GIFtS: annotation landscape analysis with GeneCards

<p>Abstract</p> <p>Background</p> <p>Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards^®is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO), pathways, interactions, phenotypes, publications and many more.</p> <p>Results</p> <p>We present the GeneCards Inferred Functionality Score (GIFtS) which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25) between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a given gene measured by GIFtS was correlated (for GIFtS>30) with the number of publications for a gene, and with the seniority of this entry in the HGNC database.</p> <p>Conclusion</p> <p>GIFtS can be a valuable tool for computational procedures which analyze lists of large set of genes resulting from wet-lab or computational research. GIFtS may also assist the scientific community with identification of groups of uncharacterized genes for diverse applications, such as delineation of novel functions and charting unexplored areas of the human genome.</p

The Next-to-Minimal Supersymmetric Standard Model

We review the theoretical and phenomenological aspects of the Next-to-Minimal Supersymmetric Standard Model: the Higgs sector including radiative corrections and the 2-loop beta-functions for all parameters of the general NMSSM; the tadpole and domain wall problems, baryogenesis; NMSSM phenomenology at colliders, B physics and dark matter; specific scenarios as the constrained NMSSM, Gauge Mediated Supersymmetry Breaking, U(1)'-extensions, CP and R-parity violation.Comment: 144 pages, 11 figures, corrections in Eqs.(2.2), (2.21), (B.9

NMSSM Higgs Benchmarks Near 125 GeV

The recent LHC indications of a SM-like Higgs boson near 125 GeV are consistent not only with the Standard Model (SM) but also with Supersymmetry (SUSY). However naturalness arguments disfavour the Minimal Supersymmetric Standard Model (MSSM). We consider the Next-to-Minimal Supersymmetric Standard Model (NMSSM) with a SM-like Higgs boson near 125 GeV involving relatively light stops and gluinos below 1 TeV in order to satisfy naturalness requirements. We are careful to ensure that the chosen values of couplings do not become non perturbative below the grand unification (GUT) scale, although we also examine how these limits may be extended by the addition of extra matter to the NMSSM at the two-loop level. We then propose four sets of benchmark points corresponding to the SM-like Higgs boson being the lightest or the second lightest Higgs state in the NMSSM or the NMSSM-with-extra-matter. With the aid of these benchmark points we discuss how the NMSSM Higgs boson near 125 GeV may be distinguished from the SM Higgs boson in future LHC searches.Comment: 40 pages, 1 figure; Minor changes and further references include

The ATLAS Trigger/DAQ Authorlist, version 1.0

This is a reference document giving the ATLAS Trigger/DAQ author list, version 1.0 of 20 Nov 2008

The ATLAS Trigger/DAQ Authorlist, version 2.0

This is the ATLAS Trigger/DAQ Authorlist, version 2.0, 31 July 200

The ATLAS Trigger/DAQ Authorlist, version 3.0

This is the ATLAS Trigger/DAQ Authorlist, version 3.0, 11 September 200

The ATLAS Trigger/DAQ Authorlist, version 3.1

This is the ATLAS Trigger/DAQ Authorlist, version 3.1, 17 September 200

Measurement of the tt¯tt¯ production cross section in pp collisions at √s=13 TeV with the ATLAS detector

A measurement of four-top-quark production using proton-proton collision data at a centre-of-mass energy of 13 TeV collected by the ATLAS detector at the Large Hadron Collider corresponding to an integrated luminosity of 139 fb−1 is presented. Events are selected if they contain a single lepton (electron or muon) or an opposite-sign lepton pair, in association with multiple jets. The events are categorised according to the number of jets and how likely these are to contain b-hadrons. A multivariate technique is then used to discriminate between signal and background events. The measured four-top-quark production cross section is found to be 26+17−15 fb, with a corresponding observed (expected) significance of 1.9 (1.0) standard deviations over the background-only hypothesis. The result is combined with the previous measurement performed by the ATLAS Collaboration in the multilepton final state. The combined four-top-quark production cross section is measured to be 24+7−6 fb, with a corresponding observed (expected) signal significance of 4.7 (2.6) standard deviations over the background-only predictions. It is consistent within 2.0 standard deviations with the Standard Model expectation of 12.0 ± 2.4 fb

Measurements of Higgs bosons decaying to bottom quarks from vector boson fusion production with the ATLAS experiment at √=13TeV

The paper presents a measurement of the Standard Model Higgs Boson decaying to b-quark pairs in the vector boson fusion (VBF) production mode. A sample corresponding to 126 fb−1 of s√=13TeV proton–proton collision data, collected with the ATLAS experiment at the Large Hadron Collider, is analyzed utilizing an adversarial neural network for event classification. The signal strength, defined as the ratio of the measured signal yield to that predicted by the Standard Model for VBF Higgs production, is measured to be 0.95+0.38−0.36 , corresponding to an observed (expected) significance of 2.6 (2.8) standard deviations from the background only hypothesis. The results are additionally combined with an analysis of Higgs bosons decaying to b-quarks, produced via VBF in association with a photon