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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5) nuclear extracts, immortalized human lung fibroblasts cells (MRC5) (MOI5) nuclear extracts, and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue and processed for proteome analysis. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files and supporting metadata materials. Experimental proteomics samples were prepared using Limited Proteolysis (LiP) methods for Label-free quantification (LFQ) and global proteomic evaluation. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and was processed and compiled using MaxQuant software (v.1.6.17.0). Processed proteomic data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files. See corresponding primary data accessions below and Viral Experiment LiP Analysis source code supporting data transparency and reuse. Experimental transcriptomics samples were collected in parallel and processed for RNA sequencing (RNA-Seq) as summarized under ACS-DP1 (https://data.pnnl.gov/group/nodes/dataset/34069).

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

A Pipeline for Assessing the Quality of Rna-Seq Datasets in GeneLab

Transcriptome profiling by RNA sequencing (RNA-seq) is a powerful approach to identify gene expression changes in organisms exposed to unique environments such as spaceflight. One of the challenges of evaluating RNA-seq data both within and across different space-relevant studies is the ability to control for technical differences, including the use of different library preparation kits, sequencing platforms, RNA yield, and person-to-person variation. To help address this issue, the National Institute of Standards and Technology (NIST, nist.gov) initiated a consortium, at the request of industry and academia, to develop a set of controls for gene expression measurements. The result was a set of 92 unlabeled, polyadenylated transcripts that range from 250 – 2,000 nucleotides in length to mimic natural eukaryotic mRNAs. These External RNA Controls Consortium (ERCC) genes can be used in any RNA-seq experiment, by adding known concentrations of the ERCC genes to samples after RNA extraction, to offer a standard measurement for data comparison. At NASA GeneLab, we employ these controls as part of our standard operating procedures for every in-house RNA-seq study to assess the limit of detection, dynamic range, and power of differential expression analysis both within and across experiments. Here we will discuss the use, benefits, and limitations of ERCC genes and other types of controls, such as universal RNA references, to generate quality control information for RNA-seq studies conducted at GeneLab.

GeneLab↗
DOE OSTI2026

EC-Bench: A Benchmark for Enzyme Commission Number Prediction

Enzymes are proteins that catalyze specific biochemical reactions in cells. Enzyme Commission (EC) numbers are used to annotate enzymes in a four-level hierarchy that classifies enzymes based on the specific chemical reactions they catalyze. Accurate EC number prediction is essential for understanding enzyme functions. Despite the availability of numerous methods for predicting EC numbers from protein sequences, there is no unified framework for evaluating and studying such methods systematically. This gap limits the ability of the community to identify the most effective approaches for enzyme annotation. We introduce EC-Bench, a benchmark for EC number prediction, consisting of 1) an initial representative set of existing methods (including homology-based, deep learning, contrastive learning, and language model methods), 2) existing and novel accuracy and efficiency performance metrics, and 3) selected datasets to allow for comprehensive comparative study. EC-Bench is open-source and provides a framework for researchers to not only compare among existing methods objectively under uniform conditions, but also to introduce and effectively evaluate performance of new methods in a comparative framework. To demonstrate the utility of EC-Bench, we perform extensive experimentation to compare the existing EC number prediction methods and establish their advantages and disadvantages in a variety of prediction tasks, namely “exact EC number prediction”, “EC number completion” and (partial or additional) “EC number recommendation”. We find wide variation in the performance of different methods, but also subtle but potentially useful differences in the performance of different methods across tasks and for different parts of the EC hierarchy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Linking groundwater variability to ecosystem carbon and water use efficiencies across India

Carbon use efficiency (CUE) and water use efficiency (WUE) are important indicators of ecosystem health, reflecting the balance between carbon uptake and allocation, and the relationship between carbon assimilation and water loss. Although India shows large spatiotemporal variation in water table depth (WTD), and increasing groundwater stress, the influence of WTD on ecosystem functioning remains underexplored. This study uses satellite-based, modeled, and in-situ datasets to (1) quantify variations in CUE and WUE under shallow (SWTD) and deep (DWTD) WTD conditions across six homogeneous meteorological regions (HMRs), (2) evaluate temporal roles of gross primary productivity (GPP), net primary productivity (NPP), and evapotranspiration (ET) in driving these efficiencies, and (3) examine temporal responses to WTD shifts. SWTD regions generally showed 12 to 18 % higher GPP, 10 to 15 % higher NPP, and 10 to 20 % higher ET than DWTD zones, especially in semi-arid croplands and forests, leading to 8 to 12 % higher CUE and WUE. However, in humid and heavily irrigated regions such as northeastern and hilly India, CUE was up to 10 % higher in DWTD zones, possibly due to reduced respiration and better soil aeration compared to SWTD areas affected by waterlogging. During the Kharif (wet) season, DWTD croplands in humid zones had higher efficiencies, while in the Rabi (dry) season, SWTD croplands in northern India benefited from irrigation and cooler temperatures. These results highlight strong influence of WTD on carbon and water use processes and support the need for region-specific groundwater strategies.

Carbon use efficiency↗
DOE OSTI2022

Aridity-Dependent Land Surface Skin Temperature Biases in CMIP5/6

Land surface skin temperature, a critical indicator of climate change, connects the water and energy cycles between the land and the atmosphere. Here, in this study, we evaluate the simulations of land surface skin temperature from the Coupled Model Intercomparison Project Phase 5 (CMIP5) and CMIP6 models with satellite-based datasets and reanalysis. We find systematic cold skin temperature biases over arid regions in CMIP5/CMIP6 simulations. Over arid and semi-arid regions, latent heat biases drive skin temperature biases by evaporative cooling. Over humid regions, surface downward shortwave and albedo biases are relatively more critical. Spatial patterns of biases remain similar in the latest CMIP6 simulations, suggesting systematic biases in land-atmosphere interactions. These biases need to be corrected or considered while using models for future projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Towards accurate prediction of configurational disorder properties in materials using graph neural networks

Abstract The prediction of configurational disorder properties, such as configurational entropy and order-disorder phase transition temperature, of compound materials relies on efficient and accurate evaluations of configurational energies. Previous cluster expansion methods are not applicable to configurationally-complex material systems, including those with atomic distortions and long-range orders. In this work, we propose to leverage the versatile expressive capabilities of graph neural networks (GNNs) for efficient evaluations of configurational energies and present a workflow combining attention-based GNNs and Monte Carlo simulations to calculate the disorder properties. Using the dataset of face-centered tetragonal gold copper without and with local atomic distortions as an example, we demonstrate that the proposed data-driven framework enables the prediction of phase transition temperatures close to experimental values. We also elucidate that the variance of the energy deviations among configurations controls the prediction accuracy of disorder properties and can be used as the target loss function when training and selecting the GNN models. The work serves as a fundamental step toward a data-driven paradigm for the accelerated design of configurationally-complex functional material systems.

Chemistry↗
DOE OSTI2023

A comparison of machine learning methods to classify radioactive elements using prompt-gamma-ray neutron activation data

The detection of illicit radiological materials is critical to establishing a robust second line of defence in nuclear security. Neutron-capture prompt-gamma activation analysis (PGAA) can be used to detect multiple radioactive materials across the entire Periodic Table. However, long detection times and a high rate of false positives pose a significant hindrance in the deployment of PGAA-based systems to identify the presence of illicit substances in nuclear forensics. In the present work, six different machine-learning algorithms were developed to classify radioactive elements based on the PGAA energy spectra. The model performance was evaluated using standard classification metrics and trend curves with an emphasis on comparing the effectiveness of algorithms that are best suited for classifying imbalanced datasets. We analyse the classification performance based on Precision, Recall, F1-score, Specificity, Confusion matrix, ROC-AUC curves, and Geometric Mean Score (GMS) measures. The tree-based algorithms (Decision Trees, Random Forest and AdaBoost) have consistently outperformed Support Vector Machine and K-Nearest Neighbours. Based on the results presented, AdaBoost is the preferred classifier to analyse data containing PGAA spectral information due to the high recall and minimal false negatives reported in the minority class.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Elucidating the photodissociation fingerprint and quantifying the determination of organic hydroperoxides in gas-phase autoxidation

Hydroperoxides are formed in the atmospheric oxidation of volatile organic compounds, in the combustion autoxidation of fuel, in the cold environment of the interstellar medium, and also in some catalytic reactions. They play crucial roles in the formation and aging of secondary organic aerosols and in fuel autoignition. However, the concentration of organic hydroperoxides is seldom measured, and typical estimates have large uncertainties. In this work, we developed a mild and environmental-friendly method for the synthesis of alkyl hydroperoxides (ROOH) with various structures, and we systematically measured the absolute photoionization cross-sections (PICSs) of the ROOHs using synchrotron vacuum ultraviolet-photoionization mass spectrometry (SVUV-PIMS). A chemical titration method was combined with an SVUV-PIMS measurement to obtain the PICS of 4-hydroperoxy-2-pentanone, a typical molecule for combustion and atmospheric autoxidation ketohydroperoxides (KHPs). We found that organic hydroperoxide cations are largely dissociated by loss of OOH. This fingerprint was used for the identification and accurate quantification of the organic peroxides, and it can therefore be used to improve models for autoxidation chemistry. The synthesis method and photoionization dataset for organic hydroperoxides are useful for studying the chemistry of hydroperoxides and the reaction kinetics of the hydroperoxy radicals and for developing and evaluating kinetic models for the atmospheric autoxidation and combustion autoxidation of the organic compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Seasonal representation of extreme precipitation indices over the United States in CMIP6 present-day simulations

Realistically representing the present-day characteristics of extreme precipitation has been a challenge for global climate models, which is due in part to deficiencies in model resolution and physics, but is also due to a lack of consistency in gridded observations. In this study, we use three observation datasets, including gridded rain gauge and satellite data, to assess historical simulations from sixteen Coupled Model Intercomparison Project Phase 6 (CMIP6) models. We separately evaluate summer and winter precipitation over the United States (US) with a comprehensive set of extreme precipitation indices, including an assessment of precipitation frequency, intensity and spatial structure. The observations exhibit significant differences in their estimates of area-average intensity distributions and spatial patterns of the mean and extremes of precipitation over the US. In general, the CMIP6 multi-model mean performs better than most individual models at capturing daily precipitation distributions and extreme precipitation indices, particularly in comparison to gauge-based data. Also, the representation of the extreme precipitation indices by the CMIP6 models is better in the summer than winter. Although the ‘standard’ horizontal-resolution can vary significantly across CMIP6 models, from ~0.7° to ~2.8°, we find that resolution is not a good indicator of model performance. Overall, our results highlight common biases in CMIP6 models and demonstrate that no single model is consistently the most reliable across all indices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Quantifying and Zoning Urban Heat Island Effects Using Unsupervised Machine Learning

This work explores the Urban Heat Island (UHI) effects in Maricopa County, Arizona, employing a simulation-based approach that combines large-scale building energy modeling with advanced spatial analysis. Utilizing the Automatic Building Energy Modeling (AutoBEM) software suite, we simulated the energy consumption for approximately 1.35 million buildings based on the Model America version 1.0 (MAv1) dataset. Our methodology incorporated spatial analysis at multiple scales, including individual buildings, clusters of zones determined by K-means clustering, and geographical level evaluation based on Zip codes. The results revealed significant variations in energy consumption and heat emissions across different building types and urban zones. High-emission hotspots identified through clustering pointed to areas most contributing to the UHI effects. Zip code-based area analysis further contextualized these findings, offering an urban context-based perspective on emission distribution and informing potential urban energy policies for mitigating UHI effects.

Chowdhury, Shovan [ORNL]↗
DOE OSTI2021

Retrospective Analysis and Bayesian Model Averaging of CMIP6 Precipitation in the Nile River Basin

The Nile River basin is one of the global hotspots vulnerable to climate change impacts because of a fast-growing population and geopolitical tensions. Previous studies demonstrated that general circulation models (GCMs) frequently show disagreement in the sign of change in annual precipitation projections. Here, we first evaluate the performance of 20 GCMs from phase six of the Coupled Model Intercomparison Project (CMIP6) benchmarked against a high-spatial-resolution precipitation dataset dating back to 1983 from Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Climate Data Record (PERSIANN-CDR). Next, a Bayesian model averaging (BMA) approach is adopted to derive probability distributions of precipitation projections in the Nile basin. Retrospective analysis reveals that most GCMs exhibit considerable (up to 64% of mean annual precipitation) and spatially heterogenous bias in simulating annual precipitation. Moreover, it is shown that all GCMs underestimate interannual variability; thus, the ensemble range is underdispersive and is a poor indicator of uncertainty. The projected changes from the BMA model show that the value and sign of change vary considerably across the Nile basin. Specifically, it is found that projected changes in the two headwaters basins, namely, the Blue Nile and Upper White Nile, are 0.03% and -1.65%, respectively; both are statistically insignificant at α = 0.05. The uncertainty range estimated from the BMA model shows that the probability of a precipitation decrease is much higher in the Upper White Nile basin whereas projected change in the Blue Nile is highly uncertain both in magnitude and sign of change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗
DOE OSTI2025

Seismic monitoring of underground vibration: database of seismic data and ground truth

Seismic waves provide valuable insights into underground activities, serving as an essential tool for monitoring anomalies that could signal containment breaches in geological repositories. We aim to test and refine underground detection and geolocation techniques to identify anomalous vibration signals indicative of potential breaches, thereby strengthening georepository safeguards. We evaluate the effectiveness of two distinct, low-maintenance sensing technologies (surface geophones and underground distributed acoustic sensing (DAS) fiber optic cable) leveraging existing datasets. This report details the experimental designs, instrumentation, and data characteristics for both seismic and DAS arrays. Additionally, we provide a ground truth database documenting relevant operational activities for each experiment.

58 GEOSCIENCES↗
DOE OSTI2025

Data for: Miscanthus × giganteus changes soil structure and increases maximum water holding capacity

The data provided include results from a comparative study evaluating the impact of Miscanthus × giganteus (miscanthus) versus maize on soil structural properties and maximum water holding capacity (MWHC) across two Iowa sites. The dataset includes MWHC values determined using the Funnel Filter Paper Drainage (FFPD) method, as well as additional measurements of MWHC following structural disruption of the soil to isolate the effect of aggregation. It also contains three-dimensional micro-computed tomography (microCT) data used to quantify total porosity and pore size distribution (PSD) of soil aggregates at a 5 µm resolution. All data are provided as raw replicate-level measurements, organized by site, crop, and depth, along with processed summary files in table form in CSV (.csv) format to support reproducibility and downstream analysis.

Misanthus x giganteus↗
DOE OSTI2025

Developing predictive models for µ opioid receptor binding using machine learning and deep learning techniques

Opioids exert their analgesic effect by binding to the µ opioid receptor (MOR), which initiates a downstream signaling pathway, eventually inhibiting pain transmission in the spinal cord. However, current opioids are addictive, often leading to overdose contributing to the opioid crisis in the United States. Therefore, understanding the structure-activity relationship between MOR and its ligands is essential for predicting MOR binding of chemicals, which could assist in the development of non-addictive or less-addictive opioid analgesics. This study aimed to develop machine learning and deep learning models for predicting MOR binding activity of chemicals. Chemicals with MOR binding activity data were first curated from public databases and the literature. Molecular descriptors of the curated chemicals were calculated using software Mold2. The chemicals were then split into training and external validation datasets. Random forest, k-nearest neighbors, support vector machine, multi-layer perceptron, and long short-term memory models were developed and evaluated using 5-fold cross-validations and external validations, resulting in Matthews correlation coefficients of 0.528–0.654 and 0.408, respectively. Furthermore, prediction confidence and applicability domain analyses highlighted their importance to the models’ applicability. Our results suggest that the developed models could be useful for identifying MOR binders, potentially aiding in the development of non-addictive or less-addictive drugs targeting MOR.

Research & Experimental Medicine↗
DOE OSTI2022

A Novel DNA Repair Gene Signature for Immune Checkpoint Inhibitor-Based Therapy in Gastric Cancer

Gastric cancer is a heterogeneous group of diseases with only a fraction of patients responding to immunotherapy. The relationships between tumor DNA damage response, patient immune system and immunotherapy have recently attracted attention. Accumulating evidence suggests that DNA repair landscape is a significant factor in driving response to immune checkpoint blockade (ICB) therapy. In this study, to explore new prognostic and predictive biomarkers for gastric cancer patients who are sensitive and responsive to immunotherapies, we developed a novel 15-DNA repair gene signature (DRGS) and its related scoring system and evaluated the efficiency of the DRGS in discriminating different molecular and immune characteristics and therapeutic outcomes of patients with gastric adenocarcinoma, using publicly available datasets. The results demonstrated that DRGS high score patients showed significantly better therapeutic outcomes for ICB compared to DRGS low score patients (p < 0.001). Integrated analysis of multi-omics data demonstrated that the patients with high DRGS score were characteristic of high levels of anti-tumor lymphocyte infiltration, tumor mutation burden (TMB) and PD-L1 expression, and these patients exhibited a longer overall survival, as compared to the low-score patients. Results obtained from HPA and IHC supported significant dysregulation of the genes in DRGS in gastric cancer tissues, and a positive correlation in protein expression between DRGS and PD-L1. Therefore, the DRGS scoring system may have implications in tailoring immunotherapy in gastric cancers. A preprint has previously been published (Yuan et al., 2021).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Transformation rate maps of dissolved organic carbon in the contiguous US

Riverine dissolved organic carbon (DOC) plays a vital role in regional and global carbon cycles. However, the processes of DOC conversion from soil organic carbon (SOC) and leaching into rivers are insufficiently understood, inconsistently represented, and poorly parameterized, particularly in land surface and Earth system models. As a first attempt to fill this gap, we propose a generic formula that directly connects SOC concentration with DOC concentration in headwater streams, where a single parameter, the transformation rate from SOC in the soil to DOC leaching flux (P r ), accounts for the overall processes governing SOC conversion to DOC and leaching from soils (along with runoff) into headwater streams. We then derive high-resolution P r maps over the contiguous US (CONUS) using SOC data from two different sources: the Harmonized World Soil Database v1.2 (HWSD) and SoilGrids 2.0. Both maps are developed following the same five major steps: (1) selecting independent catchments where observed riverine DOC data are available with reasonable quality; (2) estimating catchment-average SOC for the independent catchments; (3) estimating the P r values for these catchments based on the generic formula and catchment-average SOC; (4) developing a predictive model of P r with machine learning (ML) techniques and catchment-scale climate, hydrology, geology, and other attributes; and (5) deriving a national map of P r based on the ML model. For evaluation, we compare the DOC concentration derived using the P r map and the observed DOC concentration values at evaluation catchments. The resulting mean absolute scaled error and coefficient of determination are 0.73 and 0.47 for the HWSD-based model and 0.58 and 0.72 for the SoilGrids-based model, respectively, suggesting the effectiveness of the overall methodology. Efforts to constrain uncertainty and evaluate sensitivity of P r to different factors are discussed. To illustrate the use of such maps, we derive a riverine DOC concentration reanalysis dataset over CONUS. The two P r maps, robustly derived and empirically validated, lay a critical cornerstone for better simulating the terrestrial carbon cycle in land surface and Earth system models. Our findings not only set a foundation for improving our predictive understanding of the terrestrial carbon cycle at the regional and global scales, but also hold promises for informing policy decisions related to decarbonization and climate change mitigation. The data presented in this study are publicly available at https://doi.org/10.5281/zenodo.14563816 (Li et al., 2024).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Evaluating and Exploring Extreme Precipitation in CHIRPS3, CHIMES, and the Climate Hazards Station Database

Between 2015 and 2019, the impacts and losses associated with droughts, floods, and hurricanes surged through the interaction of increasing exposure and more extreme weather and climate (Funk 2021). In 2020, the Aon-Benfield Reinsurance Company reported that cyclones, floods, and droughts resulted in $165 billion (USD) in losses. For 2020, EM-DAT lists 363 flood, landslide, storm, and drought events impacting some 98 million people. As hazards mount, models indicate more variable precipitation, and observations indicate increasing extremes in humid regions, yet the small number of available gauge observations is declining. In this talk we briefly introduce two new resources: version 3 of the 1981-near present Climate Hazards center Infrared Precipitation with Stations (CHIRPS3) archive, and the 2000-near present Climate Hazards IMErg with Stations archive (CHIMES). The satellite-only CHIRP3 and CHIME components are based, respectively, on geostationary thermal infrared Cold Cloud Duration (CCD) values and the NASA GPM IMERGlate product. These archives benefit from thousands of station observations. In addition to standard global sources, the Climate Hazards station database includes about 5,000 additional stations in humid tropical and sub-tropical areas associated with likely increases in extreme rainfall. While effectively monitoring extreme precipitation is important to humanitarian agencies like FEWS NET, and to hydrologic modeling applications (a, b), evaluations of the widely used CHIRPS2 product indicate a propensity to underestimate extremes. Here, we explain the source of this problem. Then, focusing on pentad totals in 12 well-gauged regions, we use the high-quality gauge-based REGEN dataset to show that CHIRP3 and CHIME perform substantially better than CHIRP2. We examine trends in extremes in these validation regions, comparing REGEN results with values from the satellite-only CHIRP2, CHIRP3, CHIME and the gauge-enhanced CHIRP2, CHIRP3, CHIME. Trends in dry and humid regions are contrasted and compared. We conclude with global evaluations of the pentad CHIRP3, CHIRPS3, CHIME, CHIMES, and Climate Hazards station database products. How does the performance of the shorter period of record CHIME compare with CHIRP3? We anticipate that the sophisticated microwave-based IMERGlate inputs into CHIME will perform better. Where do we see the largest increases in extremes in these products? How well might CHIRPS3 and CHIMES perform in the context of humanitarian assistance efforts?

C Funk↗