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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 271 records · Page 15
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DOE OSTI2021

A New Era of Nuclear Criticality Experiments: The First 10 Years of Godiva IV Operations at NCERC

The work presented in this paper focuses on the first 10 years (2011–2020) of Godiva IV operations at the National Criticality Experiments Research Center (NCERC). Godiva IV is a fast burst critical assembly constructed of approximately 65 kg of highly enriched uranium fuel alloyed with 1.5% molybdenum for strength. Godiva is one of the last such critical assemblies in the United States and can be used for studies of super-prompt-critical behavior as well as irradiations and demonstrations. An overview of the startup of Godiva IV at NCERC is given followed by a summary of the experiments performed utilizing Godiva IV over the first 10 years of operation at NCERC.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

A New Era of Nuclear Criticality Experiments: The First 10 Years of Flattop Operations at NCERC

The Flattop critical assembly was built and operated from 1958 through 2004 at the Pajarito Site (Technical Area-18), home to the Los Alamos Critical Experiments Facility. Flattop was disassembled in 2005 and refurbished over the course of 3 years. In 2008, Flattop was installed in the National Criticality Experiments Research Center (NCERC) located in the Device Assembly Facility at the Nevada National Security Site. Startup of Flattop with a uranium core occurred in 2011. This paper details the first 10 years of Flattop operations at NCERC (2011–present).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

A New Era of Nuclear Criticality Experiments: The First 10 Years of Comet Operations at NCERC

Comet is a general-purpose, heavy-duty, vertical-lift assembly designed for flexibility in conducting a variety of critical experiments. It is currently located at the National Criticality Experiments Research Center (NCERC) in Nevada. In the past, Comet resided at Technical Area-18 in Los Alamos, New Mexico, as part of the Los Alamos Critical Experiments Facility (LACEF). The Comet assembly was relocated to NCERC in 2008 and became fully operational in June of 2011. The first critical experiment performed on Comet at NCERC was a verification of one of the previous configurations of the Zeus experiment series. Over the next 10 years, many additional experiments followed including other Zeus configurations as well as completely new designs. This paper discusses the Comet vertical-lift assembly, the transition from LACEF to NCERC, and a selection of experiments that have been performed on Comet during its first 10 years of operation at NCERC.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

A New Era of Nuclear Criticality Experiments: The First 10 Years of Planet Operations at NCERC

Planet is a vertical-lift assembly machine currently located at the National Criticality Experiments Research Center (NCERC) at the Nevada National Security Site. In the past, Planet resided at Technical Area-18 in Los Alamos, New Mexico, as part of the Los Alamos Critical Experiments Facility (LACEF). Following the de-inventorying of LACEF, the Planet assembly was relocated to NCERC in 2008 and became fully operational in June of 2011. The Class Foils experiment, which involves stacking highly enriched uranium foils to obtain a critical configuration, was the first critical experiment performed on Planet. As a major component of the Nuclear Criticality Safety Class taught for the U.S. Department of Energy (DOE) Nuclear Criticality Safety Program, the Class Foils experiment allows personnel from all over the DOE complex to handle nuclear material and to complete the approach to critical safely and successfully. This paper describes the Planet vertical assembly and recent engineering upgrade and a selection of the experiments that have been performed on Planet since its transition to NCERC 10 years ago.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Evaluation of Digital Nautical Chart data for confirmation and expansion of GeoNames data

Here, this work examines how Digital Nautical Chart (DNC) data may contribute to the evolution and refinement of GeoNames data for near-shore features. GeoNames features are point data with one or more possible place names. DNC Earth Cover Text (ECRText) objects are map labels positioned nearby their real word counterpart. ECRText feature map position strikes a compromise between association with real features and cartographic readability. This work explores whether ECRText features can confirm (or expand names for) existing locations or contribute new locations through data conflation. Due to name variations and spatial position, conflating these data are nontrivial. Previous work engaged in a brief examination using the trigram string matching algorithm under coarse proximity constraints, indicating that ECRText could provide additional value to GeoNames. This work builds on that study, by engaging in a deeper examination of spatial proximity and exploring conflation agreement across an ensemble of string matching approaches. The result finds strong ensemble agreement about ECRText features which already exist in GeoNames but mixed results about which features contribute new information, as well as exploring why some of these matching techniques fail. With an eye toward automation, computational efficiency was found not to be a constraint in sustaining updates.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Determinants of residential mobility: an adaptive retrospective survey method

This study introduces a survey instrument to collect retrospective life-course events, focusing on residential relocation, and it utilizes the survey to evaluate determinants of residential mobility. Here, the survey consists of seven modules collecting information about household structure and household demographics, latest residential relocation, current and previous home, employment, education, vehicle ownership, and travel behavior. The time window of the life-course calendar in the survey is customized according to the latest residential relocation as an anchor point to assist with memory recollection and balance the required input from participants. The survey is used to collect data from a sample of 514 respondents in Sydney, Australia, and another sample of 404 respondents in Chicago, Illinois, in the US. The Cox proportional hazard model is used to analyze residential mobility. The results show primary school commencement is a salient determinant of residential relocation, but its impact is significantly higher in Chicago compared to Sydney.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

El valor de los metadatos para las estaciones de recuperación de recursos del agua

Spanish: Los metadatos hacen referencia a información descriptiva (como ubicación del sensor, unidad de medida, rango de medida, fecha de calibración, fecha de limpieza, si ocurrió algún evento como episodio de lluvia/fallo operativo/vertido tóxico . . .) que es esencial para convertir los grandes volúmenes de datos que se recogen actualmente en las instalaciones de tratamiento de agua y que están sin procesar en información y recursos útiles. Con el avance de la digitalización en el sector del agua, es fundamental evitar los cementerios de datos y, por otro lado, utilizar los datos almacenados para resolver problemas actuales y futuros. Este artículo se centra en el papel crucial que tienen los metadatos para responder a desafíos futuros y posiblemente impredecibles. El objetivo de este documento es presentar el ‘reto de los metadatos’ y destacar la necesidad de tener en cuenta los metadatos cuando se recoge información como parte de las buenas prácticas de digitalización. English: Metadata refers to descriptive information (such as sensor location, measurement unit, measurement range, calibration date, cleaning date, if any event occurred such as rain event/operating failure/toxic spill, . . .) essential to convert large volumes of raw data that are currently collected at water treatment facilities into useful information and resources. With the advance of digitalization in the water sector, it is fundamental to avoid data graveyards and, on the other hand, using collected data to address current and future problems. This paper focuses on the crucial role that metadata has in responding to future and possibly unpredictable challenges. The aim of this document is to present the ‘metadata challenge’ and to highlight the need to consider metadata when collecting information as part of good digitalization practices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Where Is the Provenance? Ethical Replicability and Reproducibility in GIScience and Its Critical Applications

As replicability and reproducibility (R&R) crises develop within emerging convergent inquiry, ethical use of provenance information is central to the establishment and preservation of trust in critical applications of GIScience and geospatial technologies. Today large volumes of geospatial data are generated at high velocity from satellite sensors and unmanned aircraft systems, citizen sensors, geolocation-based data services, global navigation satellite systems, and so on. The extensive use of these data for applications such as disaster and humanitarian response raises the issue of R&R from competing perspectives of location privacy and geospatial data quality. Although geospatial data can be integrated and linked with contextual information to identify individuals’ movements, steps taken to ensure privacy can complicate the multiuser development of high-quality geospatial workflows. Provenance information as digital records of historical (retrospective) and potential future (prospective) geospatial processes is often overlooked, misunderstood, or inadequately addressed. We explore the relationship between provenance information, location privacy, and geospatial data quality in the context of R&R with a focus on disaster analytics. Here, we argue that in the era of big data and deep learning, GIScientists and associated institutions bear greater responsibility both for geospatial workflow quality and for location privacy. Given vastly heterogenous computational landscapes, we provide practical recommendations for ethically driven provenance and R&R research and development within the GIScience community and beyond.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Editorial announcements and information — ICFA Beam Dynamics Newsletter No. 85

This is a general information article of the ICFA Beam Dynamics Newsletter No. 85. It contains foreword from the Editor-in-Chief and the issue editor, a workshop and conference report section, a recent Ph.D. thesis section, a forthcoming beam dynamics events section, and a section of announcements from the beam dynamics panel.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

TranSyT , an innovative framework for identifying transport systems

The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE’s release, software development for the automatic integration of transport reactions into models has stalled. Here, in this paper, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here, we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable, federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data Findable, Accessible, Interoperable, and Reusable (FAIR).

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
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 OSTI2023

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗