FunSimMat: a comprehensive functional similarity database

Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. However, there exists no comprehensive resource of functional similarity values although such a database would facilitate the use of functional similarity measures in different applications. Here, we describe FunSimMat (Functional Similarity Matrix, http://funsimmat.bioinf.mpi-inf.mpg.de/), a large new database that provides several different semantic similarity measures for GO terms. It offers various precomputed functional similarity values for proteins contained in UniProtKB and for protein families in Pfam and SMART. The web interface allows users to efficiently perform both semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. All results can be downloaded in tab-delimited files for use with other tools. An additional XML–RPC interface gives automatic online access to FunSimMat for programs and remote services

The AutoAnnotator - Standardized annotation of protein-encoding BioBricks

For protein-encoding BioBricks a large number of useful parameters, such as the amino acid sequence or the molecular weight, can easily be computed. Furthermore alignments against databases and predictions of various features, for instance transmembrane regions, are very interesting and informative when viewing a part. However, this information is not presented or very hard to find in most part descriptions and requires the user to use external websites to obtain it. To resolve this issue we propose a standardized table containing this information. For this purpose we developed a web tool, called the AutoAnnotator, in JavaScript gathering this information and providing the standardized table for the user to copy

Measurement of the Higgs boson width and evidence of its off-shell contributions to ZZ production

Since the discovery of the Higgs boson in 2012, detailed studies of its properties have been ongoing. Besides its mass, its width—related to its lifetime—is an important parameter. One way to determine this quantity is to measure its off-shell production, where the Higgs boson mass is far away from its nominal value, and relating it to its on-shell production, where the mass is close to the nominal value. Here we report evidence for such off-shell contributions to the production cross-section of two Z bosons with data from the CMS experiment at the CERN Large Hadron Collider. We constrain the total rate of the off-shell Higgs boson contribution beyond the Z boson pair production threshold, relative to its standard model expectation, to the interval [0.0061, 2.0] at the 95% confidence level. The scenario with no off-shell contribution is excluded at a p-value of 0.0003 (3.6 standard deviations). We measure the width of the Higgs boson as $\Gamma$$_H$=3.2$^{+2.4}_{−1.7}$MeV, in agreement with the standard model expectation of 4.1 MeV. In addition, we set constraints on anomalous Higgs boson couplings to W and Z boson pairs

Measurement of the Higgs boson width and evidence of its off-shell contributions to ZZ production

Since the discovery of the Higgs boson in 2012, detailed studies of its properties have been ongoing. Besides its mass, its width—related to its lifetime—is an important parameter. One way to determine this quantity is to measure its off-shell production, where the Higgs boson mass is far away from its nominal value, and relating it to its on-shell production, where the mass is close to the nominal value. Here we report evidence for such off-shell contributions to the production cross-section of two Z bosons with data from the CMS experiment at the CERN Large Hadron Collider. We constrain the total rate of the off-shell Higgs boson contribution beyond the Z boson pair production threshold, relative to its standard model expectation, to the interval [0.0061, 2.0] at the 95% confidence level. The scenario with no off-shell contribution is excluded at a p-value of 0.0003 (3.6 standard deviations). We measure the width of the Higgs boson as ΓH=3.2+2.4−1.7MeV, in agreement with the standard model expectation of 4.1 MeV. In addition, we set constraints on anomalous Higgs boson couplings to W and Z boson pairs

Measurement of the Inclusive and Differential Higgs Boson Production Cross Sections in the Decay Mode to a Pair of τ Leptons in pp Collisions at s =13 TeV

Copyright © 2022 CERN, for the CMS Collaboration. Measurements of the inclusive and differential fiducial cross sections of the Higgs boson are presented, using the τ lepton decay channel. The differential cross sections are measured as functions of the Higgs boson transverse momentum, jet multiplicity, and transverse momentum of the leading jet in the event, if any. The analysis is performed using proton-proton collision data collected with the CMS detector at the LHC at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 138 fb−1. These are the first differential measurements of the Higgs boson cross section in the final state of two τ leptons. In final states with a large jet multiplicity or with a Lorentz-boosted Higgs boson, these measurements constitute a significant improvement over measurements performed in other final states.SCOAP3

Search for resonances decaying to three W bosons in the hadronic final state in proton-proton collisions at ps=13 TeV

A search for Kaluza-Klein excited vector boson resonances, W KK , decaying in cascade to three W bosons via a scalar radion R , W KK → W R → W W W , in a final state containing two or three massive jets is presented. The search is performed with √ s = 13     TeV proton-proton collision data collected by the CMS experiment at the CERN LHC during 2016–2018, corresponding to an integrated luminosity of 138     fb − 1 . Two final states are simultaneously probed, one where the two W bosons produced by the R decay are reconstructed as separate, large-radius, massive jets, and one where they are merged into a single large-radius jet. The observed data are in agreement with the standard model expectations. Limits are set on the product of the W KK resonance cross section and branching fraction to three W bosons in an extended warped extra-dimensional model and are the first of their kind at the LHC

Precision measurement of the W boson decay branching fractions in proton-proton collisions at ? s=13 TeV

The leptonic and inclusive hadronic decay branching fractions of the W boson are measured using proton-proton collision data collected at √ s = 13     TeV by the CMS experiment at the CERN LHC, corresponding to an integrated luminosity of 35.9     fb − 1 . Events characterized by the production of one or two W bosons are selected and categorized based on the multiplicity and flavor of reconstructed leptons, the number of jets, and the number of jets identified as originating from the hadronization of b quarks. A binned maximum likelihood estimate of the W boson branching fractions is performed simultaneously in each event category. The measured branching fractions of the W boson decaying into electron, muon, and tau lepton final states are ( 10.83 ± 0.10 ) % , ( 10.94 ± 0.08 ) % , and ( 10.77 ± 0.21 ) % , respectively, consistent with lepton flavor universality for the weak interaction. The average leptonic and inclusive hadronic decay branching fractions are estimated to be ( 10.89 ± 0.08 ) % and ( 67.32 ± 0.23 ) % , respectively. Based on the hadronic branching fraction, three standard model quantities are subsequently derived: the sum of squared elements in the first two rows of the Cabibbo–Kobayashi–Maskawa (CKM) matrix ∑ i j | V i j | 2 = 1.984 ± 0.021 , the CKM element | V c s | = 0.967 ± 0.011 , and the strong coupling constant at the W boson mass scale, α S ( m 2 W ) = 0.095 ± 0.033

Search for flavor-changing neutral current interactions of the top quark and the Higgs boson decaying to a bottom quark-antiquark pair at root s=13 TeV

A search for flavor-changing neutral current interactions of the top quark (t) and the Higgs boson (H) is presented. The search is based on a data sample corresponding to an integrated luminosity of 137 fb−1 recorded by the CMS experiment at the LHC in proton-proton collisions at s√ = 13 TeV. Events containing exactly one lepton (muon or electron) and at least three jets, among which at least two are identified as originating from the hadronization of a bottom quark, are analyzed. A set of deep neural networks is used for kinematic event reconstruction, while boosted decision trees distinguish the signal from the background events. No significant excess over the background predictions is observed, and upper limits on the signal production cross sections are extracted. These limits are interpreted in terms of top quark decay branching fractions (B) to the Higgs boson and an up (u) or a charm quark (c). Assuming one nonvanishing extra coupling at a time, the observed (expected) upper limits at 95% confidence level are B(t → Hu) < 0.079 (0.11)% and B(t → Hc) < 0.094 (0.086)%

Infrastructure and clinical practice for the detection and management of trauma-associated haemorrhage and coagulopathy

Early detection and management of post-traumatic haemorrhage and coagulopathy have been associated with improved outcomes, but local infrastructures, logistics and clinical strategies may differ. To assess local differences in infrastructure, logistics and clinical management of trauma-associated haemorrhage and coagulopathy, we have conducted a web-based survey amongst the delegates to the 15th European Congress of Trauma and Emergency Surgery (ECTES) and the 2nd World Trauma (WT) Congress held in Frankfurt, Germany, 25-27 May 2014. 446/1,540 delegates completed the questionnaire yielding a response rate of 29 %. The majority specified to work as consultants/senior physicians (47.3 %) in general (36.1 %) or trauma/orthopaedic surgery (44.5 %) of level I (70 %) or level II (19 %) trauma centres. Clinical assessment (> 80 %) and standard coagulation assays (74.6 %) are the most frequently used strategies for early detection and monitoring of bleeding trauma patients with coagulopathy. Only 30 % of the respondents declared to use extended coagulation assays to better characterise the bleeding and coagulopathy prompted by more individualised treatment concepts. Most trauma centres (69 %) have implemented local protocols based on international and national guidelines using conventional blood products, e.g. packed red blood cell concentrates (93.3 %), fresh frozen plasma concentrates (93.3 %) and platelet concentrates (83 %), and antifibrinolytics (100 %). 89 % considered the continuous intake of anticoagulants including new oral anticoagulants and platelet inhibitors as an increasing threat to bleeding trauma patients. This study confirms differences in infrastructure, logistics and clinical practice for the detection and management of trauma-haemorrhage and trauma-associated coagulopathy amongst international centres. Ongoing work will focus on geographical differences