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At least 415 records · Page 23

BrainXcan identifies brain features associated with behavioral and psychiatric traits using large-scale genetic and imaging data

Advances in brain MRI have enabled many discoveries in neuroscience. Case-control comparisons of brain MRI features have highlighted potential causes of psychiatric and behavioral disorders. However, due to the cost and difficulty of collecting MRI data, most studies have small sample sizes, limiting their reliability. Furthermore, reverse causality complicates interpretation because many observed brain differences are the result rather than the cause of the disease. Here we propose a method (BrainXcan) that leverages the power of large-scale genomewide association studies (GWAS) and reference brain MRI data to discover new mechanisms of disease etiology and validate existing ones. BrainXcan tests the association with genetic predictors of brain MRI-derived features and complex traits to pinpoint relevant brain-wide and region-specific features. Requiring only genetic data, BrainXcan allows us to test a host of hypotheses on mental illness, across many MRI modalities, using public data resources. For example, our method shows that reduced axonal density across the brain is associated with schizophrenia risk, consistent with the disconnectivity hypothesis. We also find that the hippocampus volume is associated with schizophrenia risk, highlighting the potential of our approach. Taken together, our results show the promise of BrainXcan to provide insights into the biology of GWAS traits.

Association study↗

Search for CP violation in events with top quarks and Z bosons at $\sqrt{s}$ = 13 and 13.6 TeV

A search for the violation of the charge-parity (CP) symmetry in the production of top quarks in association with Z bosons is presented, using events with at least three charged leptons and additional jets. The search is performed in a sample of proton-proton collision data collected by the CMS experiment at the CERN LHC in 2016–2018 at a center-of-mass energy of 13 TeV and in 2022 at 13.6 TeV, corresponding to a total integrated luminosity of 173 fb –1 . For the first time in this final state, observables that are odd under the CP transformation are employed. Also for the first time, physics-informed machine-learning techniques are used to construct these observables. While for standard model (SM) processes the distributions of these observables are predicted to be symmetric around zero, CP-violating modifications of the SM would introduce asymmetries. Two CP-odd operators $\mathcal{O}$$^{I}_{tW}$ and $\mathcal{O}$$^{I}_{tZ}$ in the SM effective field theory are considered that may modify the interactions between top quarks and electroweak bosons. The obtained results are consistent with the SM prediction within two standard deviations, and exclusion limits on the associated Wilson coefficients of –2.7 < $c$$^{I}_{tW}$ < 2.5 and –0.2 < $c$$^{I}_{tZ}$ < 2.0 and are set at 95 % confidence level. The largest discrepancy is observed in $c$$^{I}_{tZ}$ where data is consistent with positive values, with an observed local significance with respect to the SM hypothesis of 2.5 standard deviations, when only linear terms are considered.

CMS↗

The interactivity of sources and dietary levels of resistant starches – impact on growth performance, starch, and nutrient digestibility, digesta oligosaccharides profile, cecal microbial metabolites, and indicators of gut health in broiler chickens

In a 21-d study, 480 Cobb 500 (off-sex) male broiler chicks were used to investigate the effects of feeding different sources and levels of resistant starches (RS) on growth performance, nutrient and energy utilization, and intestinal health in broiler chickens. The birds were allocated to 10 dietary treatments in a 3 × 3 + 1 factorial arrangement. The factors were 3 RS-sources (RSS): banana starch (BS), raw potato starch (RPS), and high-amylose corn starch (HCS); each at 3 levels (RSL) 25, 50, or 100 g/kg plus a corn-soybean meal control diet. Birds and feed were weighed on d 0, 8, and 21. On d 21, samples of jejunal tissue and digesta were collected for chemical analysis. Data were analyzed using the mixed model procedure of JMP with factor levels nested with the control. In the 0 to 21 phase, the birds fed the RPS diets had higher (P = 0.011) FI than those fed HCS or control diets, and FCR was greater (P = 0.030) in birds that received BS diets than in other diets. RSS × RSL was significant (P < 0.05) for total tract nutrient retention, AME, and AMEn on d 21. The starch digestibility was higher (P < 0.001) in birds that received the control diet than in RS diets, and decreased as RS levels increased, except for HCS. The apparent metabolizable energy (AME) and nitrogen-corrected AME (AMEn) were higher (P < 0.001) in birds fed 100 g/kg HCS diet, with both decreasing with increasing levels of BS and RPS, except for HCS. Relative ileal oligosaccharides profile showed significant (P < 0.05) RSS × RSL with a higher relative abundance of Hex(3) (P = 0.01) and Pent(3) (P = 0.001) in HCS diets. In conclusion, RS may influence gut health and growth performance in broiler chickens through modulation of cecal SCFA and nutrient digestion, but these depend largely on the botanical origin and concentrations of individual RS.

60 APPLIED LIFE SCIENCES↗

High-precision measurement of the W boson mass with the CMS experiment

In the standard model of particle physics, the masses of the W and Z bosons, the carriers of the weak interaction, are uniquely related. A precise determination of their masses is important because quantum loops of heavy, undiscovered particles could modify this relationship. Although the Z mass is known to the remarkable precision of 22 parts per million (2.0 MeV), the W mass is known much less precisely. A global fit to measured electroweak observables predicts the W mass with 6 MeV uncertainty [1$-$3]. Reaching a comparable experimental precision would be a sensitive and fundamental test of the standard model, made even more urgent by a recent challenge to the global fit prediction by a measurement from the CDF Collaboration at the Fermilab Tevatron collider [4]. Here we report the measurement of the W mass by the CMS Collaboration at the CERN LHC, based on a large data sample of $W \to \mu \nu$ events collected in 2016 at the proton-proton collision energy of 13 TeV. The measurement exploits a high-granularity maximum likelihood fit to the kinematic properties of muons produced in W decays. By combining an accurate determination of experimental effects with marked in situ constraints of theoretical inputs, we reach a precise measurement of the W mass, of 80 360.2 $\pm$ 9.9 MeV, in agreement with the standard model prediction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

An infrared, Raman, and X-ray database of battery interphase components

Further improvements to lithium-ion and emerging battery technologies can be enabled by an improved understanding of the chemistry and working mechanisms of interphases that form at electrochemically active battery interfaces. However, it is difficult to collect and interpret spectra of interphases for several reasons, including the presence of a variety of compounds. To address this challenge, we herein present a vibrational spectroscopy and X-ray diffraction data library of ten compounds that have been identified as interphase constituents in lithium-ion or emerging battery chemistries. The data library includes attenuated total reflectance Fourier transform infrared spectroscopy, Raman spectroscopy, and X-ray diffraction data, collected in inert atmospheres provided by custom sample chambers. The data library presented in this work (and online repository) simplifies access to reference data that is otherwise either diffusely spread throughout the literature or non-existent, and provides energy storage researchers streamlined access to vital interphase-relevant data that can accelerate battery research efforts.

25 ENERGY STORAGE↗

Quantifying fission yields at the National Ignition Facility using depleted uranium foil experiments

There are programs for high-Z shell experiments at the National Ignition Facility (NIF). For shells made of actinide material, a quantitative fission diagnostic is needed in order to determine how much fission took place and whether the fission was sufficient to produce a non-negligible heat source in the burning capsule. Here, we present a viable coupled experimental and theoretical technique for making quantitative fission measurements possible. The proposed scheme involves using a well-characterized set of depleted uranium foils outside an NIF capsule to verify the conversion of xenon and krypton fission fragments collected at the Radiochemical Analysis of Gaseous Samples (RAGS) facility into total fission yield. We present the calculations needed for this conversion, including the decays in and out of fission fragment chains during the RAGS pump-down of the NIF chamber.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

High Multiplicity Trigger for long-lived particles in CMS detector

Searches for long-lived particles (LLPs) at the CMS experiment often involve unconventional event topologies that are difficult to efficiently select using standard trigger strategies. To improve sensitivity to such signatures during LHC Run 3 operation, a dedicated High Multiplicity Trigger (HMT) has been developed and deployed in the CMS trigger system. The trigger targets events containing unusually large numbers of hits in the CMS cathode strip chamber (CSC) muon detectors, a characteristic signature of several LLP scenarios involving displaced decays in the muon system. The HMT implementation, trigger logic, rate dependence with pileup, and operational stability are described. Optimized hit multiplicity thresholds are used to maintain acceptable trigger rates under high-luminosity and high-pileup conditions while preserving high efficiency across a broad range of LLP lifetimes and kinematic regimes. The trigger performance is evaluated using both simulated event samples and proton-proton collision data collected during Run 3 of the LHC. The HMT substantially extends the CMS sensitivity to non-standard signatures associated with LLP decays and provides a flexible platform for future searches for physics beyond the Standard Model.

47 OTHER INSTRUMENTATION↗

Machine-learning techniques for model-independent searches in dijet final states

Anomaly detection methods used in a recent search for new phenomena by CMS at the CERN LHC are presented. The methods use machine learning to detect anomalous jets produced in the decay of new massive particles without depending on a specific theory model. The effectiveness of these approaches in enhancing sensitivity to various simulated signal samples is studied and compared using data collected in proton–proton collisions at a center-of-mass energy of 13 TeV. In an example analysis, the capabilities of anomaly detection methods are further demonstrated by identifying large-radius jets consistent with Lorentz-boosted hadronically decaying top quarks in a model-agnostic framework.

CMS↗

Search for low-mass resonances decaying into two jets and produced in association with a photon or a jet at √s = 13 TeV with the ATLAS detector

A search is performed for localized excesses in the low-mass dijet invariant mass distribution, targeting a hypothetical new particle decaying into two jets and produced in association with either a high transverse momentum photon or a jet. The search uses the full Run 2 data sample from LHC proton-proton collisions collected by the ATLAS experiment at a center-of-mass energy of 13 TeV during 2015–2018. Two variants of the search are presented for each type of initial-state radiation: one that makes no jet flavor requirements and one that requires both of the jets to have been identified as containing b-hadrons. No excess is observed relative to the Standard Model prediction, and the data are used to set upper limits on the production cross section for a benchmark Z' model and, separately, for generic, beyond the Standard Model scenarios which might produce a Gaussian-shaped contribution to dijet invariant mass distributions. The results extend the current constraints on dijet resonances to the mass range between 200 and 650 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Test of lepton flavor universality in semileptonic 𝐵$^+_𝑐$ meson decays in proton-proton collisions at $\sqrt{𝑠}$ = 13 TeV

A measurement of the ratio of branching fractions 𝑅⁢(𝐽/𝜓) =ℬ⁡(𝐵$^+_𝑐$ →𝐽/𝜓⁢𝜏 + ⁢𝜈 𝜏 )/ℬ⁡(𝐵$^+_𝑐$ →𝐽/𝜓⁢𝜇 + ⁢𝜈 𝜇 ) in the 𝐽/𝜓 →𝜇 + ⁢𝜇 − , 𝜏 + →𝜇 + ⁢𝜈 𝜇 ⁢$\bar{𝜈}$ 𝜏 decay channel is presented. This measurement uses a sample of proton-proton collision data collected at a center-of-mass energy of 13 TeV by the CMS experiment in 2018, corresponding to an integrated luminosity of 59.7 fb −1 . The measured ratio, 𝑅⁢(𝐽/𝜓) = 0.1⁢7$^{+0.18}_{−0.17}⁢$(stat)$^{+0.21}_{−0.22⁢}$(syst)$^{+0.19}_{−0.18}$⁢(theo) =0.17 ± 0.33, agrees with the value of 0.2582 ± 0.0038 predicted by the standard model, which assumes lepton flavor universality. By testing lepton flavor universality, this measurement is a probe of new physics using 𝐵$^+_𝑐$ mesons, which are currently only produced at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

First Measurement of 𝐴 = 4 Hypernuclei and Antihypernuclei at the LHC

In this Letter, the first evidence of the $^4_{\bar{Λ}}$$\overline{He}$ antihypernucleus is presented, along with the first measurement at the LHC of the production of (anti)hypernuclei with mass number 𝐴 = 4, specifically (anti)⁢$^4_Λ$H and (anti)⁢$^4_Λ$He. In addition, the antiparticle-to-particle ratios for both hypernuclei ($^4_{\bar{Λ}}$$\bar{H}$⁡/$^4_Λ$H and $^4_{\bar{Λ}}$$\overline{He}$/$^4_Λ$He) are shown, which are sensitive to the baryochemical potential of the strongly interacting matter created in heavy-ion collisions. The results are obtained from a data sample of central Pb-Pb collisions, collected during the 2018 LHC data taking at a center-of-mass energy per nucleon pair of $\sqrt{𝑠_{NN}}$ = 5.02 TeV. The yields measured for the average of the charge-conjugated states are found to be [0.78 ± 0.19⁢(stat) ± 0.17⁢(syst)] × 10 −6 for the (anti)⁢$^4_Λ$H and [1.08 ± 0.34⁢(stat)± 0.20⁢(syst)] × 10 −6 for the (anti)⁢$^4_Λ$He, and the measured antiparticle-to-particle ratios are in agreement with unity. The presence of (anti)⁢$^4_Λ$H and (anti)⁢$^4_Λ$He excited states is expected to strongly enhance the production yield of these hypernuclei. The yield values exhibit a combined deviation of 3.3⁢𝜎 from the theoretical ground-state-only expectation, while the inclusion of the excited states in the calculations leads to an agreement within 0.6⁢𝜎 with the present measurements. Additionally, the measured (anti)$^4_Λ$H and (anti)⁢$^4_Λ$He masses are compatible with the world-average values within the uncertainties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient

Abstract Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.

Microbiology↗

NERSC_Lightweight Distributed Metric Service (NERSC_LDMS) v4.4.2

Miscellany This LDMS Loftsman/Helm Chart horizontally scales LDMS daemons in order to achieve a 1Hz sample rate from over 5,000 nodes, collecting 38k metrics per minute on Perlmutter. This LMDS Configuration relies on already running `ldmsd` producers running on nodes, which produce metrics via sampler plugins. The Helm chart distributes the collection of metrics from producer acrross many aggregator and storage `ldmsd` daemons, ensuring no damon is overloaded and data loss is avoided.

Stile, John [Lawrence Berkeley National Laboratory↗

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-contrast machine learning improves schistosomiasis diagnostic performance

Schistosomiasis currently affects over 250 million people and remains a public health burden despite ongoing global control efforts. Conventional microscopy is a practical tool for diagnosis and screening ofSchistosoma haematobium, but identification of eggs requires a skilled microscopist. Here we present a machine learning (ML)-based strategy for automated detection ofS. haematobiumthat combines two imaging contrasts, brightfield (BF) and darkfield (DF), to improve diagnostic performance. We collected BF and DF images of urine samples, many of them containingS. haematobiumeggs, during two different field studies in Côte d’Ivoire using a mobile phone-based microscope, the SchistoScope. We then trained separate egg-detection ML models and compared the patient-level performance of BF and DF models alone to combinations of BF and DF models, using annotations from trained microscopists as the gold standard. We found that models trained on DF images, and almost all BF and DF combinations, performed significantly better than models trained on BF images only. When models were trained on images from the first field study (n = 349 patients, 748 images of each contrast), patient-level classification performance on patient images from the second study (n = 375 patients, 752 images of each contrast) met the WHO Diagnostic Target Product Profile (TPP) sensitivity and specificity for the monitoring and evaluation use case (sensitivity for all models and combinations was >75% when evaluated at a confidence score threshold that resulted in specificity >96.5%). When we used images from both field studies for the training set, performance of the models was improved. Overall, this work shows that the use of DF and BF increases the performance of ML models on images from devices with low-cost optics, while retaining the portability, power, and time-to-results of the WHO’s diagnostic TPP. DF requires no additional sample preparation and does not increase the complexity of the imaging system. It thus offers a practical means to improve performance of automated diagnostics forS. haematobiumas well as other microscopy-based diagnostics.

Infectious Diseases↗

2014-2015 Puget Sound Regional Travel Study

The 2014-2015 Puget Sound Regional Travel Study collected information about household and individual travel patterns for residents throughout a four-county region in Washington State. Study results were used to update the region's travel and land-use models and to calibrate local traffic and travel models. The study also helped the Puget Sound Regional Council (PSRC) and its regional partners develop plans that accommodate the diverse travel needs and preferences of residents. The Resource Systems Group administered the study on behalf of PSRC. Global positioning system (GPS)-equipped smartphones were used to provide data pertaining to the daily travel of 547 individual participants. Because the region's university students may have been underrepresented in the initial 2014 household travel study, the PSRC added a college-population travel survey in fall 2014. In spring 2015, a second household data collection effort was conducted to increase the frequency of data collection and to collect GPS data as well as a sample of longitudinal data from households that completed the 2014 survey.

1Hz data↗

2008 East Tennessee Household Travel Survey

The 2008 East Tennessee Household Travel Survey, conducted by NuStats, was a comprehensive study of travel behavior in Knox, Blount, Anderson, Jefferson, Loudon, Roane, Sevier, and Union counties. The purpose of the survey was to collect weekday travel characteristics of households in the eight-county region during a 24-hour timeframe. The data will be used by the Knoxville Regional Transportation Planning Organization and local agencies to update transportation and air quality models and to identify transportation needs in the region. The survey collected demographic and travel data from a sample of 1,400 households between February and May 2008. In total, 12,012 trips were reported by 3,301 persons.

1Hz data↗

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (August 2015)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken August 29, 2015 at a location (KB1) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Sediment samples from a deep soil pit were collected from 0 to 234 cm depth below surface at discrete depths every ~10-20 cm for microbial analyses. 13 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0131241. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores).This dataset includes a zip file of 2216 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type

54 ENVIRONMENTAL SCIENCES↗