1,143 research outputs found
A Polynomial Spectral Calculus for Analysis of DG Spectral Element Methods
We introduce a polynomial spectral calculus that follows from the summation
by parts property of the Legendre-Gauss-Lobatto quadrature. We use the calculus
to simplify the analysis of two multidimensional discontinuous Galerkin
spectral element approximations
Towards Reliable Automatic Protein Structure Alignment
A variety of methods have been proposed for structure similarity calculation,
which are called structure alignment or superposition. One major shortcoming in
current structure alignment algorithms is in their inherent design, which is
based on local structure similarity. In this work, we propose a method to
incorporate global information in obtaining optimal alignments and
superpositions. Our method, when applied to optimizing the TM-score and the GDT
score, produces significantly better results than current state-of-the-art
protein structure alignment tools. Specifically, if the highest TM-score found
by TMalign is lower than (0.6) and the highest TM-score found by one of the
tested methods is higher than (0.5), there is a probability of (42%) that
TMalign failed to find TM-scores higher than (0.5), while the same probability
is reduced to (2%) if our method is used. This could significantly improve the
accuracy of fold detection if the cutoff TM-score of (0.5) is used.
In addition, existing structure alignment algorithms focus on structure
similarity alone and simply ignore other important similarities, such as
sequence similarity. Our approach has the capacity to incorporate multiple
similarities into the scoring function. Results show that sequence similarity
aids in finding high quality protein structure alignments that are more
consistent with eye-examined alignments in HOMSTRAD. Even when structure
similarity itself fails to find alignments with any consistency with
eye-examined alignments, our method remains capable of finding alignments
highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Mutant screen reveals the Piccolo's control over depression and brain-gonad crosstalk
Successful sexual reproduction involves a highly complex, genetically encoded interplay between animal physiology and behavior. Here we developed a screen to identify genes essential for rat reproduction based on an unbiased methodology involving mutagenesis via the Sleeping Beauty transposon. As expected, our screen identified genes where reproductive failure was connected to gametogenesis (Btrc, Pan3, Spaca6, Ube2k) and embryogenesis (Alk3, Exoc6b, Slc1a3, Tmx4, Zmynd8). In addition, our screen identified Atg13 (longevity) Dlg1 and Pclo (neuronal disorders), previously not associated with reproduction. Dominant Pclo traits caused epileptiform activity and affected genes supporting GABAergic synaptic transmission (Gabra6, Gabrg3), and animals exhibited a compromised crosstalk between the brain and gonads via disturbed GnRH signaling. Recessive Pclo traits disrupted conspecific recognition required for courtship/mating and were mapped to allelic markers for major depressive disorder (Grm5, Htr2a, Sorcs3, Negr1, Drd2). Thus, Pclo-deficiency in rats link neural networks controlling sexual motivation to Pclo variants that have been associated with human neurological disorders
Partial Wave Analysis of
BES data on are presented. The
contribution peaks strongly near threshold. It is fitted with a
broad resonance with mass MeV, width MeV. A broad resonance peaking at 2020 MeV is also required
with width MeV. There is further evidence for a component
peaking at 2.55 GeV. The non- contribution is close to phase
space; it peaks at 2.6 GeV and is very different from .Comment: 15 pages, 6 figures, 1 table, Submitted to PL
Measurements of the observed cross sections for exclusive light hadrons containing at , 3.650 and 3.6648 GeV
By analyzing the data sets of 17.3, 6.5 and 1.0 pb taken,
respectively, at , 3.650 and 3.6648 GeV with the BES-II
detector at the BEPC collider, we measure the observed cross sections for
, , ,
and at the three energy
points. Based on these cross sections we set the upper limits on the observed
cross sections and the branching fractions for decay into these
final states at 90% C.L..Comment: 7 pages, 2 figure
Partial wave analysis of J/\psi \to \gamma \phi \phi
Using events collected in the BESII detector, the
radiative decay is
studied. The invariant mass distribution exhibits a near-threshold
enhancement that peaks around 2.24 GeV/.
A partial wave analysis shows that the structure is dominated by a
state () with a mass of
GeV/ and a width of GeV/. The
product branching fraction is: .Comment: 11 pages, 4 figures. corrected proof for journa
Direct Measurements of Absolute Branching Fractions for D0 and D+ Inclusive Semimuonic Decays
By analyzing about 33 data sample collected at and around 3.773
GeV with the BES-II detector at the BEPC collider, we directly measure the
branching fractions for the neutral and charged inclusive semimuonic decays
to be and , and determine the ratio of the two branching
fractions to be
Measurements of the observed cross sections for exclusive light hadron production in e^+e^- annihilation at \sqrt{s}= 3.773 and 3.650 GeV
By analyzing the data sets of 17.3 pb taken at GeV
and 6.5 pb taken at GeV with the BESII detector at the
BEPC collider, we have measured the observed cross sections for 12 exclusive
light hadron final states produced in annihilation at the two energy
points. We have also set the upper limits on the observed cross sections and
the branching fractions for decay to these final states at 90%
C.L.Comment: 8 pages, 5 figur
Search for the Rare Decays J/Psi --> Ds- e+ nu_e, J/Psi --> D- e+ nu_e, and J/Psi --> D0bar e+ e-
We report on a search for the decays J/Psi --> Ds- e+ nu_e + c.c., J/Psi -->
D- e+ nu_e + c.c., and J/Psi --> D0bar e+ e- + c.c. in a sample of 5.8 * 10^7
J/Psi events collected with the BESII detector at the BEPC. No excess of signal
above background is observed, and 90% confidence level upper limits on the
branching fractions are set: B(J/Psi --> Ds- e+ nu_e + c.c.)<4.8*10^-5, B(J/Psi
--> D- e+ nu_e + c.c.) D0bar e+ e- + c.c.)<1.1*10^-5Comment: 10 pages, 4 figure
Measurements of psi(2S) decays to octet baryon-antibaryon pairs
With a sample of 14 million psi(2S) events collected by the BESII detector at
the Beijing Electron Positron Collider (BEPC), the decay channels psi(2S)->p
p-bar, Lambda Lambda-bar, Sigma0 Sigma0-bar, Xi Xi-bar are measured, and their
branching ratios are determined to be (3.36+-0.09+-0.24)*10E-4,
(3.39+-0.20+-0.32)*10E-4, (2.35+-0.36+-0.32)*10E-4, (3.03+-0.40+-0.32)*10E-4,
respectively. In the decay psi(2S)->p p-bar, the angular distribution parameter
alpha is determined to be 0.82+-0.17+-0.04.Comment: 8 pages, 8 figure
- …