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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies

Abstract BioPortal (https://bioportal.bioontology.org) is the world’s most comprehensive repository of biomedical ontologies. It provides infrastructure for finding, sharing, searching, and utilizing biomedical ontologies. Launched in 2005, BioPortal now includes 1549 ontologies (1182 of them public). Its open, freely accessible website enables anyone (i) to browse the ontology library, (ii) to search for terms across ontologies, (iii) to browse mappings between terms, (iv) to see popularity ratings and recommendations on which ontologies are most relevant to their use cases, (v) to annotate text with ontology terms, (vi) to submit an ontology, and (vii) to request ontology changes. The library of ontologies can be accessed programmatically via a REST application programming interface (API). Recent enhancements include a BioPortal knowledge graph that integrates knowledge from multiple ontologies; a unified data model for interoperability with other knowledge sources; ontology popularity ratings and recommendations for relevant ontologies; and the ability to request ontology changes via a simple user interface that automatically converts user change requests to GitHub Pull Requests that specify the edits that will be made to the ontology upon approval.

Vendetti, Jennifer↗
DOE OSTI2022

Third data release of the Hyper Suprime-Cam Subaru Strategic Program

This work presents the third data release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP), a wide-field multi-band imaging survey with the Subaru 8.2 m telescope. HSC-SSP has three survey layers (Wide, Deep, and UltraDeep) with different area coverages and depths, designed to address a wide array of astrophysical questions. This third release from HSC-SSP includes data from 278 nights of observing time and covers about 670 deg 2 in all five broad-band filters (grizy) at the full depth (~26 mag at 5σ depending on filter) in the Wide layer. If we include partially observed areas, the release covers 1470 deg 2 . The Deep and UltraDeep layers have ~80% of the originally planned integration times, and are considered done, as we have slightly changed the observing strategy in order to compensate for various time losses. There are a number of updates in the image processing pipeline. Of particular importance is the change in the sky subtraction algorithm; we subtract the sky on small scales before the detection and measurement stages, which has significantly reduced the number of false detections. Thanks to this and other updates, the overall quality of the processed data has improved since the previous release. However, there are limitations in the data (for example, the pipeline is not optimized for crowded fields), and we encourage the user to check the quality assurance plots as well as a list of known issues before exploiting the data. The data release website is https://hsc-release.mtk.nao.ac.jp.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Passive spiral galaxies deeply captured by Subaru Hyper Suprime-Cam

Abstract This paper presents a thousand passive spiral galaxy samples at z = 0.01–0.3 based on a combined analysis of the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP PDR3) and the GALEX–SDSS–WISE Legacy Catalog (GSWLC-2). Among 54871 gri galaxy cutouts taken from the HSC-SSP PDR3 over 1072 deg2, we conducted a search with deep-learning morphological classification for candidates of passive spirals below the star-forming main sequence derived by ultraviolet to mid-infrared spectral energy distribution fitting in the GSWLC-2. We then classified the candidates into 1100 passive spirals and 1141 secondary samples based on visual inspections. Most of the latter cases are considered to be passive ringed S0 or pseudo-ringed galaxies. The remaining secondary samples have ambiguous morphologies, including two peculiar objects with diamond-shaped stellar wings. The selected passive spirals have a similar distribution to the general quiescent galaxies on the EWHδ–Dn4000 diagram and concentration indices. Moreover, we detected an enhanced passive fraction of spiral galaxies in X-ray clusters. Passive spirals in galaxy clusters are preferentially located in the midterm or late infall phase on the phase–space diagram, supporting the ram pressure scenario, which has been widely advocated in previous studies. The source catalog and gri-composite images are available on the HSC-SSP PDR3 website 〈https://hsc.mtk.nao.ac.jp/ssp/data-release/〉. Future updates, including integration with a citizen science project dedicated to the HSC data, will achieve more effective and comprehensive classifications.

Shimakawa, Rhythm (ORCID:0000000344422750)↗
DOE OSTI2023

Galaxy Cruise: Deep Insights into Interacting Galaxies in the Local Universe

Abstract We present the first results from GALAXY CRUISE, a community (or citizen) science project based on data from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). The current paradigm of galaxy evolution suggests that galaxies grow hierarchically via mergers, but our observational understanding of the role of mergers is still limited. The data from HSC-SSP are ideally suited to improve our understanding with improved identifications of interacting galaxies thanks to the superb depth and image quality of HSC-SSP. We launched a community science project, GALAXY CRUISE, in 2019 and have collected over two million independent classifications of 20686 galaxies at z < 0.2. We first characterize the accuracy of the participants’ classifications and demonstrate that it surpasses previous studies based on shallower imaging data. We then investigate various aspects of interacting galaxies in detail. We show that there is a clear sign of enhanced activities of super-massive black holes and star formation in interacting galaxies compared to those in isolated galaxies. The enhancement seems particularly strong for galaxies undergoing violent mergers. We also show that the mass growth rate inferred from our results is roughly consistent with the observed evolution of the stellar mass function. The second season of GALAXY CRUISE is currently underway and we conclude with future prospects. We make the morphological classification catalog used in this paper publicly available at the GALAXY CRUISE website, which will be particularly useful for machine-learning applications.

Tanaka, Masayuki↗
DOE OSTI2024

GALAXY CRUISE: Spiral and ring classifications for bright galaxies at z = 0.01–0.3

Abstract This paper presents a morphology classification catalog of spiral and ring features of 59854 magnitude-limited galaxies (r < 17.8 mag, and additional 628005 subsamples down to r = 20 mag) at z = 0.01–0.3 based on the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program. We employ two deep-learning classifiers to determine the spiral and ring structures separately based on GALAXY CRUISE Data Release 1, which is dedicated to Hyper Suprime-Cam data. The number of spiral and ring galaxies contain 31864 and 8808 sources, respectively, which constitute 53% and 15% of the sample. A notable result of this study is the construction of a large sample of ring galaxies utilizing high-quality imaging data delivered by the Subaru Hyper Suprime-Cam. However, the accurate identification of ring galaxies remains difficult at a limited seeing resolution. Additionally, we confirm that most spiral galaxies are located on the star-forming main sequence, whereas ring galaxies preferentially reside in the green valley at stellar masses of 1010.5–1011 solar mass. Furthermore, decreasing fractions of spiral and ring galaxies are observed toward the centers of the galaxy clusters. The obtained morphology catalog is publicly available on the GALAXY CRUISE website.

Shimakawa, Rhythm (ORCID:0000000344422750)↗
DOE OSTI2020

Review of Particle Physics

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,324 new measurements from 878 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on High Energy Soft QCD and Diffraction and one on the Determination of CKM Angles from B Hadrons. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 98 review articles. Volume 2 consists of the Particle Listings and contains also 22 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Pariicle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print and as a web version optimized for use on phones as well as an Android app.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Review of Particle Physics

Abstract The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 2,143 new measurements from 709 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Among the 120 reviews are many that are new or heavily revised, including a new review on Machine Learning, and one on Spectroscopy of Light Meson Resonances. The Review is divided into two volumes. Volume 1 includes the Summary Tables and 97 review articles. Volume 2 consists of the Particle Listings and contains also 23 reviews that address specific aspects of the data presented in the Listings. The complete Review (both volumes) is published online on the website of the Particle Data Group (pdg.lbl.gov) and in a journal. Volume 1 is available in print as the PDG Book. A Particle Physics Booklet with the Summary Tables and essential tables, figures, and equations from selected review articles is available in print, as a web version optimized for use on phones, and as an Android app.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Filling-enforced obstructed atomic insulators

Topological band theory has achieved great success in the high-throughput search for topological band structures both in paramagnetic and magnetic crystal materials. However, a significant proportion of materials are topologically trivial insulators at the Fermi level. In this paper, we show that, remarkably, for a subset of the topologically trivial insulators, knowing only their electron number and the Wyckoff positions of the atoms we can separate them into two groups: the obstructed atomic insulator (OAI) and the atomic insulator (AI). The interesting group, the OAI, have a center of charge not localized on the atoms. Using the theory of topological quantum chemistry, in this work we first derive the necessary and sufficient conditions for a topologically trivial insulator to be a filling enforced obstructed atomic insulator (feOAI) in the 1651 Shubnikov space groups. Remarkably, the filling enforced criteria enable the identification of obstructed atomic bands without knowing the representations of the band structures. Hence, no calculations are needed for the filling enforced criteria, although they are needed to obtain the band gaps. With the help of the Topological Quantum Chemistry website, we have performed a high-throughput search for feOAIs and have found that 957 ICSD entries (638 unique materials) are paramagnetic feOAIs, among which 738 (475) materials have an indirect gap. The metallic obstructed surface states of feOAIs are also showcased by several material examples. Published by the American Physical Society 2024

Materials Science↗
DOE OSTI2021

Albedo Data Sets for Bifacial PV Systems

For use by the PV and financial communities to better estimate the performance and to reduce the risk of bifacial PV systems, data sets of ground albedo and associated meteorological data were developed by using existing measurement network data and data contributed by the PV industry. The data sets include time-series data as well as summary information of tabular monthly and yearly data and plots of monthly and hourly albedo values. Complete information is presented in a user's guide and data are available for download from NREL's DuraMAT website.

albedo↗
DOE OSTI2021

The Value of Diversity in the Renewable Energy Industry and Research Community

Part of creating a successful solar industry is developing a capable workforce. It has been repeatedly shown that organizations and companies are more productive when they have diverse and inclusive cultures. The solar industry in the U.S. performs well in some aspects (non-white workforce, positive work environment) but drastically under-performs in many others. We discuss these metrics and how this impacts the renewable energy industry and the solar research community. We highlight some initial actions which are necessary to begin to remediate these deficiencies, such as demographic tracking, recruiting strategies, and mentoring. We also present the historical and ongoing efforts to improve the diversity and inclusion of the Photovoltaic Specialists Conference, particularly through the work of this year’s Diversity and Inclusion (D&I) oversight committee. This year’s D&I committee is implementing diversity tracking, a women’s lunch, a diversity lunch, childcare resources, pronouns on badges, gender-neutral restrooms, addressing accessibility issues, and publishing a diversity statement and code of conduct to the PVSC website.

diversity↗
DOE OSTI2023

Global harmonization of immediate‐release solid oral drug product bioequivalence recommendations and the impact on generic drug development

Immediate-release (IR) solid oral drug products constitute a significant portion of approved drug products and products under development. Bioequivalence (BE) assessment for these oral products is important for establishing therapeutic equivalence for generic products to their respective comparator products. In December 2022, the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) published the first new draft guideline on BE for IR solid oral dosage forms (M13A). To support the development of ICH M13A, we comprehensively reviewed the landscape of oral IR products approved by the U.S. Food and Drug Administration (FDA) and compared BE recommendations for these products in the current U.S. FDA and European Medicines Agency (EMA) BE guidances. We utilized databases including Drugs@FDA, Orange Book, and product-specific guidances (PSGs) published on the U.S. FDA and EMA websites to collect information. Oral IR products account for 46% of all FDA-approved new drug applications currently listed in Orange Book with 82.5% solids, 0.9% semi-solids, and 16.6% liquids. For all published U.S. FDA PSGs for solid oral IR products, in vivo BE studies with pharmacokinetic (PK) endpoints account for 88% of BE approaches recommended. Of these PK BE studies, 86.5% recommended fasting and fed BE studies, while only 15.9% EMA PSGs recommended both fasting and fed BE studies. This review helps clarify the scope of U.S. solid oral IR products impacted by the new ICH M13A draft guideline and demonstrates how recommendations in draft ICH M13A could significantly harmonize BE recommendations for IR oral products to facilitate global drug development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Information theory and machine learning illuminate large‐scale metabolomic responses of Brachypodium distachyon to environmental change

SUMMARY Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC‐MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC‐MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ–condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)‐based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML‐based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co‐accumulation analysis further identified condition‐specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio‐Analytic Resource for Plant Biology website ( https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi‐bin/efpWeb.cgi ), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Compilation of a Solar Mirror Materials Database and an Analysis of Natural and Accelerated Mirror Exposure and Degradation

The National Renewable Energy Laboratory (NREL) has been conducting exposure experiments on solar reflectors for over four decades. Thousands of mirror samples from over one hundred suppliers have been exposed to and monitored in a range of relevant environments. These test conditions include outdoor test settings and several controlled laboratory environments. These samples have been rigorously individually characterized using a series of reflectance measurements, visual inspections, and in some cases, in-depth composition analysis to identify degradation modes, reflectance losses, and other mirror properties integral to understanding the solar reflector's life cycle. Here, this paper compiles the decades of measurement data into a concise statistical analysis. It includes exposure and degradation data for numerous reflector types, including secondary-surface reflector permutations of polymer and glass superstrates with silver and aluminum reflectors as well as front-surface reflectors. The results herein are intended to analyze environmental stressors and degradation trends among various historical and state-of-the-art solar reflectors. It may be used to support solar reflector design, effective testing methodology, and inform manufacturing decisions moving forward. Presented are the results of the compiled database and an initial analysis for degradation rate modeling using full-spectrum and wavelength-dependent approaches. The database is a growing resource hosted on a live, publicly accessible website. In conjunction with the analysis presented here, it provides a valuable resource to the solar reflector manufacturing and testing industry.

14 SOLAR ENERGY↗
DOE OSTI2024

Development of learning objectives to support undergraduate virology curriculum guidelines

It has become increasingly important for microbiology educators to help students learn critical concepts of the discipline. This is particularly true in virology, where current challenges include increasing rates of vaccine hesitancy, misinformation about the COVID-19 pandemic, and controversy surrounding research on pathogens with pandemic potential. Having students learn virology can attract more people to the field and increase the number of people who can engage in meaningful discourse about issues relating to the discipline. However, the limited number of virologists who teach undergraduates, combined with the fact that many institutions lack stand-alone virology courses, results in virology often being taught as a limited number of lectures within an undergraduate microbiology course (if it is covered at all), which may or may not be taught by an individual trained as a virologist. To provide a framework to teach virology to undergraduate students, a team of virology educators, with support from the American Society for Virology (ASV), developed curriculum guidelines for use in a stand-alone undergraduate virology course or a virology section within another course. These guidelines are available at the ASV website (https://asv.org/curriculum-guidelines/). To assist educators in implementing these guidelines, we created examples of measurable learning objectives. This perspective provides details about the virology curriculum guidelines and learning objectives and accompanies the perspective by Boury et al. in this issue of the Journal of Microbiology & Biology Education about the recent revision of the microbiology curriculum guidelines overseen by the American Society for Microbiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hybrid Organic Inorganic Perovskites: Physical Properties and Applications (in 4 Volumes)

This four-volume handbook gives a state-of-the-art overview of hybrid organic inorganic perovskites, both two dimensional (2D) and three dimensional (3D), from synthesis and characterization and simulation to optoelectronic devices (such as solar cells and light emitting diodes), spintronics devices and catalysis application. The editors, coming from academia and national laboratory, are known for their didactic skills as well as their technical expertise. Coordinating the efforts of 30 expert authors in 21 chapters, they construct the story of hybrid perovskite structural and optical properties, electronic and spintronic response, laser action, and catalysis from varied viewpoints: materials science, chemical engineering, and energy engineering. The four volumes are arranged according to the focus material properties. Volume 1 is focused on the material physical properties including structure, deposition characteristic and the structure of the electronic bands and excitons of these compounds. Volume 2 covers the hybrid perovskite optical properties including the ultrafast optical response, photoluminescence and laser action. Volume 3 contains the spin response of these compounds including application such as spin valves, photogalvanic effect, and magnetic response of light emitting diodes and solar cell devices. Finally, and highly relevant to tomorrow's energy challenges, volume 4 is focused on the physics and device properties of the most relevant applications of the hybrid perovskites, namely photovoltaic solar cells. The text contains many high-quality colorful illustrations and examples, as well as thousands of up-to-date references to peer-reviewed articles, reports and websites for further reading. This comprehensive and well-written handbook is a must-have reference for universities, research groups and companies working with the hybrid organic inorganic perovskites.

applications↗
DOE OSTI2022

Experiences with Porting the FLASH Code to Ookami, an HPE Apollo 80 A64FX Platform

We present initial experiences with running the community simulation code FLASH, developed at the University of Chicago for multi-scale multi-physics applications, on Ookami, a technology testbed featuring the A64FX processor developed by Fujitsu. Our effort focused largely on running FLASH “right out of the box” to see which combinations of compilers and software implementations (e.g. MPI) allowed the code to run with minimal modification. FLASH was one application in a larger effort to deploy Ookami; it served as a test for different versions of newly installed software, and as a cornerstone for the FAQ page of the Ookami website. Here, we report on our results with different compilers and other software, along with our initial scaling results and attempts to utilize the A64FX’s SVE instructions and NUMA architecture. We found that FLASH readily ran with different compilers and MPI implementations, and showed the expected good scaling with no turning. However, more work must be done to fully take advantage of the A64FX’s architectural features and produce a significant speedup for FLASH on Ookami.

79 ASTRONOMY AND ASTROPHYSICS↗