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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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At least 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

End-of-Century Changes in Orographic Precipitation with the Intermediate Complexity Atmospheric Research Model over the Western United States

Abstract Downscaled precipitation projections were created using the Intermediate Complexity Atmospheric Research (ICAR) model over the western United States to increase the physical realism in orographic precipitation changes. End-of-century simulations from eight models in phase 5 of the Coupled Model Intercomparison Project (CMIP5) were downscaled with ICAR and compared to the widely utilized statistically downscaled dataset, localized constructed analogs (LOCAs), to understand where and why projections of cool-season (September–May) precipitation differed. ICAR and LOCA precipitation projections were similar, but their sign differed in hydrologically relevant regions likely due to ICAR’s simulation of microphysics and mesoscale dynamics with high-resolution topography (6 km). In the Pacific Northwest, cool-season precipitation projections from ICAR showed an increase on the windward side of the Cascades and no significant change within the lee. This difference between the windward and leeward side was attributed to reduced zonal wind speeds, allowing more time for microphysical processes within ICAR. This contrast is enhanced by rain’s faster fall speed compared to snow, limiting transport into the lee. Meanwhile, LOCA projected an increase in precipitation across the Cascades. In the Upper Colorado River basin, LOCA projected an increase in precipitation in high elevation regions (>3000 m), but ICAR projected no significant change or a decrease in precipitation. High elevation differences were most evident in the spring and fall and were also attributed to a snow-to-rain transition and dynamical processes that impacted orographic enhancement within ICAR. Idealized, controlled studies are needed to better isolate individual processes, but these results underscore the importance of including microphysics and mesoscale dynamics within regional-scale precipitation projections. Significance Statement A set of global climate model simulations was downscaled using an atmospheric model that contains key physical equations, referred to as Intermediate Complexity Atmospheric Research (ICAR). ICAR was used to examine projected changes in end-of-century cool-season precipitation over mountains in the western United States. Precipitation projections from ICAR were similar to projections that used statistical relationships to downscale climate projections. However, projections differed between ICAR and statistically downscaled datasets in whether they increased, decreased, or stayed the same in specific, hydrologically relevant regions such as the eastern Cascades and high elevation areas of the Upper Colorado River basin. These differences were attributed to the simulation of physical processes in ICAR. The results highlight the importance of kilometer-scale atmospheric processes in regional climate projections.

Currier, William Ryan [NOAA/Physical Sciences Labo↗
DOE OSTI2023

Structure of coagulation factor VIII bound to a patient-derived anti-C1 domain antibody inhibitor

The development of pathogenic antibody inhibitors against coagulation factor VIII (FVIII) occurs in ~30% of congenital hemophilia A patients receiving FVIII replacement therapy as well as in all cases of acquired hemophilia A. KM33 is an anti-C1 domain antibody inhibitor previously isolated from a severe hemophilia A patient. In addition to potently blocking FVIII binding to von Willebrand factor and phospholipid surfaces, KM33 disrupts FVIII binding to lipoprotein receptor-related protein 1 (LRP1), which drives FVIII hepatic clearance and antigen presentation in dendritic cells. Here, we report on the structure of FVIII bound to NB33, a recombinant derivative of KM33, by single-particle cryo-electron microscopy. Furthermore, structural analysis reveals the NB33 epitope localizes to FVIII residues R2090-S2094 and I2158-R2159 which constitute membrane-binding loops in the C1 domain. Further analysis reveals multiple FVIII lysine and arginine residues, previously shown to mediate binding to LRP1, dock onto an acidic cleft at the NB33 variable domain interface, thus blocking a putative LRP1 binding site. Together, these results demonstrate a novel mechanism of FVIII inhibition by a patient-derived antibody inhibitor and provide structural evidence toward engineering FVIII with reduced LRP1-mediated clearance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes

Background: Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776. Results: The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome). Conclusions: Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

Background: Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation. Results: The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent ‘CheY-like’ two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes - algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs) - a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade. Conclusion: The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

The indigenous gut microbiota are thought to play a crucial role in the development and maintenance of the abnormal inflammatory responses that are the hallmark of inflammatory bowel disease. Direct tests of the role of the gut microbiome in these disorders are typically limited by the fact that sampling of the microbiota generally occurs once disease has become manifest. This limitation could potentially be circumvented by studying patients who undergo total proctocolectomy with ileal pouch anal anastomosis (IPAA) for the definitive treatment of ulcerative colitis. A subset of patients who undergo IPAA develops an inflammatory condition known as pouchitis, which is thought to mirror the pathogenesis of ulcerative colitis. Following the development of the microbiome of the pouch would allow characterization of the microbial community that predates the development of overt disease. We monitored the development of the pouch microbiota in four patients who underwent IPAA. Mucosal and luminal samples were obtained prior to takedown of the diverting ileostomy and compared to samples obtained 2, 4 and 8 weeks after intestinal continuity had been restored. Through the combined analysis of 16S rRNA-encoding gene amplicons, targeted 16S amplification and microbial cultivation, we observed major changes in structure and function of the pouch microbiota following ileostomy. There is a relative increase in anaerobic microorganisms with the capacity for fermentation of complex carbohydrates, which corresponds to the physical stasis of intestinal contents in the ileal pouch. Compared to the microbiome structure encountered in the colonic mucosa of healthy individuals, the pouch microbial community in three of the four individuals was quite distinct. In the fourth patient, a community that was much like that seen in a healthy colon was established, and this patient also had the most benign clinical course of the four patients, without the development of pouchitis 2 years after IPAA. The microbiota that inhabit the ileal-anal pouch of patients who undergo IPAA for treatment of ulcerative colitis demonstrate significant structural and functional changes related to the restoration of fecal flow. Our preliminary results suggest once the pouch has assumed the physiologic role previously played by the intact colon, the precise structure and function of the pouch microbiome, relative to a normal colonic microbiota, will determine if there is establishment of a stable, healthy mucosal environment or the reinitiation of the pathogenic cascade that results in intestinal inflammation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

Mucosal biopsy is the most common sampling technique used to assess microbial communities associated with the intestinal mucosa. Biopsies disrupt the epithelium and can be associated with complications such as bleeding. Biopsies sample a limited area of the mucosa, which can lead to potential sampling bias. In contrast to the mucosal biopsy, the mucosal brush technique is less invasive and provides greater mucosal coverage, and if it can provide equivalent microbial community data, it would be preferable to mucosal biopsies. Results: We compared microbial samples collected from the intestinal mucosa using either a cytology brush or mucosal biopsy forceps. We collected paired samples from patients with ulcerative colitis (UC) who had previously undergone colectomy and ileal pouch anal anastomosis (IPAA), and profiled the microbial communities of the samples by sequencing V4-V6 or V4-V5 16S rRNA-encoding gene amplicons. Comparisons of 177 taxa in 16 brush-biopsy sample pairs had a mean R2 of 0.94. We found no taxa that varied significantly between the brush and biopsy samples after adjusting for multiple comparisons (false discovery rate ≤0.05). We also tested the reproducibility of DNA amplification and sequencing in 25 replicate pairs and found negligible variation (mean R2 = 0.99). A qPCR analysis of the two methods showed that the relative yields of bacterial DNA to human DNA were several-fold higher in the brush samples than in the biopsies. Conclusions: Mucosal brushing is preferred to mucosal biopsy for sampling the epithelial-associated microbiota. Although both techniques provide similar assessments of the microbial community composition, the brush sampling method has relatively more bacterial to host DNA, covers a larger surface area, and is less traumatic to the epithelium than the mucosal biopsy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Extensive horizontal gene transfer, duplication, and loss of chlorophyll synthesis genes in the algae

Two non-homologous, isofunctional enzymes catalyze the penultimate step of chlorophyll a synthesis in oxygenic photosynthetic organisms such as cyanobacteria, eukaryotic algae and land plants: the light independent (LIPOR) and light-dependent (POR) protochlorophyllide oxidoreductases. Whereas the distribution of these enzymes in cyanobacteria and land plants is well understood, the presence, loss, duplication, and replacement of these genes have not been surveyed in the polyphyletic and remarkably diverse eukaryotic algal lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Burn wound healing and treatment: review and advancements

Burns are a prevalent and burdensome critical care problem. The priorities of specialized facilities focus on stabilizing the patient, preventing infection, and optimizing functional recovery. Research on burns has generated sustained interest over the past few decades, and several important advancements have resulted in more effective patient stabilization and decreased mortality, especially among young patients and those with burns of intermediate extent. However, for the intensivist, challenges often exist that complicate patient support and stabilization. Furthermore, burn wounds are complex and can present unique difficulties that require late intervention or life-long rehabilitation. In addition to improvements in patient stabilization and care, research in burn wound care has yielded advancements that will continue to improve functional recovery. This article reviews recent advancements in the care of burn patients with a focus on the pathophysiology and treatment of burn wounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Chelator-mediated Fenton post-treatment enhances methane yield from lignocellulosic residues via microbial community modulation

Advancing biomethane production from anaerobic digestion (AD) is essential for building a more reliable and resilient bioenergy system. However, incomplete conversion of lignocellulose-rich agricultural waste remains a key limitation, often leaving energy-dense residues in the digestate by-product. In this study, we introduce a novel application of chelator-mediated Fenton (CMF) post-treatment to recover untapped biomethane potential from these recalcitrant residues, representing a significant departure from conventional pre-treatment strategies. By systematically varying pH, iron-chelator concentration, and hydrogen peroxide dosage, we identified reaction conditions (pH 6–8, 5 mM Fe 2+ -dihydroxybenzene, 3–4 wt.% H 2 O 2 ) that enhanced lignocellulose deconstruction and increased dissolved organic carbon (DOC) availability for methanogenesis. CMF post-treatment led to up to a tenfold increase in biomethane potential compared to untreated controls. Microbial community analysis revealed enrichment of cellulolytic species, suggesting enhanced hydrolytic activity as a driver of improved conversion. Application of the CMF post-treatment method to isolated poplar lignin further demonstrated its versatility for diverse lignocellulosic substrates. These findings position CMF post-treatment as a promising strategy to enhance AD efficiency and valorize digestate.

Martinez, Daniella Victoria [Sandia National Labor↗
DOE OSTI2023

Providing Geospatial Intelligence through a Scalable Imagery Pipeline

This chapter describes ORNL’s (Oak Ridge National Laboratory’s) contributions to imagery preprocessing for geospatial intelligence research and development (R&D) in four sections. First, we discuss challenges involved in building an effective imagery preprocessing workflow and the world-class high-performance computing (HPC) resources at ORNL available to process petabytes of imagery data. Second, we highlight how we developed imagery preprocessing tools over three decades while paving the way for our current cutting-edge machine learning and computer vision algorithms that are impacting humanitarian and disaster response efforts. Third, we discuss how PIPE modules work together to turn raw images into analysis-ready datasets. Fourth, we look toward the future and discuss planned advancements to PIPE and computing trends that will affect geospatial intelligence R&D.

Reith, Andrew↗
DOE OSTI2019

Tumor-Infiltrating Lymphocytes in a Contemporary Cohort of Women with Ductal Carcinoma In Situ (DCIS)

Background: Growing evidence suggests that the tumor immune microenvironment influences breast cancer development and prognosis. Density of tumor-infiltrating lymphocytes (TILs) within invasive breast cancer is correlated with response to therapy, especially in triple-negative disease. The clinical relevance and outcomes of TILs within ductal carcinoma in situ (DCIS) are less understood. Methods: Our institutional database of 668 patients with pure DCIS from 2010 to 2018 was queried. TILs were evaluated by International TILs Working Group guidelines. Percentage of TILs was assessed from the densest focus (hotspot) in one high-power field of stroma touching the basement membrane. Statistical methods included cluster analyses (to define sparse versus dense TILs), logistic, and Cox regression models. Results: Sixty-nine patients with DCIS and TILs were evaluated, of whom 54 (78%) were treated by breast-conserving surgery. Thirteen (19%) patients had ipsilateral recurrence. Each recurrence (n = 13) was matched to four controls (n = 56) based on date of surgery. Median follow-up was 6.7 years. TILs were defined as sparse (< 45%) or dense (≥ 45%). Dense TILs were associated with younger age (p = 0.045), larger tumor size (p < 0.001), high nuclear grade (p = 0.010), comedo histology (p = 0.033), necrosis (p = 0.027), estrogen receptor (ER) negativity (p = 0.037), and ipsilateral recurrence (p = 0.001). Nine patients with dense TILs had mean time to recurrence of 73.5 months compared with four patients with sparse TILs with mean time to recurrence of 97.9 months (p = 0.003). Conclusions: Dense TILs were significantly associated with age, tumor size, nuclear grade, comedo histology, necrosis, and ER status and was a significant predictor of recurrence in patients with pure DCIS.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Enhanced material identification via momentum-integrated muon scattering tomography

Cosmic ray muons, originating from interactions in the upper atmosphere, possess high energy and unique penetrative capabilities suitable for non-traditional radiographic inspection. This study explores their application in various fields such as nuclear fuel cask monitoring, nuclear reactor imaging, and archaeology, leveraging the principle of multiple Coulomb scattering for imaging dense materials. While muon scattering tomography has shown promise, accurately measuring muon momentum remains challenging. This research introduces the Momentum Integrated Point-of-Closest Approach (mPoCA) algorithm, integrating muon momentum data into the traditional Point-of-Closest Approach (PoCA) framework. Utilizing the Cherenkov muon spectrometer, renowned for precise muon momentum estimation, the mPoCA algorithm offers a novel imaging approach. Simulations conducted with GEANT4 evaluate the mPoCA algorithm’s performance against the standard PoCA method, demonstrating superior image resolution and enhanced material identification capabilities, particularly in distinguishing materials like uranium and lead. These findings underscore the potential of the mPoCA algorithm for advancing muon scattering tomography applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

ShopperWorkerRatio

These data characterize spatial and temporal variation in the ratio between shoppers and workers in public places - points of interest - in the United States between 2019 and 2020. The underlying data on foot traffic to public places is collected by SafeGraph, a commercial data aggregator. We estimate the ratio of shoppers to workers based on recorded visit duration.These data may be useful for understanding how use of public spaces have changed during the Coronavirus pandemic, and more generally for understanding activity patterns in public.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2017

Metrics for the technical performance evaluation of light water reactor accident-tolerant fuel

The safe, reliable, and economic operation of the nation’s nuclear power reactor fleet has always been a top priority for the nuclear industry. Continual improvement of technology, including advanced materials and nuclear fuels, remains central to the industry’s success. Enhancing the accident tolerance of light water reactors (LWRs) became a topic of serious discussion following the 2011 Great East Japan Earthquake, resulting tsunami, and subsequent damage to the Fukushima Daiichi nuclear power plant complex. The overall goal for the development of accident-tolerant fuel (ATF) for LWRs is to identify alternative fuel system technologies to further enhance the safety, competitiveness, and economics of commercial nuclear power. Designed for use in the current fleet of commercial LWRs or in reactor concepts with design certifications (GEN-III+), fuels with enhanced accident tolerance would endure loss of active cooling in the reactor core for a considerably longer period of time than the current fuel system while maintaining or improving performance during normal operations. The complex multiphysics behavior of LWR nuclear fuel in the integrated reactor system makes defining specific material or design improvements difficult; as such, establishing desirable performance attributes is critical in guiding the design and development of fuels and cladding with enhanced accident tolerance. Research and development of ATF in the United States is conducted under the U.S. Department of Energy (DOE) Fuel Cycle Research and Development Advanced Fuels Campaign. The DOE is sponsoring multiple teams to develop ATF concepts within multiple national laboratories, universities, and the nuclear industry. Concepts under investigation offer both evolutionary and revolutionary changes to the current nuclear fuel system. This study summarizes the technical evaluation methodology proposed in the United States to aid in the optimization and prioritization of candidate ATF designs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗