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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Centralized Interactive Phenomics Resource: an integrated online phenomics knowledgebase for health data users

Development of clinical phenotypes from electronic health records (EHRs) can be resource intensive. Several phenotype libraries have been created to facilitate reuse of definitions. However, these platforms vary in target audience and utility. Here, we describe the development of the Centralized Interactive Phenomics Resource (CIPHER) knowledgebase, a comprehensive public-facing phenotype library, which aims to facilitate clinical and health services research. The platform was designed to collect and catalog EHR-based computable phenotype algorithms from any healthcare system, scale metadata management, facilitate phenotype discovery, and allow for integration of tools and user workflows. Phenomics experts were engaged in the development and testing of the site. The knowledgebase stores phenotype metadata using the CIPHER standard, and definitions are accessible through complex searching. Phenotypes are contributed to the knowledgebase via webform, allowing metadata validation. Data visualization tools linking to the knowledgebase enhance user interaction with content and accelerate phenotype development. The CIPHER knowledgebase was developed in the largest healthcare system in the United States and piloted with external partners. The design of the CIPHER website supports a variety of front-end tools and features to facilitate phenotype development and reuse. Health data users are encouraged to contribute their algorithms to the knowledgebase for wider dissemination to the research community, and to use the platform as a springboard for phenotyping. CIPHER is a public resource for all health data users available at https://phenomics.va.ornl.gov/ which facilitates phenotype reuse, development, and dissemination of phenotyping knowledge.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Agricultural Management Affects the Active Rhizosphere Bacterial Community Composition and Nitrification

Cropping system diversity provides yield benefits that may result from shifts in the composition of root-associated bacterial and fungal communities, which either enhance nutrient availability or limit nutrient loss. We investigated whether temporal diversity of annual cropping systems (four versus two crops in rotation) influences the composition and metabolic activities of root-associated microbial communities in maize at a developmental stage when the peak rate of nitrogen uptake occurs. We monitored total (DNA-based) and potentially active (RNA-based) bacterial communities and total (DNA-based) fungal communities in the soil, rhizosphere, and endosphere. Cropping system diversity strongly influenced the composition of the soil microbial communities, which influenced the recruitment of the resident microbial communities and, in particular, the potentially active rhizosphere and endosphere bacterial communities. The diversified cropping system rhizosphere recruited a more diverse bacterial community (species richness), even though there was little difference in soil species richness between the two cropping systems. In contrast, fungal species richness was greater in the conventional rhizosphere, which was enriched in fungal pathogens; the diversified rhizosphere, however, was enriched in Glomeromycetes. While cropping system influenced endosphere community composition, greater correspondence between DNA- and RNA-based profiles suggests a higher representation of active bacterial populations. Cropping system diversity influenced the composition of ammonia oxidizers, which coincided with diminished potential nitrification activity and gross nitrate production rates, particularly in the rhizosphere. The results of our study suggest that diversified cropping systems shift the composition of the rhizosphere’s active bacterial and total fungal communities, resulting in tighter coupling between plants and microbial processes that influence nitrogen acquisition and retention.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Towards FAIR Workflows for Federated Experimental Sciences

A de-centralized, peer-to-peer AI metadata framework is demonstrated which can enable end-to-end metadata & lineage tracking for distributed Machine Learning pipelines spanning edge, High Performance Computing, and cloud environments. With a specific example of end-to-end microscopy algorithm and datasets, the proposed method shows how to enable reproducibility, audit trail, provenance of metadata artifacts. The emerging needs of automation in experimental sciences, ML-centric workflows, and FAIR metadata management across federated compute environments is addressed.

machine learning↗
DOE OSTI2022

Historic Context, Character-Defining Elements, And Photographic Record For A 26.45-Mile Segment Of The 138-Kilovolt Power Transmission System, Areas 3, 5, 6, And 23, Nevada National Security Site, Nye County, Nevada

The subject of this report is the 138-kilovolt (kV) power transmission line on the Nevada National Security Site (NNSS) (see Figure 1). The NNSS, formerly the Nevada Test Site (NTS), was the main continental nuclear test site for the United States between 1951 and 1992. Known as the battleground of the Cold War, the NNSS hosted a total of 928 nuclear tests during that period. It also served as the location of numerous scientific advancements in the fields of rocketry, big-hole drilling, nuclear waste management, and defense. From its construction in the 1960s through the present day, the 138 kV line has provided electrical power to the numerous buildings, facilities, experiments, and tests on the NNSS. The Department of Energy (DOE), in consultation with the Nevada State Historic Preservation Officer (SHPO), has determined that it may contribute to the character and significance of the Mercury Historic District (MHD) on the NNSS, as well as other historic districts that have not been recorded or evaluated yet. The purpose of this report is to fulfill two of the stipulations in the Memorandum of Agreement DEGM58-22NA25553 between the U.S. Department of Energy and the Nevada State Historic Preservation Officer Regarding Installation of a 138-kilovolt Transmission Line from the Mercury Switching Station to the U1a Facility and the Removal of the Historic 138-kilovolt Transmission Line from the Mercury Switching Station to the U1a Facility in Areas 1, 3, 5, 6, and 23 of the Nevada National Security Site (MOA). The MOA was executed as part of the DOE’s obligations under Section 106 of the National Historic Preservation Act (NHPA) to mitigate the adverse effects of two undertakings on historic properties. In particular, this report fulfills MOA Stipulations III.C.1-3, which state that the Department of Energy (DOE) will prepare the following: A historic context for the 138 kV transmission line and identification of the line’s characterdefining elements; High-quality digital images of the 26.45-mile segment of the 138 kV transmission line that is subject to the two undertakings for which the MOA was executed; and Photograph catalogs and map keys showing photograph viewpoints and directions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Report series: Evaluation, Finding of Effect, and Mitigation Documentation for the 1960s Dormitories and 1950s Quonset Hut Foundations, Mercury, Area 23, Nevada National Security Site, Nye County, Nevada [3 Reports Consolidated]

The U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO) plans to modernize the town of Mercury at the Nevada National Security Site (NNSS) in Nye County, Nevada, to meet current and future National Weapons Science, Global and Homeland Security Programs, and Environmental Management mission requirements. These plans—including anticipated demolitions, consolidations, and rebuilding at Mercury—are considered an undertaking subject to review under Title 54 U.S.C. § 306108, commonly known as Section 106 of the National Historic Preservation Act, Title 54 U.S.C. § 300101, et seq., and its implementing regulations, 36 C.F.R. Part 800. Desert Research Institute (DRI) completed an architectural survey of Mercury in 2017. This effort resulted in the identification, recording, and evaluation of the Mercury Historic District, as well as the identification of its contributing components. This district was recommended eligible to the National Register of Historic Places (NRHP or National Register) under Criteria A and C, but was unevaluated under Criteria B and D at that time. The Mercury Historic District contains 153 individual landscapes, buildings, and structures. Of these resources, DRI recommends all except one as contributing elements of the historic district during its period of significance corresponding to nuclear testing from 1951 through 1992. During most of the Cold War, the land now called the NNSS was referred to as the Nevada Test Site (NTS). This report evaluates resources dating to the 1950s and 1960s between Jangle and Knothole Streets and south of Ranger Avenue in Mercury prior to the proposed demolition of all resources in that area between Sandstone and Greenhouse Avenues as a phase of the larger modernization program mentioned above. Although the Mercury Historic District as a whole is eligible to the National Register, further evaluation of these properties, as detailed in this report, indicates that none are individually eligible under any of the Secretary of Interior’s Significance Criteria, either at the national or local level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Volume I. Introduction to DUNE

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay -- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. This TDR is intended to justify the technical choices for the far detector that flow down from the high-level physics goals through requirements at all levels of the Project. Volume I contains an executive summary that introduces the DUNE science program, the far detector and the strategy for its modular designs, and the organization and management of the Project. The remainder of Volume I provides more detail on the science program that drives the choice of detector technologies and on the technologies themselves. It also introduces the designs for the DUNE near detector and the DUNE computing model, for which DUNE is planning design reports. Volume II of this TDR describes DUNE's physics program in detail. Volume III describes the technical coordination required for the far detector design, construction, installation, and integration, and its organizational structure. Volume IV describes the single-phase far detector technology. A planned Volume V will describe the dual-phase technology.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Mechanism of Lithium Ion Exchange Into Spinel Manganese Oxide

Lithium manganese oxide (LMO) is an effective absorbent for lithium recovery from brines, characterized by its high adsorption capacity, excellent regeneration performance, and selectivity. Here, this study investigates the mechanisms of material degradation during lithium loading and unloading in LMO, employing a combination of time‐resolved Raman spectroscopy, X‐ray diffraction, and X‐ray photoelectron spectroscopy. Key findings reveal that the A 1g vibrational mode wavenumber shifts from 635 cm −1 at the onset of lithium ion exchange to 656 cm −1 after 12 min, indicating local symmetry loss and manganese (Mn) loss during lithium intercalation. The proposed lithium exchange mechanism involves initial occupation of tetrahedral interstitial voids, followed by migration into interstitial sites between Mn octahedral sites. Computational modeling suggests that the loss of symmetry in MnO cubane‐like groups occurs as lithium migrates, significantly affecting the Raman spectra. Importantly, the study demonstrates that after 100 cycles of lithium/hydrogen loading, a 24% loss in Mn is observed, which correlates with decreased structural stability; however, the structural integrity of LMO is enhanced when subjected to multiple cycles without complete loading. Here, these insights contribute to the understanding of LMO's performance in lithium recovery applications and highlight potential strategies to optimize its use in future technologies.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

A successful start for mLife

mLife made its debut with the publication of the inaugurating issue on March 30, 2022. We are pleased to have published 42 high-quality articles, including reviews, research articles, and application notes, which cover microbial genetics, biochemistry and physiology, ecology and evolution, pathogenic and public health microbiology, and so forth. Nine of the articles concern technical innovations and applications in areas including genome editing, single-cell analysis, and database. To pay tribute to the great microbiologist Carl Woese on the 10th anniversary of his death, the Journal published a special section containing three thought-provoking articles in the last issue of the year. mLife and its collaborating publisher Wiley have made great efforts to increase the Journal's national and continental representation. As a result, the Journal received submissions from over 20 countries in five continents last year. The authors of the published articles are from China, United States, Great Britain, France, Canada, Ger many, Japan, Switzerland, and Austria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Process mining for healthcare: Characteristics and challenges

Process mining techniques can be used to analyse business processes using the data logged during their execution. These techniques are leveraged in a wide range of domains, including healthcare, where it focuses mainly on the analysis of diagnostic, treatment, and organisational processes. Despite the huge amount of data generated in hospitals by staff and machinery involved in healthcare processes, there is no evidence of a systematic uptake of process mining beyond targeted case studies in a research context. When developing and using process mining in healthcare, distinguishing characteristics of healthcare processes such as their variability and patient-centred focus require targeted attention. Against this background, the Process-Oriented Data Science in Healthcare Alliance has been established to propagate the research and application of techniques targeting the data-driven improvement of healthcare processes. This paper, an initiative of the alliance, presents the distinguishing characteristics of the healthcare domain that need to be considered to successfully use process mining, as well as open challenges that need to be addressed by the community in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DOME: Directional medical embedding vectors from Electronic Health Records

Motivation: The increasing availability of Electronic Health Record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data. On the other hand, scalable approaches that only require summary-level data do not incorporate temporal dependencies between concepts. Methods: We introduce a DirectiOnal Medical Embedding (DOME) algorithm to encode temporally directional relationships between medical concepts, using summary-level EHR data. Specifically, DOME first aggregates patient-level EHR data into an asymmetric co-occurrence matrix. Then it computes two Positive Pointwise Mutual Information (PPMI) matrices to correspondingly encode the pairwise prior and posterior dependencies between medical concepts. Following that, a joint matrix factorization is performed on the two PPMI matrices, which results in three vectors for each concept: a semantic embedding and two directional context embeddings. They collectively provide a comprehensive depiction of the temporal relationship between EHR concepts. Results: We highlight the advantages and translational potential of DOME through three sets of validation studies. First, DOME consistently improves existing direction-agnostic embedding vectors for disease risk prediction in several diseases, for example achieving a relative gain of 5.5% in the area under the receiver operating characteristic (AUROC) for lung cancer. Second, DOME excels in directional drug-disease relationship inference by successfully differentiating between drug side effects and indications, correspondingly achieving relative AUROC gain over the state-of-the-art methods by 10.8% and 6.6%. Finally, DOME effectively constructs directional knowledge graphs, which distinguish disease risk factors from comorbidities, thereby revealing disease progression trajectories. The source codes are provided at https://github.com/celehs/Directional-EHRembedding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Developing expert scientific consensus on the environmental and societal effects of marine artificial structures prior to decommissioning

Thousands of artificial (‘human-made’) structures are present in the marine environment, many at or approaching end-of-life and requiring urgent decisions regarding their decommissioning. No consensus has been reached on which decommissioning option(s) result in optimal environmental and societal outcomes, in part, owing to a paucity of evidence from real-world decommissioning case studies. To address this significant challenge, we asked a worldwide panel of scientists to provide their expert opinion. They were asked to identify and characterise the ecosystem effects of artificial structures in the sea, their causes and consequences, and to identify which, if any, should be retained following decommissioning. Experts considered that most of the pressures driving ecological and societal effects from marine artificial structures (MAS) were of medium severity, occur frequently, and are dependent on spatial scale with local-scale effects of greater magnitude than regional effects. The duration of many effects following decommissioning were considered to be relatively short, in the order of days. Overall, environmental effects of structures were considered marginally undesirable, while societal effects marginally desirable. Experts therefore indicated that any decision to leave MAS in place at end-of-life to be more beneficial to society than the natural environment. However, some individual environmental effects were considered desirable and worthy of retention, especially in certain geographic locations, where structures can support improved trophic linkages, increases in tourism, habitat provision, and population size, and provide stability in population dynamics. The expert analysis consensus that the effects of MAS are both negative and positive for the environment and society, gives no strong support for policy change whether removal or retention is favoured until further empirical evidence is available to justify change to the status quo. The combination of desirable and undesirable effects associated with MAS present a significant challenge for policy- and decision-makers in their justification to implement decommissioning options. Decisions may need to be decided on a case-by-case basis accounting for the trade-off in costs and benefits at a local level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Kinetics and transport of hydrogen in graphite at high temperature and the effects of oxidation, irradiation and isotopics

The kinetics of uptake and desorption impact the performance of graphite as a vector for tritium in high-temperature fission reactors and in the blanket of fusion reactors. Graphite components in these reactors are exposed to temperatures > 500 °C and H 2 partial pressures of few Pa and desorption temperatures are limited to < 1600 °C; limited data is available at these conditions. Here we review the mechanisms for uptake in, transport and desorption of hydrogen from graphite at high temperature, compiling data on uptake rates, diffusion coefficients and activation energies and providing a discussion of the impact of irradiation, pre-oxidation and isotope. At FHR conditions, trapping impacts uptake rates, leading to a reduction in apparent diffusivity by 35 to 80% compared to higher partial-pressure uptake. Timelines for desorption are not clearly defined; extrapolating from available data, at 1150 °C desorbing 80% of tritium uptaken at FHR conditions may take from 100 to 10,000 h.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or “suspects,” were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. Here, we propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cric searchable image database as a public platform for conventional pap smear cytology data

Amidst the current health crisis and social distancing, telemedicine has become an important part of mainstream of healthcare, and building and deploying computational tools to support screening more efficiently is an increasing medical priority. The early identification of cervical cancer precursor lesions by Pap smear test can identify candidates for subsequent treatment. However, one of the main challenges is the accuracy of the conventional method, often subject to high rates of false negative. While machine learning has been highlighted to reduce the limitations of the test, the absence of high-quality curated datasets has prevented strategies development to improve cervical cancer screening. The Center for Recognition and Inspection of Cells (CRIC) platform enables the creation of CRIC Cervix collection, currently with 400 images (1,376 × 1,020 pixels) curated from conventional Pap smears, with manual classification of 11,534 cells. This collection has the potential to advance current efforts in training and testing machine learning algorithms for the automation of tasks as part of the cytopathological analysis in the routine work of laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The 2021 update of the EPA’s adverse outcome pathway database

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon

Abstract Acoustic telemetry has been used extensively to study the behavior of aquatic animals. The Juvenile Salmon Acoustic Telemetry System (JSATS) is one such system; it was developed for studying juvenile salmonids but has been used to study numerous species. A recent innovation of the JSATS system is an acoustic transmitter that is small enough to be implanted through injection or small incision that doesn’t require sutures. Use of the JSATS system involves deploying cabled acoustic receivers at hydroelectric dams, or other structures, and autonomous acoustic receivers in free-flowing sections of a river. The raw detections from acoustic-tagged fish are processed to remove potential false positives. The clean detections (5,147,996 total) are used to generate detection events and to compute 3-D trajectories (403,900 total), which are used to assign fish to a passage route through a dam. Controlled field testing involving a high-accuracy Global Positioning System receiver is done to validate the submeter accuracy of the trajectories. The JSATS dataset could be reused for expanding the understanding of near-dam fish behavior.

59 BASIC BIOLOGICAL SCIENCES↗