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At least 1,711 records · Page 95

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗

Optical follow-up observation for GW event S190510g using Subaru/Hyper Suprime-Cam

Abstract A gravitational wave event, S190510g, which was classified as a binary-neutron-star coalescence at the time of preliminary alert, was detected by LIGO/Virgo collaboration on 2019 May 10. At 1.7 hours after the issue of its preliminary alert, we started a target-of-opportunity imaging observation in the Y band to search for its optical counterpart using the Hyper Suprime-Cam (HSC) on the Subaru Telescope. The observation covers a 118.8 deg2 sky area corresponding to $11.6\%$ confidence in the localization skymap released in the preliminary alert and $1.2\%$ in the updated skymap. We divided the observed area into two fields based on the availability of HSC reference images. For the fields with the HSC reference images, we applied an image subtraction technique; for the fields without the HSC reference images, we sought individual HSC images by matching a catalog of observed objects with the PS1 catalog. The search depth is 22.28 mag in the former method and the limit of search depth is 21.3 mag in the latter method. Subsequently, we performed visual inspection and obtained 83 candidates using the former method and 50 candidates using the latter method. Since we only have the one-day photometric data, we evaluated the probability of candidates being located inside the 3D skymap by estimating their distances with photometry of associated extended objects. We found three candidates are likely located inside the 3D skymap and concluded they could be a counterpart of S190510g, while most of the 133 candidates were likely to be supernovae because the number density of candidates was consistent with the expected number of supernova detections. By comparing our observational depth with a light-curve model of such a kilonova reproducing AT2017gfo, we show that early deep observations with the Subaru/HSC can capture the rising phase of the blue component of a kilonova at the estimated distance of S190510g (∼230 Mpc).

79 ASTRONOMY AND ASTROPHYSICS↗

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.

59 BASIC BIOLOGICAL SCIENCES↗

The metabolic origins of non-photorespiratory CO 2 release during photosynthesis: a metabolic flux analysis

Respiration in the light (R L ) releases CO 2 in photosynthesizing leaves and is a phenomenon that occurs independently from photorespiration. Since R L lowers net carbon fixation, understanding R L could help improve plant carbon-use efficiency and models of crop photosynthesis. Although R L was identified more than 75 years ago, its biochemical mechanisms remain unclear. To identify reactions contributing to R L , we mapped metabolic fluxes in photosynthesizing source leaves of the oilseed crop and model plant camelina (Camelina sativa). We performed a flux analysis using isotopic labeling patterns of central metabolites during 13 CO 2 labeling time course, gas exchange, and carbohydrate production rate experiments. To quantify the contributions of multiple potential CO 2 sources with statistical and biological confidence, we increased the number of metabolites measured and reduced biological and technical heterogeneity by using single mature source leaves and quickly quenching metabolism by directly injecting liquid N 2 ; we then compared the goodness-of-fit between these data and data from models with alternative metabolic network structures and constraints. Our analysis predicted that R L releases 5.2 μmol CO2 g –1 FW h –1 of CO 2 , which is relatively consistent with a value of 9.3 μmol CO 2 g –1 FW h –1 measured by CO 2 gas exchange. The results indicated that ≤10% of R L results from TCA cycle reactions, which are widely considered to dominate R L . Further analysis of the results indicated that oxidation of glucose-6-phosphate to pentose phosphate via 6-phosphogluconate (the G6P/OPP shunt) can account for >% of CO 2 released by R L .

59 BASIC BIOLOGICAL SCIENCES↗

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Abstract Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

54 ENVIRONMENTAL SCIENCES↗

Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes

Abstract Stomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.

54 ENVIRONMENTAL SCIENCES↗

The cross-section measurement for the 3 H($e, e'K^+)nnΛ$ reaction

The small binding energy of the hypertriton leads to predictions of the non-existence of bound hypernuclei for isotriplet three-body systems such as nnΛ. However, invariant mass spectroscopy at GSI has reported events that may be interpreted as the bound nnΛ state. The nnΛ state was sought by missing-mass spectroscopy via the (e, e'K + ) reaction at Jefferson Lab’s experimental Hall A. The present experiment has higher sensitivity to the nnΛ-state investigation in terms of better precision by a factor of about three. The analysis shown in this article focuses on the derivation of the reaction cross-section for the 3 H(γ*, K + )X reaction. Events that were detected in an acceptance, where a Monte Carlo simulation could reproduce the data well (|δp/p| < 4%), were analyzed to minimize the systematic uncertainty. No significant structures were observed with the acceptance cuts, and the upper limits of the production cross-section of the nnΛ state were obtained to be 21 and $31 nbsr -1 at the 90% confidence level when theoretical predictions of (-B Λ , Γ) = (0.25, 0.8) MeV and (0.55, 4.7) MeV, respectively, were assumed. The cross-section result provides valuable information for examining the existence of nnΛ.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Climate change, malaria and neglected tropical diseases: a scoping review

Abstract To explore the effects of climate change on malaria and 20 neglected tropical diseases (NTDs), and potential effect amelioration through mitigation and adaptation, we searched for papers published from January 2010 to October 2023. We descriptively synthesised extracted data. We analysed numbers of papers meeting our inclusion criteria by country and national disease burden, healthcare access and quality index (HAQI), as well as by climate vulnerability score. From 42 693 retrieved records, 1543 full-text papers were assessed. Of 511 papers meeting the inclusion criteria, 185 studied malaria, 181 dengue and chikungunya and 53 leishmaniasis; other NTDs were relatively understudied. Mitigation was considered in 174 papers (34%) and adaption strategies in 24 (5%). Amplitude and direction of effects of climate change on malaria and NTDs are likely to vary by disease and location, be non-linear and evolve over time. Available analyses do not allow confident prediction of the overall global impact of climate change on these diseases. For dengue and chikungunya and the group of non-vector-borne NTDs, the literature privileged consideration of current low-burden countries with a high HAQI. No leishmaniasis papers considered outcomes in East Africa. Comprehensive, collaborative and standardised modelling efforts are needed to better understand how climate change will directly and indirectly affect malaria and NTDs.

60 APPLIED LIFE SCIENCES↗

Generalizability of heat-related health risk associations observed in a large healthcare claims database of patients with commercial health insurance

Extreme ambient heat is unambiguously associated with higher risk of illness and death. The Optum Labs Data Warehouse (OLDW), a database of medical claims from US-based patients with commercial or Medicare Advantage health insurance, has been used to quantify heat-related health impacts. Whether results for the insured sub-population are generalizable to the broader population has to our knowledge not been documented. We sought to address this question, for the US population in California from 2012 to 2019. We examined changes in daily rates of emergency department (ED) encounters and in-patient hospitalization encounters for all-causes, heat-related outcomes, renal disease, mental/behavioral disorders, cardiovascular disease, and respiratory disease. OLDW was the source for health data for insured individuals in California, and health data for the broader population were gathered from the California Department of Health Care Access and Information (HCAI). We defined extreme heat exposure as any day in a group of 2 or more days with maximum temperatures exceeding the county-specific 97.5 th percentile and used a space-time-stratified case–crossover design to assess and compare the impacts of heat on health. Average incidence rates of medical encounters differed by dataset. However, rate ratios for ED encounters were similar across datasets for all causes (ratio of incidence rate ratios (rIRR) = 0.989; 95% confidence interval (CI) = 0.973, 1.011), heat-related causes (rIRR = 1.080; 95% CI = 0.999, 1.168), renal disease (rIRR = 0.963; 95% CI = 0.718, 1.292), and mental health disorders (rIRR = 1.098; 95% CI = 1.004, 1.201). Rate ratios for inpatient encounters were also similar. This work presents evidence that OLDW can continue to be a resource for estimating the health impacts of extreme heat.

54 ENVIRONMENTAL SCIENCES↗

Output-weighted sampling for multi-armed bandits with extreme payoffs

We present a new type of acquisition function for online decision-making in multi-armed and contextual bandit problems with extreme payoffs. Specifically, we model the payoff function as a Gaussian process and formulate a novel type of upper confidence bound acquisition function that guides exploration towards the bandits that are deemed most relevant according to the variability of the observed rewards. This is achieved by computing a tractable likelihood ratio that quantifies the importance of the output relative to the inputs and essentially acts as an attention mechanism that promotes exploration of extreme rewards. Our formulation is supported by asymptotic zero-regret guarantees, and its performance is demonstrated across several synthetic benchmarks, as well as two realistic examples involving noisy sensor network data. Finally, we provide a JAX library for efficient bandit optimization using Gaussian processes.

Science & Technology - Other Topics↗

Exascale applications: skin in the game

As noted in Wikipedia, skin in the game refers to having ‘incurred risk by being involved in achieving a goal’, where ‘ skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion’. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

97 MATHEMATICS AND COMPUTING↗

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗

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↗

Probing the axion-electron coupling with NuSTAR observations of galaxies

We search for the existence of ultralight axions coupling to electrons and photons using data from the NuSTAR telescope directed toward the galaxies M82, M87, and M31. We focus on electron bremsstrahlung and Compton scattering for axion production in stars, summing over the stellar populations found in the target galaxies when computing the axion luminosity. We then compute the hard x-ray signal that arises from the conversion of these axions to photons in each galaxy’s magnetic fields, inferred from analog galaxies in cosmological magnetohydrodynamic simulations. Analyzing NuSTAR data toward these galaxies between roughly 20 to 70 keV, we find no evidence for axions and set leading constraints on the combined axion-electron and axion-photon coupling at the level of |𝑔 𝑎⁢𝑒⁢𝑒 ×𝑔 𝑎⁢𝛾⁢𝛾 | ≲ 8.3 ×10 −27 GeV −1 for 𝑚 𝑎 ≲ 10 −10 eV at 95% confidence, with M82 providing the most stringent constraints.

Axion-like particles↗

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]↗

Rare multinucleon decays with the full data sets of the M AJORANA D EMONSTRATOR

The M AJORANA D EMONSTRATOR was an ultra-low-background experiment designed for neutrinoless double-beta decay (0⁢𝜈⁢𝛽⁢𝛽) investigation in 76 Ge . Located at the Sanford Underground Research Facility in Lead, South Dakota, the D EMONSTRATOR utilized modular high-purity Ge detector arrays within shielded vacuum cryostats, operating deep underground. The arrays, with a capacity of up to 40.4 kg (27.2 kg enriched to ∼88% in 76 Ge ), have accumulated the full data set, totaling 64.5 kg yr of enriched active exposure and 27.4 kg yr of exposure for natural detectors. Here, our updated search improves previously explored three-nucleon decay modes in Ge isotopes, setting new partial lifetime limits of 1.83 × 10 26 yr (90% confidence level) for 76 Ge (𝑝⁢𝑝⁢𝑝) → 73 Cu 𝑒 + ⁢𝜋 + ⁢𝜋 + and 76 Ge (𝑝⁢𝑝⁢𝑛) → 73 Zn 𝑒 + ⁢𝜋 + . The partial lifetime limit for the fully inclusive triproton decay mode of 76 Ge is found to be 2.1×10 25 yr. Furthermore, we have updated limits for corresponding multinucleon decays.

baryon & lepton number symmetries↗

Dark energy survey year 3 results: Cosmological constraints from cluster abundances, weak lensing, and galaxy clustering

Galaxy clusters provide a unique probe of the late-time cosmic structure and serve as a powerful independent test of the Λ⁢CDM model. This work presents the first set of cosmological constraints derived with ∼16,000 optically selected redMaPPer clusters across nearly 5000 deg 2 using DES year 3 datasets. Our analysis leverages a consistent modeling framework for galaxy cluster cosmology and DES-Y3 joint analyses of galaxy clustering and weak lensing (3 × 2⁢pt), ensuring direct comparability with the DES-Y3 3 × 2⁢pt analysis. Here, we obtain constraints of 𝑆 8 = 0.864 ± 0.035 and Ω m = $0.26⁢5^{+0.019}_{−0.031}$ from the cluster-based data vector. We find that cluster constraints and 3 × 2⁢pt constraints are consistent under the Λ⁢CDM model with a posterior predictive distribution (PPD) value of 0.53. The consistency between clusters and 3 × 2⁢pt provides a stringent test of Λ⁢CDM across different mass and spatial scales. Jointly analyzing clusters with 3 × 2⁢pt further improves cosmological constraints, yielding 𝑆 8 = $0.81⁢1^{+0.022}_{−0.020}$ and Ω m = $0.29⁢4^{+0.022}_{−0.033}$, a 24% improvement in the Ω m − 𝑆 8 figure of merit over 3 × 2⁢pt alone. Moreover, we find no significant deviation from the Planck CMB constraints with a probability to exceed (PTE) value of 0.6, significantly reducing previous 𝑆 8 tension claims. Finally, combining DES 3 × 2⁢pt, DES clusters, and Planck CMB places an upper limit on the sum of neutrino masses of ∑𝑚 𝜈 < 0.26 eV at 95% confidence under the Λ⁢CDM model. These results establish optically selected clusters as a key cosmological probe and pave the way for cluster-based analyses in upcoming stage-IV surveys such as LSST, Euclid, and Roman.

Abbott, T. M. C. [NSF’s National Optical-Infrared ↗

First Search for Dark Sector 𝑒 + ⁢𝑒 − Explanations of the MiniBooNE Anomaly at MicroBooNE

We present MicroBooNE’s first search for dark sector 𝑒 + ⁢𝑒 − explanations of the long-standing MiniBooNE anomaly. The MiniBooNE anomaly has garnered significant attention over the past 20 years including previous MicroBooNE investigations into both anomalous electron and photon excesses, but its origin still remains unclear. In this Letter, we provide the first direct test of dark sector models in which dark neutrinos, produced through neutrino-induced scattering, decay into missing energy and visible 𝑒 + ⁢𝑒 − pairs comprising the MiniBooNE anomaly. Many such models have recently gained traction as a viable solution to the anomaly while evading past bounds. Using an exposure of 6.87 × 10 20 protons-on-target in the Booster Neutrino Beam, we implement a selection targeting forward-going, coherently produced 𝑒 + ⁢𝑒 − events. After unblinding, we observe 95 events, which we compare with the constrained background-only prediction of 69.7 ±17.3. This analysis sets the world’s first direct limits on these dark sector models and, at the 95% confidence level, excludes the entirety of the single dark neutrino and majority of the dual dark neutrino, parameter space that is viable as a solution to the MiniBooNE anomaly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗