Displaying publications 21 - 40 of 231 in total

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  1. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Phys Rev Lett, 2016 Feb 19;116(7):071801.
    PMID: 26943527 DOI: 10.1103/PhysRevLett.116.071801
    A search for narrow resonances in proton-proton collisions at sqrt[s]=13  TeV is presented. The invariant mass distribution of the two leading jets is measured with the CMS detector using a data set corresponding to an integrated luminosity of 2.4  fb^{-1}. The highest observed dijet mass is 6.1 TeV. The distribution is smooth and no evidence for resonant particles is observed. Upper limits at 95% confidence level are set on the production cross section for narrow resonances with masses above 1.5 TeV. When interpreted in the context of specific models, the limits exclude string resonances with masses below 7.0 TeV, scalar diquarks below 6.0 TeV, axigluons and colorons below 5.1 TeV, excited quarks below 5.0 TeV, color-octet scalars below 3.1 TeV, and W^{'} bosons below 2.6 TeV. These results significantly extend previously published limits.
  2. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016 03 08;76:128.
    PMID: 27471431
    The cross section for [Formula: see text] production in the all-jets final state is measured in pp collisions at a centre-of-mass energy of 8 [Formula: see text] at the LHC with the CMS detector, in data corresponding to an integrated luminosity of 18.4 [Formula: see text]. The inclusive cross section is found to be [Formula: see text] [Formula: see text]. The normalized differential cross sections are measured as a function of the top quark transverse momenta, [Formula: see text], and compared to predictions from quantum chromodynamics. The results are reported at detector, parton, and particle levels. In all cases, the measured top quark [Formula: see text] spectra are significantly softer than theoretical predictions.
  3. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016 03 17;76:155.
    PMID: 27471433
    New sets of parameters ("tunes") for the underlying-event (UE) modelling of the pythia8, pythia6 and herwig++ Monte Carlo event generators are constructed using different parton distribution functions. Combined fits to CMS UE proton-proton ([Formula: see text]) data at [Formula: see text] and to UE proton-antiproton ([Formula: see text]) data from the CDF experiment at lower [Formula: see text], are used to study the UE models and constrain their parameters, providing thereby improved predictions for proton-proton collisions at 13[Formula: see text]. In addition, it is investigated whether the values of the parameters obtained from fits to UE observables are consistent with the values determined from fitting observables sensitive to double-parton scattering processes. Finally, comparisons are presented of the UE tunes to "minimum bias" (MB) events, multijet, and Drell-Yan ([Formula: see text] lepton-antilepton+jets) observables at 7 and 8[Formula: see text], as well as predictions for MB and UE observables at 13[Formula: see text].
  4. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Phys Rev Lett, 2016 Apr 29;116(17):172302.
    PMID: 27176516 DOI: 10.1103/PhysRevLett.116.172302
    Results on two-particle angular correlations for charged particles produced in pp collisions at a center-of-mass energy of 13 TeV are presented. The data were taken with the CMS detector at the LHC and correspond to an integrated luminosity of about 270  nb^{-1}. The correlations are studied over a broad range of pseudorapidity (|η|<2.4) and over the full azimuth (ϕ) as a function of charged particle multiplicity and transverse momentum (p_{T}). In high-multiplicity events, a long-range (|Δη|>2.0), near-side (Δϕ≈0) structure emerges in the two-particle Δη-Δϕ correlation functions. The magnitude of the correlation exhibits a pronounced maximum in the range 1.0
  5. Wu T, Wang X, Zhang Z, Gong F, Song T, Chen Z, et al.
    J Bioinform Comput Biol, 2016 06;14(3):1650013.
    PMID: 27225342 DOI: 10.1142/S021972001650013X
    A nuclear export signal (NES) is a protein localization signal, which is involved in binding of cargo proteins to nuclear export receptor, thus contributes to regulate localization of cellular proteins. Consensus sequences of NES have been used to detect NES from protein sequences, but suffer from poor predictive power. Some recent peering works were proposed to use biochemical properties of experimental verified NES to refine NES candidates. Those methods can achieve high prediction rates, but their execution time will become unacceptable for large-scale NES searching if too much properties are involved. In this work, we developed a novel computational approach, named NES-REBS, to search NES from protein sequences, where biochemical properties of experimental verified NES, including secondary structure and surface accessibility, are utilized to refine NES candidates obtained by matching popular consensus sequences. We test our method by searching 262 experimental verified NES from 221 NES-containing protein sequences. It is obtained that NES-REBS runs in 2-3[Formula: see text]mins and performs well by achieving precision rate 47.2% and sensitivity 54.6%.
  6. Jelen MM, Chen Z, Kocjan BJ, Hošnjak L, Burt FJ, Chan PKS, et al.
    J Virol, 2016 Jun 01;90(11):5503-5513.
    PMID: 27030261 DOI: 10.1128/JVI.03149-15
    Human papillomavirus 11 (HPV11) is an etiological agent of anogenital warts and laryngeal papillomas and is included in the 4-valent and 9-valent prophylactic HPV vaccines. We established the largest collection of globally circulating HPV11 isolates to date and examined the genomic diversity of 433 isolates and 78 complete genomes (CGs) from six continents. The genomic variation within the 2,800-bp E5a-E5b-L1-upstream regulatory region was initially studied in 181/207 (87.4%) HPV11 isolates collected for this study. Of these, the CGs of 30 HPV11 variants containing unique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes were fully sequenced. A maximum likelihood tree based on the global alignment of 78 HPV11 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (lineages A and B) and four sublineages (sublineages A1, A2, A3, and A4). HPV11 (sub)lineage-specific SNPs within the CG were identified, as well as the 208-bp representative region for CG-based phylogenetic clustering within the partial E2 open reading frame and noncoding region 2. Globally, sublineage A2 was the most prevalent, followed by sublineages A1, A3, and A4 and lineage B.

    IMPORTANCE: This collaborative international study defined the global heterogeneity of HPV11 and established the largest collection of globally circulating HPV11 genomic variants to date. Thirty novel complete HPV11 genomes were determined and submitted to the available sequence repositories. Global phylogenetic analysis revealed two HPV11 variant lineages and four sublineages. The HPV11 (sub)lineage-specific SNPs and the representative region identified within the partial genomic region E2/noncoding region 2 (NCR2) will enable the simpler identification and comparison of HPV11 variants worldwide. This study provides an important knowledge base for HPV11 for future studies in HPV epidemiology, evolution, pathogenicity, prevention, and molecular assay development.

  7. Haiyan G, Lijuan H, Shaoyu L, Chen Z, Ashraf MA
    Saudi J Biol Sci, 2016 Jul;23(4):524-30.
    PMID: 27298587 DOI: 10.1016/j.sjbs.2016.02.020
    In the study, we evaluated chemical composition and antimicrobial, antibiofilm, and antitumor activities of essential oils from dried leaf essential oil of leaf and flower of Agastache rugosa for the first time. Essential oil of leaf and flower was evaluated with GC and GC-MS methods, and the essential oil of flower revealed the presence of 21 components, whose major compounds were pulegone (34.1%), estragole (29.5%), and p-Menthan-3-one (19.2%). 26 components from essential oil of leaf were identified, the major compounds were p-Menthan-3-one (48.8%) and estragole (20.8%). At the same time, essential oil of leaf, there is a very effective antimicrobial activity with MIC ranging from 9.4 to 42 μg ml(-1) and potential antibiofilm, antitumor activities for essential oils of flower and leaf essential oil of leaf. The study highlighted the diversity in two different parts of A. rugosa grown in Xinjiang region and other places, which have different active constituents. Our results showed that this native plant may be a good candidate for further biological and pharmacological investigations.
  8. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Phys Rev Lett, 2016 Jul 15;117(3):031802.
    PMID: 27472109 DOI: 10.1103/PhysRevLett.117.031802
    A search for narrow resonances decaying into dijet final states is performed on data from proton-proton collisions at a center-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 18.8  fb^{-1}. The data were collected with the CMS detector using a novel technique called data scouting, in which the information associated with these selected events is much reduced, permitting collection of larger data samples. This technique enables CMS to record events containing jets at a rate of 1 kHz, by collecting the data from the high-level-trigger system. In this way, the sensitivity to low-mass resonances is increased significantly, allowing previously inaccessible couplings of new resonances to quarks and gluons to be probed. The resulting dijet mass distribution yields no evidence of narrow resonances. Upper limits are presented on the resonance cross sections as a function of mass, and compared with a variety of models predicting narrow resonances. The limits are translated into upper limits on the coupling of a leptophobic resonance Z_{B}^{'} to quarks, improving on the results obtained by previous experiments for the mass range from 500 to 800 GeV.
  9. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Phys Rev Lett, 2016 Jul 29;117(5):051802.
    PMID: 27517765 DOI: 10.1103/PhysRevLett.117.051802
    A search for the resonant production of high-mass photon pairs is presented. The analysis is based on samples of proton-proton collision data collected by the CMS experiment at center-of-mass energies of 8 and 13 TeV, corresponding to integrated luminosities of 19.7 and 3.3  fb^{-1}, respectively. The interpretation of the search results focuses on spin-0 and spin-2 resonances with masses between 0.5 and 4 TeV and with widths, relative to the mass, between 1.4×10^{-4} and 5.6×10^{-2}. Limits are set on scalar resonances produced through gluon-gluon fusion, and on Randall-Sundrum gravitons. A modest excess of events compatible with a narrow resonance with a mass of about 750 GeV is observed. The local significance of the excess is approximately 3.4 standard deviations. The significance is reduced to 1.6 standard deviations once the effect of searching under multiple signal hypotheses is considered. More data are required to determine the origin of this excess.
  10. Permuth JB, Pirie A, Ann Chen Y, Lin HY, Reid BM, Chen Z, et al.
    Hum Mol Genet, 2016 08 15;25(16):3600-3612.
    PMID: 27378695 DOI: 10.1093/hmg/ddw196
    Rare and low frequency variants are not well covered in most germline genotyping arrays and are understudied in relation to epithelial ovarian cancer (EOC) risk. To address this gap, we used genotyping arrays targeting rarer protein-coding variation in 8,165 EOC cases and 11,619 controls from the international Ovarian Cancer Association Consortium (OCAC). Pooled association analyses were conducted at the variant and gene level for 98,543 variants directly genotyped through two exome genotyping projects. Only common variants that represent or are in strong linkage disequilibrium (LD) with previously-identified signals at established loci reached traditional thresholds for exome-wide significance (P  P≥5.0 ×10 -  7) were detected for rare and low-frequency variants at 16 novel loci. Four rare missense variants were identified (ACTBL2 rs73757391 (5q11.2), BTD rs200337373 (3p25.1), KRT13 rs150321809 (17q21.2) and MC2R rs104894658 (18p11.21)), but only MC2R rs104894668 had a large effect size (OR = 9.66). Genes most strongly associated with EOC risk included ACTBL2 (PAML = 3.23 × 10 -  5; PSKAT-o = 9.23 × 10 -  4) and KRT13 (PAML = 1.67 × 10 -  4; PSKAT-o = 1.07 × 10 -  5), reaffirming variant-level analysis. In summary, this large study identified several rare and low-frequency variants and genes that may contribute to EOC susceptibility, albeit with possible small effects. Future studies that integrate epidemiology, sequencing, and functional assays are needed to further unravel the unexplained heritability and biology of this disease.
  11. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(7):372.
    PMID: 28280445 DOI: 10.1140/epjc/s10052-016-4205-7
    Inclusive jet production in pPb collisions at a nucleon-nucleon (NN) center-of-mass energy of [Formula: see text] is studied with the CMS detector at the LHC. A data sample corresponding to an integrated luminosity of 30.1 nb[Formula: see text] is analyzed. The jet transverse momentum spectra are studied in seven pseudorapidity intervals covering the range [Formula: see text] in the NN center-of-mass frame. The jet production yields at forward and backward pseudorapidity are compared and no significant asymmetry about [Formula: see text] is observed in the measured kinematic range. The measurements in the pPb system are compared to reference jet spectra obtained by extrapolation from previous measurements in pp collisions at [Formula: see text]. In all pseudorapidity ranges, nuclear modifications in inclusive jet production are found to be small, as predicted by next-to-leading order perturbative QCD calculations that incorporate nuclear effects in the parton distribution functions.
  12. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(8):460.
    PMID: 28747851 DOI: 10.1140/epjc/s10052-016-4292-5
    Results are reported from a search for the pair production of top squarks, the supersymmetric partners of top quarks, in final states with jets and missing transverse momentum. The data sample used in this search was collected by the CMS detector and corresponds to an integrated luminosity of 18.9[Formula: see text] of proton-proton collisions at a centre-of-mass energy of 8[Formula: see text] produced by the LHC. The search features novel background suppression and prediction methods, including a dedicated top quark pair reconstruction algorithm. The data are found to be in agreement with the predicted backgrounds. Exclusion limits are set in simplified supersymmetry models with the top squark decaying to jets and an undetected neutralino, either through a top quark or through a bottom quark and chargino. Models with the top squark decaying via a top quark are excluded for top squark masses up to 755[Formula: see text] in the case of neutralino masses below 200[Formula: see text]. For decays via a chargino, top squark masses up to 620[Formula: see text] are excluded, depending on the masses of the chargino and neutralino.
  13. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(8):469.
    PMID: 28303084 DOI: 10.1140/epjc/s10052-016-4293-4
    The differential cross section and charge asymmetry for inclusive [Formula: see text] production at [Formula: see text] are measured as a function of muon pseudorapidity. The data sample corresponds to an integrated luminosity of 18.8[Formula: see text] recorded with the CMS detector at the LHC. These results provide important constraints on the parton distribution functions of the proton in the range of the Bjorken scaling variable x from [Formula: see text] to [Formula: see text].
  14. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(8):451.
    PMID: 28303083 DOI: 10.1140/epjc/s10052-016-4286-3
    A measurement of the double-differential inclusive jet cross section as a function of jet transverse momentum [Formula: see text] and absolute jet rapidity [Formula: see text] is presented. The analysis is based on proton-proton collisions collected by the CMS experiment at the LHC at a centre-of-mass energy of 13[Formula: see text]. The data samples correspond to integrated luminosities of 71 and 44[Formula: see text] for [Formula: see text] and [Formula: see text], respectively. Jets are reconstructed with the anti-[Formula: see text] clustering algorithm for two jet sizes, R, of 0.7 and 0.4, in a phase space region covering jet [Formula: see text] up to 2[Formula: see text] and jet rapidity up to [Formula: see text] = 4.7. Predictions of perturbative quantum chromodynamics at next-to-leading order precision, complemented with electroweak and nonperturbative corrections, are used to compute the absolute scale and the shape of the inclusive jet cross section. The cross section difference in R, when going to a smaller jet size of 0.4, is best described by Monte Carlo event generators with next-to-leading order predictions matched to parton showering, hadronisation, and multiparton interactions. In the phase space accessible with the new data, this measurement provides a first indication that jet physics is as well understood at [Formula: see text] as at smaller centre-of-mass energies.
  15. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(5):237.
    PMID: 28280427 DOI: 10.1140/epjc/s10052-016-4067-z
    A search for a massive resonance [Formula: see text]decaying into a W and a Higgs boson in the [Formula: see text] ([Formula: see text], [Formula: see text]) final state is presented. Results are based on data corresponding to an integrated luminosity of 19.7[Formula: see text] of proton-proton collisions at [Formula: see text] [Formula: see text], collected using the CMS detector at the LHC. For a high-mass ([Formula: see text]1[Formula: see text]) resonance, the two bottom quarks coming from the Higgs boson decay are reconstructed as a single jet, which can be tagged by placing requirements on its substructure and flavour. Exclusion limits at 95 % confidence level are set on the production cross section of a narrow resonance decaying into WH, as a function of its mass. In the context of a little Higgs model, a lower limit on the [Formula: see text] mass of 1.4[Formula: see text] is set. In a heavy vector triplet model that mimics the properties of composite Higgs models, a lower limit on the [Formula: see text] mass of 1.5[Formula: see text] is set. In the context of this model, the results are combined with related searches to obtain a lower limit on the [Formula: see text] mass of 1.8[Formula: see text], the most restrictive to date for decays to a pair of standard model bosons.
  16. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(7):379.
    PMID: 28280447 DOI: 10.1140/epjc/s10052-016-4105-x
    Jet multiplicity distributions in top quark pair ([Formula: see text]) events are measured in pp collisions at a centre-of-mass energy of 8 TeV with the CMS detector at the LHC using a data set corresponding to an integrated luminosity of 19.7[Formula: see text]. The measurement is performed in the dilepton decay channels ([Formula: see text], [Formula: see text], and [Formula: see text]). The absolute and normalized differential cross sections for [Formula: see text] production are measured as a function of the jet multiplicity in the event for different jet transverse momentum thresholds and the kinematic properties of the leading additional jets. The differential [Formula: see text] and [Formula: see text] cross sections are presented for the first time as a function of the kinematic properties of the leading additional [Formula: see text] jets. Furthermore, the fraction of events without additional jets above a threshold is measured as a function of the transverse momenta of the leading additional jets and the scalar sum of the transverse momenta of all additional jets. The data are compared and found to be consistent with predictions from several perturbative quantum chromodynamics event generators and a next-to-leading order calculation.
  17. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(10):536.
    PMID: 28316485 DOI: 10.1140/epjc/s10052-016-4346-8
    A measurement of the decorrelation of azimuthal angles between the two jets with the largest transverse momenta is presented for seven regions of leading jet transverse momentum up to 2.2[Formula: see text]. The analysis is based on the proton-proton collision data collected with the CMS experiment at a centre-of-mass energy of 8[Formula: see text] corresponding to an integrated luminosity of 19.7[Formula: see text]. The dijet azimuthal decorrelation is caused by the radiation of additional jets and probes the dynamics of multijet production. The results are compared to fixed-order predictions of perturbative quantum chromodynamics (QCD), and to simulations using Monte Carlo event generators that include parton showers, hadronization, and multiparton interactions. Event generators with only two outgoing high transverse momentum partons fail to describe the measurement, even when supplemented with next-to-leading-order QCD corrections and parton showers. Much better agreement is achieved when at least three outgoing partons are complemented through either next-to-leading-order predictions or parton showers. This observation emphasizes the need to improve predictions for multijet production.
  18. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(8):439.
    PMID: 28303081 DOI: 10.1140/epjc/s10052-016-4261-z
    A search for new physics is performed using events with two isolated same-sign leptons, two or more jets, and missing transverse momentum. The results are based on a sample of proton-proton collisions at a center-of-mass energy of 13[Formula: see text] recorded with the CMS detector at the LHC, corresponding to an integrated luminosity of 2.3 [Formula: see text]. Multiple search regions are defined by classifying events in terms of missing transverse momentum, the scalar sum of jet transverse momenta, the transverse mass associated with a [Formula: see text] boson candidate, the number of jets, the number of [Formula: see text] quark jets, and the transverse momenta of the leptons in the event. The analysis is sensitive to a wide variety of possible signals beyond the standard model. No excess above the standard model background expectation is observed. Constraints are set on various supersymmetric models, with gluinos and bottom squarks excluded for masses up to 1300 and 680[Formula: see text], respectively, at the 95 % confidence level. Upper limits on the cross sections for the production of two top quark-antiquark pairs (119[Formula: see text]) and two same-sign top quarks (1.7[Formula: see text]) are also obtained. Selection efficiencies and model independent limits are provided to allow further interpretations of the results.
  19. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  20. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2016;76(6):325.
    PMID: 28280439 DOI: 10.1140/epjc/s10052-016-4156-z
    A measurement of the forward-backward asymmetry [Formula: see text] of oppositely charged lepton pairs ([Formula: see text] and [Formula: see text]) produced via [Formula: see text] boson exchange in pp collisions at [Formula: see text] [Formula: see text] is presented. The data sample corresponds to an integrated luminosity of 19.7[Formula: see text] collected with the CMS detector at the LHC. The measurement of [Formula: see text] is performed for dilepton masses between 40[Formula: see text] and 2[Formula: see text] and for dilepton rapidity up to 5. The [Formula: see text] measurements as a function of dilepton mass and rapidity are compared with the standard model predictions.
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