1,828 research outputs found

    NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline.

    Get PDF
    BACKGROUND: Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means of predicting and assessing neoantigens from tumor variants that may stimulate immune response. RESULTS: Here we offer NeoPredPipe (Neoantigen Prediction Pipeline) as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on predicted neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes. Given an example dataset we show how NeoPredPipe is able to rapidly provide insights into neoantigen heterogeneity, burden, and immune stimulation potential. CONCLUSIONS: Through the integration of widely adopted tools for neoantigen discovery NeoPredPipe offers a contiguous means of processing single and multi-region sequence data. NeoPredPipe is user-friendly and adaptable for high-throughput performance. NeoPredPipe is freely available at https://github.com/MathOnco/NeoPredPipe

    Immunosuppressive niche engineering at the onset of human colorectal cancer

    Get PDF
    The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune “cold” ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC

    Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

    Get PDF
    This paper presents measurements of the W+μ+νW^+ \rightarrow \mu^+\nu and WμνW^- \rightarrow \mu^-\nu cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

    Search for chargino-neutralino production with mass splittings near the electroweak scale in three-lepton final states in √s=13 TeV pp collisions with the ATLAS detector

    Get PDF
    A search for supersymmetry through the pair production of electroweakinos with mass splittings near the electroweak scale and decaying via on-shell W and Z bosons is presented for a three-lepton final state. The analyzed proton-proton collision data taken at a center-of-mass energy of √s=13  TeV were collected between 2015 and 2018 by the ATLAS experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 139  fb−1. A search, emulating the recursive jigsaw reconstruction technique with easily reproducible laboratory-frame variables, is performed. The two excesses observed in the 2015–2016 data recursive jigsaw analysis in the low-mass three-lepton phase space are reproduced. Results with the full data set are in agreement with the Standard Model expectations. They are interpreted to set exclusion limits at the 95% confidence level on simplified models of chargino-neutralino pair production for masses up to 345 GeV

    Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

    Get PDF
    Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

    Single-mode cavities at frequencies of 172 and 178 MHz

    Get PDF
    In the report presented here the projects of two accelerating cavities with strong damping of higher modes (HOM) with special vacuum loads are presented. The designs of the cavities and loads are described. The design parameters of cavities, their spectra of higher modes and calculation results of the beam phase motion stability are given for the VEPP-2000 and NANOHANA Projects

    Measurement of jet fragmentation in Pb+Pb and pp collisions at √s NN =5.02 TeV with the ATLAS detector

    Get PDF
    This paper presents a measurement of jet fragmentation functions in 0.49 nb −1 of Pb+Pb collisions and 25 pb −1 of pp collisions at √ sNN =5.02 TeV collected in 2015 with the ATLAS detector at the LHC. These measurements provide insight into the jet quenching process in the quark-gluon plasma created in the aftermath of ultra-relativistic collisions between two nuclei. The modifications to the jet fragmentation functions are quantified by dividing the measurements in Pb+Pb collisions by baseline measurements in pp collisions. This ratio is studied as a function of the transverse momentum of the jet, the jet rapidity, and the centrality of the collision. In both collision systems, the jet fragmentation functions are measured for jets with transverse momentum between 126 GeV and 398 GeV and with an absolute value of jet rapidity less than 2.1. An enhancement of particles carrying a small fraction of the jet momentum is observed, which increases with centrality and with increasing jet transverse momentum. Yields of particles carrying a very large fraction of the jet momentum are also observed to be enhanced. Between these two enhancements of the fragmentation functions a suppression of particles carrying an intermediate fraction of the jet momentum is observed in Pb+Pb collisions. A small dependence of the modifications on jet rapidity is observed

    Search for long-lived particles produced in pp collisions at √s=13 TeV that decay into displaced hadronic jets in the ATLAS muon spectrometer

    Get PDF
    A search for the decay of neutral, weakly interacting, long-lived particles using data collected by the ATLAS detector at the LHC is presented. The analysis in this paper uses 36.1 fb−1 of proton-proton collision data at √s=13 TeV recorded in 2015–2016. The search employs techniques for reconstructing vertices of long-lived particles decaying into jets in the muon spectrometer exploiting a two-vertex strategy and a novel technique that requires only one vertex in association with additional activity in the detector that improves the sensitivity for longer lifetimes. The observed numbers of events are consistent with the expected background and limits for several benchmark signals are determined

    Search for Higgs bosons produced via vector-boson fusion and decaying into bottom quark pairs in √s =13 TeV pp collisions with the ATLAS detector

    Get PDF
    A search for the bb ¯ decay of the Standard Model Higgs boson produced through vector-boson fusion is presented. Three mutually exclusive channels are considered: two all-hadronic channels and a photon-associated channel. Results are reported from the analysis of up to 30.6 fb −1 of pp data at s √ =13 TeV collected with the ATLAS detector at the LHC. The measured signal strength relative to the Standard Model prediction from the combined analysis is 2.5 +1.4 −1.3 for inclusive Higgs boson production and 3.0 +1.7 −1.6 for vector-boson fusion production only

    Measurements of inclusive and differential fiducial cross-sections of tt production with additional heavy-flavour jets in proton-proton collisions at √ s= 13 TeV with the ATLAS detector

    Get PDF
    This paper presents measurements of tt production in association with additional b-jets in pp collisions at the LHC at a centre-of-mass energy of 13 TeV. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 36.1 fb−1. Fiducial cross-section measurements are performed in the dilepton and lepton-plus-jets tt decay channels. Results are presented at particle level in the form of inclusive cross-sections of tt final states with three and four b-jets as well as differential cross-sections as a function of global event properties and properties of b-jet pairs. The measured inclusive fiducial cross-sections generally exceed the ttbb predictions from various next-to-leading-order matrix element calculations matched to a parton shower but are compatible within the total uncertainties. The experimental uncertainties are smaller than the uncertainties in the predictions. Comparisons of state-of-the-art theoretical predictions with the differential measurements are shown and good agreement with data is found for most of them
    corecore