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%A B. Rost
%T Twilight zone of protein sequence alignments
%J Protein Eng., Design and Seln
%V 12
%N 2
%P 85-94
%M FEB
%D 1999
%K jrnl, MolBio, c1999, c199x, c19xx, zz0521, protein, sequence, alignment,
   twilight zone
%X "Seq. al. unambiguously distinguish between protein pairs of similar and
   non-similar structure when the pairwise seq. identity is high (> 40% for long
   alignments). The signal gets blurred in the twilight zone of 20-35% seq.
   identity. Here, more than a million seq. al. were analysed ..."
   -- [doi:10.1093/protein/12.2.85]['21].
   (NB. sequence *identity*.)
   [Also search for: MolBio protein alignment].

%A Z. Zhang
%A et al
%T Moderate mutation rate in the SARS coronavirus genome and its implications
%J BMC Evol. Biol.
%V 4
%M JUN
%D 2004
%K jrnl, MolBio, c2004, c200x, c20xx, zz0521, SARS CoV, SARSCoV, SARS1,
   coronavirus, mutation, mutations, rate, diversity
%X "... Sixteen complete genomic seqs. with available clinical histories during
   the SARS outbreak were analyzed. ... The mutation rate in the SARS-CoV genome
   was est. to be 0.80-2.38x10^{-3} nucleotide subs. per site per year which is
   in the same order of magnitude as other RNA viruses. The non-synonymous &
   synonymous subs. rates were est. to be 1.16-3.30x10^{-3} & 1.67-4.67x10^{-3}
   per site per year, resp.. The most recent common ancestor of the 16 seqs was
   inferred to be present as early as the spring of 2002. The est. mutation
   rates in the SARS-CoV using multiple strategies were not unusual among
   coronaviruses & moderate compared to those in other RNA viruses. ..."
   -- [doi:10.1186/1471-2148-4-21]['21].
   [Also search for: SARS mutation].

%A J. Westbrook
%A et al
%T Appendix 3.6.2 The Protein Data Bank exchange dictionary
%B Int. Tables for Crystallography, Vol. G. Definition and exchange of
   crystallographic data
%I Springer
%P 195-198
%D 2005
%K chapter, MolBio, c2005, c200x, c20xx, zz0521, protein, data, mmCIF, CIF,
   PDBx, PDBML
%X "... A key strength of the mmCIF technology is the extensibility afforded by
   a framework based on a s/w-accessible data dictionary. ..."
   -- [app3.6.3]['21].
   Also see [wwpdb]['21],
   at [wwpdb]['21].

%A P. M. D. Fitzgerald
%A et al
%T Chapter 4.5. The Macromolecular dictionary (mmCIF)
%B Int. Tables for Crystallography, Vol. G. Definition and exchange of
   crystallographic data
%I Springer
%P 295-443
%D 2005
%K chapter, MolBio, c2005, c200x, c20xx, zz0521, protein, data, mmCIF, CIF,
   PDB, PDBx, PDBML
%X "Volume G describes the std data exchange & archival file format (CIF) used
   throughout crystallography. It provides in-depth information vital for
   small-molecule, inorganic and macromolecularcrystallographer ..."
   -- [wwpdb]['21].
   Also see [wwpdb]['21],
   at [wwpdb]['21].

%A V. D. Menachery
%A et al ...
%A Zhengli-Li Shi
%A R. S. Baric
%T A SARS-like cluster of circulating bat coronaviruses shows potential for
   human emergence
%J NatureMedicine
%V 21
%P 1508-1513
%M NOV
%D 2015
%K jrnl, MolBio, c2015, c201x, c20xx, zz0521, risk, risks, SARSCoV, SARS CoV,
   MERS, corona virus, coronavirus, SHC014, Zhengli-Li Shi, bat lady, batwoman,
   Wuhan Institute of Virology, WIV, laboratory, China, bats, spike protein,
   ACE2
%X "... we examine the disease potential of a SARS-like virus, SHC014-CoV, which
   is currently circulating in Chinese horseshoe bat popns. Using the SARS-CoV
   reverse genetics system, we generated & characterized a chimeric virus
   expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV
   backbone. The results indicate that group 2b viruses encoding the SHC014
   spike in a wild-type backbone can efficiently use multiple orthologs of the
   SARS receptor human angiotensin converting enzyme II (ACE2), replicate
   efficiently in primary human airway cells & achieve in vitro titers
   equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments
   demonstrate replication of the chimeric virus in mouse lung with notable
   pathogenesis. Evaluation of available SARS-based immune-therapeutic &
   prophylactic modalities revealed poor efficacy; both monoclonal antibody &
   vaccine approaches failed to neutralize & protect from infection with CoVs
   using the novel spike protein. On the basis of these findings, we
   synthetically re-derived an infectious full-length SHC014 recombinant virus
   & demonstrate robust viral replication both in vitro & in vivo. Our work
   suggests a potential risk of SARS-CoV re-emergence from viruses currently
   circulating in bat popns."
   -- [doi:10.1038/nm.3985]['21].

%A A. G. Wrobel
%A et al ...
%T SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on
   virus evolution and furin-cleavage effects
%J NatureStructAndMolBio
%V 27
%P 763-767
%M JUL
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0521, SARS-CoV-2, SARS2, covid-19,
   covid19, RaTG13, virus, horseshoe bats, Wuhan, China, pandemic, origin,
   spike protein, ACE2, furin cleavage, glycoprotein
%X "SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary
   host. Here, we investigate the relationship of spike (S) glycoprotein from
   SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. ...
   there are key differences in their properties, inc. a more stable precleavage
   form of human S & about 1,000-fold tighter binding of SARS-CoV-2 to human
   receptor. ... suggest that cleavage at the furin-cleavage site decreases the
   overall stability of SARS-CoV-2 S & facilitates the adoption of the open
   conformation that is required for S to bind to the ACE2 receptor."
   -- [doi:10.1038/s41594-020-0468-7]['21].
   [Also search for: MolBio RATG13] and [also search for: SARS origin].

%A J. W. Rausch
%A et al ...
%A M. F. Kearney
%T Low genetic diversity may be an Achilles heel of SARS-CoV-2
%J PNAS
%M OCT
%D 2020
%K jrnl, MolBio, c2020, c202x, c20xx, zz0521, SARS CoV 2, Nsp14, SARSCoV2,
   Ebola, H1N1, HBV, HIV, HIV1, flu, HCV, RNA virus, coronavirus,
   diversity, APD, ACE2
%K "... SARS-CoV-2 genetic diversity is remarkably low, almost entirely the
   product of genetic drift, and should not be expected to impede development
   of a broadly protective vaccine. ... coronaviruses evolved nonstructural
   protein 14 (nsp14), which ... excises misincorporated ribonucleotides from
   nascent strands ... This error-correcting capacity was unknown among RNA
   viruses prior to its discovery in SARS-CoV-1 ... error rate more than
   10-fold lower than that of other RNA viruses ..."
   -- [doi:10.1073/pnas.2017726117]['21].
   Paper includes the diversity (avg pairwise dist.) of several viruses.
   (* Also see [doi:10.1073/pnas.2008281117][8/'21]. *)
   [Also search for: SARS mutation].

%A Yang Zhou
%A et al
%T Platypus and echidna genomes reveal mammalian biology and evolution
%J Nature
%V 592
%P 756-762
%M APR
%D 2021
%K jrnl, MolBio, biol, c2021, c202x, c20xx, zz0521, mammal, therian, monotreme,
   platypus, Ornithorhynchus anatinus, echidna, Tachyglossus aculeatus,
   Australia, genome, nGenome, chromosome, sex, multiX, multiY
%X "... generate and analyse reference genomes of the platypus (Ornithorhynchus
   anatinus) & echidna (Tachyglossus aculeatus), which represent the only two
   extant monotreme lineages ... We provide evidence that the monotreme sex
   chromosome complex originated from an ancestral chromosome ring
   configuration ..."
   -- [doi:10.1038/s41586-020-03039-0]['21].

%A B. Halford
%T Pfizer unveils its oral SARS-CoV-2 inhibitor
%J Chem. & Eng. News (ISSN 0009-2347)
%V 99
%N 13
%M APR
%D 2021
%K MolBio, c2021, c202x, c20xx, zz0521, PF-07321332, PF07321332, SARS2,
   SARS-CoV-2, SARSCoV2, Mpro, 3CLpro, protease, inhibitor, drug, coronavirus
%X "... The compound, which is currently in Phase 1 clinical trials, is the
   first orally administered compound in the clinic that targets the main
   protease ..."
   -- [www]['21].
   [Also search for: MolBio 3CLpro inhibitor].

%A M. C. Wibowo
%A et al
%T Reconstruction of ancient microbial genomes from the human gut
%J Nature
%M MAY
%D 2021
%K MolBio, jrnl, c2021, c202x, c20xx, zz0521, human, gut, microbiome,
   microbiota, health, diet, ancient, modern, Methanobrevibacter smithii,
   genome, microbe, faeces, faecal
%X "... we performed a large-scale de novo assembly of microbial genomes from
   palaeofaeces. From eight authenticated human palaeofaeces samples
   (1,000-2,000 years old) with well-preserved DNA from southwestern USA &
   Mexico, we reconstructed 498 medium- & high-quality microbial genomes. Among
   the 181 genomes with the strongest evidence of being ancient & of human gut
   origin, 39% represent previously undescribed species-level genome bins. ..."
   -- [doi:10.1038/s41586-021-03532-0]['21].

%A J. D. Bloom
%A et al ...
%T Investigate the origins of COVID-19
%J Science
%V 372
%N 6543
%P 694
%M MAY
%D 2021
%K letter, MolBio, c2021, c202x, c20xx, zz0521, covid-19, covid19, WHO,
   investigation, SARS2, SARSCoV2, SARS-CoV-2, bat, virus, origin, origins,
   theories, Wuhan laboratory, lab, accident, China, controversial
%X "... In May 2020, the World Health Assembly requested that the WHO
   director-general work closely with partners to determine the origins of
   SARS-CoV-2. ... Although there were no findings in clear support of either a
   natural spillover or a lab accident, the team assessed a zoonotic spillover
   from an intermediate host as 'likely to very likely,' & a lab. incident as
   'extremely unlikely'. Furthermore, the two theories were not given balanced
   consideration. Only 4 of the 313 pages of the report & its annexes addressed
   the possibility of a laboratory accident. ... As [18]scientists with relevant
   expertise, we agree with the WHO director-general, the United States & 13
   other countries, & the European Union that greater clarity about the origins
   of this pandemic is necessary & feasible to achieve. We must take hypotheses
   about both natural & lab.  spillovers seriously until we have suff.data. A
   proper investigation should be transparent, objective, data-driven, inclusive
   of broad expertise, subject to independent oversight, & responsibly managed
   to minimize the impact of conflicts of interest. ..."
   -- [doi:10.1126/science.abj0016]['21].
   [Also search for: SARS2 origin] and [also search for: Wuhan laboratory].
   (Also see SciMag[18/10/21]['21].)

%A M. Elsman
%A N. Hallenberg
%T Integrating region memory management
%J JFP
%V 31
%N e4
%M FEB
%D 2021
%K jrnl, JFP, FP, c2021, c202x, c20xx, zz0521, garbage collection, GC,
   memory management, region, generation, MLton, MLkit
%X "We present a region-based memory management scheme with support for
   generational garbage collection. The scheme features a compile-time region
   inference alg., which associates values with logical regions ..."
   -- [doi:10.1017/S0956796821000010]['21].

%T Metcalfe's law
%D 1993
%K Metcalfe, law, c1993, c199x, c19xx, zz0521, laws, telecommunications,
   Gilder
%X "Metcalfe's law states that the value of a telecommunications network is
   proportional to the square of the number of connected users of the system
   (n^2). First formulated in this form by George Gilder in 1993,[1] and
   attributed to Robert Metcalfe in regard to Ethernet ..."
   -- [wikip]['21].
   [Also search for: funny laws].

%A J. Taylor
%T Melbourne professor quits after health department pressures her over
   data breach
%J The Guardian
%M MAR
%D 2020
%K newspaper, c2020, c202x, c20xx, zz0521, Australia, University of Melbourne,
   UniMelb, Vanessa Teague, data, privacy, deidentification, reidentification,
   Medicare, medical, federal government, health department, PBS, MBS, data,
   blunder
%X 8 March 2020: "... an open government data website by the federal government,
   of 2.5 million Australians' Medicare & PBS payment history dating back to
   1984 that had supposedly been de-identified so people were anonymous. Teague
   & her colleagues reported that the dataset had several samples where people
   were able to be identified. ... Beauchamp [health dept secretary] also
   requested Teague cease her work on the dataset. ..."
   -- [www][8/3/2020].
   Also see 'MBS/PBS data publication 23 March 2018'
   "On 1 August 2016, the Department of Health published on data.gov.au a
   collection of Medicare Benefits Schedule and Pharmaceutical Benefits Schedule
   related data. The data consisted of claims information for a 10% sample of
   people who had made a claim for payment of Medicare Benefits since 1984, or
   for payment of Pharmaceutical Benefits since 2003. ..."
   -- OAIC .gov.au [www]['21].
   [Also search for: data reidentification].

%A J. W. Weiss
%A J. M. Jacobson
%T Learning on knowledge graph dynamics provides an early warning of
   impactful research
%J NatureBiotech
%M MAR
%D 2021
%K jrnl, c2021, c202x, c20xx, zz0521, DELPHI, publish, perish, JIF, impact,
   quality, bibliometrics, scientific literature, publications, research,
   academia
%X "The sci. ecosystem relies[!] on citation-based metrics that provide only
   imperfect, inconsistent & easily manipulated[!] measures of research quality.
   Here we describe DELPHI (Dynamic Early-warning by Learning to Predict High
   Impact), a framework that provides an early-warning signal for 'impactful'
   research by autonomously learning high-dimensional relationships among
   features calc. across time from the sci. lit.. We prototype this framework &
   deduce its performance & scaling properties on time-structured publication
   graphs from 1980 to 2019 drawn from 42 biotechnology-related journals,
   inc. over 7.8 million individual nodes, 201 million relationships & 3.8
   billion calculated metrics. We demonstrate the framework's performance by
   correctly identifying 19/20 seminal biotechnologies from 1980 to 2014 via a
   blinded retrospective study & provide 50 research papers from 2018 that
   DELPHI predicts will be in the top 5% of time-rescaled node centrality in the
   future. We propose DELPHI as a tool to aid in the construction of
   diversified, impact-optimized funding portfolios."
   -- [doi:10.1038/s41587-021-00907-6]['21] (via AK).
   GROAN.  [Also search for: publish perish].

%A S. Gakkhar
%A M. Marcolli
%T Syntactic structures and the general Markov models
%J arXiv
%M APR
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, syntax, syntactic structures, Markov model,
   evolution, trees, human, natural language, linguistics
%X "... studying syntactic structures data from Longobardi (2017b), Collins
   (2010), Ceolin et al. (2020) & Koopman (2011) using general Markov models
   initiated in Shu et al. (2017), exploring the question of how consistent the
   data is with the idea that general Markov models. The ideas explored ... are
   more generally applicable than to the setting of syntactic structures, & can
   be used when analyzing consistency of data with general Markov models.
   Additionally, we give an interpretation of the methods of Ceolin et al.
   (2020) as an infinite sites evolutionary model & compare it to the Markov
   model & explore each in the context of evolutionary processes acting on human
   language syntax.
   -- 2104.08462@[arXiv]['21].
   [Also search for: natural language evolution].

%A R. E. Tarjan
%A M. Yannakakis
%T Simple linear-time algorithms to test chordality of graphs, test acyclicity
   of hyper-graphs, and selectively reduce acyclic hypergraphs
%J SIAM J. on Comp.
%V 13
%N 3
%P 566-579
%D 1984
%K jrnl, c1984, c198x, c19xx, zz0521, simplicial, chordal, graph, graphs, maths,
   acyclic, algorithm, test
%X "Chordal gs. arise naturally in the study of Gaussian elim'n on sparse
   symmetric matrices; acyclic hypergraphs arise in the study of rel'l data
   bases. Rose, Tarjan & Lueker [SIAM J.Comput., 5 ('76), pp. 266-283] have
   given a linear-time alg. to test whether a graph is chordal, which Y. has
   modified to test whether a hypergraph is acyclic. Here we develop a
   simplified linear-time test for g.chordality & hyperg. acyclicity. The test
   uses a new kind of g. (& hyperg.) search, which we call maximum cardinality
   search. A variant of the method gives a way to selectively reduce acyclic
   hypergs., which is needed for evaluating queries in acyclic rel. DBs."
   -- [doi"10.1137/0213035]['21].
   [Also search for: chordal].

%A S. M. Fleming
%T Know Thyself: The Science of Self-Awareness
%I BasicBooks
%P 304
%M APR
%D 2021
%K book, text, c2021, c202x, c20xx, zz0521, mind, self, consciousness,
   awareness, metacognition, thought, thinking
%X 1st ed 2021; hb us $20; uk us isbn:1541672844; uk us isbn13:978-1541672840
   "... Metacognition, or thinking about thinking, is the most important tool
   we have for understanding our own mind. ..."

%A D. Nguyen
%A A. Vullikanti
%T Differentially private densest subgraph detection
%X arXiv
%M MAY
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, differential privacy, dense subgraph
%X "Densest subgraph detection ... However, in many domains, the n/wk is private
   & returning a densest SG can reveal info. about the n/wk. Differential
   privacy ... handle such settings. We study the densest SG problem in the edge
   privacy model, in which the edges of the g. are private. We present the first
   sequential & parallel DP algs. for this problem. We show that our algs. have
   an additive approximation guarantee. We evaluate [them] on a large # of
   real-world n/wks, & observe a good privacy-accuracy tradeoff when the n/wk
   has high density."
   -- 2105.13287@[arXiv]['21].
      (I am told: It's a typical g.DP problem. Adding noise to the answers of
      an existing subgraph mining alg., so the true answer is protected.)
   [Also search for: differential privacy].

%A S. Hossenfelder
%T Superdeterminism: A guide for the perplexed
%J arXiv
%M OCT
%D 2020
%K TR, physics, c2020, c202x, c20xx, zz0521, determinism, superdeterminism,
   quantum mechanics, weirdnes, predestination, predetermined, free will,
   Sabine Hossenfelder
%X "Superdeterminism is presently the only known consistent description of
   nature that is local, deterministic, and can give rise to the observed
   correlations of quantum mechanics. I here want to explain what makes this
   approach promising and offer the reader some advice for how to avoid common
   pitfalls. In particular, I explain why superdeterminism is not a threat to
   science, is not necessarily finetuned, what the relevance of future input is,
   and what the open problems are."
   -- 2010.01324@[arXiv]['21].
   [Also search for: superdeterminism] & [also search for: Sabine Hossenfelder].

%A A. N. Pearson
%A et al
%T Measuring the thermodynamic cost of timekeeping
%J Phys. Rev. X
%V 11
%N 021029
%M MAY
%D 2021
%K jrnl, physics, c2021, c202x, c20xx, zz0521, time, thermodynamics, entropy,
   clock, clocks, accuracy
%X "All clocks, in some form or another, use the evolution of nature toward
   higher entropy states to quantify the passage of time. Because of the stat.
   nature of the second law & corr. entropy flows, fluctuations fundamentally
   limit the performance of any clock. This suggests a deep relation between the
   increase in entropy & the quality of clock ticks. Indeed, minimal models for
   autonomous clocks in the quantum realm revealed that a linear reln can be
   derived, where for a limited regime every bit of entropy linearly increases
   the accuracy of quantum clocks. But can such a linear relation persist as we
   move toward a more classical system? We answer this in the affirmative by
   presenting the first experimental investigation of this thermodynamic reln in
   a nanoscale clock. We stochastically drive a nanometer-thick membrane & read
   out its displacement with a radio-freq. cavity, allowing us to identify the
   ticks of a clock. We show theoretically that the max. possible accuracy for
   this classical clock is proportional to the entropy created per tick, similar
   to the known limit for a weakly coupled q.clock but with a different
   proportionality const.. We measure both the accuracy & the entropy. Once
   nonthermal noise is accounted for, we find that there is a linear reln
   between accuracy & entropy and that the clock operates within an order of
   magnitude of the theoretical bound."
   -- [doi:10.1103/PhysRevX.11.021029]['21].
   [Also search for: physics time].

%A Zuhe Zhang
%A B. Rubinstein
%A C. Dimitrakakis
%T On the differential privacy of Bayesian inference
%D 2015
%K c2015, c201x, c20xx, zz0521, differential privacy, stats, network, BN, Bnet,
   graphical model
%X "... how to communicate findings of Bayesian inference to third parties,
   while preserving the strong guarantee of differential privacy. ... four
   different algs. for private Bayesian inference on probabilistic graphical
   models. These include two mechanisms for adding noise to the Bayesian
   updates, either directly to the posterior parameters, or to their Fourier
   transform so as to preserve update consistency. We also utilise a recently
   introduced posterior sampling mechanism, for which we prove bounds for the
   specific but general case of discrete Bayesian networks ..."
   -- [inr'a]['21],
   Also see DP@[wikip]['21].
   [Also search for: differential privacy].

%A A. Wood
%A et al
%T Differential privacy: A primer for a non-technical audience
%J Vanderbilt J. of Entertainment and Technology Law
%V V 21
%N 17
%M JAN
%D 2018
%O Berkman Klein Center Research Publication No. 2019-2
%K eJrnl, c2018, c201x, c20xx, zz0521, differential privacy, DBMS, law, legal,
   deidentification, reidentification, data, stats
%X "... primarily studied in the context of the collection, analysis, & release
   of aggregate statistics. These range from simple stat.estimations, such as
   avgs, to machine learning. Tools for differentially private analysis are now
   in early stages of implementation & use across a variety of academic,
   industry, & government settings. Interest in the concept is growing among
   potential users of the tools, as well as within legal & policy communities,
   as it holds promise as a potential approach to satisfying legal requirements
   for privacy protection when handling personal information. ..."
   -- [doi:10.2139/ssrn.3338027]['21],
      [wikip]['21].

%A T. Akutsu
%A T. Mori
%A N. Nakamura
%A S. Kozawa
%A Y. Ueno
%A T. N. Sato
%T Tree edit distance with variables. Measuring the similarity between
   mathematical formulas
%J arXiv
%M MAY
%D 2021
%K TR, c2021, c202x, c20xx, zz0521, mathematical formula, tree edit distance,
   parse tree, variable, similarity, similar, formulae
%X "... propose tree edit dist. with variables, which is an extn of the [TED]
   to handle trees with variables & has a potential application to measuring the
   similarity between math. formulas, esp., those appearing in math. models of
   biol. sys.. ... show that the problem is NP-complete for ordered trees. [&]
   show for unordered trees that the problem of deciding whether or not the
   distance is 0 is graph isomorphism complete but can be solved in polynomial
   time if the max. outdegree of input trees is bounded by a constant. This
   distance model is then extended for measuring the difference/similarity
   between two systems of differential equns, for which results of preliminary
   computational experiments using biological models are provided."
   -- 2105.04802@[arXiv]['21].