5,677 research outputs found
MODBASE, a database of annotated comparative protein structure models and associated resources.
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/)
Pseudorapidity Distribution of Charged Particles in PbarP Collisions at root(s)= 630GeV
Using a silicon vertex detector, we measure the charged particle
pseudorapidity distribution over the range 1.5 to 5.5 using data collected from
PbarP collisions at root s = 630 GeV. With a data sample of 3 million events,
we deduce a result with an overall normalization uncertainty of 5%, and typical
bin to bin errors of a few percent. We compare our result to the measurement of
UA5, and the distribution generated by the Lund Monte Carlo with default
settings. This is only the second measurement at this level of precision, and
only the second measurement for pseudorapidity greater than 3.Comment: 9 pages, 5 figures, LaTeX format. For ps file see
http://hep1.physics.wayne.edu/harr/harr.html Submitted to Physics Letters
Exact solution of a two-type branching process: Clone size distribution in cell division kinetics
We study a two-type branching process which provides excellent description of
experimental data on cell dynamics in skin tissue (Clayton et al., 2007). The
model involves only a single type of progenitor cell, and does not require
support from a self-renewed population of stem cells. The progenitor cells
divide and may differentiate into post-mitotic cells. We derive an exact
solution of this model in terms of generating functions for the total number of
cells, and for the number of cells of different types. We also deduce large
time asymptotic behaviors drawing on our exact results, and on an independent
diffusion approximation.Comment: 16 page
A Hybrid Likelihood Model for Sequence-Based Disease Association Studies
In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values<0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing. © 2013 Chen et al
Construction and Performance of Large-Area Triple-GEM Prototypes for Future Upgrades of the CMS Forward Muon System
At present, part of the forward RPC muon system of the CMS detector at the
CERN LHC remains uninstrumented in the high-\eta region. An international
collaboration is investigating the possibility of covering the 1.6 < |\eta| <
2.4 region of the muon endcaps with large-area triple-GEM detectors. Given
their good spatial resolution, high rate capability, and radiation hardness,
these micro-pattern gas detectors are an appealing option for simultaneously
enhancing muon tracking and triggering capabilities in a future upgrade of the
CMS detector. A general overview of this feasibility study will be presented.
The design and construction of small (10\times10 cm2) and full-size trapezoidal
(1\times0.5 m2) triple-GEM prototypes will be described. During detector
assembly, different techniques for stretching the GEM foils were tested.
Results from measurements with x-rays and from test beam campaigns at the CERN
SPS will be shown for the small and large prototypes. Preliminary simulation
studies on the expected muon reconstruction and trigger performances of this
proposed upgraded muon system will be reported.Comment: 7 pages, 25 figures, submitted for publication in conference record
of the 2011 IEEE Nuclear Science Symposium, Valencia, Spai
Performance of a Large-Area GEM Detector Prototype for the Upgrade of the CMS Muon Endcap System
Gas Electron Multiplier (GEM) technology is being considered for the forward
muon upgrade of the CMS experiment in Phase 2 of the CERN LHC. Its first
implementation is planned for the GE1/1 system in the region of the muon endcap mainly to control muon level-1 trigger rates
after the second long LHC shutdown. A GE1/1 triple-GEM detector is read out by
3,072 radial strips with 455 rad pitch arranged in eight -sectors.
We assembled a full-size GE1/1 prototype of 1m length at Florida Tech and
tested it in 20-120 GeV hadron beams at Fermilab using Ar/CO 70:30 and
the RD51 scalable readout system. Four small GEM detectors with 2-D readout and
an average measured azimuthal resolution of 36 rad provided precise
reference tracks. Construction of this largest GEM detector built to-date is
described. Strip cluster parameters, detection efficiency, and spatial
resolution are studied with position and high voltage scans. The plateau
detection efficiency is [97.1 0.2 (stat)]\%. The azimuthal resolution is
found to be [123.5 1.6 (stat)] rad when operating in the center of
the efficiency plateau and using full pulse height information. The resolution
can be slightly improved by 10 rad when correcting for the bias due
to discrete readout strips. The CMS upgrade design calls for readout
electronics with binary hit output. When strip clusters are formed
correspondingly without charge-weighting and with fixed hit thresholds, a
position resolution of [136.8 2.5 stat] rad is measured, consistent
with the expected resolution of strip-pitch/ = 131.3 rad. Other
-sectors of the detector show similar response and performance.Comment: 8 pages, 32 figures, submitted to Proc. 2014 IEEE Nucl. Sci.
Symposium, Seattle, WA, reference adde
MODBASE: a database of annotated comparative protein structure models and associated resources
MODBASE () is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence–structure alignment, model building and model assessment (). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, ), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, ) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, )
Overview of large area triple-GEM detectors for the CMS forward muon upgrade
In order to cope with the harsh environment expected from the high luminosity LHC, the CMS forward muon system requires an upgrade. The two main challenges expected in this environment are an increase in the trigger rate and increased background radiation leading to a potential degradation of the particle ID performance. Additionally, upgrades to other subdetectors of CMS allow for extended coverage for particle tracking, and adding muon system coverage to this region will further enhance the performance of CMS
A novel application of Fiber Bragg Grating (FBG) sensors in MPGD
We present a novel application of Fiber Bragg Grating (FBG) sensors in the
construction and characterisation of Micro Pattern Gaseous Detector (MPGD),
with particular attention to the realisation of the largest triple (Gas
electron Multiplier) GEM chambers so far operated, the GE1/1 chambers of the
CMS experiment at LHC. The GE1/1 CMS project consists of 144 GEM chambers of
about 0.5 m2 active area each, employing three GEM foils per chamber, to be
installed in the forward region of the CMS endcap during the long shutdown of
LHC in 2108-2019. The large active area of each GE1/1 chamber consists of GEM
foils that are mechanically stretched in order to secure their flatness and the
consequent uniform performance of the GE1/1 chamber across its whole active
surface. So far FBGs have been used in high energy physics mainly as high
precision positioning and re-positioning sensors and as low cost, easy to
mount, low space consuming temperature sensors. FBGs are also commonly used for
very precise strain measurements in material studies. In this work we present a
novel use of FBGs as flatness and mechanical tensioning sensors applied to the
wide GEM foils of the GE1/1 chambers. A network of FBG sensors have been used
to determine the optimal mechanical tension applied and to characterise the
mechanical tension that should be applied to the foils. We discuss the results
of the test done on a full-sized GE1/1 final prototype, the studies done to
fully characterise the GEM material, how this information was used to define a
standard assembly procedure and possible future developments.Comment: 4 pages, 4 figures, presented by Luigi Benussi at MPGD 2015 (Trieste,
Italy). arXiv admin note: text overlap with arXiv:1512.0848
Development and performance of Triple-GEM detectors for the upgrade of the muon system of the CMS experiment
The CMS Collaboration is evaluating GEM detectors for the upgrade of the muon system. This contribution will focus on the R&D performed on chambers design features and will discuss the performance of the upgraded detector
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