674 research outputs found

    Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

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    <p>Abstract</p> <p>Background</p> <p>The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences.</p> <p>Results</p> <p>Prior to our study, mRNA sequences for only 1,556 partial or complete ovine genes were publicly available. Therefore, we developed a composite <it>de novo </it>transcriptome assembly method for next-generation sequence data to combine known ovine mRNA and EST sequences, mRNA sequences from mouse and cow, and sequences assembled <it>de novo </it>from short read RNA-Seq data into a composite reference transcriptome, and identified transcripts from over 12 thousand previously undescribed ovine genes. Gene expression analysis based on these data revealed substantially different expression profiles in standard versus delayed bone healing in an ovine tibial osteotomy model. Hundreds of transcripts were differentially expressed between standard and delayed healing and between the time points of the standard and delayed healing groups. We used the sheep sequences to design quantitative RT-PCR assays with which we validated the differential expression of 26 genes that had been identified by RNA-seq analysis. A number of clusters of characteristic expression profiles could be identified, some of which showed striking differences between the standard and delayed healing groups. Gene Ontology (GO) analysis showed that the differentially expressed genes were enriched in terms including <it>extracellular matrix</it>, <it>cartilage development</it>, <it>contractile fiber</it>, and <it>chemokine activity</it>.</p> <p>Conclusions</p> <p>Our results provide a first atlas of gene expression profiles and differentially expressed genes in standard and delayed bone healing in a large-animal model and provide a number of clues as to the shifts in gene expression that underlie delayed bone healing. In the course of our study, we identified transcripts of 13,987 ovine genes, including 12,431 genes for which no sequence information was previously available. This information will provide a basis for future molecular research involving the sheep as a model organism.</p

    Search for resonant WZ production in the fully leptonic final state in proton–proton collisions at √s=13 TeV with the ATLAS detector

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    Measurement of exclusive pion pair production in proton–proton collisions at √s=7 TeV with the ATLAS detector

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    Measurement of the nuclear modification factor of b-jets in 5.02 TeV Pb+Pb collisions with the ATLAS detector

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    Searches for lepton-flavour-violating decays of the Higgs boson into eτ and μτ in \sqrt{s} = 13 TeV pp collisions with the ATLAS detector

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    Abstract This paper presents direct searches for lepton flavour violation in Higgs boson decays, H → eτ and H → μτ, performed using data collected with the ATLAS detector at the LHC. The searches are based on a data sample of proton-proton collisions at a centre-of-mass energy s s \sqrt{s} = 13 TeV, corresponding to an integrated luminosity of 138 fb−1. Leptonic (τ → ℓνℓντ) and hadronic (τ → hadrons ντ) decays of the τ-lepton are considered. Two background estimation techniques are employed: the MC-template method, based on data-corrected simulation samples, and the Symmetry method, based on exploiting the symmetry between electrons and muons in the Standard Model backgrounds. No significant excess of events is observed and the results are interpreted as upper limits on lepton-flavour-violating branching ratios of the Higgs boson. The observed (expected) upper limits set on the branching ratios at 95% confidence level, B B \mathcal{B} (H → eτ) < 0.20% (0.12%) and B B \mathcal{B} (H → μτ ) < 0.18% (0.09%), are obtained with the MC-template method from a simultaneous measurement of potential H → eτ and H → μτ signals. The best-fit branching ratio difference, B B \mathcal{B} (H → μτ) → B B \mathcal{B} (H → eτ), measured with the Symmetry method in the channel where the τ-lepton decays to leptons, is (0.25 ± 0.10)%, compatible with a value of zero within 2.5σ

    Measurement of the total cross section and ρ -parameter from elastic scattering in pp collisions at √s=13 TeV with the ATLAS detector

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    Measurement of the polarisation of W bosons produced in top-quark decays using dilepton events at root s=13 TeV with the ATLAS experiment

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    A measurement of the polarisation of WW bosons produced in top-quark decays is presented, using proton-proton collision data at a centre-of-mass energy of s=13\sqrt{s} = 13 TeV. The data were collected by the ATLAS detector at the Large Hadron Collider and correspond to an integrated luminosity of 139 fb1^{-1}. The measurement is performed selecting ttˉt\bar{t} events decaying into final states with two charged leptons (electrons or muons) and at least two bb-tagged jets. The polarisation is extracted from the differential cross-section distribution of the cosθ\cos{\theta^{*}} variable, where θ\theta^{*} is the angle between the momentum direction of the charged lepton from the WW boson decay and the reversed momentum direction of the bb-quark from the top-quark decay, both calculated in the WW boson rest frame. Parton-level results, corrected for the detector acceptance and resolution, are presented for the cosθ\cos{\theta^{*}} angle. The measured fractions of longitudinal, left- and right-handed polarisation states are found to be f0=0.684±0.005(stat.)±0.014(syst.)f_{0} = 0.684 \pm 0.005\,\mathrm{(stat.)} \pm 0.014\,\mathrm{(syst.)}, fL=0.318±0.003(stat.)±0.008(syst.)f_{\mathrm{L}} = 0.318 \pm 0.003\,\mathrm{(stat.)} \pm 0.008\,\mathrm{(syst.)} and fR=0.002±0.002(stat.)±0.014(syst.)f_{\mathrm{R}} = -0.002 \pm 0.002\,\mathrm{(stat.)} \pm 0.014\,\mathrm{(syst.)}, in agreement with the Standard Model prediction

    Search for pair-produced scalar and vector leptoquarks decaying into third-generation quarks and first- or second-generation leptons in pp collisions with the ATLAS detector

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    Abstract A search for pair-produced scalar and vector leptoquarks decaying into quarks and leptons of different generations is presented. It uses the full LHC Run 2 (2015–2018) data set of 139 fb −1 collected with the ATLAS detector in proton–proton collisions at a centre-of-mass energy of s s \sqrt{s} = 13 TeV. Scalar leptoquarks with charge −(1/3)e as well as scalar and vector leptoquarks with charge +(2/3)e are considered. All possible decays of the pair-produced leptoquarks into quarks of the third generation (t, b) and charged or neutral leptons of the first or second generation (e, μ, ν) with exactly one electron or muon in the final state are investigated. No significant deviations from the Standard Model expectation are observed. Upper limits on the production cross-section are provided for eight models as a function of the leptoquark mass and the branching ratio of the leptoquark into the charged or neutral lepton. In addition, lower limits on the leptoquark masses are derived for all models across a range of branching ratios. Two of these models have the goal of providing an explanation for the recent B-anomalies. In both models, a vector leptoquark decays into charged and neutral leptons of the second generation with a similar branching fraction. Lower limits of 1980 GeV and 1710 GeV are set on the leptoquark mass for these two models

    Evidence of off-shell Higgs boson production from ZZ leptonic decay channels and constraints on its total width with the ATLAS detector

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    Search for flavour-changing neutral-current couplings between the top quark and the photon with the ATLAS detector at root s = 13 TeV

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    This letter documents a search for flavour-changing neutral currents (FCNCs), which are strongly sup-pressed in the Standard Model, in events with a photon and a top quark with the ATLAS detector. The analysis uses data collected in pp collisions at &amp; RADIC;s =13 TeV during Run 2 of the LHC, corresponding to an integrated luminosity of 139 fb-1. Both FCNC top-quark production and decay are considered. The final state consists of a charged lepton, missing transverse momentum, a b-tagged jet, one high-momentum photon and possibly additional jets. A multiclass deep neural network is used to classify events either as signal in one of the two categories, FCNC production or decay, or as background. No significant ex-cess of events over the background prediction is observed and 95% CL upper limits are placed on the strength of left-and right-handed FCNC interactions. The 95% CL bounds on the branching fractions for the FCNC top-quark decays, estimated (expected) from both top-quark production and decay, are B(t &amp; RARR; u &amp; gamma; ) &lt; 0.85 (0.88+0.37 -0.25) x 10-5 and B(t &amp; RARR; c &amp; gamma; ) &lt; 4.2 (3.40+1.35-0.95) x 10-5 for a left-handed tq &amp; gamma; cou-pling, and B(t &amp; RARR; u &amp; gamma; ) &lt; 1.2 (1.20+0.50 -0.33) x10-5 and B(t &amp; RARR; c &amp; gamma; ) &lt; 4.5 (3.70+1.47 -1.03) x10-5 for a right-handed coupling. &amp; COPY; 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons .org /licenses /by /4 .0/). Funded by SCOAP3
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