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

Glookbib search for: zz0717

%A C. Holst
%A et al
%T Alcohol drinking patterns and risk of diabetes: A cohort study of
   70,551 men and women from the general Danish population
%J Diabetologia
%V ?
%P 1-10
%M JUL
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0717, diabetes, moderate alcohol consumption,
   drink, drinking, human health, risk, risks, sugar, zzAlcohol, positive
%X "Alcohol consumption is inversely associated with diabetes, but little is
   known about the role of drinking patterns. We examined the assoc. between
   alcohol drinking patterns & diabetes risk in men & women from the general
   Danish population. ... Danish Health Examination Survey 2007-2008. Of the
   76,484 survey participants, 28,704 men and 41,847 women ... consumption of
   alcohol over 3-4 days per week is assoc. with the lowest risk of diabetes,
   even after taking avg. weekly a.consumption into account."  (online 27/7.)
   -- [doi:10.1007/s00125-017-4359-3]['17].
   [Also search for: zzAlcohol].

%A M. Mitzenmacher
%A T. Morgan
%T Reconciling graphs and sets of sets
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, set, graph, reconcile, reconciliation
%X "We explore a generalization of set reconciliation, where the goal is to
   reconcile sets of sets. Alice & Bob each have a parent set consisting of s
   child sets, each containing at most h elements from a universe of size u.
   They want to reconcile their sets of sets in a scenario where the total
   number of differences between all of their child sets (under the minimum
   difference matching between their child sets) is d. We give several
   algorithms for this problem, & discuss applications to reconciliation
   problems on graphs, databases, & collections of documents. We specifically
   focus on graph reconciliation, providing protocols based on sets of sets
   reconciliation for random graphs from G(n,p) & for forests of rooted trees."
   -- 1707.05867@[arXiv]['17].

%A K. U. Linderstrom-Lang
%T Proteins and Enzymes
%I StanfordUP
%S Lane Medical Lectures, Medical Sciences, Volume VI, 115 pages
%D 1952
%K c1952, c195x, c19xx, zz0717, MolBio, protein, primary, secondary, tertiary,
   structure, origin, terminology
%X 1st ed 1952; pb, asin:B009NI2YAY.
   Kister (2013) attributes the coining of the terms primary-, secondary-,
   and tertiary-structure to L-L (1952).
   [Also search for: MolBio super secondary],  R and R (1973).

%A G. H. Gonnet
%A C. Korostensky
%T Optimal scoring matrices for estimating distances between aligned sequences
%I ETH Zurich
%M JUL
%D 1999
%K TR, MolBio, c1999, c199x, c19xx, zz0717, scoring, matrix, matrices, PAM,
   DNA alignment, distance, Dayhoff, phylogenetric trees
%X "Seq. alignment is typically the 1st step in many research areas of
   bioinformatics, where some form of score or distance is derived. ... Since
   those scores and distances are the basis for further studies, it is important
   that they can be estimated as well as possible. ... we prove that the scores
   obtained from Dayhoff matrices (or from any other matrix) are not consistent
   for tree construction. Then we show how this can be corrected and how to
   create an optimal scoring matrix to estimate distances. This scoring matrix
   is optimal within a large class of estimators. ..."
   -- ps@[ethz]['17].
   And a later 2004 version
   -- pdf@[gonnet.com]['17].

%A A. Prlic
%A et al
%A S. Willis
%T BioJava: an open-source framework for bioinformatics in 2012
%J J. Bioinformatics
%V 28
%N 20
%P 2693-2695
%M AUG
%D 2012
%K jrnl, MolBio, c2012, c201x, c20xx, zz0717, biology, platform, BioJava, Java,
   openSource, protein structure, sequence alignment
%X "BioJava is an open-source project for processing of biological data in the
   Java programming language. We have recently released a new version (3.0.5),
   which is a major update to the code base that greatly extends its
   functionality. ..."
   -- [doi:10.1093/bioinformatics/bts494]['17].
   Also see [www]['17].
   [Also search for: BioJava].

%A A. S. Konagurthu
%A A. M. Lesk
%T Structure description and identification using the tableau representation of
   protein folding patterns
%P 51-59
%B Protein Supersecondary Structures
%E A. E. Kister
%S Methods in Molec. Biol.
%I Springer
%D 2013
%K chapter, MolBio, c2013, c201x, c20xx, zz0717, protein, structure, 3D, fold,
   folding, tableau, motif, pattern, super secondary structure, superSecondary,
   AMLesk, ArunK, MMB
%X "... a concise tableau representation of protein folding patterns, based on
   the order & contact patterns of elts of secondary struct.: helices & strands
   of sheet. The tableaux provide a DB, derived from the protein data bank,
   minable for studies on the general principles of protein architecture, inc.
   investigation of the relationship between local supersecondary structure of
   proteins & the complete folding topology. This chapter outlines the tableaux
   representation of protein folding patterns & methods to use them to identify
   structural & substructural similarities."  [online July 2012.]
   -- [doi:10.1007/978-1-62703-065-6_4]['17].
   [Also search for: MolBio protein tableau].

%A I. Sillitoe
%A et al ...
%A C. A. Orengo
%T CATH: comprehensive structural and functional annotations for
   genome sequences
%J NAR
%M JAN
%D 2015
%K jrnl, NAR, MolBio, c2015, c201x, c20xx, zz0717, CATH, protein, structure, 3D,
   domain, domains, CATH40
%X "The latest version of the CATH-Gene3D protein structure classification
   database (4.0, [www]) provides
   annotations for over 235,000 protein domain structs. & inc. 25 million domain
   predictions. This article provides an update on the major developments in the
   2 years since the last publn in this j. including: sig. improvements to the
   predictive power of our functional families (FunFams); the release of our
   'current' putative domain assignments (CATH-B); a new, strictly non-redundant
   data set of CATH domains suitable for homology benchmarking experiments
   (CATH-40) and a number of improvements to the web pages."
   -- [doi:10.1093/nar/gku947]['17].

%A S. Shukla
%A et al
%T The Onion Genomic Resource: A genomics and bioinformatics driven resource for
   onion breeding
%J Plant Gene
%V 8
%P 9-15
%M DEC
%D 2016
%K jrnl, MolBio, c2016, c201x, c20xx, zz0717, plant, onion, Allium cepa L.,
   onions, crop, genome, nGenome, OGR
%X "... one of the most challenging plant species to be worked on ... houses
   information of assembly of 20,204 publicly available onion expressed sequence
   tags (ESTs), available 20,755 assembled transcripts and 249,987 unigenes from
   Allium cepa transcriptome shotgun assembly (TSA) along with their annotations
   and functional significance. ..."
   -- [doi:10.1016/j.plgene.2016.09.003]['17].
   Also see oniongenome.[net]['17].
   (NB. about 15GB! human 3GB.)

%A A. M. Calvin
%A et al
%T Childhood intelligence in relation to major causes of death in
   68 year follow-up: prospective population study
%J BMJ
%V 357
%P j2708
%M JUN
%D 2017
%K jrnl, BMJ, c2017, c201x, c20xx, zz0717, human, health, medicine, IQ, ageing,
   lifespan, longevity, risks
%X "... Childhood intelligence was inversely associated with all major causes of
   death. The age and sex adjusted hazard ratios (& 95% c.i.) per 1 SD (about
   15 points) advantage in intelligence test score were strongest for
   respiratory disease (0.72, 0.70 to 0.74), coronary heart disease (0.75,
   0.73 to 0.77), and stroke (0.76, 0.73 to 0.79). Other notable associations
   (all P < 0.001) were observed for deaths from injury (0.81, 0.75 to 0.86),
   smoking related cancers (0.82, 0.80 to 0.84), digestive disease (0.82,
   0.79 to 0.86), and dementia (0.84, 0.78 to 0.90). ..."
   -- [doi:10.1136/bmj.j2708]['17].

%A Y.-J. Feng
%A et al ...
%A P. Zhang
%T Phylogenomics reveals rapid, simultaneous diversification of three major
   clades of Gondwanan frogs at the Cretaceous-Paleogene boundary
%J PNAS
%V ?
%P ?-?
%M JUL
%D 2017
%K jrnl, PNAS, MolBio, c2017, c201x, c20xx, zz0717, animal, amphibian, Anura,
   frog, Hyloidea, Microhylidae, Natatanura, evolution, phylogenetic, tree,
   Cretaceous Paleogene bounday, K-Pg, KPg, KPB
%X "... using a molecular dataset of unprecedented size, inc. 88-kb characters
   from 95 nuclear genes of 156 frog species, [+] 20 fossil-based calibrations,
   our analyses result in the most strongly supported phylogeny of all major
   f.lineages and provide a timescale of f.evolution that suggests much younger
   divergence times than suggested by earlier studies. Unexpectedly, our
   divergence-time analyses show that three species-rich clades (Hyloidea,
   Microhylidae, & Natatanura), which together comprise ~ 88% of extant anuran
   species, simultaneously underwent rapid diversification at the
   Cretaceous-Paleogene (K-Pg) boundary (KPB) [66Mya]. [&] anuran families &
   subfamilies containing arboreal species originated near or after the KPB. ...
   suggest that the K-Pg mass extinction may have triggered explosive radiations
   of frogs by creating new ecological opportunities. ..."
   -- [doi:10.1073/pnas.1704632114]['17].
   (Also see the [bbc][3/7/2017].)

%A K. Kupferschmidt
%T Labmade smallpox is possible, study shows
%V Science
%V 357
%N 6347
%P 115-116
%M JUL
%D 2017
%K news, views, c2017, c201x, c20xx, zz0717, MolBio, smallpox, virux, variola,
   horsepox, poliovirus, disease, risk, risks, danger, security,
   mail order, GeneArt
%X "... Ever since virologists stitched together DNA seqs to make a poliovirus
   from scratch 15 years ago - a feat that triggered an intense debate about the
   risks of synthetic biology - researchers have said the same might be possible
   for a much more complex virus that causes the most feared infectious disease
   in human history: smallpox. ... In 2016, David Evans, a virologist at the U.
   of Alberta in Edmonton, Canada, led a team that quietly synthesized horsepox,
   a virus believed to have gone extinct decades ago, from DNA fragments ordered
   online and delivered in the mail. ..."
-- [doi:10.1126/science.357.6347.115]['17].

%A S. Kelk
%A F. Pardi
%A C. Scornavacca
%A L. van Iersel
%T Finding the most parsimonious or likely tree in a network with respect to an
   alignment
%J arXiv
%M JUL
%D 2017
%K TR, MolBio, c2017, c201x, c20xx, zz0717, multiple sequence alignment,
   parsimony, evolutionary, phylogenetic, tree, network
%X "Phylogenetic networks are often constructed by merging multiple conflicting
   phylogenetic signals into a directed acyclic graph. It is interesting to
   explore whether a n/wk constructed in this way induces biol.-relevant
   phylogenetic signals that were not present in the input. Here we show that,
   given a multiple alignment A for a set of taxa X & a rooted phylogenetic n/wk
   N whose leaves are labelled by X, it is NP-hard to locate the most
   parsimonious ph.tree displayed by N (wrt A) even when the level of N - the
   max. # of reticulation nodes within a biconnected component - is 1 & A
   contains only 2 distinct states. (If, additionally, gaps are allowed the
   problem becomes APX-hard.) We also show that under the same condns, &
   assuming a simple binary symmetric model of character evolution, finding the
   most likely tree displayed by the n/wk is NP-hard. These -ve results contrast
   with earlier work on parsimony in which it is shown that if A consists of a
   single column the problem is fixed parameter tractable in the level. We
   conclude with a discussion of why, despite the NP-hardness, both the
   parsimony & likelihood problem can likely be well-solved in practice."
   -- 1707.03648@[arXiv]['17].
   [Also search for: MolBio phylogenetic].

%A G. Rocklin
%A et al ...
%A D. Baker
%T Global analysis of protein folding using massively parallel design,
   synthesis, and testing
%J Nature
%V 357
%N 6347
%P 168-175
%M JUL
%D 2017
%K jrnl, MolBio, c2017, c201x, c20xx, zz0717, protein, fold, folds, folding,
   structure, 3D, design, Rosetta
%X "... We combined computational protein design, next-gen. gene synthesis, & a
   high-throughput protease susceptibility assay to measure folding & stability
   for > 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000
   point mutants, & 30,000 -ve control seqs.. ... identified > 2500 stable
   designed proteins in four basic folds - a # sufficient to enable us to
   systematically examine how seq. determines folding & stability in uncharted
   protein space. Iteration between design & experiment increased the design
   success rate from 6% to 47%, produced stable proteins unlike those found in
   nature for topologies where design was initially unsuccessful, & revealed
   subtle contributions to stability as designs became increasingly optimized.
   Our approach achieves the long-standing goal of a tight feedback cycle
   between computation & experiment & has the potential to transform
   computational protein design into a data-driven science."
   -- [doi:10.1126/science.aan0693]['17].

%A D. Graur
%T An upper limit on the functional fraction of the human genome
%J Genome Biol. Evol.
%V ?
%P evx121
%M JUL
%D 2017
%K jrnl, eJrnl, MolBio, c2017, c201x, c20xx, zz0717, human genome, junk DNA,
   useless, functional, purpose
%X "For the human pop'n to maintain a const. size from generation to generation,
   an increase in fertility must compensate for the reduction in the mean
   fitness of the pop'n caused, among others, by deleterious mutations. The
   required increase in fertility due to this mutational load depends on the
   # of sites in the genome that are functional, the mutation rate, & the
   fraction of deleterious mutations among all mutations in functional regions.
   These dependencies & the fact that there exists a max. tolerable replacement
   level fertility can be used to put an upper limit on the fraction of the
   h.genome that can be functional. Mutational load considerations lead to the
   conclusion that the functional fraction within the human genome cannot exceed
   25%, and is probably considerably lower."
   -- [doi:10.1093/gbe/evx121]['17].
   [Also search for: MolBio junk DNA].

%A J. B. Losos
%T Improbable Destinies: Fate, Chance, and the Future of Evolution
%I RiverheadBooks
%D 2017
%K book, text, c2017, c201x, c20xx, zz0717, biology, origins, life,
   convergent, divergent, chance, contingency
%X 1st ed 2017; hb us$18; uk us isbn:0399184929; uk us isbn13:978-0399184925.
   "Earth's natural history is full of fascinating instances of convergence:
   phenomena like eyes and wings and tree-climbing lizards that have evolved
   independently, multiple times. But evolutionary biologists also point out
   many examples of contingency, cases where the tiniest change - a random
   mutation or an ancient butterfly sneeze - caused evolution to take a
   completely different course. ..."
   (Also see [www]['17].)

%A M. Kwiek
%T Academic top earners. Research productivity, prestige generation, and
   salary patterns in European universities
%J Sci. and Public Policy
%M MAY
%D 2017
%K c2017, c201x, c20xx, zz0717, scientific research, university, academic,
   salary, work, jobs, success, funding, grants, Europe
%X "... While, in the Anglo-Saxon countries, the U.research mission typically
   pays off at an individual level, in Continental Europe, it pays off only in
   combination with administrative & related duties. Seeking future financial
   rewards solely through res. does not seem to be a viable strategy in Europe,
   but seeking satisfaction in res. through solving res. puzzles is also
   becoming difficult, with the growing emphasis on the 'relevance' &
   'applicability' of fundable research. Thus, both the traditional 'investment
   motivation' & 'consumption motivation' to perform research decrease, creating
   severe policy implications. The primary data come from 8,466 usable cases."
   -- [doi:10.1093/scipol/scx020]['17].

%T Let's talk about sex robots
%J Nature
%V 547
%N 7662
%P 138
%M JUL
%D 2017
%K editorial, news, views, c2017, c201x, c20xx, zz0717, doll, robot, sex,
   sexbot, humanoid, android, Jia Jia, JiaJia, Roxy, Roxxy, Roxxxy, Sinthetics,
   Realdoll, report, human, society
%X "... Enabling robots to read human behaviour and to respond in appropriate
   ways is a burgeoning area of research. As is the study of how humans will
   react to these potentially clever, personalized & ever-available companions.
   But there is another aspect of human-robot relationships that is rarely
   mentioned, & it's one on which robots could have just as great an impact as
   any other. Sex.  That reticence changed, at least in the United Kingdom, last
   week. A flurry of press reports followed the publication of a consultation
   report ..."
   -- [doi:10.1038/547138a]['17].
   (That report: 'Our Sexual Future with Robots',
   -- Foundation for Responsible Robotics
      [www]['17], pp.42 inc. refs.)

%A A. V. Whillians
%A et al
%T Buying time promotes happiness
%J PNAS
%V ?
%P ?-?
%M JUL
%D 2017
%K jrnl, PNAS, c2017, c201x, c20xx, zz0717, happiness, well being, wellbeing,
   satisfaction, time, wealth, society, USA
%X "... provide evidence that using money to buy time can provide a buffer
   against this time famine, thereby promoting happiness. Using large, diverse
   samples from the United States, Canada, Denmark, & The Netherlands (n=6,271),
   we show that individuals who spend money on time-saving services report
   greater life satisfaction. A field experiment provides causal evidence that
   working adults report greater happiness after spending money on a time-saving
   purchase than on a material purchase. Together, these results suggest that
   using money to buy time can protect people from the detrimental effects of
   time pressure on life satisfaction."
   -- [doi:10.1073/pnas.1706541114]['17].
   [Also search for: happiness well being].

%A E. Travers
%A C. D. Frith
%A N. Shea
%T Learning rapidly about the relevance of visual cues requires conscious
   awareness
%J Quarterly J. of Experimental Psychology
%M JUN
%D 2017
%K jrnl, c2017, c201x, c20xx, zz0717, brain, mind, consciousness, human,
   behaviour, learning, psychology, cognition, awareness, cue
%X "Humans have been shown capable of performing many cognitive tasks using
   info. of which they are not consciously aware. This raises Qs about what role
   consciousness actually plays in cognition. Here, we explored whether
   participants can learn cue-target contingencies in an attentional learning
   task when the cues were presented below the level of c.awareness, & how this
   differs from learning about c.cues. Participants' manual (Experiment 1) &
   saccadic (Exp.2) response speeds were influenced by both c. & unc. cues.
   However, participants were only able to adapt to reversals of the cue-target
   contingencies (Exp.1) or changes in the reliability of the cues (Exp.2) when
   consciously aware of the cues. Therefore, although visual cues can be
   processed unconsciously, learning about cues over a few trials requires
   c.awareness of them. Finally, we discuss implications for cognitive theories
   of consciousness."
   -- 7becr@[psyarxiv]['17],
   or e4cz7@[osf.io]['17],
   or [doi10.17605/OSF.IO/E4CZ7]['17].
   [Also search for: consciousness].

%A C. Kabadayi
%A M. Osvath
%T Ravens parallel great apes in flexible planning for tool-use and bartering
%J Science
%V 357
%N 6347
%P 202-204
%M JUL
%D 2017
%K c2017, c201x, c20xx, zz0717, animal, bird, raven, crow, corvid, corvids,
   behaviour, planning, learning, intelligence, memory
%X "... Corvids, however, have shown evidence of planning their food hoarding,
   although this has been suggested to reflect a specific caching adaptation
   rather than domain-general planning. Here, we show that ravens plan for
   events unrelated to caching - tool-use and bartering - with delays of up to
   17 hours, exert self-control, and consider temporal distance to future
   events. Their performance parallels that seen in apes and suggests that
   planning evolved independently in corvids, which opens new avenues for the
   study of cognitive evolution."
   -- [doi:10.1126/science.aam8138]['17].

%A A. M. Khalili
%T On the mathematics of beauty: beautiful music
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, music, beauty, Dyson distribution,
   regularity, randomness
%X "...  we will study the simplest kind of beauty that can be found in a simple
   piece of music & can be appreciated universally. The proposed model suggest
   that there is a link between beautiful music & the Dyson distribution which
   seems to be the result of a deeper optimisation process between randomness &
   regularity. Then we show that beautiful music need to satisfy a more
   fundamental law that seeks to deliver the highest amount of information
   using the least amount of energy. The proposed model is tested on a set of
   beautiful music pieces."
   -- 1707.06510@[arXiv]['17].

%A P. Ball
%T How quantum trickery can scramble cause and effect
%J Nature
%V 546
%P 590-592
%M JUN
%D 2017
%K views, c2017, c201x, c20xx, zz0717, physics, quantum theory, mechanics,
   qubit, qubits, information, paths, Walther, causal, ambiguity, causality,
   indeterminacy, Copenhagen interpretation, superposition, Chiribella, Brukner
%X "... Albert Einstein is heading out for his daily stroll & has to pass
   through two doorways. First he walks through the green door, & then through
   the red one. Or wait - did he go through the red first & then the green? ...
   Walther's group has shown that it is impossible to say in which order these
   photons pass through a pair of gates as they zip around the lab. It's not
   that this information gets lost or jumbled - it simply doesn't exist. In
   Walther's experiments, there is no well-defined order of events. This finding
   in 2015 ..."   [11 refs.]
   -- [doi:10.1038/546590a]['17].

%A D. Castelvecchi
%T The strange topology that is reshaping physics
%J Nature
%V 547
%N 7663
%P ?-?
%M JUL
%D 2017
%K news, views, c2017, c201x, c20xx, zz0717, physics, quantum, chemistry,
   topology, topological, effects, Thouless, Hall effect, insulator, Hasan
%X "Topological effects might be hiding inside perfectly ordinary materials,
   waiting to reveal bizarre new particles or bolster quantum computing. ...
   In the past decade, they have found that topology provides unique insight
   into the physics of materials, such as how some insulators can sneakily
   conduct electricity along a single-atom layer on their surfaces. ... Some of
   the most fundamental properties of subatomic particles are, at their heart,
   topological. Take the spin of the electron, for example ..."
   -- [doi:10.1038/547272a]['17].
   Also see 'Topological quantum chemistry',
   -- [doi:10.1038/nature23268]['17].

%A J. Y. Halpern
%A R. Pass
%T A knowledge-based analysis of the blockchain protocol
%J arXiv
%M JUL
%D 2017
%K TR, c2017, c201x, c20xx, zz0717, blockchain, block chain, protocol,
   bitCoin, bitCoins, virtual currency
%X "At the heart of the Bitcoin is a blockchain protocol, a protocol for
   achieving consensus on a public ledger that records bitcoin transactions. To
   the extent that a blockchain protocol is used for applications such as
   contract signing and making certain transactions (such as house sales)
   public, we need to understand what guarantees the protocol gives us in terms
   of agents' knowledge. Here, we provide a complete characterization of agent's
   knowledge when running a blockchain protocol using a variant of common
   knowledge that takes into account the fact that agents can enter and leave
   the system, it is not known which agents are in fact following the protocol
   (some agents may want to deviate if they can gain by doing so), and the fact
   that the guarantees provided by blockchain protocols are probabilistic. We
   then consider some scenarios involving contracts and show that this level of
   knowledge suffices for some scenarios, but not others."
   -- 1707.08751@[arXiv]['17].