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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Analysis of genomic signatures associated with Variovorax endosphere colonization

This repository contains the analysis code and supporting datasets associated with the study “Genomic signatures in Variovorax enabling colonization of the Populus endosphere.” Beals DG, Carper DL, Hochanadel LH, Jawdy SS, Klingeman DM, Piatkowski BT, Weston DJ, Doktycz MJ, Pelletier DA. 2026. Genomic signatures in Variovorax enabling colonization of the Populus endosphere. mSystems 11:e01605-25. https://doi.org/10.1128/msystems.01605-25 The scripts are organized sequentially (01–07) and document the workflows used for: Sequence-read alignment and feature counting Orthogroup and KEGG Ortholog annotation Count normalization Statistical analysis and aggregation Generation of manuscript figures and tables Repository contents The uncompressed files are the finalized, formatted datasets used to generate the figures and tables reported in the study, including the supplemental CSV files referenced in the manuscript. The accompanying ZIP archive contains the complete codebase and example data_input/ and data_output/ directories illustrating the organization and execution of the analytical workflow. Individual scripts identify the corresponding manuscript analyses and figure panels. Raw sequencing data Raw sequencing reads are available through the NCBI Sequence Read Archive under BioProject accession PRJNA1322484.

Beals, Delaney [ORNL] (ORCID:0000000306274574)↗
DOE OSTI2022

A Pilot Study of Whole-Blood Transcriptomic Analysis to Identify Genes Associated with Repetitive Low-Level Blast Exposure in Career Breachers

Repetitive low-level blast exposure is one of the major occupational health concerns among US military service members and law enforcement. This study seeks to identify gene expression using microRNA and RNA sequencing in whole-blood samples from experienced breachers and unexposed controls. We performed experimental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System, and microRNA analysis using NanoString Technology nCounter miRNA expression panel in whole-blood total RNA samples from 15 experienced breachers and 14 age-, sex-, and race-matched unexposed controls. We identified 10 significantly dysregulated genes between experienced breachers and unexposed controls, with FDR corrected <0.05: One upregulated gene, LINC00996 (long intergenic non-protein coding RNA 996); and nine downregulated genes, IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin-like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin-associated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobulin heavy variable 4-34). The dysregulated gene expressions reported here have been associated with chronic inflammation and immune response, suggesting that these pathways may relate to the risk of lasting neurological symptoms following high exposures to blast over a career.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Gait Characterization and Analysis of Hereditary Amyloidosis Associated with Transthyretin Patients: A Case Series

Hereditary amyloidosis associated with transthyretin (ATTRv), is a rare autosomal dominant disease characterized by length-dependent symmetric polyneuropathy that has gait impairment as one of its consequences. The gait pattern of V30M ATTRv amyloidosis patients has been described as similar to that of diabetic neuropathy, associated with steppage, but has never been quantitatively characterized. In this study we aim to characterize the gait pattern of patients with V30M ATTRv amyloidosis, thus providing information for a better understanding and potential for supporting diagnosis and disease progression evaluation. We present a case series in which we conducted two gait analyses, 18 months apart, of five V30M ATTRv amyloidosis patients using a 12-camera, marker based, optical system as well as six force platforms. Linear kinematics, ground reaction forces, and angular kinematics results are analyzed for all patients. All patients, except one, showed a delayed toe-off in the second assessment, as well as excessive pelvic rotation, hip extension and external transverse rotation and knee flexion (in stance and swing phases), along with reduced vertical and mediolateral ground reaction forces. The described gait anomalies are not clinically quantified; thus, gait analysis may contribute to the assessment of possible disease progression along with the clinical evaluation.

Vilas-Boas, Maria do Carmo (ORCID:000000025012789X↗
DOE OSTI2023

Variability and associated uncertainty in image analysis for soiling characterization in solar energy systems

The accumulation of soiling on photovoltaic modules and on the mirrors of concentrating solar power systems causes non-negligible energy losses with economic consequences. These challenges can be mitigated, or even prevented, through appropriate actions if the magnitude of soiling is known. Particle counting analysis is a common procedure to characterize soiling, as it can be easily performed on micrographs of glass coupons or solar devices that have been exposed to the environment. Particle counting does not, however, yield invariant results across institutions. The particle size distribution analysis is affected by the operator of the image analysis software and the methodology utilized. The results of a round-robin study are presented in this work to explore and elucidate the uncertainty related to particle counting and its effect on the characterization of the soiling of glass surfaces used in solar energy conversion systems. An international group of soiling experts analyzed the same 8 micrographs using the same open-source ImageJ software package. The variation in the particle analyses results were investigated to identify specimen characteristics with the lowest coefficient of variation (CV) and the least uncertainty among the various operators. The mean particle diameter showed the lowest CV among the investigated characteristics, whereas the number of particles exhibited the largest CV. Additional parameters, such as the fractional area coverage by particles and parameters related to the distribution's shape yielded intermediate CV values. These results can provide insights on the magnitude inter-lab variability and uncertainty for optical and microscope-based soiling monitoring and characterization.

14 SOLAR ENERGY↗
DOE OSTI2024

Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy

The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Analysis of nonlinear features associated with radio-frequency sheaths

An analytic study is conducted of nonlinear features that arise when radio-frequency (RF) sheath boundary conditions are solved self-consistently with the electromagnetic fields in a magnetized plasma. An instability associated with RF sheath–plasma interactions is identified and shown to be closely linked with sheath–plasma resonance and the occurrence of multiple solutions. It is proposed that this instability serves as a physical mechanism that enables jumping from one solution branch to another, providing a physical basis for the prediction of an RF sheath hysteresis in the time domain. It is further shown that this instability can lead to non-intuitive features such as spontaneous symmetry breaking in an otherwise completely symmetric problem. In plane-stratified geometry, two analytically solvable examples are considered for the cases of an unbounded half-space and a bounded domain

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

LBNL CRADA (FP00009949) with the American Public Power Association: Electricity Reliability Metrics, Analysis, and Planning (Final Technical Report)

LBNL and APPA (the team) jointly examined the extent to which differences in distribution feeder characteristics are correlated with differences in their reliability performance when exposed to three different types of natural hazards (wildlife, weather, and vegetation). The team employed data-driven approaches to quantify the relationships between various measures of feeder reliability and a suite of feeder characteristics individually and jointly via a statistically-based clustering method.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

CHRNA5 rs16969968 polymorphism is associated with lung cancer risk: A meta‐analysis

Abstract Objective To evaluate the genetic association between rs16969968 and lung cancer risk by meta‐analysis. Data source We searched eligible studies from MEDLINE, Web of Science and EMBASE up to Dec, 2017. Study selection Association studies concerning rs16969968 and lung cancer risk were included. We assessed the association strength between this polymorphism and risk of lung cancer by calculating odds ratios (OR) and 95% confidence interval (95%CI). Results A total of 26 data sets comprising 30 772 lung cancers and 90 954 controls were included. rs16969968 was found to be associated with lung cancer risk in population of European ancestry in all models (A vs. G: OR = 1.30, 95%CI 1.27‐1.33, P < 0.001; AA + GA vs. GG: OR = 1.38, 95%CI 1.33‐1.43, P < 0.001; AA vs. GG + GA: OR = 1.45, 95%CI 1.38‐1.53, P < 0.001), consistent with previous genome‐wide association study (GWAS). However, no association was observed in Asians (A vs. G: OR = 1.19. 95%CI 0.95‐1.49, P = 0.131). The minor allele A may increase the risk of lung cancer in both smokers (OR = 1.33, 95%CI 1.29‐1.39, P < 0.001) and nonsmokers (OR = 1.25, 95%CI 1.12‐1.39, P < 0.001). There was no obvious publication bias in all analyses. Conclusions Our analysis provided more evidence that rs16969968 is a susceptibility locus of lung cancer in the Caucasians and that it may be not associated with the risk in the Asians.

Zhou, Wei↗
DOE OSTI2024

TRUST Contact Thermal Conductance (TRUST-CTC) Report: FY24

The objective of the Delivery Environments (DE) Testbeds to Reduce Uncertainties in Simulations and Tests (TRUST) project is to quantify and help increase confidence in specific areas of computational and experimental capabilities that are applicable to current and future delivery environments. More complete quantification of confidence in experimental and computational capabilities and the sufficient increase of confidence in those capabilities is critical to improving weapons engineering design, qualification, and assessment efforts that are critical to the current and future stockpile. Staff development will include cross-discipline collaboration to provide engineers with experience in both numerical simulations and experimental methods. This work uses and provides feedback on analysis tools and experimental results databases for efficient and responsive engineering which are currently under development. TRUST currently includes five testbeds and their associated engineering analysis baseline models (EABMs): 1. contact thermal conductivity, (CTC) 2. nonlinear dynamics, (ND) 3. sensors in environments for accelerometers, (SEA) 4. sensors in environments for fiber optic displacement gages, and (SEFOD) 5. sensors in environments for thermocouples (SETC). The TRUST project uses single-feature testbeds to quantify uncertainties in specific models and experiments and to identify capability development needs that can help to reduce these uncertainties. Each testbed is designed, configured, and tested in collaboration with groups with design and experimental capability: E-14 and MPA-CINT. The complementary simulations are conducted using W-13 analysis tools and stored in model repositories with plans for incremental progress toward EABM requirements. W-13 extends and exercises the testbed simulations in collaboration with experimentalists for uncertainty quantification of current and future materials, geometries, and environments. Additionally, TRUST is intended to provide engineers in W-13 and E-14 with experience in both numerical simulations and experimental methods through cross-discipline collaborations. Following the introduction to the TRUST project, the remainder of this report focuses on experimental and analytical efforts conducted in Fiscal Year (FY) 2024 relevant to the TRUST Contact Thermal Conductance (CTC) testbed.

42 ENGINEERING↗
DOE OSTI2024

TRUST Sensors in Environments: Fiber Optic Displacement (SE-FOD) Report, Release FY24

The objective of the Delivery Environments (DE) Testbeds to Reduce Uncertainty in Simulations and Tests (TRUST) project is to quantify and help increase confidence in specific areas of computational and experimental capabilities that are applicable to the development, on-target assessment, and qualification of current and future delivery environments. More complete quantification of confidence in experimental and computational capabilities and the sufficient increase of confidence in those capabilities is critical to improving weapons engineering design, qualification, and assessment efforts that are critical to the current and future stockpile. This work uses and provides feedback on analysis tools and experimental results databases for efficient and responsive engineering which are currently under development. Under the TRUST work package, there are five testbeds and their associated engineering analysis baseline models (EABMs): 1. Contact Thermal Conductivity (CTC), 2. Nonlinear Dynamics (ND), 3. Sensors in Environments: Accelerometers (SE-A), 4. Sensors in Environments: Fiber Optic Displacement Gauges (SE-FOD), and 5. Sensors in Environments: Thermocouples (SE-TC). The TRUST project uses single-feature testbeds to quantify uncertainties in specific models and experiments and to identify capability development needs that can help to reduce these uncertainties. Each testbed is designed, configured, and tested in collaboration with groups with design and experimental capability: E-14 and MPA-CINT. The complementary simulations are conducted using W-13 analysis tools and stored in model repositories with plans for incremental progress toward EABM requirements. W-13 extends and exercises the testbed simulations in collaboration with experimentalists for uncertainty quantification of current and future materials, geometries, and environments. Additionally, TRUST is intended to provide engineers in W-13 and E-14 with experience in both numerical simulations and experimental methods through cross-discipline collaborations. Following the introduction to the TRUST project, the remainder of this report focuses on experimental, modeling and simulation, and analysis efforts conducted in FY24 relevant to the TRUST Sensors in Environments: Fiber Optic Displacement (SE-FOD) testbed.

42 ENGINEERING↗
DOE OSTI2021

TRUST End-of-Year Report

The objective of the Delivery Environments (DE) Testbeds to Reduce Uncertainties in Simulations and Tests (TRUST) work package is to quantify and help increase confidence in specific areas of computational and experimental capabilities that are applicable to current and future delivery environments. More complete quantification of confidence in experimental and computational capabilities and the sufficient increase of confidence in those capabilities is critical to improving weapons engineering design, qualification, and assessment efforts that are critical to the current and future stockpile. Staff development will include cross-discipline training to provide engineers with experience in both numerical simulations and experimental methods. This work will use and provide feedback on analysis tools and experimental results databases for efficient and responsive engineering which are currently under development: engineering common model framework (ECMF), engineering quantification of margins and uncertainties (EQMU), and the test information management system (TIMS). TRUST includes four testbeds and their associated engineering analysis baseline models (EABMs): 1. contact thermal conductivity (CTC); 2. nonlinear dynamics (ND); 3. sensors in environments for accelerometers (SEA); 4. sensors in environments for fiber optic displacement gages (SEFOD).

42 ENGINEERING↗
DOE OSTI2022

Genome assembly PYCC 8100

The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, and variation in gene content, or possible domestication routes have not been investigated. Here, we address these issues and update the circumscription of T. delbrueckii, which is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other one to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition were more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.

Sampaio, Jose P.↗
DOE OSTI2022

Autogenous acid production using a regulated bio-oxidation method for economical recovery of REEs and critical metals from coal-based resources

Acid is a necessary component for the successful leaching of minerals containing REEs (rare earth elements) and other sources. Pyrite (FeS2), which is present in REE containing minerals, can be used to produce acid. Pyrite is utilized as a source to create ferric sulfate and sulfuric acid in the presence of A. Ferroxidans. Such microorganism-based bio-oxidation necessitates the establishment of optimal conditions for continual acid production. For efficient acid generation, additional optimization was done by varying residence time, solid percentage, and airflow rate. A step-by-step analysis and associated details are offered in this work, which used pyrite to create acid for leaching. For the bio-oxidation of pyrite with varying purity, an automated bioreactor was used. Scanning electron microscopy with energy-dispersive X-ray spectroscopy was used to examine the morphology and elemental content of bioleaching sediments. Eh and pH measurements were continuously done to ensure healthy operation of the bioreactors. The analysis suggested that, the Eh value in the range of ∼ 640–680 mV, pH range of ∼ 1.3–1.5 and residence time of 4–6 days with 6% solid feed are favorable conditions of operation.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Quantitative Proteomic Analysis of the Senescence-Associated Secretory Phenotype by Data-Independent Acquisition

Cellular senescence is a complex stress response that induces an essentially permanent cell cycle arrest and a complex secretory phenotype termed the senescence-associated secretory phenotype (SASP), which drives numerous aging pathologies. Characterization of the SASP can provide insights into aging and disease mechanisms, aging biomarker candidates, and targets for counteracting the deleterious effects of senescent cells. Here we describe a mass spectrometry (MS)-compatible protocol to (1) generate senescent cells using different stimuli, (2) collect conditioned medium containing proteins secreted by senescent cells (i.e., SASP), and (3) prepare the SASP for quantitative proteomic analysis using data-independent acquisition (DIA) MS. Basic Protocol 1: Generating ionizing radiation-induced senescent and control cells Alternate Protocol 1: Generating doxorubicin-induced senescent and control cells Alternate Protocol 2: Generating oncogenic RAS-induced senescent and control cells Alternate Protocol 3: Generating mitochondrial dysfunction-induced senescent and control cells Alternate Protocol 4: Generating atazanavir/ritonavir-induced senescent and control cells Support Protocol: A multiple-assay approach to confirm the phenotype of senescent cells Basic Protocol 2: Generating conditioned medium from senescent cells cultured in low serum and quiescent control cells Alternate Protocol 5: Generating conditioned medium from senescent cells cultured in complete medium and quiescent control cells Basic Protocol 3: Quantitative proteomic analysis of the SASP.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Analysis of Tank 38H (HTF-38-25-36, -32) and Tank 43H (HTF-43-25-33, -35) Samples for Support of the Enrichment Control and Corrosion Control Programs

Savannah River National Laboratory (SRNL) analyzed samples from Tank 38H and Tank 43H to support the Enrichment Control Program (ECP) and Corrosion Control Program (CCP). The results indicate the concentrations of most soluble species in the Tank 38H surface sample are similar to the previous Tank 38H surface sample. The current Tank 38H subsurface sample shows similar Na, free hydroxide, and anions in comparison to the previous subsurface sample. The current Tank 38H subsurface sample appears brown in color. Measurement of the wt.% insoluble solids in the Tank 38H subsurface sample and associated uncertainty analysis indicates that the calculated average wt.% insoluble solids is 5.5 ± 3.6 wt.%. Significant differences in the concentrations of major components between the Tank 38H surface and subsurface samples indicate stratification of solution species between these two locations within the Tank 38H. The current Tank 43H surface sample is ~ 10% diluted versus the previous Tank 43H surface sample and the Tank 43H subsurface sample is similar in composition to the previous Tank 43H subsurface sample. Information provided by SRMC on tank additions since the last ECP sampling indicates that a total of about 4,062 gallons of water was added to Tank 43H. This addition could account for the observed relatively small dilution of ~ 10% in the Tank 43H surface sample. Similar solution compositions measured in the current Tank 43H surface and subsurface samples indicate a minimal stratification within the tank.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗