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%A Z. Merali
%T Pulsar discoverer Jocelyn Bell Burnell wins $3-million Breakthrough Prize
%J Nature
%V 561
%P 161
%M SEP
%D 2018
%K Jocelyn Bell, news, c201, c201x, c20xx, zz0918, astronomy, physics, pulsar,
   pulsars, Hewish, Nobel(not) prize, NobelPrize, women, STEM, science
%X "Fifty years after discovering pulsars - compact rotating stars that emit
   beams of radiation - astrophysicist Jocelyn Bell Burnell has been awarded
   one of the most lucrative prizes in science: a US$3-million Breakthrough
   prize. ... In 1974, Hewish shared the Nobel Prize in Physics with fellow
   radio astronomer Martin Ryle, for pioneering research in astrophysics.
   Hewish was cited for his 'decisive role in the discovery of pulsars' - while
   Bell Burnell was overlooked. Bell Burnell herself has previously stated
   that she does not mind the oversight because she understands that
   Nobel prizes are not usually awarded to research students. ..."
   -- [doi:10.1038/d41586-018-06210-w]['18].
   [Also search for: Bell pulsar].

%T Celebrate the mathematics of Emmy Noether
%J Nature
%V 561
%N ?
%P 149-150
%M SEP
%D 2018
%K Noether, Emmy, c2018, c201x, c20xx, zz0918, maths, math, mathematician,
   mathematics, STEM, women, woman, Noetherian, ring, biog
%X Emmy Noether (23/3/1882 - 14/4/1935).
   "Emmy Noether was a force in mathematics - & knew it. She was fully
   confident in her capabilities & ideas. Yet a century on, those ideas, &
   their contribution to science, often go unnoticed. Most physicists are aware
   of her fundamental theorem, which puts symmetry at the heart of physical law.
   But how many know anything of her & her life? ..."
   -- editorial@[doi:10.1038/d41586-018-06658-w]['18].
   (*See EM@[wikip]['21].*)

%A S. R. Eddy
%T A probabilistic model of local sequence alignment that simplifies statistical
   significance estimation
%J PLoS Computational Biol.
%M MAY
%D 2008
%K jrnl, eJrnl, MolBio, c2008, c200x, c20xx, zz0918, HMMER, HMM, HMMER2,
   protein, alignment, profile
%X "... Optimal local seq. alignment scores follow Gumbel distributions, but
   determining an important param. of the distribution (L) requires
   time-consuming computational simulation. Moreover, optimal alignment scores
   are less powerful than probabilistic scores that integrate over alignment
   uncertainty ('Forward' scores), but the expected distribution of Forward
   scores remains unknown. Here, I conjecture that both expected score distns
   have simple, predictable forms when full probabilistic modeling methods are
   used. For a probabilistic model of local seq. alignment, optimal alignment
   bit scores ('Viterbi' scores) are Gumbel-distributed with constant L = log 2,
   & the high scoring tail of Forward scores is exponential with the same
   constant L. Simulation studies support these conjectures over a wide range of
   profile/seq. comparisons, using 9,318 profile-hidden Markov models from the
   Pfam database. This enables efficient & accurate determination of
   expectation values (E-values) for both Viterbi & Forward scores for
   probabilistic local alignments."
   -- [doi:10.1371/journal.pcbi.1000069]['18], [hmmer.org]['18].
   [Also search for: HMMER].

%A J. J. Walsh
%A et al ...
%A M. S. Tremblay
%T Associations between 24 hour movement behaviours and global cognition in
   US children: a cross-sectional observational study
%X The Lancet
%V ?
%M SEP
%D 2018
%K jrnl, c2018, c201x, c20xx, zz0918, health, human, child, early childhood,
   children, development, health, electronic devices, internet, www, web,
   device, TV, tablet, screen, screens, time, cognition, exercise
%X "... Complete movement behaviour data were available for 4520 participants.
   The mean # of guideline recommendations met was 1.1 (SD 0.9). Overall, 2303
   (51%) participants met the sleep recommendation, 1655 (37%) met screen time,
   & 793 (18%) met the physical activity r.. 3190 (71%) participants met at
   least one r., whereas 216 (5%) of participants met all three recommendations.
   Global cognition was + assoc. with each additional recommendation met
   (b=1.44, 95% CI 0.82-2.07, p < 0.0001). Compared with meeting none of the
   recommendations, associations with superior global cognition were found in
   participants who met all three recommendations (b=3.89, 95% CI 1.43 to 6.34,
   p=0.0019), the screen time recommendation only (b=4.25, 2.50-6.01,
   p < 0.0001), & both the screen time and the sleep recommendations (b=5.15,
   3.56-6.74, p < 0.0001).  ..."
   -- [doi:10.1016/S2352-4642(18)30278-5]['18].
   (Also see the [bbc][27/9/2018].)

%A J. P. A. Ioannidis
%A R. Klavans
%A K. W. Boyack
%T Thousands of scientists publish a paper every five days
%J Nature
%V 561
%P 167-169
%M SEP
%D 2018
%K news, views, c2018, c201x, c20xx, zz0918, publish, perish, scientific,
   research, paper, papers, Scopus, guest authorship, implausibly prolific,
   questionable, dubious, publication, glut, Hindex, KPI, KPIs
%X "... We searched Scopus for authors who had published more than 72 papers
   (the equivalent of one paper every 5 days) in any one calendar year between
   2000 and 2016, a figure that many would consider implausibly prolific. We
   found more than 9,000 individuals, and made every effort to count only
   'full papers' - articles, conference papers, substantive comments and
   reviews - not editorials, letters to the editor and the like. We hoped that
   this could be a useful exercise in understanding what scientific authorship
   means. ..."
   --  [doi:10.1038/d41586-018-06185-8]['18].
   [Also search for: publish perish] & [also search for: implausibly prolific].

%A T. Gagie
%A G. Gourdel
%A G. Navarro
%A J. Simpson
%T The read-optimized Burrows-Wheeler transform
%M SEP
%D 2018
%K TR, c2018, c201x, c20xx, zz0918, BWT, MolBio, FM index, FMindex
%X "The advent of high-throughput sequencing has resulted in massive genomic
   datasets, some consisting of assembled genomes but others consisting of raw
   reads. We consider how to reduce the amount of space needed to index a set of
   reads, in particular how to reduce the number of runs in the Burrows-Wheeler
   Transform (BWT) that is the basis of FM-indexing. The best current
   fully-functional index for repetitive collections (Gagie et al., SODA 2018)
   uses space proportional to this number.
   -- 1809.07320@[arXiv]['18].