Search engine run on: http://users.monash.edu.au/

Glookbib search for: zz0220

%A A. M. Garsia
%A M. L. Wachs
%T A new algorithm for minimum cost binary trees
%J SIAM J. Comput.
%V 6
%N 4
%P 622-642
%D 1977
%K jrnl, c1977, c197x, c19xx, zz0220, minimum cost binary tree, optimum,
   search trees, Huffman code, linearithmic, Garsia Wachs, algorithm, Hu-Tucker
%X "A new alg. for constructing minimum cost binary trees in O(n log n) time is
   presented. [It] is similar to the well-known Hu-Tucker alg.. Our proof of
   validity is based on finite variational methods & is therefore quite
   different & somewhat simpler than the proof for the H.-T. alg. Our proof
   also yields some additional information about the structure of min. cost b.
   trees. This permits a linear time implementation ... in a special case."
   -- [doi:10.1137/0206045]['20].
   Also see GW@[wikip]['20].
   ("An alg. is said to run in quasilinear time (aka log-linear time) if
   T(n)=O(n log^k(n)) for some +ve const. k; linearithmic is the case k=1."
   TC@[wikip]['20].)
   (Also see R.S.Bird JFP [doi:10.1017/S0956796819000194][21/1/'20].)
   [Also search for: binary code tree].

%A J. Calvo-Zaragoza
%A J. Oncina
%A C. De la Higuera
%T Computing the expected edit distance from a string to a PFA
%J 21st Int. Conf. Implementation and Application of Automata
%P 39-50
%D 2016
%K conf, c2016, c201x, c20xx, zz0220, string, strings, FSA, FSM, PFSA, PFSM,
   PFA, median, expected, mean, average, distribution, edit distance
%X "... compare  a  witness  string with a distribution. One possibility is to
   compute the prob. of the string for that distn. [or] giving a more global
   view, is to compute the expected edit dist. from a string randomly drawn to
   the witness string. This # is often used to measure the performance of a
   prediction, the goal then being to return the median string, or the string
   with smallest exp. dist.. To be able to measure this, computing the dist.
   between a hypothesis & that distn is necessary. This paper proposes two
   solns for computing this value, when the distn is defined with a
   probabilistic finite state automaton. The 1st is exact but [cost] can be
   exponential in the length of the input string, ... the 2nd is a F_{pras}."
   -- [www]['20].

%A T. Bingmann
%A P. Sanders
%A M. Schimek
%T Communication-efficient string sorting
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, sort, sorting, string, strings, algorithm,
   parallel, distributed, bandwidth, multiway merge, merging
%X "There has been surprisingly little work on algs. for sorting strings on
   distributed-memory parallel machines. We develop efficient algs. for this
   problem based on the multi-way merging principle. These algs. inspect only
   chars. that are needed to determine the sorting order. [&] communication
   volume is reduced by also communicating (roughly) only those chars. & by
   communicating repetitions of the same prefixes only once. Experiments on up
   to 1280 cores reveal that these algs. are often more than five times faster
   than prev. algs."
   -- 2001.08516@[arXiv]['20].

%A Duc Hung Pham
%A K. V. Palem
%A M. V. Panduranga Rao
%T A polynomial time parallel algorithm for graph isomorphism using a
   quasipolynomial number of processors
%J arXiv
%M FEB
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, graph, graphs, isomorphism, maths, parallel,
   algorithm, color refinement, WL, quasipolynomial, processor, Babai
%X "... Babai made a breakthrough in 2015 ... Based on Babai's alg., we prove
   that GI can further be solved by a parallel alg. that runs in polynomial time
   using a quasipolynomial # of processors. We achieve that result by
   identifying the bottlenecks in B's algs. & parallelizing them. In particular,
   we prove that color refinement can be computed in parallel logarithmic time
   using a polynomial # of proc., & the k-dimensional WL refinement can be
   computed in parallel polynomial time using a quasipolynomial # of ps.. Our
   work suggests that Graph Isomorphism & GI-complete problems can be computed
   efficiently in a parallel computer, & provides insights on speeding up
   parallel GI programs in practice."
   -- 2002.04638@[arXiv]['20].
   [Also search for: maths graph isomorphism].

%A K. Gregor
%A F. Besse
%A D. Jimenez Rezende
%A I. Danihelka
%A D. Wierstra
%T Towards conceptual compression
%J NIPS
%D 2016
%K conf, NIPS, NIPS29, NN, ANN, c2016, c201x, c20xx, zz0220, image, images,
   representation, concept, abstraction, compress, compression
%X "We introduce convolutional DRAW, a homogeneous deep generative model
   [for] latent variable image modeling. The alg. naturally stratifies info.
   into higher & lower level details, creating abstract features & as such
   addressing one of the fundamentally desired properties of representation
   learning. [&] the hierarchical ordering of its latents creates the
   opportunity to selectively store global info. about an image, yielding a high
   quality 'conceptual compression' framework."
   -- [www]['20],
      1604.08772@[arXiv]['20].

%A A. Aszodi
%A W. R. Taylor
%T Estimating polypeptide alpha-carbon distances from
   multiple sequence alignments
%J J. Math. Chem
%V 17
%N 2
%P 167-184
%M JUN
%D 1995
%K jrnl, MolBio, c1995, c199x, c19xx, zz0220, protein structure, prediction,
   MSA, alignment, CA, carbona, Amino Acid, distance
%X "The hydrophobic amino acids that make up the core of a protein can be
   expected to be closer together than the rest of the residues in the molecule
   & are likely to remain conserved during evolution due to their important
   role. ... a general theoretical framework is provided for estimating
   interresidue distances from residue hydrophobicity & conservation deduced
   from multiple alignments. While the accurate prediction of individual
   distances by statistical procedures is theoretically impossible, the method
   is able to match the distn of pred. dists. to a prescribed distn with good
   accuracy."
   -- [doi:10.1007/BF01164846]['20].

%A K. T. Simons
%A C. Kooperberg
%A E. Huang
%A D. Baker
%T Assembly of protein tertiary structures from fragments with similar
   local sequences using simulated annealing and Bayesian scoring functions
%J J. Molec. Biol.
%V 268
%N 1
%P 209-225
%M APR
%D 1997
%K jrnl, JMB, MolBio, c1997, c199x, c19xx, zz0220, protein structure prediction,
   fragment library
%X "...  simple simulated annealing procedure to assemble native-like structures
   from fragments of unrelated protein structures with similar local seqs. using
   Bayesian scoring fns. ... investigate the effects of multiple seq. info. &
   different types of conformational constraints on the overall performance of
   the method, & the ability of a variety of recently developed scoring fns to
   recognize the native-like conformations in the ensembles of simulated
   structures."
   -- [doi:10.1006/jmbi.1997.0959]['20].
   [Also search for: MolBio protein structure library] (and/or Rosetta).

%A R. L. Tatusov
%A M. Y. Galperin
%A D. A. Natale
%A E. V. Koonina
%T The COG database: a tool for genome-scale analysis of protein functions and
   evolution
%J NAR
%V 28
%N 1
%P 33-36
%M JAN
%D 2000
%K jrnl, NAR, MolBio, c2000, c200x, c20xx, zz0220, COG, database, protein,
   evolution, Orthologous, COGs, KOGs, POGs
%X "... The database of Clusters of Orthologous Groups of proteins (COGs) is an
   attempt on a phylogenetic classn of the proteins encoded in 21 complete
   genomes of bacteria, archaea & eukaryotes (www.ncbi.nlm.nih.gov/COG). The
   COGs were constructed by applying the criterion of consistency of
   genome-specific best hits to the results of an exhaustive comparison of all
   protein sequences from these genomes. The DB comprises 2091 COGs that include
   56-83% of the gene products from each of the complete bacterial & archaeal
   genomes and ~35% of those from the yeast Saccharomyces cerevisiae genome. The
   COG DB is accompanied by the COGNITOR program that is used to fit new
   proteins into the COGs  ..."
   -- [doi:10.1093/nar/28.1.33]['20].
   Also see [COG][2O2O].

%A S. J. Wheelan
%A A. Marchler-Bauer
%A S. H. Bryant
%T Domain size distributions can predict domain boundaries
%J Bioinformatics
%V 16
%N 7
%P 613-618
%M JUL
%D 2000
%K jrnl, MolBio, c2000, c200x, c20xx, zz0220, protein, domain, domains, size,
   chain, length, boundary
%X " The sizes of protein domains observed in the 3D-structure database follow a
   surprisingly narrow distn. Structural domains are furthermore formed from a
   single-chain continuous segment in over 80% of instances. These observations
   imply that some choices of domain boundaries on an otherwise uncharacterized
   sequence are more likely than others, based solely on the size & segment
   number of predicted domains. ... We find that domain boundary predictions are
   surprisingly successful for sequences up to 400 residues long & that guessing
   domain boundaries in this way can improve the sensitivity of threading
   analysis."
   -- [doi:10.1093/bioinformatics/16.7.613]['20].

%A M. Remmert
%A A. Biegert
%A A. Hauser
%A J. Soding
%T HHblits: lightning-fast iterative protein sequence searching by
   HMM-HMM alignment
%J Nature Methods
%V 9
%P 173-175
%D 2012
%K jrnl, MolBio, HHblits, HH blits, c2012, c201x, c20xx, zz0220, protein,
   profile HMM, amino acid, multiple sequence alignment, MSA, hhblitz, blitz,
   HHsearch, HHsuite, MSA, PSIBLAST
%X "... We present an open-source, general-purpose tool that represents both
   query & database seqs. by profile hidden Markov models (HMMs): 'HMM-HMM-based
   lightning-fast iterative seq. search' (HHblits). Compared to the seq.-search
   tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter,
   has 50-100% higher sensitivity & generates more accurate alignments."
   -- [doi:10.1038/nmeth.1818]['20],
    & HH@[g'thub]['22],
      HH@[wikip]['22],
      hhblits@[lmu.de]['20] dead?
   [Also search for: MolBio protein alignment].

%A J. G. Greener
%A S. M. Kandathil
%A D. T. Jones
%T Deep learning extends de novo protein modelling coverage of genomes using
   iteratively predicted structural constraints
%J NatureComms
%V 10
%N #3977
%M SEP
%D 2019
%K jrnl, MolBio, c2019, c201x, c20xx, zz0220, protein structure prediction, NN,
   ANN, DMPfold, CASP, CASP12
%X "The inapplicability of AA covariation methods to small protein families ...
   Recently, deep learning has shown promise in allowing accurate
   residue-residue contact prediction even for shallow sequence alignments. ...
   introduce DMPfold ... predict inter-atomic distance bounds, the main chain
   hydrogen bond n/wk, & torsion angles ... Applied to all Pfam domains without
   known structures, confident models for 25% of these so-called dark families
   were produced in under a week on a small 200 core cluster. DMPfold provides
   models for 16% of human proteome UniProt entries without structures,
   generates accurate models with fewer than 100 seqs. in some cases, & is
   freely available."
   -- [doi:10.1038/s41467-019-11994-0]['20],
      1811.12355@[arXiv]['20].
   [Also search for: MolBio protein deep learning].

%A A. W. Senior
%A et al ...
%A D. Hassabis
%T Improved protein structure prediction using potentials from deep learning
%J Nature
%V 577
%P 706-710
%M JAN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0220, protein structure prediction,
   AlphaFold, google, deep, ANN, NN, CNN, CASP, CASP13, free modelling, FM,
   contacts, HHblits, details
%X "... we show that we can train a neural network to make accurate predictions
   of the distances between pairs of residues, which convey more info. about the
   struct. than contact predictions. Using this info., we construct a potential
   of mean force that can accurately describe the shape of a protein. We find
   that the resulting potential can be optimized by a simple gradient descent
   alg. to generate structs. without complex sampling procedures. The resulting
   system, named AlphaFold, achieves high accuracy, even for seqs. with fewer
   homologous seqs.. In the recent Critical Assessment of Protein Structure
   Prediction (CASP13) - a blind assessment of the state of the field -
   AlphaFold created high-accuracy structs. (with template modelling (TM)
   scores of 0.7 or higher) for 24 out of 43 free modelling domains, whereas
   the next best method, which used sampling & contact info., achieved such
   accuracy for only 14 out of 43 domains. ..."
      "... a CNN trained on PDB structures ... predicts a discrete prob. distn
      P(dij|S, MSA(S)) for every ij pair in any 64x64 region of the LxL
      distance matrix ..."
   -- [doi:/10.1038/s41586-019-1923-7]['20],
   &  preprint@[UCL]['22].
   [Also search for: CASP MolBio] and see AF@[wikip]['22].

%A H. Imachi
%A et al ...
%A K. Takai
%T Isolation of an archaeon at the prokaryote-eukaryote interface
%J Nature
%V 577
%P 519-525
%M JAN
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0220, evolution, origins, tree of life,
   E3, phylogenetic, prokaryote, eukaryote, archae, Asgard loki, Lokiarchaeota,
   Candidatus Prometheoarchaeum syntrophicum, organelle, coccus
%X "... Current data suggest that eukaryotes may have emerged from an archaeal
   lineage known as 'Asgard' archaea. Despite the eukaryote-like genomic
   features that are found in these a., the evolutionary transition from archaea
   to e. remains unclear ... Here we report the decade-long isolation of an
   Asgard archaeon related to Lokiarchaeota from deep marine sediment. The
   archaeon - 'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1 - is an
   anaerobic, extremely slow-growing, small coccus (around 550nm dia.) that
   degrades amino acids through syntrophy. Although eukaryote-like intracellular
   complexes have been proposed for A.archaea, the isolate has no visible
   organelle-like structure. Instead, Ca. P. syntrophicum is morphologically
   complex & has unique protrusions that are long & often branching. On the
   basis of the available data obtained from cultivation & genomics, & reasoned
   interpretations of the existing literature, we propose a hypothetical model
   for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3)
   model."
   -- [doi:10.1038/s41586-019-1916-6]['20].
   (Also see Lokiarchaeota@[wikip]['20].)
   [Also search for: MolBio tree life].

%A A. B. Barron
%A B. Hare
%T Prosociality and a sociosexual hypothesis for the evolution of same-sex
   attraction in humans
%J Frontiers in Psychol.
%V 10
%N 2955
%M JAN
%D 2019
%K jrnl, c2020, c202x, c20xx, zz0220, human, evolution, same, sex, SSSA,
   attraction, sexuality, society, behaviour
%X "... develop a novel argument for the evolution of SSSA that focuses on the
   likely adaptive social consequences of SSSA. We argue that SSAT evolved as
   just one of a suite of traits responding to strong seln for ease of social
   integration or prosocial behavior. A strong driver of recent human behavioral
   evolution has been seln for reduced reactive aggression, increased social
   affiliation, social communication, & ease of social integration. In many
   prosocial mammals sex has adopted new social fns in contexts of social
   bonding, social reinforcement, appeasement, & play. We argue that for humans
   the social fns & benefits of sex apply to same-sex sexual behavior as well as
   heterosexual behavior. [so] we propose a degree of SSSA, was selected for in
   recent human evolution for its non-conceptive social benefits. ..."
    -- [doi:10.3389/fpsyg.2019.02955]['20].

%A A. K. Wesselink
%A et al ...
%A K. J. Rothman
%T Seasonal patterns in fecundability in North America and Denmark: a
   preconception cohort study
%J Hum. Reprod.
%M JAN
%D 2020
%K jrnl, c2020, c202x, c20xx, zz0220, human, reproduction, birth, conception,
   pregnancy, fecund, fecundity, baby, babies, stats, periodic, season,
   seasonal, cyclic, model, USA, Denmark
%X "... Initiation of pregnancy attempts peaked in September, with stronger
   seasonality in N.America than in Denmark (48 vs. 16% higher prob. initiating
   attempts in Sept. compared with March). After accounting for seasonal
   variation in initiation of pregnancy attempts, we observed modest seasonal
   variation in fecundability, with a peak in the late fall & early winter in
   both cohorts, but stronger peak/low ratios in N.A. (1.16; 95% [CI]: 1.05,
   1.28) than in D. (1.08; 95% CI: 1.00, 1.16). When we stratified the NA data
   by latitude, we observed the strongest seasonal variation in the southern USA
   (peak/low ratio of 1.45 [95% CI: 1.14, 1.84]), with peak fecundability in
   late November. ..."
   -- [doi:10.1093/humrep/dez265]['20].
   (auth1@[bu]['20].)

%A R. Wu
%A et al
%T A new coronavirus associated with human respiratory disease in China
%J Nature
%V 579
%P 265-269
%M FEB
%D 2020
%K jrnl, MN908947.3, c2020, c202x, c20xx, zz0220, 2019-nCoV, 2019nCoV, covid 19,
   covid19, WH-Human-1, SARS2, SARS-CoV-2, SARSCoV2, genome, WHHuman1, MolBio,
   coronavirus, corona virus, Wuhan, China, RNA, virus, viral, Coronaviridae,
   Betacoronavirus, Sarbecovirus, zoonotic disease, infection, bat, bats
%X "... a novel RNA virus from the family Coronaviridae, designed here as
   WH-Human-1 coronavirus. Phylogenetic analysis of the complete viral genome
   (29,903 nucleotides) revealed that the virus was most closely related
   (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus
   Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in
   China. This outbreak highlights the ongoing capacity of viral spill-over from
   animals to cause severe disease in humans."
   -- [doi:10.1038/s41586-020-2008-3][2/2020]  (online Feb 2020)..
   "GenBank: MN908947.3 ...
   Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome.
   Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ..." (~30Kb)
   -- [ncbi][12/2/2020].
   (Also see [wikip]['20].)
   [Also search for: MolBio SARS].

%A R. S. Bird
%T An optimal, purely functional implementation of the Garsia-Wachs algorithm
%J JFP
%V 30
%N e3
%M JAN
%D 2020
%K JFP, FP, c2020, c202x, c20xx, zz0220, Garsia Wachs algorithm,
   minimum cost binary tree, code, search trees, optimum
%X "The Garsia-Wachs alg. ... for building a binary leaf tree whose cost is as
   small as possible. ... described in more detail below, but the task is
   essentially the same as that of building a Huffman coding tree with the added
   constraint that the fringe of the tree has to be exactly the given list of
   inputs (in H.coding, the fringe of the tree can be any permutation of the
   input) ..."
   -- [doi:10.1017/S0956796819000194]['20].
   [Also search for: Garsia Wachs algorithm].

%A M. Allen
%T Liability for climate change
%J Nature
%V 421
%N 6926
%P 891-892
%M FEB
%D 2003
%K news views, c2003, c200x, c20xx, zz0220, climate change, global warming, CO2,
   world, extreme weather, attribution, cause, causation, causality, storms,
   flooding, flood, floods, temperature, drought
%X -- [doi:10.1038/421891a]['20].
   [Also search for: extreme weather attribution].

%A R. Garnaut
%T The Garnaut Review 2011: Australia in the Global Response to Climate
%I CUP
%P 244
%M JUL
%D 2011
%K book, text, CUP, c2011, c201x, c20xx, zz0220, Australia, climate change,
   global warming, greenhouse gas, gases, CO2, coal, oil, fossil fuel,
   economics, GFC, sustainability, environment, wind, solar, politics, enquiry
%X 1st edn 2011; pb us$43; uk us isbn:1107691680; uk us isbn13:978-1107691681.
   "In this update to the 2008 Garnaut Climate Change Review, Ross Garnaut
   re-examines the case for action in the aftermath of the global financial
   crisis and recent developments by major countries to reduce emissions and
   prepare for a low-carbon future. He guides the reader through the climate
   change debate, and explains why Australia's contribution is vital to the
   national interest and matters to the global effort. He outlines a set of
   policies through which Australia can contribute its fair share without
   damaging Australian prosperity. The Garnaut Review 2011: Australia in the
   Global Response to Climate Change extends the analysis to contemporary
   economic, political and environmental conditions in a way that is clear and
   easy to understand. It is an essential resource for all who care about the
   future of our economy and environment."
   [Also search for: climate change].

%A A. van de Rijt
%A S. Moon Kang
%A M. Restivo
%A A. Patil
%T Field experiments of success-breeds-success dynamics
%J PNAS
%V 111
%N 19
%P 6934-6939
%M SEP
%D 2014
%K jrnl, PNAS, c2014, c201x, c20xx, zz0220, deRijt, success, luck, social,
   feedback, Matthew effect, principle, preferential attachment,
   rich get richer, human behaviour, experiment, grants, kickstarter, Hindex
%X "... Some scholars have suggested such inequality merely reflects
   hard-to-observe personal differences in ability. Others have proposed that
   one fortunate success may trigger another, thus producing arbitrary
   differentiation. We conducted randomized experiments through intervention in
   live social systems to test for success-breeds-success dynamics. Results show
   that different kinds of success (money, quality ratings, awards, and
   endorsements) when bestowed upon arbitrarily selected recipients all produced
   significant improvements in subsequent rates of success as compared with the
   control group of nonrecipients. However, greater amounts of initial success
   failed to produce much greater subsequent success, suggesting limits ..."
   -- [doi:10.1073/pnas.1316836111][20].
   (Also see Sci Show, ABC radio[www][8/2/20].)
   [Also search for: success luck].

%A P. A. Stott
%A N. Christidis
%A F. E. Otto
%A et al ...
%A F. W. Zwiers
%T Attribution of extreme weather and climate-related events
%J Wiley Interdisciplinary Reviews: Climate Change
%V 7
%P 1
%P 23-41
%D 2016
%K c2016, c201x, c20xx, zz0220, extreme, world, weather attribution, WWA,
   climate change, global warming, CO2, human activity, cause, causality, stats
%X "... Event attribution studies seek to determine to what extent anthropogenic
   climate change has altered the probability or magnitude of particular
   events. ..."
   -- [doi:10.1002/wcc.380]['20].
   [Also search for: extreme weather attribution].

%A M. J. Lerchenmueller
%A O. Sorenson
%A A. B. Jena
%T Gender differences in how scientists present the importance of their
   research: observational study
%J BMJ
%V 367
%P l6573
%D 2019
%K BMJ, c2020, c202x, c20xx, zz0220, scientific research, publications, papers,
   title, titles, citations, gender, publish, perish, gender, women, STEM
%X "... this study was to analyze whether men and women differ in how positively
   they frame their research findings and to analyze whether the positive
   framing of research is associated with higher downstream citations. ..."
   -- [doi:10.1136/bmj.l6573]['20].
      "... Clinical articles involving a male first or last author were
      more likely to present research findings positively in titles and
      abstracts compared with articles in which both the first and last
      author were women, particularly in the highest impact journals.
      Positive presentation of research findings was associated with
      higher downstream citations. ..."
   [Also search for: publish perish].

%A E. Worthington
%T Murdoch University drops financial claim against whistleblower academic
   after backlash
%I ABC
%M JAN
%D 2020
%K news, c2020, c202x, c20xx, zz0220, Australia, Murdoch University, WA,
   student, students, welfare, overseas, international, Schroder-Turk,
   whistleblower, academic, scandal, administration, NTEU
%X "... A West Australian university is withdrawing a multi-million-dollar
   financial damages claim filed against a whistleblower academic who spoke on
   the ABC's Four Corners last year. Associate Professor Gerd Schroder-Turk
   was one of three Murdoch University academics who appeared on the program
   raising concerns about the welfare of international students.  He took
   legal action in the Federal Court seeking an injunction to stop the
   university from removing him from his position on the university's senate
   after the broadcast.  In response, Murdoch University counter-sued Dr
   Schroder-Turk for costs and damages.  Murdoch claimed that since
   Dr Schroder-Turk's comments the U.'s reputation had been damaged ..."
   --[abc][13/1/2020].

%A N. Phillips
%A B. Nogrady
%T The race to decipher how climate change influenced Australia's record fires
%J Nature
%V 577
%P 610-612
%M JAN
%D 2020
%K news, views, c2020, c202x, c20xx, zz0220, world, Australia, Victoria, NSW,
   risk, risks, climate change, extreme weather attribution, WWA, bush fires,
   bushfire, drought, cause, causality, CO2, greenhouse gas, gases,
   human activity, Sophie Lewis, Perkins-Kirkpatrick
%X "On 1 January, the air in Canberra was the worst of any city in the world.
   With unprecedented bush fires raging nearby, a thick blanket of smoke
   smothered Australia's capital for weeks, ..."
   -- [doi:10.1038/d41586-020-00173-7]['20].
   [Also search for: extreme weather attribution].

%A R. Van Noorden
%T Highly cited researcher banned from journal board for citation abuse
%J Nature
%V 578
%P 200-201
%M FEB
%D 2020
%K news, views, VanNorden, c2020, c202x, c20xx, zz0220, publish, perish,
   research, coerce, coercive, citations, papers, gIndex, Hindex, KPI, KPIs,
   impact, university management, JTB, journals, Kuo-Chen Chou, KCChou,
   KuoChenChou, academic misconduct, peer review, research, refereeing, scam,
   abuse, misuse, ethics
%X "A US-based biophysicist [Kuo-Chen Chou] who is one of the world's most
   highly cited researchers has been removed from the editorial board of one
   journal and barred as a reviewer for another, after repeatedly manipulating
   the peer-review process to amass citations to his own work. ... asked authors
   of dozens of papers he was editing to cite a long list of his publications -
   sometimes more than 50 ..."
   -- [doi:10.1038/d41586-020-00335-7]['20].
   [Also search for: peer review]  and  [also search for: KuoChenChou].

%A A. Cayley
%T Desiderata and suggestions: No.2. The theory of groups: Graphical
   representation
%J Amr. J. Maths.
%V 1
%N 2
%P 174-176
%D 1878
%K jrnl, maths, c1878, c187x, c18xx, zz0220, group, graph, diagram, permutation,
   generators, representation theory, theorem
%X -- [doi:10.2307/2369306]['20],
      2369306@[Jstore]['20].
   Also see CayleyG@[wikip]['20].
   [Also search for: permutation group].

%A F. Harary
%A G. E. Uhlenbeck
%T On the number of Husimi trees, I
%J PNAS
%V 39
%N 4
%P 315-322
%M APR
%D 1955
%K jrnl, PNAS, c1953, c195x, c19xx, zz0220, Husimi tree, cactus graph, cacti,
   block, cycles, maths, count, counting
%X "... A H.tree is a connected graph s.t. no line [edge] lies on more
   than one cycle. ..."
   --  [doi:10.1073/pnas.39.4.315]['20].
   Also see, "Meanwhile, ... H.tree commonly came to refer to gs. in which every
   block is a complete g. ... This usage had little to do with the work of H.,
   & the more pertinent term block g. is now used for this family; however,
   because of this ambiguity this phrase has become less frequently used to
   refer to cactus graphs."
   -- CactusGraph@[wikip]['20].

%T SymPy
%D ? 2009+ on ?
%K TR, c201x, c20xx, zz0220, Python, symbolic maths, mathematics, SymPy, mpmath,
   galgebra, computer algebra, library
%X "SymPy is a Python library for symbolic mathematics. It aims to become a
   full-featured computer algebra system (CAS) while keeping the code as simple
   as possible in order to be comprehensible and easily extensible. SymPy is
   written entirely in Python."
   -- [www]['20],  (via njh).

%A Zhengfeng Ji
%A A. Natarajan
%A T. Vidick
%A J. Wright
%A H. Yuen
%T MIP* = RE
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, MIP, RE, spooky, quantum prover, computing,
   physics, entanglement, game, Halting Problem, entangled value,
   undecidability, Tsirelson, commuting, correlation, Connes, embedding,
   conjecture
%X "We show that the class MIP* of languages that can be decided by a classical
   verifier interacting with multiple all-powerful quantum provers sharing
   entanglement is equal to the class RE of rec. enum. langs.. ... builds upon
   the q. low-degree test of (Natarajan & Vidick, FOCS 2018) by integrating
   recent developments from (Natarajan & Wright, FOCS 2019) & combining them
   with the recursive compression framework of (Fitzsimons et al., STOC 2019).
   An immediate byproduct of our result is that there is an efficient reduction
   from the Halting Problem to the problem of deciding whether a two-player
   nonlocal game has entangled value 1 or at most 1/2. Using a known connection,
   undecidability of the entangled value implies a -ve answer to Tsirelson's
   problem: we show, by providing an explicit e.g., that the closure C_{qa} of
   the set of q.tensor product correlations is strictly included in the set
   C_{qc} of q.commuting correlns. Following work of (Fritz, Rev. Math. Phys.
   2012) & (Junge et al., J. Math. Phys. 2011) our results provide a refutation
   of Connes' embedding conjecture from the theory of von Neumann algebras."
   -- 2001.04383@[arXiv]['20].
   (I'm glad that's clear.)  Not yet peer reviewed.
   (Also see discussion at [doi:10.1038/d41586-020-00120-6]['20].)

%A B. Greene
%T Until the End of Time: Mind, Matter, and Our Search for Meaning in an
   Evolving Universe
%I Knopf
%P 448
%M FEB
%D 2020
%K book, text, c2020, c202x, c20xx, zz0220, time, entropy, meaning, human,
   science, physics, cosmology, free will
%X "... explores how life and mind emerged from the initial chaos, and how our
   minds, in coming to understand their own impermanence, seek in different ways
   to give meaning to experience: in narrative, myth, religion, creative
   expression, science, the quest for truth ..."
   1st ed 2020; hb us$21; uk us isbn:1524731676; uk us isbn13:978-1524731670.
   [Also search for: consciousness]  and  [also search for: arrow time].

%T Stan Modelling Language, ver.3.9.0
%D DEC
%D 2015
%K Stan, c2015, c201x, c20xx, zz0220, probabilistic programming language, PLD,
   stats, probability, model
%X "Stan is a state-of-the-art platform for statistical modeling and
   high-performance statistical computation. Thousands of users rely on Stan
   for statistical modeling, data analysis, and prediction in the social,
   biological, and physical sciences, engineering, and business. ..."
   -- Stan@[www]['20] home.
   "Stan is a probabilistic programming language for statistical inference
   written in C++. ..."
   -- Stan@[wikip]['20]  (via njh).

%A E. Dijkstra
%D ?
%T Quote
%K Dijkstra, Edsger, EWD, c19xx, zz0220, quote, quotable, SE, SWE, SWEng,
   computer programming, proof, verification, logic, formal,
   Software Engineering, crisis
%X "The required techniques of effective reasoning are pretty formal, but
   as long as programming is done by people that don't master them, the
   software crisis will remain with us and will be considered an incurable
   disease. And you know what incurable diseases do: they invite the quacks
   and charlatans in, who in this case take the form of Software Engineering
   gurus."
   -- [www]['20]  (via AK).

%A K. B. Korb
%A E. P. Nyberg
%A L. Hope
%T A new causal power theory
%B Causality in the Sciences
%I OUP
%D 2011
%K chapter, c2011, c201x, c20xx, zz0220, cause, causality, causal power, KBKorb,
   Bnet, Bayesian network, mutual, information, intervention, stats
%X (In, uk us isbn:0199574138; uk us isbn13:978-0199574131.)
   "The causal power of C over E is (roughly) the degree to which changes in C
   cause changes in E. A formal measure of causal power would be v.useful, as an
   aid to understanding & modelling complex stochastic systems. Previous
   attempts to measure causal power, such as those of Good (1961), Cheng (1997),
   & Glymour (2001), while useful, suffer from one fundamental flaw: they only
   give sensible results when applied to v.restricted types of causal system,
   all of which exhibit causal transitivity. Causal Bayesian networks, however,
   are not in general transitive. The chapter develops an information-theoretic
   alternative, causal information, which applies to any kind of causal B. n/w.
   Causal information is based upon three ideas. First ... that the system can
   be rep. causally as a B.n/wk. Second ... uses hypothetical interventions to
   select the causal from the non-causal paths connecting C to E. Third ... a
   variation on the information-theoretic measure mutual information to
   summarize the total causal influence of C on E. ... gives sensible results
   for a much wider variety of complex stochastic systems than prev. attempts &
   promises to simplify the interpretation & application of B.networks."
   -- [doi:10.1093/acprof:oso/9780199574131.003.0030]['20].
   [Also search for: Bnet information].

%A J. Cockx
%A A. Abel
%T Elaborating dependent (co)pattern matching: No pattern left behind
%J JFP
%V 30
%P #e2
%M JAN
%D 2020
%K jrnl, JFP, c2020, c202x, c20xx, zz0220, FP, programing languages, types,
   dependent, typed, type, check, checking, co pattern, copattern, Agda
%X "... dependently typed language, we can guarantee correctness of our
   programmes by providing formal proofs. To check them, the typechecker
   elaborates these programs and proofs into a low-level core language. However,
   this core language is by nature hard to understand by mere humans, so how can
   we know we proved the right thing? ...  A definition by copattern matching
   consists of a list of clauses that are elaborated to a case tree ...  present
   an algorithm elaborating definitions by dependent copattern matching to a
   core language with inductive data types, coinductive record types, an
   identity type, and constants defined by well-typed case trees. ...
   reimplement the alg. used by Agda to check left-hand sides of defns by
   pattern matching. ...  Thus, we take another step towards the formally
   verified implementation of a practical dependently typed language.
   -- [doi:10.1017/S0956796819000182]['20].

%A S. Cipolla
%A F. Durastante
%A F. Tudisco
%T Nonlocal pagerank
%J arXiv
%M JAN
%D 2020
%K TR, c2020, c202x, c20xx, zz0220, PageRank, non local, page rank, importance,
   ranking, ranks
%X "... introduce & study a nonlocal version of the PageRank. ... the random
   walker explores the graph using longer excursions than just moving between
   neighboring nodes. [So] the corr. ranking of the nodes, which takes into
   account a long-range interaction between them, does not exhibit concentration
   phenomena typical for spectral rankings taking into account just local
   interactions. We show that the predictive value of the rankings obtained
   using our proposals is considerably improved on different real world
   problems."
   -- 2001.10421@[arXiv]['20].
   [Also search for: pagerank].