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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

IGM damping wing constraints on the tail end of reionization from the enlarged XQR-30 sample

ABSTRACT The attenuation of Lyα photons by neutral hydrogen in the intergalactic medium (IGM) at z ≳ 5 continues to be a powerful probe for studying the epoch of reionization. Given a framework to estimate the intrinsic (true) Lyα emission of high-z sources, one can infer the ionization state of the IGM during reionization. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high signal-to-noise quasar spectra between $5.8\lesssim \, z\lesssim \, 6.6$ obtained with VLT/X-shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Lyα emission profiles (obtained via covariance matrix reconstruction of the Lyα and N v emission lines from unattenuated high-ionization emission line profiles; C iv, Si iv + O iv], and C iii]) and (ii) distribution of ionized regions within the IGM using synthetic damping wing profiles drawn from a 1.63 Gpc3 reionization simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionization. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14 -0.12}$ and $0.29\substack{+0.14 -0.13}$ at z = 6.15 and 6.35. Further, we also report 68th percentile upper limits of $\bar{x}_{\mathrm{H\, {\small I}}{}} \lt 0.21$, 0.20, 0.21, and 0.18 at z = 5.8, 5.95, 6.05, and 6.55. These results imply reionization is still ongoing at $5.8\lesssim \, z\lesssim \, 6.55$, consistent with previous results from XQR-30 (dark fraction and Lyα forest) along with other observational probes considered in the literature.

Greig, B. (ORCID:0000000240852094)↗
DOE OSTI2021

ECO: the Evidence and Conclusion Ontology, an update for 2022

The Evidence and Conclusion Ontology (ECO) is a community resource that provides an ontology of terms used to capture the type of evidence that supports biomedical annotations and assertions. Consistent capture of evidence information with ECO allows tracking of annotation provenance, establishment of quality control measures, and evidence-based data mining. ECO is in use by dozens of data repositories and resources with both specific and general areas of focus. ECO is continually being expanded and enhanced in response to user requests as well as our aim to adhere to community best-practices for ontology development. The ECO support team engages in multiple collaborations with other ontologies and annotating groups. Here we report on recent updates to the ECO ontology itself as well as associated resources that are available through this project. ECO project products are freely available for download from the project website (https://evidenceontology.org/) and GitHub (https://github.com/evidenceontology/evidenceontology). ECO is released into the public domain under a CC0 1.0 Universal license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗
DOE OSTI2016

The Human Phenotype Ontology in 2017

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

ECO, the Evidence & Conclusion Ontology: community standard for evidence information

The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures and query of evidence. ECO contains over 1500 terms and is in use by many leading biological resources including the Gene Ontology, UniProt and several model organism databases. ECO is continually being expanded and revised based on the needs of the biocuration community.

Biochemistry & Molecular Biology↗
DOE OSTI2018

RNAcentral: a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality.

Sweeney, Blake A.↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Interactions and Dynamics Within CHIP/Hsp70 Complexes

Interactions between the E3 ubiquitin ligase CHIP (C‐terminus of Hsp70 interacting protein) and the chaperone Hsp70 represent the physical intersection of two competing protein quality control efforts: refolding, and degradation. Interaction with CHIP allows for the formation of a productive encounter complex that facilitates ubiquitination of Hsp70‐bound substrates, thereby targeting those proteins for proteasomal degradation. Central to the CHIP/Hsp70 interaction are changes in structure and dynamics that occur upon binding. Although recruitment of Hsp70 to CHIP via interaction with the CHIP tetratricopeptide repeat (TPR) domain is well established, alterations in structure and dynamics of CHIP and Hsp70 upon binding are not well understood. Using NMR we describe residue‐level changes in dynamics to the CHIP‐TPR domain that occur upon binding Hsp70. We also utilize small angle X‐ray scattering (SAXS) and electron paramagnetic resonance (EPR) to identify motions with the CHIP/Hsp70 complex. Independent SAXS and EPR experiments both point to a mobile Hsp70 substrate binding domain that is only partially constrained through interactions with the CHIP‐TPR. Building upon static models of the full‐length CHIP/Hsp70 complex, afforded by our recent crystal structure of the CHIP‐TPR/Hsp70‐lid‐tail complex, we have assembled a dynamic model of the CHIP‐Hsp70 complex. This dynamic model sheds light on the function of the CHIP/Hsp70 chaperoned ubiquitination complex and how CHIP harnesses dynamics of Hsp70 to overcome significant distance separations identified in earlier static models of the CHIP/Hsp70 complex. Support or Funding Information The authors acknowledge financial support from the US National Science Foundation (Award No. MCB 1552113 to RCP), the American Heart Association (Award No. 16SDG26960000 to RCP), the Burroughs Wellcome Fund (Award No. 1014031 to RCP), and institutional support from Miami University through the Robert H. and Nancy J. Blayney Professorship (to RCP). The Advanced Light Source is supported by the US Department of Energy under contract number DE‐AC03‐76SF00098 at Lawrence Berkeley National Laboratory.

Mannion, Matthew M.↗
DOE OSTI2015

Dose Reconstruction for the Million Worker Study: Status and Guidelines

The primary aim of the epidemiologic study of one million U.S. radiation workers and veterans (the Million-Worker study) is to provide scientifically valid information on the level of radiation risk when exposures are received gradually over time, and not acutely as was the case for Japanese atomic bomb survivors. The primary outcome of the epidemiological study is cancer mortality but other causes of death such as cardiovascular disease and cerebrovascular disease will be evaluated. The success of the study is tied to the validity of the dose reconstruction approaches to provide unbiased estimates of organ-specific radiation absorbed doses and their accompanying uncertainties. The dosimetry aspects for the Million-Worker study are challenging in that they address diverse exposure scenarios for diverse occupational groups being studied over a period of up to 70 years. The dosimetric issues differ among the varied exposed populations that are considered: atomic veterans, DOE workers exposed to both penetrating radiation and intakes of radionuclides, nuclear power plant workers, medical radiation workers, and industrial radiographers. While a major source of radiation exposure to the study population comes from external gamma-ray or x-ray sources, for certain of the study groups there is a meaningful component of radionuclide intakes that require internal radiation dosimetry measures. Scientific Committee 6-9 has been established by NCRP to produce a report on the comprehensive organ dose assessment (including uncertainty analysis) for the Million-Worker study. The Committee’s report will cover the specifics of practical dose reconstruction for the ongoing epidemiologic studies with uncertainty analysis discussions and will be a specific application of the guidance provided in NCRP Reports 158, 163, 164, and 171. The main role of the Committee is to provide guidelines to the various groups of dosimetrists involved in the various components of the Million-Worker study to make sure that certain dosimetry criteria are respected: calculation of annual absorbed doses in the organs of interest, separation of low-LET and high-LET components, evaluation of uncertainties, and quality assurance and quality control. Lastly, we recognize that the Million-Worker study and its approaches to dosimetry are a work in progress and that there will be flexibility and changes in direction as new information is obtained, both with regard to dosimetry and with regard to the epidemiologic features of the study components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Setup and Characterization of a 137 CS Dosimetry Calibration Source in a Space-constrained Environment

Proper characterization of 137 Cs sources used for dosimeter calibration and performance testing is crucial for accurate and precise knowledge of air kerma rate and delivered dose. A 269 GBq 137 Cs source was relocated to a new facility, which had a footprint of approximately 2.8 m × 3.6 m and a 3.4 m high ceiling. A small room size, such as in the new facility, may significantly increase backscatter from the walls or room return. Due to the limited source strength, a relatively close irradiation position of 1.00 m from the source was selected to decrease required exposure times. Proximity to the small but cylindrical source has the potential to alter the 1/r 2 relationship (inverse square law) of air kerma rate with distance associated with point sources. Practical tutorials concerning dosimetry irradiation facilities are largely absent from the archival literature. For those reasons, standard characterization experiments were repeated multiple times, great care was taken with positioning, several experiments were added to the standard ones, an ion chamber and dosimeters were used rather than film for greater accuracy and precision, and practical details of the process were recorded. The impacts of room size and finite source dimensions were quantified and mitigated by the efforts reported here. Finally, recommendations for simple but thorough facility characterization, beam calibration, and quality control resulted.

42 ENGINEERING↗
DOE OSTI2024

Self-consistent quasiparticle G W and hybrid functional calculations for Al/InAs/Al heterojunctions: Band offset and spin-orbit coupling effects

The electronic structure of surfaces and interfaces plays a key role in the properties of quantum devices. Here, we study the electronic structure of realistic Al/InAs/Al heterojunctions using a combination of density functional theory with hybrid functionals and state-of-the-art quasiparticle G W (QSGW) calculations. We find a good agreement between QSGW calculations and hybrid functional calculations, which themselves compare favorably well with angle-resolved photoemission spectroscopy experiments. Our paper confirms the need for well-controlled quality of the interfaces to obtain the needed properties of InAs/Al heterojunctions. A detailed analysis of the effects of spin-orbit coupling on the spin splitting of the electronic states shows a linear scaling in k space, related to the two-dimensional nature of some interface states. The good agreement by QSGW and hybrid functional calculations opens the door towards trustable use of an effective approximation to QSGW for studying very large heterojunctions. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗
DOE OSTI2017

Insight into 3D micro-CT data: exploring segmentation algorithms through performance metrics

Three-dimensional (3D) micro-tomography (µ-CT) has proven to be an important imaging modality in industry and scientific domains. Understanding the properties of material structure and behavior has produced many scientific advances. An important component of the 3D µ-CT pipeline is image partitioning (or image segmentation), a step that is used to separate various phases or components in an image. Image partitioning schemes require specific rules for different scientific fields, but a common strategy consists of devising metrics to quantify performance and accuracy. The present article proposes a set of protocols to systematically analyze and compare the results of unsupervised classification methods used for segmentation of synchrotron-based data. Additionally, the proposed dataflow for Materials Segmentation and Metrics (MSM) provides 3D micro-tomography image segmentation algorithms, such as statistical region merging (SRM), k-means algorithm and parallel Markov random field (PMRF), while offering different metrics to evaluate segmentation quality, confidence and conformity with standards. Both experimental and synthetic data are assessed, illustrating quantitative results through the MSM dashboard, which can return sample information such as media porosity and permeability. The main contributions of this work are: (i) to deliver tools to improve material design and quality control; (ii) to provide datasets for benchmarking and reproducibility; (iii) to yield good practices in the absence of standards or ground-truth for ceramic composite analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Operando Temperature Measurements of Photovoltaic Laser Power Converter Devices Under Continuous High-Intensity Illumination

Photovoltaic devices that operate under extremely high irradiances, such as laser power converters (LPCs), may also operate at elevated temperatures, even under active cooling, as the result of large temperature gradients. We demonstrate the operation of GaAs LPC devices under orders of magnitude of irradiances up to 150 W/cm 2 in a monochromatic laser simulator with an active cooling stage. The steady-state open-circuit voltage (V OC ) as a function of irradiance is known to droop at high irradiance as the result of junction heating, but the junction temperature can be difficult to measure by conventional methods. Fast, transient V OC measurements under these extreme operating conditions are used here to determine the junction temperature. Empirical V OC temperature coefficients of the devices at each irradiance of interest are determined and used as an integral part of this technique. We show that the thermal design of different LPC devices strongly affects the operating temperature of the junctions. Knowledge of the operating temperature can be a strong tool for understanding the nature of loss mechanisms and improving the design for the operation of photovoltaic LPCs at high irradiances. Furthermore, this technique can be used for laboratory devices during initial design as well as to characterize mass-produced and packaged devices for quality control.

14 SOLAR ENERGY↗
DOE OSTI2015

Quantifying Solar Cell Cracks in Photovoltaic Modules by Electroluminescence Imaging

This article proposes a method for quantifying the percentage of partially and totally disconnected solar cell cracks by analyzing electroluminescence images of the photovoltaic module taken under high- and low-current forward bias. The method is based on the analysis of the module's electroluminescence intensity distribution, applied at module and cell level. These concepts are demonstrated on a crystalline silicon photovoltaic module that was subjected to several rounds of mechanical loading and humidity-freeze cycling, causing increasing levels of solar cell cracks. The proposed method can be used as a diagnostic tool to rate cell damage or quality of modules after transportation. Moreover, the method can be automated and used in quality control for module manufacturers, installers, or as a diagnostic tool by plant operators and diagnostic service providers.

14 SOLAR ENERGY↗
DOE OSTI2022

Evaluation of PV Module Packaging Strategies of Monofacial and Bifacial PERC Using Degradation Pathway Network Modeling

As the PV industry is rapidly expanding, it is important to thoroughly investigate the long-term impact of packaging strategies on the performance of PV modules. In this study, the variants in sets differ on the basis of manufacturer (A/B), encapsulant (EVA/POE), rear encapsulant (UV-cutoff/opaque/transparent), module architecture (GB/DG) and cell type (monofacial/bifacial). The minimodules were exposed for 2520 hours in modified damp heat, with or without full spectrum light. Every 504 hours, stepwise electrical characterization techniques were employed to track changes in minimodules. Degradation pathway modeling using network structural equation modeling was employed to study pairwise relationships between variables and service lifetime prediction in minimodules. Through this study, differences in quality control are identified in minimodules made by different manufacturers. Minimodules with UV-cutoff rear encapsulant show relatively better stability, whereas the ones with opaque rear encapsulant show greater power loss. In addition, GB having UV-cutoff rear encapsulation and GB with POE having opaque rear encapsulation were identified to be stable as they lack a best model fit. Here, the primary power loss mechanism in degrading variants is interconnect corrosion.

14 SOLAR ENERGY↗
DOE OSTI2016

Protection heater design validation for the LARP magnets using thermal imaging

Protection heaters are essential elements of a quench protection scheme for high-field accelerator magnets. Various heater designs fabricated by LARP and CERN have been already tested in the LARP high-field quadrupole HQ and presently being built into the coils of the high-field quadrupole MQXF. In order to compare the heat flow characteristics and thermal diffusion timescales of different heater designs, we powered heaters of two different geometries in ambient conditions and imaged the resulting thermal distributions using a high-sensitivity thermal video camera. We observed a peculiar spatial periodicity in the temperature distribution maps potentially linked to the structure of the underlying cable. Two-dimensional numerical simulation of heat diffusion and spatial heat distribution have been conducted, and the results of simulation and experiment have been compared. Imaging revealed hot spots due to a current concentration around high curvature points of heater strip of varying cross sections and visualized thermal effects of various interlayer structural defects. Furthermore, thermal imaging can become a future quality control tool for the MQXF coil heaters.

43 PARTICLE ACCELERATORS↗
DOE OSTI2017

Status of Long Coil Production for the MQXFB Nb3Sn Prototype Quadrupole for the HiLumi LHC

The High luminosity LHC upgrade target is to increase the integrated luminosity by a factor 10, resulting in an integrated luminosity of 3000 fb-1. One major improvement foreseen is the reduction of the beam size at the collision points. This requires the development of 150 mm single aperture quadrupoles for the interaction regions. These quadrupoles are under development in a joint collaboration between CERN and the US-LHC Accelerator Research Program (LARP). The chosen approach for achieving a nominal quadrupole field gradient of 132.6 T/m is based on the Nb3Sn technology. The coils with a length of 7281 mm will be the longest Nb3Sn coils fabricated so far for accelerator magnets. The production of the long coils was launched in 2016 based on practise coils made from copper. This paper provides a status of the production of the first low grade and full performance coils and describes the production process and applied quality control. Furthermore an outlook for the prototype assembly is provided.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Correlations Between In-Line X-ray Diffraction Data and In-Field Critical Current of Long, 4-μm Thick Film REBCO Tapes Made by Advanced MOCVD

REBa 2 Cu 3 O 7-δ (REBCO, RE = rare earth) tapes with high critical current can be very impactful in high magnetic field applications at low temperatures and power applications at high temperatures. A pilot-scale Advanced Metal Organic Chemical Vapor Deposition (MOCVD) method was used to fabricate 50-m-long, 4+μm-thick REBCO tape in a single pass. Critical currents 3.3x that of commercial HTS tapes were achieved at 20 K, 12 T in these 50-m-long tapes. An in-line 2D X-ray Diffraction (XRD) system has been used to assess the quality of the long tapes in real-time, during manufacturing. The key peaks of REBCO, REO, and BZO phases were identified and utilized for tape quality analysis. Furthermore, a 20-m tape made by Advanced MOCVD was tested over its entire length by reel-to-reel (R2R) scanning Hall-probe microscopy (SHPM) at 65 K, 0.25 T, 2 T, and 4 T. 4-mm-wide strands of Advanced MOCVD tapes showed mean critical currents at 65 K of 530 A, 200 A, and 104 A at 0.25 T, 2 T, and 4 T respectively. The combined use of in-line and offline characterization techniques provides a reliable approach for assessing long REBCO tapes during manufacturing, serving as an effective feedback source for quality control in scaled-up REBCO tape deposition processes. This advancement contributes to the production of longer and more uniform high-performance REBCO tapes for large-scale, high-field superconducting applications

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗