An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Untangling the effects of overexploration and overexploitation on organizational performance: The moderating role of environmental dynamism

Because a firm's optimal knowledge search behavior is determined by unique firm and industry conditions, organizational performance should be contingent oil the degree to which a firm's actual level of knowledge search deviates from the optimal level. It is thus hypothesized that deviation from the optimal search, in the form of either overexploitation or overexploration, is detrimental to organizational performance. Furthermore, the negative effect of search deviation oil organizational performance varies with environmental dynamism: that is, overexploitation is expected to become more harmful. whereas overexploration becomes less so with all increase in environmental dynamism. The empirical analyses yield results consistent with these arguments. Implications for research and practice are correspondingly discussed

Differential cross-sections for events with missing transverse momentum and jets measured with the ATLAS detector in 13 TeV proton-proton collisions

Measurements of inclusive, diferential cross-sections for the production of events with missing transverse momentum in association with jets in proton-proton collisions at √s = 13 TeV are presented. The measurements are made with the ATLAS detector using an integrated luminosity of 140 fb−1 and include measurements of dijet distributions in a region in which vector-boson fusion processes are enhanced. They are unfolded to correct for detector resolution and efficiency within the fiducial acceptance, and are designed to allow robust comparisons with a wide range of theoretical predictions. A measurement of differential cross sections for the Z → νν process is made. The measurements are generally well-described by Standard Model predictions except for the dijet invariant mass distribution. Auxiliary measurements of the hadronic system recoiling against isolated leptons, and photons, are also made in the same phase space. Ratios between the measured distributions are then derived, to take advantage of cancellations in modelling effects and some of the major systematic uncertainties. These measurements are sensitive to new phenomena, and provide a mechanism to easily set constraints on phenomenological models. To illustrate the robustness of the approach, these ratios are compared with two common Dark Matter models, where the constraints derived from the measurement are comparable to those set by dedicated detector-level searches

Measurement of ZZ production cross-sections in the four-lepton final state in pp collisions at √s = 13.6 TeV with the ATLAS experiment

This paper reports cross-section measurements of ZZ production in pp collisions at √s = 13.6TeV at the Large Hadron Collider. The data were collected by the ATLAS detector in 2022, and correspond to an integrated luminosity of 29 fb−1. Events in the ZZ → 4ℓ (ℓ = e, μ) final states are selected and used to measure the inclusive and differential cross-sections in a fiducial region defined close to the analysis selections. The inclusive cross-section is further extrapolated to the total phase space with a requirement of 66 <mZ < 116 GeV for both Z bosons, yielding 16.8 ± 1.1 pb. The results are well described by the Standard Model predictions

Inclusive and diferential cross-section measurements of ttZ¯ production in pp collisions at √s = 13 TeV with the ATLAS detector, including EFT and spin-correlation interpretations

Measurements of both the inclusive and diferential production cross sections of a top-quark-top-antiquark pair in association with a Z boson (ttZ¯ ) are presented. Final states with two, three or four isolated leptons (electrons or muons) are targeted. The measurements use the data recorded by the ATLAS detector in pp collisions at √s = 13 TeV at the Large Hadron Collider during the years 2015–2018, corresponding to an integrated luminosity of 140 fb−1. The inclusive cross section is measured to be σttZ¯ = 0.86±0.04 (stat.)±0.04 (syst.) pb and found to be in agreement with the most advanced Standard Model predictions. The differential measurements are presented as a function of a number of observables that probe the kinematics of the ttZ¯ system. Both the absolute and normalised differential cross-section measurements are performed at particle level and parton level for specific fiducial volumes, and are compared with NLO+NNLL theoretical predictions. The results are interpreted in the framework of Standard Model effective field theory and used to set limits on a large number of dimension-6 operators involving the top quark. The first measurement of spin correlations in ttZ¯ events is presented: the results are in agreement with the Standard Model expectations, and the null hypothesis of no spin correlations is disfavoured with a significance of 1.8 standard deviations

The ATLAS trigger system for LHC Run 3 and trigger performance in 2022

The ATLAS trigger system is a crucial component of the ATLAS experiment at the LHC. It is responsible for selecting events in line with the ATLAS physics programme. This paper presents an overview of the changes to the trigger and data acquisition system during the second long shutdown of the LHC, and shows the performance of the trigger system and its components in the proton-proton collisions during the 2022 commissioning period as well as its expected performance in proton-proton and heavy-ion collisions for the remainder of the third LHC data-taking period (2022–2025)

Observation of quantum entanglement with top quarks at the ATLAS detector

Entanglement is a key feature of quantum mechanics with applications in fields such as metrology, cryptography, quantum information and quantum computation. It has been observed in a wide variety of systems and length scales, ranging from the microscopic to the macroscopic. However, entanglement remains largely unexplored at the highest accessible energy scales. Here we report the highest-energy observation of entanglement, in top–antitop quark events produced at the Large Hadron Collider, using a proton–proton collision dataset with a centre-of-mass energy of √s = 13 TeV and an integrated luminosity of 140 inverse femtobarns (fb)−1 recorded with the ATLAS experiment. Spin entanglement is detected from the measurement of a single observable D, inferred from the angle between the charged leptons in their parent top- and antitop-quark rest frames. The observable is measured in a narrow interval around the top–antitop quark production threshold, at which the entanglement detection is expected to be significant. It is reported in a fiducial phase space defined with stable particles to minimize the uncertainties that stem from the limitations of the Monte Carlo event generators and the parton shower model in modelling top-quark pair production. The entanglement marker is measured to be D = −0.537 ± 0.002 (stat.) ± 0.019 (syst.) for 340 GeV < mtt < 380 GeV. The observed result is more than five standard deviations from a scenario without entanglement and hence constitutes the first observation of entanglement in a pair of quarks and the highest-energy observation of entanglement so far

Measurements of the production cross-section for a Z boson in association with b- or c-jets in proton–proton collisions at √s = 13 TeV with the ATLAS detector

This paper presents a measurement of the production cross-section of a Z boson in association with bor c-jets, in proton–proton collisions at √s = 13 TeV with the ATLAS experiment at the Large Hadron Collider using data corresponding to an integrated luminosity of 140 fb−1. Inclusive and differential cross-sections are measured for events containing a Z boson decaying into electrons or muons and produced in association with at least one b-jet, at least one c-jet, or at least two b-jets with transverse momentum pT > 20 GeV and rapidity |y| < 2.5. Predictions from several Monte Carlo generators based on next-to-leading-order matrix elements interfaced with a parton-shower simulation, with different choices of flavour schemes for initial-state partons, are compared with the measured cross-sections. The results are also compared with novel predictions, based on infrared and collinear safe jet flavour dressing algorithms. Selected Z+ ≥ 1 c-jet observables, optimized for sensitivity to intrinsic-charm, are compared with benchmark models with different intrinsic-charm fractions

Measurement of diferential cross-sections in tt¯ and tt¯+jets production in the lepton+jets fnal state in pp collisions at √s = 13 TeV using 140 fb−1 of ATLAS data

Diferential cross-sections for top-quark pair production, inclusively and in association with jets, are measured in pp collisions at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC using an integrated luminosity of 140 fb−1. The events are selected with one charged lepton (electron or muon) and at least four jets. The differential cross-sections are presented at particle level as functions of several jet observables, including angular correlations, jet transverse momenta and invariant masses of the jets in the final state, which characterise the kinematics and dynamics of the top-antitop system and the hard QCD radiation in the system with associated jets. The typical precision is 5%–15% for the absolute differential cross-sections and 2%–4% for the normalised differential cross-sections. Next-to-leading-order and next-to-next-to-leading-order QCD predictions are found to provide an adequate description of the rate and shape of the jet-angular observables. The description of the transverse momentum and invariant mass observables is improved when next-to-next-to-leading-order QCD corrections are included

Measurement of the VH,H → ττ process with the ATLAS detector at 13 TeV

A measurement of the Standard Model Higgs boson produced in association with a W or Z boson and decaying into a pair of τ-leptons is presented. This search is based on proton-proton collision data collected at √s = 13 TeV by the ATLAS experiment at the LHC corresponding to an integrated luminosity of 140 fb−1. For the Higgs boson candidate, only final states with at least one τ-lepton decaying hadronically (τ →hadrons + vτ ) are considered. For the vector bosons, only leptonic decay channels are considered: Z → ℓℓ and W → ℓvℓ, with ℓ = e, μ. An excess of events over the expected background is found with an observed (expected) significance of 4.2 (3.6) standard deviations, providing evidence of the Higgs boson produced in association with a vector boson and decaying into a pair of τ-leptons. The ratio of the measured cross-section to the Standard Model prediction is μττ VH = 1.28 +0.30 −0.29 (stat.) +0.25 −0.21 (syst.). This result represents the most accurate measurement of the VH(ττ) process achieved to date