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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 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Thousands of small, novel genes predicted in global phage genomes

Small genes (<150nucleotides) have been systematically overlooked in phage genomes. We employ a large scale comparative genomics approach to predict >40,000 small-gene families in 2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000families encode predicted anti-CRISPR proteins, and more than500families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Fremin, Brayon↗
DOE OSTI2025

Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases

Background Large language models (LLMs) are increasingly used medicine for diverse applications including differential diagnostic support. The training data used to create LLMs such as the Generative Pretrained Transformer (GPT) predominantly consist of English-language texts, but LLMs could be used across the globe to support diagnostics if language barriers could be overcome. Initial pilot studies on the utility of LLMs for differential diagnosis in languages other than English have shown promise, but a large-scale assessment on the relative performance of these models in a variety of European and non-European languages on a comprehensive corpus of challenging rare-disease cases is lacking. Methods We created 4917 clinical vignettes using structured data captured with Human Phenotype Ontology (HPO) terms with the Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema. These clinical vignettes span a total of 360 distinct genetic diseases with 2525 associated phenotypic features. We used translations of the Human Phenotype Ontology together with language-specific templates to generate prompts in English, Chinese, Czech, Dutch, French, German, Italian, Japanese, Spanish, and Turkish. We applied GPT-4o, version gpt-4o-2024-08-06, and the medically fine-tuned Meditron3-70B to the task of delivering a ranked differential diagnosis using a zero-shot prompt. An ontology-based approach with the Mondo disease ontology was used to map synonyms and to map disease subtypes to clinical diagnoses in order to automate evaluation of LLM responses. Findings For English, GPT-4o placed the correct diagnosis at the first rank 19.9% and within the top-3 ranks 27.0% of the time. In comparison, for the nine non-English languages tested here the correct diagnosis was placed at rank 1 between 16.9% and 20.6%, within top-3 between 25.4% and 28.6% of cases. The Meditron3 model placed the correct diagnosis within the first 3 ranks for 20.9% of cases in English and between 19.9% and 24.0% for the other nine languages. Interpretation The differential diagnostic performance of LLMs across a comprehensive corpus of rare-disease cases was largely consistent across the ten languages tested. This suggests that the utility of LLMs in clinical settings may extend to non-English clinical settings.

Artificial intelligence↗
DOE OSTI2020

Application of emerging monitoring techniques at the Illinois Basin – Decatur Project

The Illinois Basin – Decatur Project is a large-scale carbon capture and storage demonstration project located in Decatur, Illinois, USA. In this project, one million metric tons of carbon dioxide (CO 2 ) was captured from an ethanol production facility and successfully injected into a deep saline reservoir over a period of three years. The scale of this project presented an opportunity to explore emerging technologies for effective long-term monitoring of the carbon capture and storage site. This research documents the application of three emerging monitoring techniques: (1) a prototype “open-path” sensor, a method of continuously monitoring atmospheric CO 2 by applying tunable diode laser absorption spectroscopy to provide a warning system for personnel safety along pipelines and at wellheads; (2) the Greenhouse Gas Laser Imaging Tomography Experiment (GreenLITE), an automated system for measuring two-dimensional spatial distribution of atmospheric CO 2 concentrations; and (3) periodic aerial imagery, a method of documenting surface-vegetation dynamics to detect vegetative responses to CO 2 leaks. The objective of this work was to assess the advantages and limitations of these monitoring techniques and quantify their reliability over an extended deployment at an active industrial site. These results will aid in determining viability of long-term monitoring on a commercial scale.

42 ENGINEERING↗
DOE OSTI2021

Screening and Validation of Molecular Targeted Radiosensitizers

The development of molecular targeted drugs with radiation and chemotherapy is critically important for improving the outcomes of patients with hard-to-treat, potentially curable cancers. However, too many preclinical studies have not translated into successful radiation oncology trials. Major contributing factors to this insufficiency include poor reproducibility of preclinical data, inadequate preclinical modeling of intertumoral genomic heterogeneity that influences treatment sensitivity in the clinic, and a reliance on tumor growth delay instead of local control (TCD50) endpoints. There exists an urgent need to overcome these barriers to facilitate successful clinical translation of targeted radiosensitizers. To this end, we have used 3-dimensional (3D) cell culture assays to better model tumor behavior in vivo. Examples of successful prediction of in vivo effects with these 3D assays include radiosensitization of head and neck cancers by inhibiting epidermal growth factor receptor or focal adhesion kinase signaling, and radioresistance associated with oncogenic mutation of KRAS. To address the issue of tumor heterogeneity, we leveraged institutional resources that allow high-throughput 3D screening of radiation combinations with small-molecule inhibitors across genomically characterized cell lines from lung, head and neck, and pancreatic cancers. This high-throughput screen is expected to uncover genomic biomarkers that will inform the successful clinical translation of targeted agents from the National Cancer Institute Cancer Therapy Evaluation Program portfolio and other sources. Screening “hits” need to be subjected to refinement studies that include clonogenic assays, addition of disease-specific chemotherapeutics, target/biomarker validation, and integration of patient-derived tumor models. The chemoradiosensitizing activities of the most promising drugs should be confirmed in TCD50 assays in xenograft models with or without relevant biomarker and using clinically relevant radiation fractionation. We predict that appropriately validated and biomarker-directed targeted therapies will have a higher likelihood than past efforts of being successfully incorporated into the standard management of hard-to-treat tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

Regulatory helix plays a key role in genetic ON-OFF switching for the 2’-deoxyguanosine sensing mRNA element

Transcriptional riboswitches, noncoding mRNA elements that operate in cis to regulate gene expression, have a promising potential in medicine, synthetic biology and directed evolution. They bind to cellular metabolites or metal ions with high specificity, leading to conformational rearrangements that facilitate the activation or premature termination of transcription for downstream genes. This elegant mechanism for feedback regulation of metabolic pathways has been identified in prokaryotes and a few in eukaryotes. Our chemical probing of the 2’-deoxyguanosine (2’-dG)-sensing riboswitch demonstrates that the overall conformational state of the full-length riboswitch (dGsw-fl) is unresponsive to the 2’-dG. Although binding proceeds as expected, dGsw-fl exclusively populates an OFF state of transcriptional inhibition. We chemically probed the structure of a known dGsw transcriptional intermediate (dGsw-int) to evaluate the possibility of a cotranscriptional regulatory role. Interestingly, apo dGsw-int adopts an alternative conformation in which a stable anti-terminator helix is formed, leading to an ON state where transcription can proceed. In the presence of 2’-dG, this anti-terminator helix is destabilized to produce a conformation reminiscent of the full-length, OFF-state dGsw. Using a fluorescence quenching assay, we demonstrate that binding 2’-dG to early transcriptional intermediates can inhibit the formation of the anti-terminator helix, locking dGsw in an OFF state. These data suggest that metabolite sensing occurs during a brief window of time between the synthesis of two transcriptional intermediates. Our studies indicate that dGsw does not function as a binary ON−OFF switch, but instead fine-tunes the transcription of downstream genes during RNA synthesis using key intermediates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mitigation and Diagnosis of Pin-Hole Formation in Polymer Electrolyte Membrane Fuel Cells

In this work, we implement a calendering technique to flatten stray fibers within the gas diffusion media, thereby mitigating pin-hole formation in the hot-pressed MEAs. We have investigated the influence of calendering on the long-term durability for several types of gas diffusion electrodes (GDEs) using a combined chemical and mechanical accelerated stress test (AST). The calendered MEAs demonstrate an average AST lifetime improvement of 77% relative to the as-fabricated MEAs.

AMR↗
DOE OSTI2025

The separatrix electron density in JET, ASDEX upgrade and alcator C-Mod H-mode plasmas: A common evaluation procedure and correlation with engineering parameters

The separatrix electron density is an important parameter for core-edge scenario integration in tokamak devices, as it influences plasma confinement, divertor detachment and disruption avoidance. This quantity has been measured in H-mode discharges on JET, ASDEX Upgrade and Alcator C-Mod by applying the same fitting function to Thomson scattering measurements, and by employing the same analysis technique based on scrape-off layer power balance. To estimate the power crossing the separatrix, the inter-ELM time derivative of the plasma energy d W /d t has been experimentally evaluated and found to be approximately a constant fraction of the absorbed heating power. Correlations between n e,sep and engineering parameters have been investigated, revealing that n e,sep scales with the divertor neutral pressure p 0,div in a similar manner across all devices. Additionally, when n e,sep is normalized to the obtained n e,sep dependency, no clear correlation with the plasma current is found. These observations are in agreement with the 2-point model, which suggests that the upstream separatrix density is mainly set by the recycling at the divertor target.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Balmer emission measurements in JET-ILW hydrogen, deuterium, tritium and deuterium-tritium low-confinement mode plasmas

Measurements of Balmer-alpha (B-α) and Balmer-gamma (B-γ), where B = H, D, or T isotopes of hydrogen, emission across the low-field side (LFS) divertor in JET ITER-like Wall (ILW), low-confinement mode (L-mode) plasma indicate that the divertor plasma was more strongly detached in deuterium, tritium and deuterium–tritium than in hydrogen plasmas. These measurements are consistent with the lower degree of detachment in hydrogen versus tritium plasmas inferred from Langmuir probes (Groth et al., 2023). The ratio of B-γ to B-α is a suitable indicator of high density/low temperature conditions because B-α emission is dominated by electron impact excitation with a small electron–ion recombination component regardless of electron temperature and density (for conditions in tokamak plasmas) whilst for B-γ the recombination component increases and the excitation component decreases as the electron temperature decreases and the electron density increases. Within the uncertainty of the measurements, the electron density at the low-field side separatrix and the power crossing the separatrix are similar to permit these comparisons. The B-©/B-α ratio is well correlated with the onset of detachment as measured by Langmuir probes (McCracken et al., 1998; Groth et al., 2023). The ratios of B-γ and B-α varied between 0.005 and 0.035 for low-recycling, high-recycling and partially detached conditions, and were 60–70 % higher in partially detached hydrogen than in tritium plasmas. In contrast, the difference between deuterium, tritium and 40–60 % deuterium–tritium is within 10 % and thus within the uncertainties of the measurements. Profiles of the B-α and B-γ emission was measured with two filtered CCDs connected to the visible lost light leg of JET’s mirror link spectroscopy system (Meigs et al., 2010; Lomanowski et al., 2014). Spatially (radial) narrower B-α profiles were measured with increasing isotope mass, while similarly broadened B-γ profiles were measured.

Balmer↗
DOE OSTI2020

An efficient Chlorella sp.-Cupriavidus necator microcosm for phenol degradation and its cooperation mechanism.

In this work, a Chlorella sp.-Cupriavidus necator (C. necator) microcosm was artificially established for phenol degradation. Additionally, the cooperation relationship between Chlorella sp. and C. necator was initially demonstrated, and then the effects of Chlorella sp./C. necator inoculation ratio, light intensity, temperature and pH on the performance of this microcosm were systematically evaluated and optimized. The optimal conditions for phenol degradation were as follows: a Chlorella sp./C. necator inoculation ratio of 1:1, a light intensity of 110 μmol m -2 s -1 , a temperature in the range of 25-32 °C and a pH in the range of 5.5-7.5. Under optimal conditions, this microcosm could degrade phenol with a maximum concentration of 1200 mg L -1 within 60 h. It was found that only when the phenol concentration was reduced to the tolerance concentration of microalgae, that is, the last stage of phenol degradation, the cooperation effect could be generated, indicating that the tolerance of microalgae to phenol may be more important than its degradation performance. Comparative transcriptomic analysis was conducted to discuss the cooperation mechanism of this microcosm subject to high phenol concentrations. The up-regulation of genes involved in photosynthesis and carbon fixation of Chlorella sp. demonstrated the CO 2 and O 2 exchange between Chlorella sp. and C. necator and their cooperation relationship. This study suggests that this microcosm has great potential for the bioremediation of phenol contaminants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Methods for Carbon Mass Closure in Polyolefin Hydrocracking

Heterogeneous catalytic hydrocracking of polyolefins is a promising approach for the processing of postconsumer plastics, but product quantification methods remain inconsistent across the literature. In systems that generate a large fraction of vapor-phase products, typical product capture methods can result in large carbon balance deficits, exceeding 50%, compromising reported yields and selectivities. Here, we identify the major sources of product loss and develop enhanced capture methods to improve the quantification accuracy. Seven supplemental techniques were evaluated, targeting either increased vapor recovery (by increasing the volatility or system volume) or enhanced retention in the liquid phase (by decreasing volatility). Among these, a flow collection approach using a continuous helium sweep and downstream gas sampling bag capture yielded the highest recovery, achieving a 96 ± 9.2% carbon balance closure. We show that the efficacy of these methods is strongly dependent on product distribution. In general, solvent addition was most effective when condensable species dominate the product distribution, while flow collection was preferred when both condensable species and light gases are present in high concentrations. These results highlight the need for method-specific workup strategies and demonstrate that no single protocol is universally optimal. We provide general guidelines for selecting and implementing robust product capture techniques, enabling accurate yield and selectivity determinations in polyolefin hydrocracking systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Using an Isotope Enabled Mass Balance to Evaluate Existing Land Surface Models

Abstract Land surface models (LSMs) play a crucial role in elucidating water and carbon cycles by simulating processes such as plant transpiration and evaporation from bare soil, yet calibration often relies on comparing LSM outputs of landscape total evapotranspiration ( ET ) and discharge with measured bulk fluxes. Discrepancies in partitioning into component fluxes predicted by various LSMs have been noted, prompting the need for improved evaluation methods. Stable water isotopes serve as effective tracers of component hydrologic fluxes, but data and model integration challenges have hindered their widespread application. Leveraging National Ecological Observation Network measurements of water isotope ratios at 16 US sites over 3 years combined with LSM‐modeled fluxes, we employed an isotope‐enabled mass balance framework to simulate ET isotope values ( δET ) within three operational LSMs (Mosaic, Noah, and VIC) to evaluate their partitioning. Models simulating δET values consistent with observations were deemed more reflective of water cycling in these ecosystems. Mosaic exhibited the best overall performance (Kling‐Gupta Efficiency of 0.28). For both Mosaic and Noah there were robust correlations between bare soil evaporation fraction and error (negative) as well as transpiration fraction and error (positive). We found the point at which errors are smallest ( x ‐intercept of the multi‐site regression) is at a higher transpiration fraction than is currently specified in the models. Which means that transpiration fraction is underestimated on average. Stable isotope tracers offer an additional tool for model evaluation and identifying areas for improvement, potentially enhancing LSM simulations and our understanding of land‐surface hydrologic processes.

58 GEOSCIENCES↗
DOE OSTI2026

A New Theoretical Framework for Parameterizing Nonequilibrium Fractionation During Evaporation From the Ocean

The evaporation model for water isotopes proposed by Craig and Gordon (1965, https://books.google.co.in/books?id=6wIKAQAAIAAJ) is used in most isotope-enabled atmospheric models for the parameterization of nonequilibrium fractionation during evaporation from the ocean. In this model, one of the most uncertain parameters is the nonequilibrium fractionation factor 𝛼 𝑘 . Many isotope models use the formulation of Merlivat and Jouzel (1979, https://doi.org/10.1029/jc084ic08p05029), which parameterizes 𝛼 𝑘 as a function of wind speed and distinguishes between a smooth and a rough regime to account for the effect of ocean waves. The resulting discontinuity in 𝛼 𝑘 between smooth and rough regimes has been disputed by several empirical studies. Here, we present a new approach to parameterizing 𝛼𝑘 by explicitly accounting for the influence of wave drag on the momentum flux near the surface. Following Cifuentes-Lorenzen et al. (2018, https://doi.org/10.1007/s10546-018-0376-0), we add a third wave-induced component to the total momentum flux, in addition to the viscous and turbulent components, and extend the definition of the eddy viscosity to account for the momentum flux due to waves and turbulent dissipation near the surface. The new scheme predicts a slight decrease of 𝛼 𝑘 with wind speed, similar to the smooth-regime parameterization of Merlivat and Jouzel (1979, https://doi.org/10.1029/jc084ic08p05029). This new parameterization is incorporated into the isotope-enabled Community Atmosphere Model, where it improves the correlation of simulated and measured vapor deuterium excess relative to the default version and a version with constant 𝛼 𝑘 , suggesting that it may be used as a valid representation of fractionation during evaporation from the ocean in future isotope models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Leaf Wax Hydrogen Isotopes Reflect Storm Track Position Over Western North America

Proxy records of past climates have yielded powerful insights into regional hydroclimate dynamics. Novel insights may be gained by reconstructing spatiotemporal changes in precipitation isotopologues in past climate states that cannot be gleaned from individual site‐level studies. In this paper, we ask whether latitudinal gradients in the stable hydrogen isotopic composition of precipitation, as inferred from sedimentary leaf wax biomarkers, reflect aspects of large‐scale climate conditions in western North America (WNA). Modern coretop samples from offshore WNA show that leaf wax hydrogen isotopes broadly track the hydrogen isotopic composition of rainfall between 20 and 40N, but with an offset corresponding to a relatively constant “apparent fractionation” value. Poleward of 40N, the leaf wax signal may be complicated by fluvial transport of leaf waxes from the continental interior. Leaf wax‐inferred precipitation hydrogen isotopes show a shift to more negative values between 30 and 40N. We use modern observational data to show that this latitudinal range marks a major transition between the subtropical arid zone and the location of the midlatitude storm tracks over the northeast Pacific. Nudged water isotope‐enabled models capture the location of the arid to mesic climate transition with fidelity. This modern data set suggests that reconstructions of the latitudinal gradient of precipitation hydrogen isotopes can constrain the sensitivity of the storm tracks to shifts in climatic boundary conditions in past climate states. This approach can yield novel insights into past, present, and future hydroclimate variability in this arid region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Characterization of volcanic tuff pores pre- and post-underground nuclear detonation using ultra-small and small angle neutron scattering

The ability to accurately model the subsurface transport of radionuclides is fundamental to the remote detection and characterization of underground nuclear explosion (UNE) events. Developing more sophisticated transport models presents a significant opportunity to enhance monitoring capabilities, particularly in the reliable prediction of signature migration. Experimentally determined characterization of geologic materials associated with transport properties is the pertinent base information for such robust model development and calibration. Here, we report results from an unprecedented study demonstrating changes to the pore and fracture network structures in geological materials in response to UNEs over nanometer to micrometer length scales. Volcanic tuffs of five different lithological formations from pre- and post-UNE environments were collected from the Nevada National Security Site. Combined ultra-small and small-angle neutron scattering techniques were used to characterize the tuff pore structure. The results demonstrate measurable differences in the specific surface area and porosity of samples pre- and post-shot from texturally similar lithological formations, indicating that pore properties can serve as a direct physical signature of a UNE. The results also provide experimentally determined transport parameters in support of advanced model development through the integration of gas migration, hydrodynamic simulations, and geologic framework models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine learning prediction of enzyme optimum pH

The relationship between pH and enzyme catalytic activity, especially the optimal pH (pH opt ) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pH opt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. Here, in this study, we proposed and evaluated various machine learning methods for predicting pH opt , conducting extensive hyperparameter optimization and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pH opt , including proximity of residues to the catalytic centre and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pH opt prediction and will potentially speed up the development of enzyme technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Multiscale and multidimensional modeling of particle acceleration and transport in solar flares

Multi-messenger, multi-viewpoint, and time-resolved observations of solar flares are now providing unprecedented constraints on particle acceleration sites, energy conversion, and energy transport. The interpretation of current observations, including microwave imaging spectroscopy from EOVSA, hard x-ray (HXR) imaging from Solar Orbiter/STIX, gamma-ray diagnostics from Fermi, and in situ measurements from Parker Solar Probe and Solar Orbiter, collectively demands modeling frameworks that go beyond traditional spatially unresolved, one-zone models or single-mechanism descriptions. This review surveys multiscale and multidimensional modeling approaches, including kinetic, magnetohydrodynamic (MHD), and macroscopic particle models, that are being developed to meet the need. Kinetic simulations reveal that three-dimensional (3D) effects, including field-line chaos and self-generated turbulence, are essential for sustained power-law particle acceleration. MHD simulations now capture flux-rope eruptions, plasmoid-unstable current sheets, and turbulent flare regions in realistic magnetic topologies. Macroscopic models coupling MHD with energetic-particle models produce spatially resolved electron distributions and synthetic HXR and microwave emissions for direct comparison with observations. Despite these advances, outstanding challenges remain in bridging kinetic and global scales, improving MHD simulations and macroscopic particle models, and achieving quantitative model-observation closure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Rapid organic carbon spiraling in a headwater stream linked with streamflow, biogeochemistry, and canopy phenology

Headwater streams are abundant worldwide and important to global biogeochemical cycles, serving as critical processors and transporters of C. C spiraling is a useful way to understand the retention and mineralization of organic C (OC) in streams. However, analyses of seasonal and interannual variability in OC spiraling are currently limited. In this study, we aimed to understand the temporal patterns and driving mechanisms of OC spiraling, which will inform our understanding of future OC changes under climate change. We used 7 y of daily data in a small headwater stream (Walker Branch, Tennessee, USA) to assess seasonal and interannual variability in OC spiraling length (S OC ) and mineralization velocity (v fOC ), as well as their potential related variables. On average, S OC in Walker Branch was ~10× shorter than in previously studied small streams, indicating strong connections between the water column and the benthic environment where OC mineralization mostly takes place. OC spiraling was faster during the more biologically active periods of spring and autumn compared with more elongated OC spiraling in summer and winter, when OC retention was lower and downstream transport was higher. Gross primary production (GPP) was most strongly related to S OC and v fOC . Photosynthetically active radiation (PAR) and NO 3 − were also positively and negatively related to v fOC , respectively. Trends toward earlier and longer canopy cover and reduced GPP and PAR may result in longer S OC and slower v fOC , reducing localized instream processing of OC and potentially shunting more OC downstream. However, long-term observations indicate reduced NO 3 − at Walker Branch, suggesting opposing effects to those of GPP and PAR, leading to faster v fOC and greater OC retention. Time-series analyses of OC spiraling in streams can enhance our understanding of current and future responses of OC processing and downstream transport to climate change, as well as implications for downstream OC dynamics.

biological activity↗