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Open Access Publications from the University of California

Scholarly Works (511 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2011)
Introns in a wide range of organisms including plants, animals and fungi are able to increase the expression of the gene that they are contained in. This process of intron-mediated enhancement (IME) is most thoroughly studied in Arabidopsis thaliana, where it has been shown that enhancing introns are typically located near the promoter and are compositionally distinct from downstream introns. In this study, we perform a comprehensive comparative analysis of several sequenced plant genomes. We find that enhancing sequences are conserved in the multi-cellular plants but are either absent or unrecognizable in algae. IME signals are preferentially located towards the 5'-end of first introns but also appear to be enriched in 5'-UTRs and coding regions near the transcription start site. Enhancing introns are found most prominently in genes that are highly expressed in a wide range of tissues. Through site-directed mutagenesis in A. thaliana, we show that IME signals can be inserted or removed from introns to increase or decrease gene expression. Although we do not yet know the specific mechanism of IME, the predicted signals appear to be both functional and highly conserved.
    Cover page: Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2016)
    Searches for pair-produced scalar leptoquarks are performed using 20 fb[Formula: see text] of proton-proton collision data provided by the LHC and recorded by the ATLAS detector at [Formula: see text] TeV. Events with two electrons (muons) and two or more jets in the final state are used to search for first (second)-generation leptoquarks. The results from two previously published ATLAS analyses are interpreted in terms of third-generation leptoquarks decaying to [Formula: see text] and [Formula: see text] final states. No statistically significant excess above the Standard Model expectation is observed in any channel and scalar leptoquarks are excluded at 95 % CL with masses up to [Formula: see text] 1050 GeV for first-generation leptoquarks, [Formula: see text] 1000 GeV for second-generation leptoquarks, [Formula: see text] 625 GeV for third-generation leptoquarks in the [Formula: see text] channel, and 200 [Formula: see text] 640 GeV in the [Formula: see text] channel.
      Cover page: Searches for scalar leptoquarks in pp collisions at s = 8 TeV with the ATLAS detectorCreative Commons 'BY' version 4.0 license
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2015)
      Measurements of the ZZ and WW final states in the mass range above the [Formula: see text] and [Formula: see text] thresholds provide a unique opportunity to measure the off-shell coupling strength of the Higgs boson. This paper presents constraints on the off-shell Higgs boson event yields normalised to the Standard Model prediction (signal strength) in the [Formula: see text], [Formula: see text] and [Formula: see text] final states. The result is based on pp collision data collected by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 20.3 fb[Formula: see text] at a collision energy of [Formula: see text] TeV. Using the [Formula: see text] method, the observed 95 [Formula: see text] confidence level (CL) upper limit on the off-shell signal strength is in the range 5.1-8.6, with an expected range of 6.7-11.0. In each case the range is determined by varying the unknown [Formula: see text] and [Formula: see text] background K-factor from higher-order quantum chromodynamics corrections between half and twice the value of the known signal K-factor. Assuming the relevant Higgs boson couplings are independent of the energy scale of the Higgs boson production, a combination with the on-shell measurements yields an observed (expected) 95 [Formula: see text] CL upper limit on [Formula: see text] in the range 4.5-7.5 (6.5-11.2) using the same variations of the background K-factor. Assuming that the unknown [Formula: see text] background K-factor is equal to the signal K-factor, this translates into an observed (expected) 95 [Formula: see text] CL upper limit on the Higgs boson total width of 22.7 (33.0) MeV.
        Cover page: Constraints on the off-shell Higgs boson signal strength in the high-mass ZZ and WW final states with the ATLAS detectorCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2014)
        A search is conducted for non-resonant new phenomena in dielectron and dimuon final states, originating from either contact interactions or large extra spatial dimensions. The LHC 2012 proton-proton collision dataset recorded by the ATLAS detector is used, corresponding to 20 fb[Formula: see text] at [Formula: see text] = 8 TeV. The dilepton invariant mass spectrum is a discriminating variable in both searches, with the contact interaction search additionally utilizing the dilepton forward-backward asymmetry. No significant deviations from the Standard Model expectation are observed. Lower limits are set on the [Formula: see text] contact interaction scale [Formula: see text] between 15.4 TeV and 26.3 TeV, at the 95 % credibility level. For large extra spatial dimensions, lower limits are set on the string scale [Formula: see text] between 3.2 TeV to 5.0 TeV.
          Cover page: Search for contact interactions and large extra dimensions in the dilepton channel using proton–proton collisions at s= 8 TeV with the ATLAS detectorCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Santa Cruz Previously Published Works (2013)
          The measurement of the jet energy resolution is presented using data recorded with the ATLAS detector in proton-proton collisions at [Formula: see text]. The sample corresponds to an integrated luminosity of 35 pb-1. Jets are reconstructed from energy deposits measured by the calorimeters and calibrated using different jet calibration schemes. The jet energy resolution is measured with two different in situ methods which are found to be in agreement within uncertainties. The total uncertainties on these measurements range from 20 % to 10 % for jets within |y|<2.8 and with transverse momenta increasing from 30 GeV to 500 GeV. Overall, the Monte Carlo simulation of the jet energy resolution agrees with the data within 10 %.
            Cover page: Jet energy resolution in proton-proton collisions at recorded in 2010 with the ATLAS detectorCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Santa Cruz Previously Published Works (2015)
            The mass of the top quark is measured in a data set corresponding to 4.6 [Formula: see text] of proton-proton collisions with centre-of-mass energy [Formula: see text] 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 [Formula: see text]-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 produced in a top-quark decay. Using these three jets the dijet mass is obtained from the two jets produced in the [Formula: see text] 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 [Formula: see text].
              Cover page: Measurement of the top-quark mass in the fully hadronic decay channel from ATLAS data at s=7TeVCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC Santa Cruz Previously Published Works (2012)
              We report a measurement of the cross section of single top-quark production in the t-channel using 1.04 fb−1 of pp collision data at s=7 TeV recorded with the ATLAS detector at the LHC. Selected events feature one electron or muon, missing transverse momentum, and two or three jets, exactly one of them identified as originating from a b quark. The cross section is measured by fitting the distribution of a multivariate discriminant constructed with a neural network, yielding σt=83±4(stat.)−19+20(syst.) pb, which is in good agreement with the prediction of the Standard Model. Using the ratio of the measured to the theoretically predicted cross section and assuming that the top-quark-related CKM matrix elements obey the relation |Vtb|≫|Vts|,|Vtd|, the coupling strength at the W-t-b vertex is determined to be |Vtb|=1.13−0.13+0.14. If it is assumed that |Vtb|⩽1 a lower limit of |Vtb|>0.75 is obtained at the 95% confidence level.
                Cover page: Measurement of the t-channel single top-quark production cross section in pp collisions at s=7 TeV with the ATLAS detectorCreative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2012)
                A search for the production of single top-quarks via flavour-changing neutral-currents is presented. Data collected with the ATLAS detector at a centre-of-mass energy of s=7 TeV, corresponding to an integrated luminosity of 2.05 fb−1, are used. Candidate events with a semileptonic top-quark decay signature are classified as signal- or background-like events by using several kinematic variables as input to a neural network. No signal is observed in the neural network output distribution and a Bayesian upper limit is placed on the production cross-section. The observed upper limit at 95% confidence level on the cross-section multiplied by the t→Wb branching fraction is measured to be σqg→t×B(t→Wb)<3.9 pb. This upper limit is converted using a model-independent approach into upper limits on the coupling strengths κugt/Λ<6.9⋅10−3 TeV−1 and κcgt/Λ<1.6⋅10−2 TeV−1, where Λ is the new physics scale, and on the branching fractions B(t→ug)<5.7⋅10−5 and B(t→cg)<2.7⋅10−4.
                  Cover page: Search for FCNC single top-quark production at s=7 TeV with the ATLAS detectorCreative Commons 'BY' version 4.0 license
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2012)
                  The results of a search for supersymmetry in events with large missing transverse momentum and heavy-flavor jets using an integrated luminosity corresponding to 2.05fb-1 of pp collisions at √s=7TeV recorded with the ATLAS detector at the Large Hadron Collider are reported. No significant excess is observed with respect to the prediction for standard model processes. Results are interpreted in a variety of R-parity conserving models in which scalar bottoms and tops are the only scalar quarks to appear in the gluino decay cascade, and in an SO(10) model framework. Gluino masses up to 600-900GeV are excluded, depending on the model considered. © 2012 CERN. Published by the American Physical Society.
                    Cover page: Search for supersymmetry in pp collisions at s=7 TeV in final states with missing transverse momentum and b-jets with the ATLAS detectorCreative Commons 'BY' version 4.0 license
                    • Article
                    • Peer Reviewed
                    UC Santa Cruz Previously Published Works (2015)
                    The distribution and orientation of energy inside jets is predicted to be an experimental handle on colour connections between the hard-scatter quarks and gluons initiating the jets. This Letter presents a measurement of the distribution of one such variable, the jet pull angle. The pull angle is measured for jets produced in tt- events with one W boson decaying leptonically and the other decaying to jets using 20.3 fb-1 of data recorded with the ATLAS detector at a centre-of-mass energy of s=8 TeV at the LHC. The jet pull angle distribution is corrected for detector resolution and acceptance effects and is compared to various models.
                      Cover page: Measurement of colour flow with the jet pull angle in tt¯ events using the ATLAS detector at s=8&nbsp;TeVCreative Commons 'BY' version 4.0 license
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