Dissemination of metabolomics results: role of MetaboLights and COSMOS.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information

User Experience document on VRC Design Guide - D6.1

This document is a comprehensive report on the first user experience (UX) workshop hosted to ensure a user centric design and usability of the PhenoMeNal Virtual Research Environment (VRE), aka. Virtual Research Community (VRC)

Determination of jet calibration and energy resolution in proton-proton collisions at \sqrts = 8 TeV using the ATLAS detector

The jet energy scale, jet energy resolution, and their systematic uncertainties are measured for jets reconstructed with the ATLAS detector in 2012 using proton–proton data produced at a centre-of-mass energy of 8 TeV with an integrated luminosity of 20fb−1. Jets are reconstructed from clusters of energy depositions in the ATLAS calorimeters using the anti-kt algorithm. A jet calibration scheme is applied in multiple steps, each addressing specific effects including mitigation of contributions from additional proton–proton collisions, loss of energy in dead material, calorimeter non-compensation, angular biases and other global jet effects. The final calibration step uses several in situ techniques and corrects for residual effects not captured by the initial calibration. These analyses measure both the jet energy scale and resolution by exploiting the transverse momentum balance in γ + jet, Z + jet, dijet, and multijet events. A statistical combination of these measurements is performed. In the central detector region, the derived calibration has a precision better than 1% for jets with transverse momentum 150GeV<pT< 1500 GeV, and the relative energy resolution is (8.4±0.6)% for pT=100GeV and (23±2)% for pT=20GeV. The calibration scheme for jets with radius parameter R=1.0, for which jets receive a dedicated calibration of the jet mass, is also discussed

Measurement of ℤℤ production in the \ell\ellνν final state with the ATLAS detector in pp collisions at \sqrts = 13 TeV

This paper presents a measurement of ZZ production with the ATLAS detector at the Large Hadron Collider. The measurement is carried out in the final state with two charged leptons and two neutrinos, using data collected during 2015 and 2016 in pp collisions at s√ = 13 TeV, corresponding to an integrated luminosity of 36.1 fb−1. The integrated cross-sections in the total and fiducial phase spaces are measured with an uncertainty of 7% and compared with Standard Model predictions, and differential measurements in the fiducial phase space are reported. No significant deviations from the Standard Model predictions are observed, and stringent constraints are placed on anomalous couplings corresponding to neutral triple gauge-boson interactions

Constraints on mediator-based dark matter and scalar dark energy models using √s = 13 TeV pp collision data collected by the ATLAS detector

Constraints on selected mediator-based dark matter models and a scalar dark energy model using up to 37 fb−1√s = 13 TeV pp collision data collected by the ATLAS detector at the LHC during 2015-2016 are summarised in this paper. The results of experimental searches in a variety of final states are interpreted in terms of a set of spin-1 and spin-0 single-mediator dark matter simplified models and a second set of models involving an extended Higgs sector plus an additional vector or pseudo-scalar mediator. The searches considered in this paper constrain spin-1 leptophobic and leptophilic mediators, spin-0 colour-neutral and colour-charged mediators and vector or pseudo-scalar mediators embedded in extended Higgs sector models. In this case, also √s = 8 TeV pp collision data are used for the interpretation of the results. The results are also interpreted for the first time in terms of light scalar particles that could contribute to the accelerating expansion of the universe (dark energy)

Search for heavy particles decaying into a top-quark pair in the fully hadronic final state in pp collisions at √s=13 TeV with the ATLAS detector

A search for new particles decaying into a pair of top quarks is performed using proton-proton collision data recorded with the ATLAS detector at the Large Hadron Collider at a center-of-mass energy of √s=13  TeV corresponding to an integrated luminosity of 36.1  fb−1. Events consistent with top-quark pair production and the fully hadronic decay mode of the top quarks are selected by requiring multiple high transverse momentum jets including those containing b-hadrons. Two analysis techniques, exploiting dedicated top-quark pair reconstruction in different kinematic regimes, are used to optimize the search sensitivity to new hypothetical particles over a wide mass range. The invariant mass distribution of the two reconstructed top-quark candidates is examined for resonant production of new particles with various spins and decay widths. No significant deviation from the Standard Model prediction is observed and limits are set on the production cross-section times branching fraction for new hypothetical Z′ bosons, dark-matter mediators, Kaluza-Klein gravitons and Kaluza-Klein gluons. By comparing with the predicted production cross sections, the Z′ boson in the topcolor-assisted-technicolor model is excluded for masses up to 3.1–3.6 TeV, the dark-matter mediators in a simplified framework are excluded in the mass ranges from 0.8 to 0.9 TeV and from 2.0 to 2.2 TeV, and the Kaluza-Klein gluon is excluded for masses up to 3.4 TeV, depending on the decay widths of the particles

Measurement of the transverse momentum distribution of Drell–Yan lepton pairs in proton–proton collisions at \sqrts=13 TeV with the ATLAS detector

This paper describes precision measurements of the transverse momentum pℓℓT (ℓ=e,μ) and of the angular variable ϕ∗η distributions of Drell–Yan lepton pairs in a mass range of 66–116 GeV. The analysis uses data from 36.1 fb−1 of proton–proton collisions at a centre-of-mass energy of s√=13TeV collected by the ATLAS experiment at the LHC in 2015 and 2016. Measurements in electron-pair and muon-pair final states are performed in the same fiducial volumes, corrected for detector effects, and combined. Compared to previous measurements in proton–proton collisions at s√=7 and 8TeV, these new measurements probe perturbative QCD at a higher centre-of-mass energy with a different composition of initial states. They reach a precision of 0.2% for the normalized spectra at low values of pℓℓT. The data are compared with different QCD predictions, where it is found that predictions based on resummation approaches can describe the full spectrum within uncertainties

Measurement of the nuclear modification factor for inclusive jets in Pb+Pb collisions at √sNN=5.02 TeV with the ATLAS detector

Measurements of the yield and nuclear modification factor, RAA, for inclusive jet production are performed using 0.49 nb−1of Pb+Pb data at √sNN=5.02 TeV and 25 pb−1of ppdata at √s=5.02 TeV with the ATLAS detector at the LHC. Jets are reconstructed with the anti-kt algorithm with radius parameter R =0.4 and are measured over the transverse momentum range of 40–1000 GeV in six rapidity intervals covering |y| < 2.8. The magnitude of RAA increases with increasing jet transverse momentum, reaching a value of approximately 0.6 at 1 TeVin the most central collisions. The magnitude of RAAalso increases towards peripheral collisions. The value of RAA is independent of rapidity at low jet transverse momenta, but it is observed to decrease with increasing rapidity at high transverse moment

Search for invisible Higgs boson decays in vector boson fusion at √s = 13 TeV with the ATLAS detector

We report a search for Higgs bosons that are produced via vector boson fusion and subsequently decay into invisible particles. The experimental signature is an energetic jet pair with invariant mass of O(1) TeV and O(100) GeV missing transverse momentum. The analysis uses 36.1fb−1of ppcollision data at √s=13 TeV recorded by the ATLAS detector at the LHC. In the signal region the 2252 observed events are consistent with the background estimation. Assuming a 125 GeV scalar particle with Standard Model cross sections, the upper limit on the branching fraction of the Higgs boson decay into invisible particles is 0.37 at 95% confidence level where 0.28 was expected. This limit is interpreted in Higgs portal models to set bounds on thewimp–nucleon scattering cross section. We also consider invisible decays of additional scalar bosons with masses up to 3 TeV for which the upper limits on the cross section times branching fraction are in the range of 0.3–1.7 pb