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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗
DOE OSTI2025

Leveraging unlabeled SEM datasets with self-supervised learning for enhanced particle segmentation

Scanning Electron Microscopes (SEMs) are widely used in experimental science laboratories, often requiring cumbersome and repetitive user analysis. Automating SEM image analysis processes is highly desirable to address this challenge. In particle sample analysis, Machine Learning (ML) has emerged as the most effective approach for particle segmentation. However, the time-intensive process of manually annotating thousands of SEM images limits the applicability of supervised learning approaches. Self-Supervised Learning (SSL) offers a promising alternative by enabling knowledge extraction from raw, unlabeled data. This study presents a framework for evaluating SSL techniques in SEM image analysis, focusing on novel methods leveraging the ConvNeXtV2 architecture for particle detection. A dataset comprising 25,000 SEM images is curated to benchmark these proposed SSL methods. The results demonstrate that ConvNeXtV2 models, with varying parameter counts, consistently outperform other techniques in particle detection across different length scales, achieving up to a 34% reduction in relative error compared to established SSL methods. Furthermore, an ablation study explores the relationship between dataset size and SSL performance, providing actionable insights for practitioners regarding model selection and resource efficiency. This research advances the integration of SSL into autonomous analysis pipelines and supports its application in accelerating materials science discovery.

Rettenberger, Luca↗
NASA NTRSDate not supplied

Enabling Cloud Services and Enhanced Data Discovery With Earthdata-Varinfo

NASA’s Earth Observing System Data and Information System (EOSDIS) contains thousands of Earth science datasets from satellites, models, and field campaigns. Each of these collections can contain hundreds of variables that describe each measurement within the dataset, therefore an automated method for generating UMM-Var records is necessary. The Unified Metadata Model for Variables (UMM-Var) provides a framework for variable metadata records in NASA’s Common Metadata Repository (CMR). The Python tool, earthdata-varinfo, was developed to solve this problem of automating the curation of UMM-Var records. Given either a collection DMR file or a netCDF-4 file, earthdata-varinfo can scrape variable metadata and return a CMR compliant UMM-Var record. Earthdata-varinfo can generate thousands of UMM-Var records in a matter of seconds, thus enabling subsetting capabilities and enhancing data discovery.

Eni Awowale↗
NASA NTRS2002

The Genesis Mission: Contamination Control and Curation

The Genesis mission, launched in August 2001, is collecting samples of the solar wind and will return to Earth in 2004. Genesis can be viewed as the most fundamental of NASA's sample return missions because it is expected to provide insight into the initial elemental and isotopic composition of the solar nebula from which all other planetary objects formed. The data from this mission will have a large impact on understanding the origins and diversity of planetary materials. The collectors consist of clean, pure materials into which the solar wind will imbed. Science and engineering issues such as bulk purity, cleanliness, retention of solar wind, and ability to withstand launch and entry drove material choices. Most of the collector materials are installed on array frames that are deployed from a clean science canister. Two of the arrays are continuously exposed for collecting the bulk solar wind; the other three are only exposed during specific solar wind regimes as measured by ion and electron monitors. Other materials are housed as targets at the focal point of an electrostatic mirror, or "concentrator", designed to enhance the flux of specific solar wind species. Johnson Space Center (JSC) has two principal responsibilities for the Genesis mission: contamination control and curation. Precise and accurate measurements of the composition of the solar atoms require that the collector materials be extremely clean and well characterized before launch and during the mission. Early involvement of JSC curation personnel in concept development resulted in a mission designed to minimize contaminants from the spacecraft and operations. A major goal of the Genesis mission is to provide a reservoir of materials for the 21 51 century. When the collector materials are returned to Earth, they must be handled in a clean manner and their condition well documented. Information gained in preliminary examination of the arrays and detailed surveys of each collector will be used to guide sample allocations to the scientific community. Samples allocated for analysis are likely to be small sections of individual collectors, therefore subdividing the materials must take place in a clean, well characterized way. A major focus of current research at JSC includes identifying and characterizing the contamination, waste, and alteration of the sample when using different subdividing, transport, and storage techniques and developing protocols for reducing their impact on the scientific integrity of the mission.

Stansbery, E. K.↗
DOE OSTI2022

A Neural Network Approach to Predict Gibbs Free Energy of Ternary Solid Solutions

Here, we present a data-centric deep learning (DL) approach using neural networks (NNs) to predict the thermodynamics of ternary solid solutions. We explore how NNs can be trained with a dataset of Gibbs free energies computed from a CALPHAD database to predict ternary systems as a function of composition and temperature. We have chosen the energetics of the FCC solid solution phase in 226 binaries consisting of 23 elements at 11 different temperatures to demonstrate the feasibility. The number of binary data points included in the present study is 102,000. We select six ternaries to augment the binary dataset to investigate their influence on the NN prediction accuracy. We examine the sensitivity of data sampling on the prediction accuracy of NNs over selected ternary systems. It is anticipated that the current DL workflow can be further elevated by integrating advanced descriptors beyond the elemental composition and more curated training datasets to improve prediction accuracy and applicability.

42 ENGINEERING↗
DOE OSTI2025

RefAHL: a curated quorum sensing reference linking diverse LuxI-type signal synthases with their acyl-homoserine lactone products

Some bacteria use acyl-homoserine lactone (AHL) signals in quorum sensing, a type of cell-cell communication. Here, we present “RefAHL,” an updated, curated collection of LuxI-type AHL synthases with their AHL products and associated metadata. RefAHL is publicly available as a community resource to help catalog LuxI-type diversity encoded in (meta) genomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling and simulation to investigate the electrification potential of medium- and heavy-duty vehicle fleets

This project involves developing and integrating new modeling tools to simulate the dynamics of electric medium- and heavy-duty fleet vehicle adoption. A technical and economic modeling tool, combining a data-driven hardware cost model with a cost-optimal charging strategy microsimulation, enables tailored analysis of the costs and benefits of electrifying individual fleets. Next, a novel text synthesis process, applied to a curated corpus of literature, quantifies trade-offs between technical, economic, and other factors in the fleet vehicle procurement decision. The outcomes of these tasks combine with knowledge from recent literature on fleet decision processes to specify the vehicle procurement model used by fleets in an agent-based model of the medium- and heavy-duty electric vehicle market. This model embodies an especially disaggregated approach to adoption modeling, internalizing factors and dynamics that conventional adoption models externalize. In particular, explicitly modeling the formation and diffusion of opinions among agents enables experiments that conventional models cannot support. Demonstrations show, for example, that increasing the extent of interactions between populations with different proclivities to electric vehicles has an asymmetrical outcome. High-proclivity electric vehicle adoption is generally unaffected as interactions increase, but low-proclivity adoption is accelerated. By representing individual fleets' requirements and costs at a high level of detail, incorporating an adoption decision model informed by a wide body of empirical research, and broadening the array of variables and dynamics available for experimentation, this integrated model offers a new way to understand the urgent challenge of eliminating emissions from the most emissions-intensive transportation sectors.

Trinko, David A.↗
DOE OSTI2020

Machine Learning for Automated Extraction of Building Geometry

As data science comes to buildings, the promise of using machine learning and novel sources of data has received much attention. Advances in machine learning and computer vision algorithms, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics – cost-effectively, and at scale. Acquisition of features such as footprint are time consuming and costly to acquire with today’s manual methods, but can be streamlined through intelligent software-based solutions applied to satellite images. When combined with aerial RGB and thermal images, full 3D geometries and thermal maps can be constructed to determine additional characteristics such as window to wall ratio, height, number of stories and envelope thermal characteristics. In this paper we present three contributions to accelerate these high potential opportunities: (1) a methodical analysis of how these features can be integrated into today’s simulation and data driven software tools to enhance efficiency measure identification and owner/operator decision making; (2) development and accuracy testing of open source deep neural network methods to extract building footprints from satellite imagery, including the curation and application of openly available GIS datasets for training and continued development by others; and (3) an open framework for drone-based image capture and creation of 3D building geometries. This work represents an important bridge between high-level studies that span diverse application areas and those that detail point solutions yet cannot be easily replicated or extended.

Touzani, Samir↗
NASA NTRS2018

The Opera Instrument: An Advanced Curation Development for Mars Sample Return Organic Contamination Monitoring

Mars Sample Return (MSR) requires strict organic contamination control (CC) and contamination knowledge (CK) as outlined by the Mars 2020 Organic Contamination Panel (OCP). This includes a need to monitor surficial organic contamination to a ng/sq. cm sensitivity level. Archiving and maintaining this degree of surface cleanliness may be difficult but has been achieved. MSR's CK effort will be very important because all returned samples will be studied thoroughly and in minute detail. Consequently, accurate CK must be collected and characterized to best interpret scientific results from the returned samples. The CK data are not only required to make accurate measurements and interpretations for carbon-depleted martian samples, but also to strengthen the validity of science investigations performed on the samples. The Opera instrument prototype is intended to fulfill a CC/CK role in the assembly, cleaning, and overall contamination history of hardware used in the MSR effort, from initial hardware assembly through post-flight sample curation. Opera is intended to monitor particulate and organic contamination using quartz crystal microbalances (QCMs), in a self-contained portable package that is cleanroom-compliant. The Opera prototype is in initial development capable of approximately 100 ng/sq. cm organic contamination sensitivity, with additional development planned to achieve 1 ng/sq. cm. The Opera prototype was funded by the 2017 NASA Johnson Space Center Innovation Charge Account (ICA), which provides funding for small, short-term projects.

Fries, M. D.↗
DOE OSTI2024

Physics-coupled data-driven design of high-temperature alloys

We present a materials design loop, which streamlines physics-coupled machine learning (ML) surrogate models to discover new alloy chemistries with improved properties. The efficacy is demonstrated by discovering a high-temperature alumina-forming austenitic (AFA) stainless steel with enhanced creep, followed by experimental validation. The ML models have been trained using a well-curated, highly consistent experimental dataset augmented with synthetic microstructural features from a computational thermodynamic approach. We have populated a large number of hypothetical AFA alloys to explore the high-dimensional composition space and have predicted their creep properties by providing the same synthetic input features obtained from the trained ML models. Uncertainties from the ML training were taken as thresholds for truncating predicted results to identify alloys with improved or deteriorated creep. Individual elemental compositions have been determined via probability density distribution analysis from the group of alloys at the top and bottom of the predicted creep values for further virtual and experimental validations. In conclusion, we anticipate that this workflow can be applied to screen desired conditions, such as chemistry and processing parameters, in high-dimensional space through physics-guided data analytics.

Alloy design↗
DOE OSTI2022

ODI notebook additive_manufacturing_video_2022

Additive Manufacturing, video dataset Two-photon lithography (TPL) is a widely used 3D nanoprinting technique that uses laser light to create objects. Challenges to large-scale adoption of this additive manufacturing method include identifying light dosage parameters and monitoring during fabrication. A research team from LLNL, Iowa State University, and Georgia Tech is applying machine learning models to tackle these challenges-i.e., accelerate the process of identifying optimal light dosage parameters and automate the detection of part quality. Funded by LLNL's Laboratory Directed Research and Development Program, the project team has curated a video dataset of TPL processes for parameters such as light dosages, photo-curable resins, and structures. Both raw and labeled versions of the datasets are available on the links in the Open Data Initiative page. The code uses the labeled dataset. Notebook compiled by Nisha Mulakken (mulakken1@llnl.gov) for LLNL Open Data Initiative, Summer 2022. Original code provided by research team. Publications: X.Y. Lee, S.K. Saha, S. Sarkar, B. Giera. "Automated detection of part quality during two-photon lithography via deep learning." Additive Manufacturing 36, December 2020: doi.org/10.1016/j.addma.2020.101444 X.Y. Lee, S.K. Saha, S. Sarkar, B. Giera. "wo Photon lithography additive manufacturing: Video dataset of parameter sweep of light dosages, photo-curable resins, and structures." Data in Brief 32, October 2020. doi.org/10.1016/j.dib.2020.106119.

Mulakken, NishaJ↗
DOE OSTI2023

Deep Green Unannotated Protein Structures

The Deep Green list is based on the identification and curation of conserved unannotated proteins in three green lineage (Viridiplantae) model organisms; Arabidopsis thaliana, Chlamydomonas reinhardtii, and Setaria viridis. Preliminary characterization of Deep Green proteins and genes was done using various informatics tools and published data sets and is presented in Knoshaug, Sun, et al., 2023, submitted. The structures of these unannotated proteins were also predicted using AlphaFold (Jumper et al., 2021). The data deposited here are the AlphaFold structural predictions having the highest pLDDT score and thus identified as the best folded structure (ranked_0). These data enable others to do in-depth structural characterizations to aid in functional characterization leading to deeper understanding of plant biology. References: Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. and Hassabis, D. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596:583-589. Knoshaug, E. P., Sun, P., Nag, A., Nguyen, H., Mattoon, E. M., Zhang, N., Liu, J., Chen, C., Cheng, J., Zhang, R., St. John, P., and Umen, J. (submitted) Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis.

09 BIOMASS FUELS↗
NASA NTRS2017

The NASA Ames Life Sciences Data Archive: Biobanking for the Final Frontier

The NASA Ames Institutional Scientific Collection involves the Ames Life Sciences Data Archive (ALSDA) and a biospecimen repository, which are responsible for archiving information and non-human biospecimens collected from spaceflight and matching ground control experiments. The ALSDA also manages a biospecimen sharing program, performs curation and long-term storage operations, and facilitates distribution of biospecimens for research purposes via a public website (https:lsda.jsc.nasa.gov). As part of our best practices, a tissue viability testing plan has been developed for the repository, which will assess the quality of samples subjected to long-term storage. We expect that the test results will confirm usability of the samples, enable broader science community interest, and verify operational efficiency of the archives. This work will also support NASA open science initiatives and guides development of NASA directives and policy for curation of biological collections.

Biobank↗
DOE OSTI2021

HangulFonts v1.0.0

The software creates the Hangul Fonts data set.The Hangul Fonts Datasets consists of all possible blocks for each font along with a set of labels and features for each block which are common across all fonts. We provide scripts to render each block and font into an image and store them together in an HDF5 file for each font and fontsize specified. Each font has 11,172 possible blocks and we have curated 35 fonts for a total of 391,020 possible images. The spoken consonants and vowel correspond to a set of "initial", "medial", and "final" labels for each block with 19, 21, and 28 classes respectively. In addition, each block can also be assigned a hierarchy label based on the block geometry. Finally, the individual glyphs (atoms) are composed across the initial, medial, and final locations along with potential scalings, translations, or rotations. These features of the data set make it uniquely positioned in the deep representation learning field because of its compositionally and hierarchical organization, while retaining diverse types of variation in the realizations.

Bouchard, Kristofer↗
DOE OSTI2021

Co-expression networks in Chlamydomonas reveal significant rhythmicity in batch cultures and empower gene function discovery

The unicellular green alga Chlamydomonas reinhardtii is a choice reference system for the study of photosynthesis and chloroplast metabolism, cilium assembly and function, lipid and starch metabolism, and metal homeostasis. Despite decades of research, the functions of thousands of genes remain largely unknown, and new approaches are needed to categorically assign genes to cellular pathways. Growing collections of transcriptome and proteome data now allow a systematic approach based on integrative co-expression analysis. We used a dataset comprising 518 deep transcriptome samples derived from 58 independent experiments to identify potential co-expression relationships between genes. We visualized co-expression potential with the R package corrplot, to easily assess co-expression and anti-correlation between genes. We extracted several hundred high-confidence genes at the intersection of multiple curated lists involved in cilia, cell division, and photosynthesis, illustrating the power of our method. Surprisingly, Chlamydomonas experiments retained a significant rhythmic component across the transcriptome, suggesting an underappreciated variable during sample collection, even in samples collected in constant light. Our results therefore document substantial residual synchronization in batch cultures, contrary to assumptions of asynchrony. We provide step-by-step protocols for the analysis of co-expression across transcriptome data sets from Chlamydomonas and other species to help foster gene function discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial DNA Database and Demonstration

2024 Annual Review meeting talk, "Microbial DNA Database and Demonstration." Description of the NETL's PW DNA Database that will be 1) curated to make it more useable, 20 include metadata linked to each sequencing set, such as qPCR and geochemistry, and 30 allow better filtering and visualization. The database is hosted on KBase so terabytes worth of data can be used directly on the program without having to download it to personal computers.

Schweitzer, Hannah↗
DOE OSTI2022

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

IDB Loader

SAND2024-08428O The IDB Loader is a database designed to hold gamma spectra. IDB is a web-accessible database of reference gamma spectra for measuring uranium (U) and plutonium (Pu) isotopic composition. The database, developed by the International Atomic Energy Agency (IAEA), provides access to well-characterized groups of gamma spectra curated by international experts in gamma spectroscopy. It was created to promote sustainability and maintenance of software used to determine the isotopic abundances of U and Pu. The IDB Loader works by uploading one set of spectral data into an existing IDB. The Data Loader package includes documentation describing the IDB's table, the format of the spectral data, and a description of the loader program. The IDB is currently hosted by the IAEA at: https://nds.iaea.org/idb Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Schwartz, Steven↗