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At least 847 records · Page 47

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Searching for quasar candidates with periodic variations from the Zwicky Transient Facility: results and implications

ABSTRACT We conduct a systematic search for quasars with periodic variations from the archival photometric data of the Zwicky Transient Facility by cross-matching with the quasar catalogues of the Sloan Digital Sky Survey and Véron-Cetty and Véron. We first select out 184 primitive periodic candidates using the generalized Lomb–Scargle periodogram and autocorrelation function and then estimate their statistical significance of periodicity based on two red-noise models, i.e. damped random walk (DRW) and single power-law (SPL) models. As such, we finally identify 106 (DRW) and 86 (SPL) candidates with the most significant periodic variations out of 143 700 quasars. We further compare DRW and SPL models using Bayes factors, which indicate a relative preference of the SPL model for our primitive sample. We thus adopt the candidates identified with SPL as the final sample and summarize its basic properties. We extend the light curves of the selected candidates by supplying other archival survey data to verify their periodicity. However, only three candidates (with 6–8 cycles of periods) meet the selection criteria. This result clearly implies that, instead of being strictly periodic, the variability must be quasi-periodic or caused by stochastic red-noise. This exerts a challenge to the existing search approaches and calls for developing new effective methods.

Chen, Yong-Jie (ORCID:0000000342807673)↗

Search for subsolar-mass black hole binaries in the second part of Advanced LIGO’s and Advanced Virgo’s third observing run

ABSTRACT We describe a search for gravitational waves from compact binaries with at least one component with mass $0.2$–$1.0 \, \mathrm{M}_\odot$ and mass ratio q ≥ 0.1 in Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO) and Advanced Virgo data collected between 2019 November 1, 15:00 utc and 2020 March 27, 17:00 utc. No signals were detected. The most significant candidate has a false alarm rate of $0.2 \, \rm {yr}^{-1}$. We estimate the sensitivity of our search over the entirety of Advanced LIGO’s and Advanced Virgo’s third observing run, and present the most stringent limits to date on the merger rate of binary black holes with at least one subsolar-mass component. We use the upper limits to constrain two fiducial scenarios that could produce subsolar-mass black holes: primordial black holes (PBH) and a model of dissipative dark matter. The PBH model uses recent prescriptions for the merger rate of PBH binaries that include a rate suppression factor to effectively account for PBH early binary disruptions. If the PBHs are monochromatically distributed, we can exclude a dark matter fraction in PBHs $f_\mathrm{PBH} \gtrsim \, 0.6$ (at 90 per cent confidence) in the probed subsolar-mass range. However, if we allow for broad PBH mass distributions, we are unable to rule out fPBH = 1. For the dissipative model, where the dark matter has chemistry that allows a small fraction to cool and collapse into black holes, we find an upper bound fDBH < 10−5 on the fraction of atomic dark matter collapsed into black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

The Atacama cosmology telescope: flux upper limits from a targeted search for extragalactic transients

ABSTRACT We have performed targeted searches of known extragalactic transient events at millimetre wavelengths using nine seasons (2013–2021) of 98, 150, and 229 GHz Atacama Cosmology Telescope (ACT) observations that mapped ∼40 per cent of the sky for most of the data volume. Our data cover 88 gamma-ray bursts (GRBs), 12 tidal disruption events (TDEs), and 203 other transients, including supernovae (SNe). We stack our ACT observations to increase the signal-to-noise ratio of the maps. In all cases but one, we do not detect these transients in the ACT data. The single candidate detection (event AT2019ppm), seen at ∼5σ significance in our data, appears to be due to active galactic nuclei activity in the host galaxy coincident with a transient alert. For each source in our search we provide flux upper limits. For example, the medians for the 95 per cent confidence upper limits at 98 GHz are 15, 18, and 16 mJy for GRBs, SNe, and TDEs, respectively, in the first month after discovery. The projected sensitivity of future wide-area cosmic microwave background surveys should be sufficient to detect many of these events using the methods described in this paper.

Hervías-Caimapo, Carlos↗

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

Abstract BioPortal (https://bioportal.bioontology.org) is the world’s most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms across ontologies, (iii) to browse mappings between terms, (iv) to see popularity ratings and recommendations on which ontologies are most relevant to their use cases, (v) to annotate text with ontology terms, (vi) to submit an ontology, and (vii) to request ontology changes. The library of ontologies can be accessed programmatically via a REST application programming interface (API). Recent enhancements include a BioPortal knowledge graph that integrates knowledge from multiple ontologies; a unified data model for interoperability with other knowledge sources; ontology popularity ratings and recommendations for relevant ontologies; and the ability to request ontology changes via a simple user interface that automatically converts user change requests to GitHub Pull Requests that specify the edits that will be made to the ontology upon approval.

Vendetti, Jennifer↗

Search for electroweak-scale dijet resonances using trigger-level analysis with the ATLAS detector in 132 fb −1 of 𝑝⁢𝑝 collisions at $\sqrt{𝑠}$ = 13 TeV

This article reports on a search for dijet resonances using 132 fb −1 of 𝑝⁢𝑝 collision data recorded at $\sqrt{𝑠}$ = 13 TeV by the ATLAS detector at the Large Hadron Collider. The search is performed solely on jets reconstructed within the ATLAS trigger to overcome bandwidth limitations imposed on conventional single-jet triggers, which would otherwise reject data from decays of sub-TeV dijet resonances. Collision events with two jets satisfying transverse momentum thresholds of 𝑝 T ≥ 85 GeV and jet rapidity separation of |𝑦*| <0.6 are analysed for dijet resonances with invariant masses from 375 to 1800 GeV. A data-driven background estimate is used to model the dijet mass distribution from multijet processes. No significant excess above the expected background is observed. Upper limits are set at 95% confidence level on coupling values for a benchmark leptophobic axial-vector 𝑍′ model and on the production cross section for a new resonance contributing a Gaussian-distributed line-shape to the dijet mass distribution.

hadron colliders↗

First Results on the Search for Lepton Number Violating Neutrinoless Double-𝛽 Decay with the LEGEND-200 Experiment

The LEGEND Collaboration is searching for neutrinoless double-beta (0⁢𝜈⁢𝛽⁢𝛽) decay by operating high-purity germanium detectors enriched in 76 Ge in a low-background liquid argon environment. Building on key technological innovations from the GERmanium Detector Array (GERDA) experiment and the MAJORANA DEMONSTRATOR experiment, LEGEND-200 has performed a first 0⁢𝜈⁢𝛽⁢𝛽 decay search based on 61.0 kg yr of data. Over half of this exposure comes from our highest performing detectors, including newly developed inverted-coaxial detectors, and is characterized by an estimated background level of 0.5$^{+0.3}_{−0.2}$ ⁢cts/(keV ton yr) in the 0⁢𝜈⁢𝛽⁢𝛽 decay signal region. A combined analysis of data from GERDA, the MAJORANA DEMONSTRATOR, and LEGEND-200, characterized by a 90% confidence level exclusion sensitivity of 2.8 ×10 26 yr on the half-life of 0⁢𝜈⁢𝛽⁢𝛽 decay, reveals no evidence for a signal and sets a new observed lower limit at 𝑇$^{⁢0𝜈}_{1/2}$ > 1.9 × 10 26 yr (90% confidence level). Assuming the decay is mediated by Majorana neutrinos, this corresponds to an upper limit on the effective Majorana mass in the range 𝑚 𝛽⁢𝛽 < 75–200 meV, depending on the adopted nuclear matrix element.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for dark matter produced in association with a Higgs boson decaying to bottom quarks in proton-proton collisions at $\sqrt{s}=13$ TeV

A search for dark matter particles produced in association with a Higgs boson decaying to a bottom quark-antiquark pair in proton-proton collisions at $\sqrt{s}=13$ TeV is presented. The data, collected with the CMS detector at the LHC, correspond to an integrated luminosity of 101 fb −1 . The analysis is performed in exclusive categories targeting both Lorentz-boosted (merged) and resolved 𝑏 jet pair topologies, covering a wide range of Higgs boson transverse momentum. A statistical combination is made with a previous search using data collected in 2016 and corresponding to an integrated luminosity of 35.9 fb −1 . The observed data agree with the standard model background predictions. Constraints are placed on models predicting new particles or interactions, such as those in the simplified frameworks of baryonic-𝑍′ and 2⁢HDM + 𝑎, where the latter is a type-II two-Higgs-doublet model featuring a heavy pseudoscalar with an additional light pseudoscalar. Upper limits at 95% confidence level are set on the production cross section for these models. For the baryonic-𝑍′ model, 𝑍′ boson masses below 2.25 TeV are excluded for a dark matter particle candidate mass of 1 GeV. In the 2⁢HDM + 𝑎 model, heavy pseudoscalar masses between 850 and 1300 GeV are excluded for a light pseudoscalar mass of 350 GeV.

Hayrapetyan, A. [Yerevan Physics Institute]↗

Search for a Dark Higgs Boson Produced in Association with Inelastic Dark Matter at the Belle II Experiment

Inelastic dark matter models that have two dark matter particles and a massive dark photon can reproduce the observed relic dark matter density without violating cosmological limits. The mass splitting between the two dark matter particles 𝜒 1 and 𝜒 2 , with 𝑚⁡(𝜒 2 ) >𝑚⁡(𝜒 1 ), is induced by a dark Higgs field and a corresponding dark Higgs boson ℎ′. We present a search for dark matter in events with two vertices, at least one of which must be displaced from the interaction region, and missing energy. Using a 365 fb −1 data sample collected at Belle II, which operates at the SuperKEKB 𝑒 + ⁢𝑒 − collider, we observe no evidence for a signal. We set upper limits on the product of the production cross section 𝜎⁡(𝑒 + ⁢𝑒 − → ℎ′⁡𝜒 1 ⁢𝜒 2 ), and the product of branching fractions ℬ⁡(𝜒 2 → 𝜒 1⁢ 𝑒 + ⁢𝑒 − ) ×ℬ⁡(ℎ′ → 𝑥 + ⁢𝑥 − ), where 𝑥 + ⁢𝑥 − indicates 𝜇 + ⁢𝜇 − , 𝜋 + ⁢𝜋 − , or 𝐾 + ⁢𝐾 − , as functions of ℎ′ mass and lifetime at the level of 10 −1 fb. We set model-dependent upper limits on the dark Higgs mixing angle at the level of 10 −5 and on the dark photon kinetic mixing parameter at the level of 10 −3 . This is the first search for dark Higgs bosons in association with inelastic dark matter.

dark matter↗

Search for new physics in final states with semivisible jets or anomalous signatures using the ATLAS detector

A search is presented for hadronic signatures of beyond the Standard Model (BSM) physics, with an emphasis on signatures of a strongly coupled hidden dark sector accessed via resonant production of a 𝑍′ mediator. The ATLAS experiment dataset collected at the Large Hadron Collider from 2015 to 2018 is used, consisting of proton-proton collisions at $\sqrt{𝑠}$ = 13 TeV and corresponding to an integrated luminosity of 140 fb −1 . The 𝑍′ mediator is considered to decay to two dark quarks, which each hadronize and decay to showers containing both dark and Standard Model particles, producing a topology of interacting and noninteracting particles within a jet known as “semivisible.” Machine learning methods are used to select these dark showers and reject the dominant background of mismeasured multijet events, including an anomaly detection approach to preserve broad sensitivity to a variety of BSM topologies. A resonance search is performed by fitting the transverse mass spectrum based on a functional form background estimation. No significant excess over the expected background is observed. Results are presented as limits on the production cross section of semivisible jet signals, parametrized by the fraction of invisible particles in the decay and the 𝑍′ mass, and by quantifying the significance of any generic Gaussian-shaped mass peak in the anomaly region.

particle dark matter↗

Proposal for a dedicated search for millicharged and fractionally charged particles at LANL

In this paper, we propose an experiment, LANSCE-mQ, aiming to detect fractionally charged and millicharged particles (mCPs) using an 800 MeV proton beam fixed target at the Los Alamos Neutron Science Center (LANSCE) facility at Los Alamos National Laboratory. This search can shed new light on numerous fundamental questions, including charge quantization, the predictions of string theories and grand unification theories, the gauge symmetry of the Standard Model, dark sector models, and the tests of cosmic reheating. We propose to install two-layer scintillation detectors made of plastic (such as EJ-200) or CeBr 3 to search for mCPs. Dedicated geant4 detector simulations and in situ measurements have been conducted to obtain a preliminary determination of the background rate. The dominant backgrounds are beam-induced neutrons and coincident dark current signals from the photomultiplier tubes, while beam-induced high-energy photons ( γ ’s) and cosmic muons are subdominant. We determined that LANSCE-mQ, the dedicated mCP experiment, has the leading mCP sensitivity for mass between ∼ 1 and 300 MeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for New Physics in Jet Multiplicity Patterns of Multilepton Events at $\sqrt{s}$ = 13 TeV

A first search for beyond the standard model physics in jet multiplicity patterns of multilepton events is presented, using a data sample corresponding to an integrated luminosity of 138 fb −1 of 13 TeV proton-proton collisions recorded by the CMS detector at the LHC. The search uses observed jet multiplicity distributions in one-, two-, and four-lepton events to explore possible enhancements in jet production rate in three-lepton events with and without bottom quarks. The data are found to be consistent with the standard model expectation. The results are interpreted in terms of supersymmetric production of electroweak chargino-neutralino superpartners with cascade decays terminating in prompt hadronic 𝑅-parity violating interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for cascade decays of charged sleptons and sneutrinos in final states with three leptons and missing transverse momentum in 𝑝⁢𝑝 collisions at $\sqrt{𝑠} = 13$ TeV with the ATLAS detector

A search for cascade decays of charged sleptons and sneutrinos using final states characterized by three leptons (electrons or muons) and missing transverse momentum is presented. The analysis is based on a dataset with 140 fb −1 of proton-proton (pp) collisions at a center-of-mass energy of $\sqrt{𝑠} = 13$ TeV recorded by the ATLAS detector at the Large Hadron Collider. This paper focuses on a supersymmetric scenario that is motivated by the muon anomalous magnetic moment observation, dark-mattter relic density abundance, and electroweak naturalness. A mass spectrum involving light Higgsinos and heavier sleptons with a bino at intermediate mass is targeted. No significant deviation from the Standard Model expectation is observed. This search enables us to place stringent constraints on this model, excluding at the 95% confidence level charged slepton and sneutrino masses up to 450 GeV when assuming a lightest neutralino mass of 100 GeV and mass-degenerate selectrons, smuons and sneutrinos.

extensions of Higgs sector↗

Search for the production of Higgs-portal scalar bosons in the NuMI beam using the MicroBooNE detector

We present the strongest experimental limits to date on the mixing angle, 𝜃, with which a new scalar particle, 𝑆, mixes with the Higgs field in the mass range 110 MeV < 𝑚 𝑆 <155 MeV. This result uses the MicroBooNE liquid argon time projection chamber to search for decays of these Higgs-portal scalar particles through the 𝑆 → 𝑒 + ⁢𝑒 − channel with the decays of kaons in the NuMI neutrino beam acting as the source of the scalar particles. The analysis uses an exposure of 2.01 × 10 21 protons on target of NuMI beam data including periods when the beam focusing system was configured to focus positively charged hadrons and separate periods when negatively charged hadrons were focused. The analysis searches for scalar particles produced from kaons decaying in flight in the beam’s decay volume and at rest in the target and absorber. At 𝑚 𝑆 =125 MeV (𝑚 𝑆 =150 MeV) we set a limit of 𝜃 < 3.19 ×10 −4 (𝜃 < 2.79 ×10 −4 ) at the 95% confidence level.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Inclusive Search for Anomalous Single-Photon Production in MicroBooNE

We present an inclusive search for anomalous production of single-photon events from neutrino interactions in the MicroBooNE experiment. The search and its signal definition are motivated by the previous observation of a low-energy excess of electromagnetic shower events from the MiniBooNE experiment. We use the Wire-Cell reconstruction framework to select a sample of inclusive single-photon final-state interactions with a final efficiency and purity of 7.0% and 40.2%, respectively. We leverage simultaneous measurements of sidebands of charged current 𝜈 𝜇 interactions and neutral current interactions producing 𝜋 0 mesons to constrain signal and background predictions and reduce uncertainties. We perform a blind analysis using a dataset collected from February 2016 to July 2018, corresponding to an exposure of 6.34 × 10 20 protons on target from the Booster Neutrino Beam at Fermilab. In the full signal region, we observe agreement between the data and the prediction, with a goodness-of-fit 𝑝 value of 0.11. We then isolate a subsample of these events containing no visible protons, and observe 93 ± 22⁢(stat) ±35⁢(syst) data events above prediction, corresponding to just above 2⁢𝜎 local significance, concentrated at shower energies below 600 MeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Search for charged lepton flavor violating 𝑍 and 𝑍′ boson decays in proton-proton collisions at $\sqrt{s}$ = 13 TeV

A search for flavor violating decays of the 𝑍 boson to charged leptons is performed using data from proton-proton collisions at $\sqrt{s}$ =13 TeV collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 138 fb −1 . Each of the decays 𝑍 → 𝑒⁢𝜇, 𝑍 → 𝑒⁢𝜏, and 𝑍 → 𝜇⁢𝜏 is considered. The data are consistent with the backgrounds expected from standard model processes. For the 𝑍 → 𝑒⁢𝜇 channel the observed (expected) 95% confidence level upper limit on the branching fraction is 1.9⁢(2.0) × 10 −7 , which is the most stringent direct limit to date on this process; the corresponding limits for the 𝑍 → 𝑒⁢𝜏 and 𝑍 → 𝜇⁢𝜏 channels are 13.8⁢(11.4) × 10 −6 and 12.0⁢(5.3) × 10 −6 , respectively. Additionally, the 𝑒⁢𝜇 final state is used to search for lepton flavor violating decays of 𝑍′ resonances in the mass range from 110 to 500 GeV. No significant excess is observed above the predicted background levels.

Hayrapetyan, A. [Yerevan Physics Institute]↗

Constraints on the polarization angle oscillations of the Crab Nebula with the Simons Array and its applications to the search for axionlike particles

Here, we present a search for polarization oscillation of the Crab Nebula, also known as Tau A, at millimeter wavelengths using observations with the Simons Array, the successor experiment to POLARBEAR. We follow up on previous work by POLARBEAR using 90 GHz band data of the 2023 observing season of the Simons Array to evaluate the variability of Tau A’s polarization angle. Tau A is widely used as a polarization angle calibration source in millimeter-wave astronomy, and thus it is necessary to validate the stability. Additionally, an interesting application of the time-resolved polarimetry of Tau A is to search for axionlike particles (ALPs). We do not detect a global signal across the frequencies considered in this analysis and place a median 95% upper bound of polarization oscillation amplitude A < 0.12° over oscillation frequencies from 3.39 yr -1 to 1.50 day -1 . This constrains the ALP-photon coupling at a median 95% upper bound of g aγγ < 3.84 × 10 -12 × (m a /10 -21 eV) in the mass range from 4.4 × 10 -22 to 7.2 × 10 -20 eV, assuming the ALP constitutes all of dark matter, its field is a stochastic Gaussian field, and it is the sole source of Tau A’s polarization angle oscillation. Additionally, we do not detect signal at the frequencies where 2.5σ hints were previously reported by POLARBEAR, but we do not exclude these signals at the 95% confidence level.

Adkins, Tylor [University of California, Berkeley]↗

General search for supersymmetric particles in scenarios with compressed mass spectra using proton-proton collisions at $\sqrt{s}$ = 13 TeV

A general search is presented for supersymmetric particles (sparticles) in scenarios featuring compressed mass spectra using proton-proton collisions at a center-of-mass energy of 13 TeV, recorded with the CMS detector at the LHC. The analyzed data sample corresponds to an integrated luminosity of 138 fb −1 . A wide range of potential sparticle signatures are targeted, including pair production of electroweakinos, sleptons, and top squarks. The search focuses on events with a high transverse momentum system from initial-state-radiation jets recoiling against a potential sparticle system with significant missing transverse momentum. Events are categorized based on their lepton multiplicity, jet multiplicity, number of 𝑏-tagged jets, and kinematic variables sensitive to the sparticle masses and mass splittings. The sensitivity extends to higher parent sparticle masses than previously probed at the LHC for production of pairs of electroweakinos, sleptons, and top squarks with mass spectra featuring small mass splittings (compressed mass spectra). The observed results demonstrate agreement with the predictions of the background-only model. Lower mass limits are set at 95% confidence level on production of pairs of electroweakinos, sleptons, and top squarks that extend to 325, 275, and 780 GeV, respectively, for the most favorable compressed mass regime cases.

Hadron colliders↗