Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Search for scalar diphoton resonances in the mass range 65-600 GeV with the ATLAS detector in pp collision data at √s = 8 TeV

A search for scalar particles decaying via narrow resonances into two photons in the mass range 65–600 GeV is performed using 20.3  fb−¹ of √s=8  TeV pp collision data collected with the ATLAS detector at the Large Hadron Collider. The recently discovered Higgs boson is treated as a background. No significant evidence for an additional signal is observed. The results are presented as limits at the 95% confidence level on the production cross section of a scalar boson times branching ratio into two photons, in a fiducial volume where the reconstruction efficiency is approximately independent of the event topology. The upper limits set extend over a considerably wider mass range than previous searches

Measurement of the top-quark mass in the fully hadronic decay channel from ATLAS data at s=7\sqrt{s}=7 TeV

The mass of the top quark is measured in a data set corresponding to 4.6 fb$^{−1}$ of proton--proton collisions with centre-of-mass energy $\sqrt{s}=7$ TeV collected by the ATLAS detector at the LHC. Events consistent with hadronic decays of top--antitop quark pairs with at least six jets in the final state are selected. The substantial background from multijet production is modelled with data-driven methods that utilise the number of identified $b$-quark jets and the transverse momentum of the sixth leading jet, which have minimal correlation. The top-quark mass is obtained from template fits to the ratio of three-jet to dijet mass. The three-jet mass is calculated from the three jets of a top-quark decay. Using these three jets the dijet mass is obtained from the two jets of the $W$ boson decay. The top-quark mass obtained from this fit is thus less sensitive to the uncertainty in the energy measurement of the jets. A binned likelihood fit yields a top-quark mass of $m_{t}$ = 175.1 $\pm$ 1.4 (stat.) $\pm$ 1.2 (syst.) GeV.publishedVersio

Electron reconstruction and identification efficiency measurements with the ATLAS detector using the 2011 LHC proton–proton collision data

Many of the interesting physics processes to be measured at the LHC have a signature involving one or more isolated electrons. The electron reconstruction and identification efficiencies of the ATLAS detector at the LHC have been evaluated using proton–proton collision data collected in 2011 at s√=7 TeV and corresponding to an integrated luminosity of 4.7 fb −1. Tag-and-probe methods using events with leptonic decays of W and Z bosons and J/ψ mesons are employed to benchmark these performance parameters. The combination of all measurements results in identification efficiencies determined with an accuracy at the few per mil level for electron transverse energy greater than 30 GeV

Monitoring and data quality assessment of the ATLAS liquid argon calorimeter

The liquid argon calorimeter is a key component of the ATLAS detector installed at the CERN Large Hadron Collider. The primary purpose of this calorimeter is the measurement of electron and photon kinematic properties. It also provides a crucial input for measuring jets and missing transverse momentum. An advanced data monitoring procedure was designed to quickly identify issues that would affect detector performance and ensure that only the best quality data are used for physics analysis. This article presents the validation procedure developed during the 2011 and 2012 LHC data-taking periods, in which more than 98% of the proton-proton luminosity recorded by ATLAS at a centre-of-mass energy of 7-8 TeV had calorimeter data quality suitable for physics analysis

死体肺移植におけるrecombinant tissue-field name="type" plasminogen activator(rt-PA)の効果について

[[sponsorship]]物理研究所[[note]]已出版;[SCI];有審查制度;具代表性[[note]]http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Drexel&SrcApp=hagerty_opac&KeyRecord=1434-6044&DestApp=JCR&RQ=IF_CAT_BOXPLO

Measurement of the tt¯ production cross-section using eμ events with b-tagged jets in pp collisions at √s=7 and 8 TeV with the ATLAS detector

The inclusive top quark pair (tt¯tt¯) production cross-section σtt¯σtt¯ has been measured in proton–proton collisions at s√=7 TeVs=7 TeV and s√=8 TeVs=8 TeV with the ATLAS experiment at the LHC, using tt¯tt¯ events with an opposite-charge eμeμ pair in the final state. The measurement was performed with the 2011 7 TeV dataset corresponding to an integrated luminosity of 4.6 fb−1fb−1 and the 2012 8 TeV dataset of 20.3 fb−1fb−1. The numbers of events with exactly one and exactly two bb-tagged jets were counted and used to simultaneously determine σtt¯σtt¯ and the efficiency to reconstruct and bb-tag a jet from a top quark decay, thereby minimising the associated systematic uncertainties. The cross-section was measured to be: σtt¯σtt¯=182.9±3.1±4.2±3.6±3.3 pb (s√=7 TeV)and=242.4±1.7±5.5±7.5±4.2 pb (s√=8 TeV), σtt¯=182.9±3.1±4.2±3.6±3.3 pb (s=7 TeV)andσtt¯=242.4±1.7±5.5±7.5±4.2 pb (s=8 TeV), where the four uncertainties arise from data statistics, experimental and theoretical systematic effects, knowledge of the integrated luminosity and of the LHC beam energy. The results are consistent with recent theoretical QCD calculations at next-to-next-to-leading order. Fiducial measurements corresponding to the experimental acceptance of the leptons are also reported, together with the ratio of cross-sections measured at the two centre-of-mass energies. The inclusive cross-section results were used to determine the top quark pole mass via the dependence of the theoretically predicted cross-section on mpoletmtpole giving a result of mpoletmtpole=172.9+2.5−2.6=172.9−2.6+2.5 GeV. By looking for an excess of tt¯tt¯ production with respect to the QCD prediction, the results were also used to place limits on the pair-production of supersymmetric top squarks t~1t~1 with masses close to the top quark mass, decaying via t~1→tχ~01t~1→tχ~10 to predominantly right-handed top quarks and a light neutralino χ~01χ~10, the lightest supersymmetric particle. Top squarks with masses between the top quark mass and 177 GeV are excluded at the 95 % confidence level

Measurements of spin correlation in top-antitop quark events from proton-proton collisions at √s=7 TeV using the ATLAS detector

Measurements of spin correlation in top quark pair production are presented using data collected with the ATLAS detector at the LHC with proton-proton collisions at a center-of-mass energy of 7 TeV, corresponding to an integrated luminosity of 4.6 fb$^{-1}$. Events are selected in final states with two charged leptons and at least two jets and in final states with one charged lepton and at least four jets. Four different observables sensitive to different properties of the top quark pair production mechanism are used to extract the correlation between the top and antitop quark spins. Some of these observables are measured for the first time. The measurements are in good agreement with the Standard Model prediction at next-to-leading-order accuracy