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1.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Landes Bioscience. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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2.
  • Jin, Ying-Hui, et al. (författare)
  • Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
  • 2020
  • Ingår i: Military Medical Research. - : BioMed Central (BMC). - 2054-9369. ; 7:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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3.
  • Aad, G., et al. (författare)
  • A measurement of the ratio of the production cross sections for W and Z bosons in association with jets with the ATLAS detector
  • 2014
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 74:12
  • Tidskriftsartikel (refereegranskat)abstract
    • The ratio of the production cross sections for W and Z bosons in association with jets has been measured in proton-proton collisions at root s = 7 TeV with the ATLAS experiment at the Large Hadron Collider. The measurement is based on the entire 2011 dataset, corresponding to an integrated luminosity of 4.6 fb(-1). Inclusive and differential cross-section ratios for massive vector bosons decaying to electrons and muons are measured in association with jets with transverse momentum p(T) > 30 GeV and jet rapidity vertical bar y vertical bar < 4.4. The measurements are compared to next-to-leading-order perturbative QCD calculations and to predictions from different Monte Carlo generators implementing leading-order matrix elements supplemented by parton showers.
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4.
  • Aad, G., et al. (författare)
  • A search for high-mass resonances decaying to tau(+)tau(-) in pp collisions at root s=8 TeV with the ATLAS detector
  • 2015
  • Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; :7
  • Tidskriftsartikel (refereegranskat)abstract
    • A search for high-mass resonances decaying into tau(+)tau(-) final states using proton-proton collisions at root s = 8 TeV produced by the Large Hadron Collider is presented. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 19.5-20.3 fb(-1). No statistically significant excess above the Standard Model expectation is observed; 95% credibility upper limits are set on the cross section times branching fraction of Z' resonances decaying into tau(+)tau(-) pairs as a function of the resonance mass. As a result, Z' bosons of the Sequential Standard Model with masses less than 2.02 TeV are excluded at 95% credibility. The impact of the fermionic couplings on the Z' acceptance is investigated and limits are also placed on a Z' model that exhibits enhanced couplings to third-generation fermions.
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5.
  • Aad, G., et al. (författare)
  • A search for t(t)over-bar resonances using lepton-plus-jets events in proton-proton collisions at root s=8 TeV with the ATLAS detector
  • 2015
  • Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; :8
  • Tidskriftsartikel (refereegranskat)abstract
    • A search for new particles that decay into top quark pairs is reported. The search is performed with the ATLAS experiment at the LHC using an integrated luminosity of 20.3 fb(-1) of proton-proton collision data collected at a centre-of-mass energy of root s = 8TeV. The lepton-plus-jets final state is used, where the top pair decays to W (+) bW(-)(b) over bar, with one W boson decaying leptonically and the other hadronically. The invariant mass spectrum of top quark pairs is examined for local excesses or deficits that are inconsistent with the Standard Model predictions. No evidence for a top quark pair resonance is found, and 95% confidence-level limits on the production rate are determined for massive states in benchmark models. The upper limits on the cross-section times branching ratio of a narrow Z' boson decaying to top pairs range from 4.2 pb to 0.03 pb for resonance masses from 0.4 TeV to 3.0 TeV. A narrow leptophobic topcolour Z' boson with mass below 1.8 TeV is excluded. Upper limits are set on the cross-section times branching ratio for a broad colour-octet resonance with Gamma/m = 15% decaying to tt. These range from 4.8 pb to 0.03 pb for masses from 0.4 TeV to 3.0 TeV. A Kaluza-Klein excitation of the gluon in a Randall-Sundrum model is excluded for masses below 2.2 TeV.
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6.
  • Aad, G, et al. (författare)
  • ATLAS Run 1 searches for direct pair production of third-generation squarks at the Large Hadron Collider.
  • 2015
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 75:10
  • Tidskriftsartikel (refereegranskat)abstract
    • This paper reviews and extends searches for the direct pair production of the scalar supersymmetric partners of the top and bottom quarks in proton-proton collisions collected by the ATLAS collaboration during the LHC Run 1. Most of the analyses use 20 [Formula: see text] of collisions at a centre-of-mass energy of [Formula: see text] TeV, although in some case an additional [Formula: see text] of collision data at [Formula: see text] TeV are used. New analyses are introduced to improve the sensitivity to specific regions of the model parameter space. Since no evidence of third-generation squarks is found, exclusion limits are derived by combining several analyses and are presented in both a simplified model framework, assuming simple decay chains, as well as within the context of more elaborate phenomenological supersymmetric models.
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7.
  • Aad, G., et al. (författare)
  • Centrality and rapidity dependence of inclusive jet production in root(NN)-N-S=5.02 TeV proton-lead collisions with the ATLAS detector
  • 2015
  • Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier. - 0370-2693 .- 1873-2445. ; 748, s. 392-413
  • Tidskriftsartikel (refereegranskat)abstract
    • Measurements of the centrality and rapidity dependence of inclusive jet production in root(NN)-N-S = 5.02 TeV proton-lead (p + Pb) collisions and the jet cross-section in root s = 2.76 TeV proton-proton collisions are presented. These quantities are measured in datasets corresponding to an integrated luminosity of 27.8 nb(-1) and 4.0 pb(-1), respectively, recorded with the ATLAS detector at the Large Hadron Collider in 2013. The p + Pb collision centrality was characterised using the total transverse energy measured in the pseudorapidity interval -4.9 < eta < -3.2 in the direction of the lead beam. Results are presented for the double-differential per-collision yields as a function of jet rapidity and transverse momentum (p(T)) for minimum-bias and centrality-selected p + Pb collisions, and are compared to the jet rate from the geometric expectation. The total jet yield in minimum-bias events is slightly enhanced above the expectation in a p(T)-dependent manner but is consistent with the expectation within uncertainties. The ratios of jet spectra from different centrality selections show a strong modification of jet production at all p(T) at forward rapidities and for large pT at mid-rapidity, which manifests as a suppression of the jet yield in central events and an enhancement in peripheral events. These effects imply that the factorisation between hard and soft processes is violated at an unexpected level in proton-nucleus collisions. Furthermore, the modifications at forward rapidities are found to be a function of the total jet energy only, implying that the violations may have a simple dependence on the hard parton-parton kinematics. (C) 2015 CERN for the benefit of the ATLAS Collaboration. Published by Elsevier B.V.
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8.
  • Aad, G., et al. (författare)
  • Comprehensive measurements of t-channel single top-quark production cross sections at root S=7 TeV with the ATLAS detector
  • 2014
  • Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - : American Physical Society. - 1550-2368 .- 1550-7998. ; 90:11, s. 112006-
  • Tidskriftsartikel (refereegranskat)abstract
    • This article presents measurements of the t-channel single top-quark ((t) over bart) and top-antiquark (_ t) total production cross sections sdtq_ and sd _ tq_, their ratio Rt sdtq_= sd _ tq_, and a measurement of the inclusive production cross section sdtq _ _ tq_ in proton-proton collisions at ffiffiffi ps = 7 TeV at the LHC. Differential cross sections for the tq and _ tq processes are measured as a function of the transverse momentum and the absolute value of the rapidity of t and _ t, respectively. The analyzed data set was recorded with the ATLAS detector and corresponds to an integrated luminosity of 4.59 fb-1. Selected events contain one charged lepton, large missing transverse momentum, and two or three jets. The cross sections are measured by performing a binned maximum-likelihood fit to the output distributions of neural networks. The resulting measurements are sdtq_ 46 = 1dstat_ = 6dsyst_ pb, sd _ tq_ = 23 +/- 1dstat_ = 3dsyst_ pb, Rt = 2.04 0.13dstat_ +/-=0.12dsyst_, and sdtq _ _ tq_ = 68 +/-= 2dstat_ = 8dsyst_ pb, consistent with the Standard Model expectation. The uncertainty on the measured cross sections is dominated by systematic uncertainties, while the uncertainty on Rt is mainly statistical. Using the ratio of sdtq _ _ tq_ to its theoretical prediction, and assuming that the top-quark-related CKM matrix elements obey the relation jVtbj = jVtsj; jVtdj, we determine jVtbj = 1.02 = 0.07.
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9.
  • Aad, G., et al. (författare)
  • Constraints on new phenomena via Higgs boson couplings and invisible decays with the ATLAS detector
  • 2015
  • Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; :11
  • Tidskriftsartikel (refereegranskat)abstract
    • The ATLAS experiment at the LHC has measured the Higgs boson couplings and mass, and searched for invisible Higgs boson decays, using multiple production and decay channels with up to 4.7 fb(-1) of pp collision data at root S = 7 TeV and 20.3 fb(-1) at root s = 8 TeV. In the current study, the measured production and decay rates of the observed Higgs boson in the gamma gamma, ZZ, WW, Z gamma, bb, tau tau, and mu mu decay channels, along with results from the associated production of a Higgs boson with a top-quark pair, are used to probe the scaling of the couplings with mass. Limits are set on parameters in extensions of the Standard Model including a composite Higgs boson, an additional electroweak singlet, and two-Higgs-doublet models. Together with the measured mass of the scalar Higgs boson in the gamma gamma and ZZ decay modes, a lower limit is set on the pseudoscalar Higgs boson mass of m(A) > 370 GeV in the "hMSSM" simplified Minimal Supersymmetric Standard Model. Results from direct searches for heavy Higgs bosons are also interpreted in the hMSSM. Direct searches for invisible Higgs boson decays in the vector-boson fusion and associated production of a Higgs boson with W/Z (Z -> ll, W/Z -> jj) modes are statistically combined to set an upper limit on the Higgs boson invisible branching ratio of 0.25. The use of the measured visible decay rates in a more general coupling fit improves the upper limit to 0.23, constraining a Higgs portal model of dark matter.
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10.
  • Aad, G, et al. (författare)
  • Constraints on the off-shell Higgs boson signal strength in the high-mass ZZ and WW final states with the ATLAS detector.
  • 2015
  • Ingår i: European Physical Journal C. Particles and Fields. - : Springer. - 1434-6044 .- 1434-6052. ; 75:7
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
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