Search engine run on: http://users.monash.edu.au/
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%T Int. Symp. on Practical Aspects of Declarative Languages
%K PADL, PADL5,PADDL03,2003, PADL6,PADL04,2004, PADL7,PADL05,2005,
PADL8,PADL06,2006, PADL10,2008, PADL11,2009, PADL12,2010, PADL16,2014,
PADL18,2016, PADL19,2017, PADL20,2018, PADL21,2019, PADL22,2020, PADL23,2021,
CFP,conf,programming,applications,FP,LP,www,HREF,http, zz0921, zz0920
%X [2021 Jan 18-19] where?, deadline 9 Oct 2020
[2020 Jan 20-21] New Orleans
[2019 Jan 14-15] Lisbon, deadline 26 Sept 2018
[2018 Jan 8-9], LA
[2017 Jan 18-20] Paris, deadline 12 Sep 2016.
[2003 Jan 13-14] New Orleans, deadline 5 Aug 2002
(.ps or .pdf, 15p, 11pt, single spaced.)
[Also search for: FP].
%A D. Shanks
%T Class number, a theory of factorization and genera...
%J Proc. Symp. Pure Math., Prov., R.I.
%K conf, c1971, c197x, c19xx, zz0920, baby step giant step algorithm,
discrete logarithm, log, Dlog, order, group, factorization, factor,
integer factorisation, primes
%X See, "... a meet-in-the-middle alg. for computing the discrete logarithm or
order of an elt in a finite abelian group due to Daniel Shanks ..."
-- BSGS@[wikip]['20] inc. the algorithm,
Also see DL@[wikip]['20].
[Also search for: discrete logarithm].
%A C. Levinthal
%T How to fold graciously
%J Mossbauer Spectroscopy in Biol. Sys.
%W Proc. of a mtg at Allerton House, Monticello, Illinois
%K conf, MolBio, c2020, c202x, c20xx, zz0920, protein fold, folding, structure,
Levinthal's paradox, energy, proteins, 3D
%X "... If we consider a protein containing 2,000 atoms with no structural
restrictions, such a macromolecule would possess 6,000 degrees of freedom.
... is the final conformation necessarily the one of lowest free energy? We
do not feel that it has to be. It obviously must be a metastable state which
is in a sufficiently deep energy well to survive possible perturbations in a
biological system. If it is the lowest energy state, we feel it must be the
result of biological evolution; i.e., the first deep metastable trough
reached during evolution happened to be the lowest energy state. You may then
ask the question, 'Is a unique folding necessary for any random 150-amino
acid sequence?' & I would answer, 'Probably not.' Some experimental support
for this statement comes from the difficulty many of us are all too aware of
in attempting to crystallize peptides. ..."
Also see Lparadox@[wikip]['20].
[Also search for: MolBio Anfinsen dogma].
%A R. Doolittle
%T Of Urfs and Orfs: A Primer on How to Analyze Derived Amino Acid Sequences
%K book, text, MolBio, c1986, c1998x, c19xx, zz0920, ORF, DNA, genetics
%X 2nd edn 1991; pb us$47; uk us isbn: 0935702547; uk us isbn13:978-0935702545.
"... seq. is 'open' when read in an appropriate frame, which is to say that
there is a long run of AA codons before the appearance of a terminator codon.
How can we find out if this 'unidentified reading frame' (URF) really codes
for a genuine protein, and how can we identify it if it exists? ..."
%A B. J. Strait
%A T. G. Dewey
%T The Shannon information entropy of protein sequences
%J Biophys. J.
%K jrnl, MolBio, c1996, c199x, c19xx, zz0920, protein sequence, entropy,
compress, compression, bits
%X "... info. ent. is est. by three methods: a k-tuplet analysis, a generalized
Zipf analysis, and a 'Chou-Fasman gambler.' ... The Zipf analysis & k-tuplet
analysis give Shannon entropies of ~2.5 bits/amino acid. This entropy is much
smaller than the value of 4.18 bits/amino acid obtained from the nonuniform
composition of amino acids in proteins. ..."
[Also search for: MolBio protein compressible].
%A Yuan-Ping Pang
%A et al ...
%A S. Brimijoin
%T Selective and irreversible inhibitors of mosquito Acetylcholinesterases for
controlling malaria and other mosquito-borne diseases
%J PLoS One
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920, AMTS 17, AMTS17, BPA 11, BPA11,
methanethiosulfonate, insect, insecticide, mosquito, aphid,
acetylcholinesterase, AChE, inhibitor, cysteine, Cys
%X "... a free [Cys] residue at the entrance of the active site of
acetylcholinesterase (AChE) in some insects but not in mammals, birds, &
fish. These insects have two AChE genes (AP & AO), & only AP-AChE carries the
Cys residue. ... Recently we reported a Cys-targeting small molecule that
irreversibly inhibited all AChE activity extracted from aphids while an
identical exposure caused no effect on the human AChE. Full inhibition of
AChE in aphids indicates that AP-AChE contributes most of the enzymatic
activity & suggests that the Cys residue might serve as a target for
developing better aphicides. ..."
[Also search for: MolBio Cys inhibitor].
%A J. A. Jaimes
%A et al
%T Phylogenetic analysis and structural modeling of SARS-CoV-2 spike protein
reveals an evolutionary distinct & proteolytically sensitive activation loop
%J J. Mol. Biol.
%K jrnl, JMB, MolBio, c2020, c202x, c20xx, zz0920, SARS-CoV-2, SARSCoV2, SARS2,
spike protein, phylogeny, tree, betacoronavirus
%X "... we perform structural modeling of the SARS-CoV-2 spike glycoprotein. Our
data provide support for the similar receptor utilization between SARS-CoV-2
and SARS-CoV, despite a relatively low amino acid similarity in the receptor
binding module. ..."
%A G. Andreatta
%A K. Tessmar-Raible
%T The still dark side of the Moon: Molecular mechanisms of lunar-controlled
rhythms and clocks
%K jrnl, JMB, MolBio, c2020, c202x, c20xx, zz0920, biology, biol, clock, cycle,
cyclic, rythm, moon, lunar, circatidal, circalunar, circadian, transcriptome,
%X "... many marine species exhibit lunar rhythms, and also the number of
documented 'lunar-rhythmic' terrestrial species is increasing. ..."
[Also search for: moon lunar].
%A K. H. Miga
%A et al ...
%A A. M. Phillippy
%T Telomere-to-telomere assembly of a complete human X chromosome
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920, human, genome, X chromosome,
Xchromosome, chromosomeX, Xchr, chrX, GRCh38, CHM13
%X "... we present a human genome assembly that surpasses the continuity of
GRCh382, along with a gapless, telomere-to-telomere assembly of a human
chromosome. This was enabled by high-coverage, ultra-long-read nanopore
seq. of the complete hydatidiform mole CHM13 genome, combined with
complementary technologies for quality improvement & validation. Focusing our
efforts on the human X chromosome3, we reconstructed the centromeric
satellite DNA array (~3.1 Mb) & closed the 29 remaining gaps ..."
%A A. D. Rathnayake
%A et al ...
%A Kyeong-Ok Chang
%T 3C-like protease inhibitors block coronavirus replication in vitro and
improve survival in MERS-CoV-infected mice
%J Sci. Trans. Med.
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0920, MERS, protease inhibitor,
3CLpro, Mpro, mouse, SARS, SARS1, MERSCov, MERS, SARS2,
Huh-7, Huh7, Vero E6, VeroE6
%X "... We describe herein the struct.-guided optimization of a series of
inhibitors of the coronavirus 3C-like protease (3CLpro), an enzyme essential
for viral replication. The optimized compounds were effective against several
human coronaviruses including MERS-CoV, SARS-CoV, and SARS-CoV-2 in an enzyme
assay & in cell-based assays using Huh-7 and Vero E6 cell lines. ... [mouse]
survival [went] from 0 to 100% ..."
[Also search for: MolBio 3CLpro inhibitor].
%A W. Vuong
%A et al ...
%A M. J. Lemieux
%T Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and
blocks virus replication
%J Nat. Comms.
%K jrnl, eJrnl, MolBio, c2020, c202x, c20xx, zz0920, SARS, SARS2, SARSCoV2,
protease, inhibitor, drug, cat, cats, feline, GC373, GC376, Cys145
%X "... prodrug GC376, a dipeptide-based p.inhibitor. Here, we show the prodrug
& its parent GC373, are effective inhibitors of the Mpro from both SARS-CoV
& SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of
SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the
nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via
reversible formation of a hemithioacetal. GC373 & GC376 are potent inhibitors
of SARS-CoV-2 replic'n in cell culture. They are strong drug candidates ..."
[Also search for: SARSCoV2 inhibitor].
%A M. Thoms
%A et al ...
%A R. Beckmann
%T Structural basis for translational shutdown and immune evasion by the Nsp1
protein of SARS-CoV-2
%K jrnl, MolBio, c2020, c202x, c20xx, zz0920, SARSCoV2, nsp1, protein,
%X "... virulence factor nonstructural protein 1 (Nsp1) also shuts down
translation of host messenger RNA. Thoms et al. determined a 2.6A resolution
cryo-electron microscopy structure of a reconstituted complex of Nsp1 bound
to the human 40S ribosomal subunit and showed that Nsp1 blocks the mRNA
entry tunnel. ..."
[Also search for: SARSCoV2 Nsp1].
%A R. Bird
%A J. Gibbons
%T Algorithm Design with Haskell
%K book, text, c2020, c202x, c20xx, zz0620, zz0920, FP, Functional Programming,
CUP, Haskell, computer programming, algorithms
%X 1st ed 2020; hb us$65; uk us isbn:1108491618; uk us isbn13:978-1108491617.
"...devoted to five main principles of algorithm design: divide & conquer,
greedy algorithms, thinning, dynamic programming, & exhaustive search. ..."
[Also search for: FP Functional Programming].
%A R. Cellan-Jones
%T Women in computing - there is good news and bad
%K News, c2020, c202x, c20xx, zz0920, computing CSci, CompSci, GCSE, women,
girls, STEM, UK, GCSE, ICT, CSci, CompSci, school, schools,
Durham University, Uni
%X "... The good news: a major university has doubled the number of women
arriving to study computer science in the space of a year. The bad: the
latest GCSE figures show the number of girls getting any kind of computing
qualification at school continues to decline. ..."
%A C. Laufkotter
%A J. Zscheischler
%A T. L. Frolicher
%T High-impact marine heatwaves attributable to human-induced global warming
%K jrnl, c2020, c202x, c20xx, zz0920, climate change, CO2, attributing, severe,
attribution, weather events, heatwave, MHW, MHWs, stats, greenhouse gas,
%X "... We show that the occurrence probs. of the duration, intensity, &
cumulative intensity of most documented, large, & impactful MHWs have
increased more than 20-fold as a result of anthropogenic climate change.
MHWs that occurred only once every hundreds to thousands of years in the
preindustrial climate are projected to become decadal to centennial events
under 1.5C warming conditions & annual to decadal events under 3C warming
%A N. DeVito
%A et al
%T How we learnt to stop worrying and love web scraping
%K views, intro, c2020, c202x, c20xx, zz0920, web scraper, webScraper,
www, HTML, BeautifulSoup, rvest, data
%X -- [doi:10.1038/d41586-020-02558-0]['20].
%A D. P. Friedman
%A C. Eastlund
%T The Little Prover
%K CompSci, CSCI, book, text, c2015, c201x, c20xx, zz0920, program, proof,
logic. correctness, theorem prover, proving, computer programming
%X 1st ed 2015; pb us$40; uk us Isbn:0262527952; uk us isbn13:978-0262527958.
"... a gentle intro. to the nuts & bolts of formal proofs about programs.
Following on from The Little Schemer, it is an excellent guide for both
thoughtful FP'ers wondering what it really means to know that a program is
correct & do-it-yourselfers who want a taste of how proof assistants like
ACL2 do their work. ...”
[Also search for: theorem prover].
%A H. Barrow
%A R. Burstall
%T Subgraph isomorphism, matching relational structures and maximal cliques
%K jrnl, IPL, c1976, c197x, c19xx, zz0920, maths, graph, maximal clique,
%X -- [doi:10.1016/0020-0190(76)90049-1]['20].
(Also see MCS@[wikip]['20].)
[Also search for: graphAlignment].
%A N. Alon
%A R. Yuster
%A U. Zwick
%K Jrnl, JACM, c1995, c199x, c19xx, zz0920, Noga, NAlon, maths, graph, path,
cycle, colour coding, randomized algorithm, randomised
%X "We describe a novel randomized method, the method of color-coding for
finding simple paths & cycles of a specified length k, & other small
subgraphs, within a given graph G=(V,E). The randomized algs obtained using
this method can be derandomized using families of perfect hash fns ..."
%A L. A. Zager
%A G. C. Verghese
%T Graph similarity scoring and matching
%J Appl. Math. Lett.
%K jrnl, AML, c2008, c200x, c20xx, zz0920, maths, graph, similarity, matching,
%X "We outline a class of g.similarity measures that uses the struct. sim. of
local n'hoods to derive pairwise sim.scores for the nodes of two different
gs., & present a related sim.measure that uses a linear update to generate
both node & edge sim.scores. ... then applied to the task of g.matching."
[Also search for: graphAlignment] and [also search for: graph MCS].
%A V. Lyubashevsky
%A C. Peikert
%A O. Regev
%T On ideal lattices and learning with errors over rings
%J Cryptology ePrint Archive: Report 2012/230
%K TR, c2012, c201x, c20xx, zz0920, ring learning with errors, RLWE, LWE,
problem, lattice, ring, homomorphic encryption, pseudorandom
%X "The 'learning with errors' (LWE) problem is to distinguish random linear
equations, which have been perturbed by a small amount of noise, from truly
uniform ones. The problem has been shown to be as hard as worst-case lattice
problems ... we show that the ring-LWE distribution is pseudorandom, assuming
that worst-case problems on ideal lattices are hard for polynomial-time
quantum algs.. Applications include the first truly practical lattice-based
public-key cryptosystem ..."
Also see RLWE@[wikip]['20] (learning with errors over rings).
[Also search for: homomorphic encryption].
%A E. Duesbury
%A J. Holliday
%A P. Willett
%T Comparison of maximum common subgraph isomorphism algorithms for the
alignment of 2D chemical structures
%J Spec. Issue: Cheminformatics in Drug Discovery
%K c2017, c201x, c20xx, zz0920, maths, graph, MCS, similarity, graphAlignment,
matching, large, maximum common subgraph, MCSG, chemical molecule, fMCS,
MaxCliquesSeq, ChemAxon, ChemAxon_MCS, algorithm, MolBio, chemical, compound,
%X "The identification of the largest substructure in common when two (or more)
molecules are overlaid ... The fastest exact algs. for the connected &
disconnected problems were found to be the fMCS & MaxCliqueSeq algs., resp.,
while the ChemAxon_MCS alg. was the fastest approximate alg. for both types
[Also search for: graphAlignment] and [also search for: MCS graph].
Also see MCS@[wikip]['20].
%A A. Conte
%A et al
%T A fast discovery algorithm for large common connected induced subgraphs
%J Spec. Issue of Discr. Maths (sub.)
%K TR, c2018, c201x, c20xx, zz0920, maths, graph, common subgraph, MCS, MCSG,
MolBio, protein, chemical, molecule
%X "... fast alg. for the classical problem of finding common subgraphs, which
are useful for detecting struct. relationships between biol. macromolecules.
Although the cost is potentially high for this hard problem, we improve
performance by several orders of mag. [v] known algs. We validate our
findings with experiments on proteins with thousands of atoms."
[Also search for: graph MCS].
%A M. Bressan
%A S. Leucci
%A A. Panconesi
%T Faster motif counting via succinct color coding and adaptive sampling
%K TR, c2020, c202x, c20xx, zz0920, maths, graph, motif, network, motifs,
pattern, count, frequent, colour
%X "... the problem of computing the dist'n of induced connected subgs., aka
graphlets or motifs, in large gs.. The current state-of-the-art algs. est.
the motif counts via uniform sampling, by leveraging the color coding
technique by Alon, Yuster & Zwick ... We extend the applicability of this
approach, by introducing a set of alg. optimizations & techniques that reduce
the running time & space usage ... improve the accuracy of the counts. ...
first show how to optimize color coding ... For 8-node motifs, we can build
[a] table in one hour for a g. with 65M nodes & 1.8B edges, which is 2000
times larger than the state of the art. We then intro. a novel adaptive
sampling scheme that breaks the 'additive error barrier' of uniform sampling,
... allows us to count not only the most freq. motifs, but also extremely
rare ones. [eg], on one graph we accurately count nearly 10,000 distinct
8-node motifs ..."
[Also search for: NAlon graph].
%A E. K. Chen
%T Quantum mechanics in a time-asymmetric universe: On the nature of the
initial quantum state
%J British J. for the Philosophy of Sci., axy068
%K jrnl, c2020, c202x, c20xx, zz0920, Eddy Keming Chen, physics, arrow of time,
asymmetric, past, future, quantum mechanics
%X "In a q.universe with a strong arrow of time, we postulate a low-entropy
boundary condition (the past hypothesis, PH) to account for the temporal
asymmetry. In this article, I show that the PH also contains enough info. to
simplify the q.ontology and define a natural initial condition. First, I
introduce 'density-matrix realism', the thesis that the q.state of the
universe is objective and impure. This stands in sharp contrast to
wave-function realism ..."
%A C. R. Harris
%A et al
%T Array programming with NumPy
%K review, c2020, c202x, c20xx, zz0920, Python, NumPy, numerical methods,
algorithms, array, arrays
%X "... NumPy is the primary array programming library for the
Python language ..."
%A Mark Zuckerberg
%T Zuckerberg quotes
%K Zuckerberg emails, Facebook, www, social media, sharing, quote, quotable,
c2012, c201x, c20xx, zz0920, UK, privacy
%X "That may be good for the world, but it's not good for us,"
Zuckerberg wrote in a 2012 email.
-- [The-G][5/12/2018], J.C.Wong.
[Also search for: Facebook].
%A Y. Sakai
%T Maximal common subsequence algorithms
%K jrnl, TCS, c2019, c201x, c20xx, zz0920, maximal common subsequence, MCS,
MCSS, LCS, algorithm, string, strings
%X "A common subseq. of two strings is maximal if inserting any char. into it
no longer yields a common subseq.. ... proposes a (sub)linearithmic-time,
linear-space alg. for finding a MCS of two strings & a linear-time alg. for
determining if a common subseq. of two strings is maximal."
%A Jin Cao
%A Dewei Zhong
%T A fast randomized algorithm for finding the maximal common subsequences
%K TR, c2020, c202x, c20xx, zz0920, multiple, string, strings,
maximal common subsequence, MCS, MCSS, LCS
%X "... we develop a randomized alg., referred to as Random-MCS, for finding a
random inst. of [MCS] of multiple strings. ... We show the complexity of our
alg. is linear in L [# strings], & therefore is suitable for large L. ...
study the occurrence prob. for a single instance of MCS & demo. via both
theor. and exp. studies that the LCS from multiple runs of Random-MCS often
yields a solution to LCS."
[Also search for: string MCS algorithm] (or try MCS -> LCS).
%A L. Jordon
%A P. Moser
%T A normal sequence compressed by PPM* but not by Lempel-Ziv 78
%K TR, c2020, c202x, c20xx, zz0920, string, compression, PPM, PPM*, LZ78
%X "... compare the difference in performance of two of the Prediction by
Partial Matching (PPM) family of compressors (PPM* and the original Bounded
PPM alg.) & the Lempel-Ziv 78 (LZ) alg.. We construct an infinite binary seq.
whose worst-case compression ratio for PPM* is 0, while Bounded PPM's & LZ's
best-case comp.ratios are at least 1/2 & 1 resp.. This seq. is an enum. of
all binary strings in order of length, i.e. all strings of length 1 followed
by all strings of length 2 & so on. It is therefore normal, & is built using
repetitions of deBruijn strings of increasing order."
%A A. Bruns
%A S. Harrington
%A E. Hurcombe
%T 'Corona? 5G? or both?': The dynamics of COVID-19/5G conspiracy theories on
%J Media Int. Au.
%K jrnl, c2020, c202x, c20xx, zz0920, covid 19, 5G, fiveG, altright, QAnon,
conspiracy theory, Trumpery, Trumpistan, misinformation, disinformation,
spread, rumour, rumours, denier, Facebook, Twitter, social media, www
%X "... Drawing on a mixture of quantitative & qualitative methods inc.
time-series analysis, n/wk analysis & in-depth close reading, our analysis
shows the dissemination of the rumour on Facebook from its obscure origins
in pre-existing conspiracist groups through greater uptake in more diverse
communities to substantial amplification by celebrities, sports stars & media
outlets. The in-depth tracing of COVID-related mis- & disinformation across
social n/wks offers important new insights into the dynamics of online ..."
-- [doi:10.1177/1329878X20946113]['20]. (auth1@QUT.)