A Pilot Study of Urine Proteomics in COVID-19–Associated Acute Kidney Injury
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60 APPLIED LIFE SCIENCES↗
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Results for “Association study”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Sexual Health and Interpersonal Relationships After Chemoradiation Therapy for Human Papillomavirus-Associated Oropharyngeal Cancer: A Cross-sectional Study
To examine sexual health, including sexual satisfaction, and perceived changes in relationships and sexual relationships of human papillomavirus (HPV) oropharyngeal cancer (OPC) survivors ≥12 months after (chemo)radiation therapy.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Studies on Dispersion of Americium-241 and Associated Risk
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Potter, Charles Augustus↗
Unveiling shared genetic regulators of plant architectural and biomass yield traits in the Sorghum Association Panel
Abstract Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural characteristics, is typically regulated by numerous genes. This study aimed to dissect the genetic regulators underlying 14 plant architectural traits and 10 biomass yield traits in the Sorghum Association Panel across two growing seasons. We identified 321 associated loci through genome-wide association studies (GWAS), involving 234 264 single nucleotide polymorphisms (SNPs). These loci include genes with known associations to biomass traits, such as maturity, dwarfing (Dw), and leafbladeless1, as well as several uncharacterized loci not previously linked to these traits. We also identified 22 pleiotropic loci associated with variation in multiple phenotypes. Three of these loci, located on chromosomes 3 (S03_15463061), 6 (S06_42790178; Dw2), and 9 (S09_57005346; Dw1), exerted significant and consistent effects on multiple traits across both growing seasons. Additionally, we identified three genomic hotspots on chromosomes 6, 7, and 9, each containing multiple SNPs associated with variation in plant architecture and biomass yield traits. Chromosome-wise correlation analyses revealed multiple blocks of positively associated SNPs located near or within the same genomic regions. Finally, genome-wide correlation-based network analysis showed that loci associated with flowering, plant height, leaf traits, plant density, and tiller number per plant were highly interconnected with other genetic loci influencing plant architectural and biomass yield traits. The pyramiding of favorable alleles related to these traits holds promise for enhancing the future development of bioenergy sorghum crops.
Singh, Anuradha (ORCID:0000000197149095)↗
Limit on Supernova Emission in the Brightest Gamma-Ray Burst, GRB 221009A
We present photometric and spectroscopic observations of the extraordinary gamma-ray burst (GRB) 221009A in search of an associated supernova. Some past GRBs have shown bumps in the optical light curve that coincide with the emergence of supernova spectral features, but we do not detect any significant light-curve features in GRB 221009A, nor do we detect any clear sign of supernova spectral features. Using two well-studied GRB-associated supernovae (SN 2013dx, M r,max =-19.54;$ SN 2016jca, M r,max =-19.04$) at a similar redshift as GRB 221009A (z = 0.151), we modeled how the emergence of a supernova would affect the light curve. If we assume the GRB afterglow to decay at the same rate as the X-ray data, the combination of afterglow and a supernova component is fainter than the observed GRB brightness. For the case where we assume the best-fit power law to the optical data as the GRB afterglow component, a supernova contribution should have created a clear bump in the light curve, assuming only extinction from the Milky Way. If we assume a higher extinction of E(B - V) = 1.74 mag (as has been suggested elsewhere), the supernova contribution would have been hard to detect, with a limit on the associated supernova of M r,max ≈ -$19.54. We do not observe any clear supernova features in our spectra, which were taken around the time of expected maximum light. The lack of a bright supernova associated with GRB 221009A may indicate that the energy from the explosion is mostly concentrated in the jet, leaving a lower energy budget available for the supernova.
79 ASTRONOMY AND ASTROPHYSICS↗
Climatological occurrences of hail and tornadoes associated with mesoscale convective systems in the United States
Hail and tornadoes are hazardous weather events responsible for significant property damage and economic loss worldwide. The most devastating occurrences of hail and tornadoes are commonly produced by supercells in the United States. However, these supercells may also grow upscale into mesoscale convective systems (MCSs) or be embedded within them. The relationship between hail and tornado occurrences with MCSs in the long-term climatology has not been thoroughly examined. In this study, radar features associated with MCSs are extracted from a 14-year MCS tracking database across the contiguous United States, and hazard reports are mapped to these MCS features. We investigate the characteristics of hail and tornadoes in relation to MCSs, considering seasonal and regional variabilities. On average, 8 %–17 % of hail events and 17 %–32 % of tornado events are associated with MCSs, depending on the criteria used to define MCSs. The highest total and MCS-associated hazard events occur from March to May, while the highest MCS-associated portion (23 % for hail and 45 % for tornadoes) is observed in winter (December–February) due to the dominance of MCSs caused by strong synoptic forcing. As hailstone size increases, the fraction associated with MCS decreases, but there is an increasing trend for tornado severity from EF0 to EF3 (Enhanced Fujita Scale). Violent tornadoes at EF4 and EF5 associated with MCSs were also observed, which are generated by supercells embedded within MCSs.
54 ENVIRONMENTAL SCIENCES↗
Novel CHI3L1 ‐Associated Angiogenic Phenotypes Define Glioma Microenvironments: Insights From Multi‐Omics Integration
ABSTRACT The CHI3L1 signaling pathway significantly influences glioma angiogenesis, but its role in the tumor microenvironment (TME) remains elusive. We propose a novelCHI3L1‐associated vascular phenotype classification for glioma through integrative analyses of multiple datasets with bulk and single‐cell transcriptome, genomics, digital pathology, and clinical data. We investigated the biological characteristics, genomic alterations, therapeutic vulnerabilities, and immune profiles within these phenotypes through a comprehensive multi‐omics approach. We constructed the vascular‐related risk (VR) score based onCHI3L1‐associated vascular signatures (CAVS) identified by machine learning algorithms. Utilizing unsupervised consensus clustering, gliomas were stratified into three distinct vascular phenotypes: Cluster A, marked by high vascularization and stromal activation with a relatively low levels of tumor‐infiltrating lymphocytes (TILs); Cluster B, characterized by moderate vascularization and stromal activity, coupled with a high density of TILs; and Cluster C, defined by low vascularization and sparse immune cell infiltration. We observed that the CAVS effectively indicated glioma‐associated angiogenesis and immune suppression by single‐cell RNA‐seq analysis. Moreover, the high‐VR‐score group exhibited enhanced angiogenic activity, reduced immune response, resistance to immunotherapy, and poorer clinical outcomes. The VR score independently predicted glioma prognosis and, combined with a nomogram, provided a robust clinical decision‐making tool. Potential drug prediction based on transcription factors for high‐risk patients was also performed. Our study reveals thatCHI3L1‐associated vascular phenotypes shape distinct immune landscapes in gliomas, offering insights for optimizing therapeutic strategies to improve patient outcomes.
Oncology↗
Singly Reduced Iridium Chromophores: Synthesis, Characterization, and Photochemistry
One-electron reduced photosensitizers have been invoked as crucial intermediates in photoredox catalysis, including multiphoton excitation and electrophotocatalytic processes. However, such reduced chromophores have been less investigated, limiting mechanistic studies of their associated electron transfer processes. Here, we report a total of 11 different examples of isolable singly reduced iridium chromophores. Chemical reduction of a cyclometalated iridium complex with potassium graphite affords a 19-electron species. Structural and spectroscopic characterizations reveal a ligand-centered reduction product. The reduced chromophore absorbs a wide range of light from ultraviolet to near-infrared and exhibits photoinduced bimolecular electron transfer reactivity. Furthermore, these studies shed light on elusive reduced iridium chromophores in both ground and excited states, providing opportunities to investigate a commonly invoked intermediate in photoredox catalysis.
14 SOLAR ENERGY↗
Denudation, solute export, landscape evolution modeling, and geographic information system data for the East River watershed, Colorado, USA (2020-2024)
This data package contains geographic information system (GIS) layers and tabular datasets associated with the study of lithologic controls on denudation, solute export, carbon-scaling relationships, and transient landscape evolution in the East River watershed near Crested Butte, Colorado, USA. The package includes GIS layers used to produce the Figure 2 map, including drainage, hillshade, lithology, sample locations, and basin polygons, together with comma-separated value (CSV) tables and matching CSV data dictionaries. One group of tables reports sample-level and catchment-level information for river-sediment samples analyzed for in situ-produced cosmogenic beryllium-10 (10Be), including sample names, outlet elevations, geographic coordinates, upstream drainage area, rock-type classes, production-rate scaling scheme, analyzed nuclide, catchment-averaged denudation rates, and associated lower and upper analytical uncertainties. Sample and catchment attributes provide the basis for comparing denudation rates across intrusive, shale, sedimentary, and mixed-lithology settings. A second group of tables reports supporting information for landscape-evolution modeling and the mapped geologic framework of the study area. Included files list parameter values and definitions for the two-phase landscape-evolution simulations, summarize full-domain model erosion fluxes and topographic metrics for different simulation configurations, provide a fixed-area carbon-model scaling table, and summarize mapped geologic units within the East River study domain, including geologic code, formation name, lithologic description, mapped area, and lithologic class grouping. Model outputs and geologic summaries support interpretation of transient landscape behavior and its relation to the mapped distribution of shale, intrusive, sedimentary, and surficial units. A third group of tables reports hydrologic and hydrochemical information used to quantify dissolved export from the watershed. Included files provide site-level values for drainage area, mean annual solute export, standard error of annual export, area-normalized solute yield, and equivalent weathering rate for five East River monitoring sites, along with metadata describing the number, sampling cadence, and date range of discharge records and partial and full total dissolved solids observations used in the solute-yield analyses. The package also contains a supplementary daily ion-load time series with daily mean discharge, discharge observation counts, dissolved concentrations, and daily loads for calcium, magnesium, sodium, potassium, chloride, sulfate, nitrate, fluoride, dissolved silica, charge-balance bicarbonate, and total dissolved solids. The package contains GIS files, comma-separated value files (.csv), CSV data dictionaries, a file-level metadata table, a package-tree text file, and a readme text file.
10Be↗
Statistical properties of sites visited by independent random walks
The set of visited sites and the number of visited sites are two basic properties of the random walk trajectory. Here, we consider two independent random walks on hyper-cubic lattices and study ordering probabilities associated with these characteristics. The first is the probability that during the time interval (0, t), the number of sites visited by a walker never exceeds that of another walker. The second is the probability that the sites visited by a walker remain a subset of the sites visited by another walker. Using numerical simulations, we investigate the leading asymptotic behaviors of the ordering probabilities in spatial dimensions d = 1, 2, 3, 4. We also study the time evolution of the number of ties between the number of visited sites. We show analytically that the average number of ties increases as a 1 ln t with a 1 = 0.970 508 in one dimension and as (ln t) 2 in two dimensions.
97 MATHEMATICS AND COMPUTING↗
Mycorrhizal status and host genotype interact to shape plant nutrition in field grown maize ( Zea mays ssp. mays )
Arbuscular mycorrhizal fungi (AMF) establish symbioses with the major cereal crops, providing plants with increased access to nutrients while enhancing their tolerance to toxic heavy metals. However, not all plant varieties benefit equally from this association. In this study, we used quantitative trait loci (QTL) mapping to evaluate the combined effect of host genotypic variation (G) and AMF across 141 genotypes on the concentration of 20 mineral elements in the leaves and grain of field grown maize (Zea mays spp. mays). Our mapping design included selective incorporation of a castor AMF-incompatibility mutation, allowing estimation of AMF, QTL and QTLxAMF effects by comparison of mycorrhizal and non-mycorrhizal plants. Overall, AMF compatibility was associated with higher concentrations of boron (B), copper (Cu), molybdenum (Mo), phosphorus (P), selenium (Se) and zinc (Zn) and lower concentrations of arsenic (As), iron (Fe), magnesium (Mg), manganese (Mn), potassium (K) and strontium (Sr). In addition to effects on individual elements, pairwise correlation matrices for element concentration differed between mycorrhizal and non-mycorrhizal plants. We mapped 22 element QTLs, including 18 associated with QTLxAMF effects that indicate plant genotype-specific differences in the impact of AMF on the host ionome. Although there is considerable interest in AMF as biofertilizers, it remains challenging to estimate the impact of AMF in the field. Our design illustrates an effective approach for field evaluation of AMF effects. Furthermore, we demonstrate the capacity of the ionome to reveal host genotype-specific variation in the impact of AMF on plant nutrition.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of Subhalos on Interpreting Highly Magnified Sources Near Lensing Caustics
Large magnification factors near gravitational lensing caustics of galaxy-cluster lenses allow the study of individual stars or compact stellar associations at cosmological distances. We study how the presence of sub-galactic subhalos, an inevitable consequence of cold dark matter, can alter the property of caustics and hence change the interpretation of highly magnified sources that lie atop them. First, we consider a galaxy-cluster halo populated with subhalos sampled from a realistic subhalo mass function calibrated to N-body simulations. Then, we compare a semianalytical approximation and an adaptive ray-shooting method that we employ to quantify the property of the caustics. As a case study, we investigate Earendel, a z = 6.2 candidate of magnified single- or multiple-star system with a lone lensed image atop the critical curve in the Sunrise Arc. We find that the source size constraint (≲0.3 pc) previously derived from macrolens models should be relaxed by a factor of a few to 10 when subhalos are accounted for, therefore allowing the possibility of a compact star cluster. The subhalos could introduce an astrometric perturbation that is ≲0$^{"}_{.}$5, which does not contradict observation. These conclusions are largely robust to changes in the subhalo population. Subhalos therefore should be seriously accounted for when interpreting the astrophysical nature of similar highly magnified sources uncovered in recent high-z observations.
Caustic curve↗
A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae
The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.
59 BASIC BIOLOGICAL SCIENCES↗
Interface models for three-dimensional Rayleigh–Taylor instability
We derive interface models for three-dimensional Rayleigh–Taylor instability (RTI), making use of a novel asymptotic expansion in the non-locality of the fluid flow. These interface models are derived for the purpose of studying universal features associated with RTI such as the Froude number in single-mode RTI, the predicted quadratic growth of the interface amplitude under multi-mode random perturbations, the optimal (viscous) mixing rates induced by the RTI and the self-similarity of horizontally averaged density profiles and the remarkable stabilization of the mixing layer growth rate which arises for the three-fluid two-interface heavy–light–heavy configuration, in which the addition of a third fluid bulk slows the growth of the mixing layer to a linear rate. Our interface models can capture the formation of small-scale structures induced by severe interface roll-up, reproduce experimental data in a number of different regimes and study the effects of multiple interface interactions even as the interface separation distance becomes exceedingly small. Compared with traditional numerical schemes used to study such phenomena, our models provide a computational speed-up of at least two orders of magnitude.
Mechanics↗
Non-Thermal Plasma as a Novel Strategy for Treating or Preventing Viral Infection and Associated Disease
Pathogenic viruses cause many human, animal, and plant diseases that are associated with substantial morbidity, mortality and socio-economic impact. Although effective strategies for combatting virus transmission and associated disease are available, global outbreaks of viral pathogens such as the virus responsible for the COVID-19 pandemic demonstrate that there is still a critical need for new approaches that can be used to interrupt the chain of viral infection and mitigate virus-associated pathogenesis. Recent studies point to non-thermal plasma (NTP), a partly ionized gas comprised of a complex mixture of reactive oxygen and nitrogen species along with physical effectors, as the potential foundation for new antiviral approaches. A more thorough understanding of the antiviral properties and safety of NTP has stimulated explorations of NTP as the basis for treatments of viral diseases. The recently described immunomodulatory properties of NTP are also being evaluated for potential use in immunotherapies of viral diseases as well as in antiviral vaccination strategies. In this review, we present the current state-of-the-art in addition to compelling arguments that NTP merits further exploration for use in the prevention and management of viral infections and associated diseases.
60 APPLIED LIFE SCIENCES↗
Aggregation and analysis of indication-symptom relationships for drugs approved in the USA
Abstract Purpose Drug indications and disease symptoms often confound adverse event reports in real-world datasets, including electronic health records and reports in the FDA Adverse Event Reporting System (FAERS). A thorough, standardized set of indications and symptoms is needed to identify these confounders in such datasets for drug research and safety assessment. The aim of this study is to create a comprehensive list of drug-indication associations and disease-symptom associations using multiple resources, including existing databases and natural language processing. Methods Drug indications for drugs approved in the USA were extracted from two databases, RxNorm and Side Effect Resource (SIDER). Symptoms for these indications were extracted from MedlinePlus and using natural language processing from PubMed abstracts. Results A total of 1361 unique drugs, 1656 unique indications, and 2201 unique symptoms were extracted from a wide variety of MedDRA System Organ Classes. Text-mining precision was maximized at 0.65 by examining Term Frequency Inverse Document Frequency (TF-IDF) scores of the disease-symptom associations. Conclusion The drug-indication associations and disease-symptom associations collected in this study may be useful in identifying confounders in other datasets, such as safety reports. With further refinement and additional drugs, indications, and symptoms, this dataset may become a quality resource for disease symptoms.
Punyala, Ananth↗
Theoretical study of the reaction mechanism and kinetics of the phenyl + propargyl association
Potential energy surface for the phenyl + propargyl radical recombination reaction has been studied at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G** level of theory for the closed-shell singlet species and at the triplet–singlet gap CASPT2/cc-pVTZ-CCSD(T)-F12/cc-pVTZ-f12//CASSCF/cc-pVTZ level of theory for the diradical species. High-pressure limit rate constants for the barrierless channels were evaluated with variable reaction coordinate transition state theory (VRC-TST). Rice–Ramsperger–Kassel–Marcus Master Equation (RRKM-ME) calculations have been performed to assess temperature- and pressure-dependent phenomenological rate constants and product branching ratios. Here, the entrance channels of the radical association reaction produce 3-phenyl-1-propyne and phenylallene which can further dissociate/isomerize into a variety of unimolecular and bimolecular products. Theoretical evidence is presented that, at combustion relevant conditions, the phenyl + propargyl recombination provides a feasible mechanism for the addition of a second five-member ring to the first six-member aromatic ring producing the prototype two-ring species indene and indenyl. Rate expressions for all important reaction channels in a broad range of temperatures and pressures have been generated for kinetic modeling.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Maize Terpene Synthase 8 (ZmTPS8) Contributes to a Complex Blend of Fungal-Elicited Antibiotics
In maize (Zea mays), fungal-elicited immune responses include the accumulation of terpene synthase (TPS) and cytochrome P450 monooxygenases (CYP) enzymes resulting in complex antibiotic arrays of sesquiterpenoids and diterpenoids, including α/β-selinene derivatives, zealexins, kauralexins and dolabralexins. To uncover additional antibiotic families, we conducted metabolic profiling of elicited stem tissues in mapping populations, which included B73 × M162W recombinant inbred lines and the Goodman diversity panel. Five candidate sesquiterpenoids associated with a chromosome 1 locus spanning the location of ZmTPS27 and ZmTPS8. Heterologous enzyme co-expression studies of ZmTPS27 in Nicotiana benthamiana resulted in geraniol production while ZmTPS8 yielded α-copaene, δ-cadinene and sesquiterpene alcohols consistent with epi-cubebol, cubebol, copan-3-ol and copaborneol matching the association mapping efforts. ZmTPS8 is an established multiproduct α-copaene synthase; however, ZmTPS8-derived sesquiterpene alcohols are rarely encountered in maize tissues. A genome wide association study further linked an unknown sesquiterpene acid to ZmTPS8 and combined ZmTPS8-ZmCYP71Z19 heterologous enzyme co-expression studies yielded the same product. To consider defensive roles for ZmTPS8, in vitro bioassays with cubebol demonstrated significant antifungal activity against both Fusarium graminearum and Aspergillus parasiticus. As a genetically variable biochemical trait, ZmTPS8 contributes to the cocktail of terpenoid antibiotics present following complex interactions between wounding and fungal elicitation.
59 BASIC BIOLOGICAL SCIENCES↗