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At least 271 records · Page 15

ThermoBase: A Database of the Phylogeny and Physiology of Thermophilic and Hyperthermophilic Organisms

Thermophiles and hyperthermophiles are those organisms which grow at high temperature (> 40°C). The unusual properties of these organisms have received interest in multiple fields of biological research, and have found applications in biotechnology, especially in industrial processes. However, there are few listings of thermophilic and hyperthermophilic organisms and their relevant environmental and physiological data. Such repositories can be used to standardize definitions of thermophile and hyperthermophile limits and tolerances and would mitigate the need for extracting organism data from diverse literature sources across multiple, sometimes loosely related, research fields. Therefore, we have developed ThermoBase, a web-based and freely available database which currently houses comprehensive descriptions for 1238 thermophilic or hyperthermophilic organisms. ThermoBase reports taxonomic, metabolic, environmental, experimental, and physiological information in addition to literature resources. This includes parameters such as coupling ions for chemiosmosis, optimal pH and range, optimal temperature and range, optimal pressure, and optimal salinity. The database interface allows for search features and sorting of parameters. As such, it is the goal of ThermoBase to facilitate and expedite hypothesis generation, literature research, and understanding relating to thermophiles and hyperthermophiles within the scientific community in an accessible and centralized repository. ThermoBase is freely available online at the Astrobiology Habitable Environments Database (AHED; https://ahed.nasa.gov), at the Database Center for Life Science (TogoDB; http://togodb.org/db/thermobase), and in the S1 File.

Thermophiles↗

Comparison of Entry Descent and Landing Aerodynamic Databases with Uncertainty Quantification Developed Using Machine Learning Techniques

When developing the aerodynamic databases for use in trajectory simulations, it is important to develop a system of metrics to qualify which aerodynamic models are best to use. Since aerodynamics are just one input into trajectory simulations, the results of these simulations do not reflect on the quality of the aerodynamic database used. This means that aerodynamic database comparisons must be done offline. While traditional metrics that focus on mean/nominal predictions are a good first step, more robust estimates of the prediction interval become important as more focused uncertainty models are developed. We explore the limitations of evaluating aerodynamic models based purely on nominal-centered response surfaces. Before elaborating and evaluating metrics based on distributed models, the value of evaluating prediction interval and confidence interval are discussed to conclude that prediction intervals are more relevant to the use of trajectory analysis. Several metrics to evaluate the prediction interval are introduced with a focus on the standard calibration metric. Finally, we compare candidate models using both mean and distributed metrics. A finalized candidate model developed using state of the art machine learning methods is compared to a baseline model developed using traditional aerodynamic database modeling techniques.

Aerodynamic Database↗

Improved Aerothermal Reliability Analysis Enabled by the Mars Sample Return Earth Entry System Aerothermal Database

The Mars Sample Return (MSR) campaign is a series of missions designed to retrieve Martian rock and soil samples for detailed study on Earth. The campaign is split into three primary phases: sample collection with the Mars2020 rover, retrieval with the Sample Return Lander (SRL) and Mars Ascent Vehicle (MAV), and then return to Earth with the Earth Return Orbiter (ERO) and Capture, Containment, and Return System (CCRS) [1]. The final sequence in the Earth return phase is the delivery and entry of the Earth Entry System (EES) sample return capsule. Due to unprecedented planetary protection concerns, the sample return capsule is subject to strict reliability requirements. To this end, the MSR-EES aerothermal team has implemented a flexible aerothermal database architecture capable of integration with state-of-the-art trajectory codes to provide a more rigorous aerothermal reliability analysis. The EES database enables the generation of environments at any location on the heatshield and can incorporate trajectory uncertainties to both statistically quantify aerothermal environments for arcjet testing and produce material response boundary conditions to rigorously select thermal protection system (TPS) sizing environments. This poster will not discuss the fundamental modeling assumptions included in the database, and will instead focus on the downstream reliability analyses that can be performed with a database of this architecture.

MSR-EES↗

Geothermal NEPA Database on OpenEI (Poster)

The National Renewable Energy Laboratory (NREL) developed the Geothermal National Environmental Policy Act (NEPA) Database as a platform for government agencies and industry to access and maintain information related to geothermal NEPA documents. The data were collected to inform analyses of NEPA timelines, and the collected data were made publically available via this tool in case others might find the data useful. NREL staff and contractors collected documents from agency websites, during visits to the two busiest Bureau of Land Management (BLM) field offices for geothermal development, and through email and phone call requests from other BLM field offices. They then entered the information into the database, hosted by Open Energy Information (http://en.openei.org/wiki/RAPID/NEPA). The long-term success of the project will depend on the willingness of federal agencies, industry, and others to populate the database with NEPA and related documents, and to use the data for their own analyses. As the information and capabilities of the database expand, developers and agencies can save time on new NEPA reports by accessing a single location to research related activities, their potential impacts, and previously proposed and imposed mitigation measures. NREL used a wiki platform to allow industry and agencies to maintain the content in the future so that it continues to provide relevant and accurate information to users.

15 GEOTHERMAL ENERGY↗

FY 2019 Nuclear Energy Infrastructure Database Accomplishments

The database, known as the Nuclear Energy Infrastructure Database (NEID), is accessed through a web-based application (at nsuf-infrastructure.inl.gov) and built specifically to track research and development (R&D) facilities and associated equipment throughout the DOE-NE complex. The NEID serves internal users (such as DOE personnel and national laboratory staff and researchers) and potential infrastructure users who will be able to view the inventory of DOE-NE-compatible R&D capabilities potentially available to them. NSUF utilizes the NEID to support the annual nuclear energy gap analysis process. Infrastructure needs are gathered from DOE-NE R&D programs and researchers at U.S. national laboratories, universities, and the U.S. nuclear industry. The fiscal year (FY) 2019 Nuclear Energy Infrastructure Database (NEID) Accomplishments report captures all the additions and improvements made to the database in FY 2019.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Advances in Metallic Fuel Database Development and Data Qualification

The Fuels Irradiation and Physics Database (FIPD [1]) is a comprehensive repository of data and documents related to Uranium-Zirconium based metallic fuel test pins. This database stores operational conditions of these pins, calculated using a suite of Argonne National Laboratory analysis codes developed during the Integral Fast Reactor (IFR) program. Key calculated data include axial distributions of power, temperature, fluence, burnup, and isotopic densities. Additionally, the FIPD holds post-irradiation examination (PIE) data such as fission gas release, gas chemistry measurements, and axial distributions derived from profilometry, gamma scanning, and neutron radiography. Complementing these data is an extensive archive of documents related to various pins and experiments. These include raw PIE records, design details, safety analyses, and operational reports. More detail about FIPD can be found in ref. [2]. The database development is an ongoing effort covering metallic fuel experiments from the Experimental Breeder Reactor II (EBR-II) and the Fast Flux Test Facility (FFTF). The recent improvements to the database and the data QA status are summarized in this paper.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Development of a Searchable Database of Cryoablation Simulations for Use in Treatment Planning

PurposeTo create and validate a planning tool for multiple-probe cryoablation, using simulations of ice ball size and shape for various ablation probe configurations, ablation times, and types of tissue ablated.Materials and MethodsIce ball size and shape was simulated using the Pennes bioheat equation. Five thousand six hundred and seventy different cryoablation procedures were simulated, using 1–6 cryoablation probes and 1–2 cm spacing between probes. The resulting ice ball was measured along three perpendicular axes and recorded in a database. Simulated ice ball sizes were compared to gel experiments (26 measurements) and clinical cryoablation cases (42 measurements). The clinical cryoablation measurements were obtained from a HIPAA-compliant retrospective review of kidney and liver cryoablation procedures between January 2015 and February 2016. Finally, we created a web-based cryoablation planning tool, which uses the cryoablation simulation database to look up the probe spacing and ablation time that produces the desired ice ball shape and dimensions.ResultsAverage absolute error between the simulated and experimentally measured ice balls was 1 mm in gel experiments and 4 mm in clinical cryoablation cases. The simulations accurately predicted the degree of synergy in multiple-probe ablations. The cryoablation simulation database covers a wide range of ice ball sizes and shapes up to 9.8 cm.ConclusionCryoablation simulations accurately predict the ice ball size in multiple-probe ablations. The cryoablation database can be used to plan ablation procedures: given the desired ice ball size and shape, it will find the number and type of probes, probe configuration and spacing, and ablation time required.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

An annotated database of Arabidopsis mutants of acyl lipid metabolism

Mutants have played a fundamental role in gene discovery and in understanding the function of genes involved in plant acyl lipid metabolism. The first mutant in Arabidopsis lipid metabolism ( fad4 ) was described in 1985. Since that time, characterization of mutants in more than 280 genes associated with acyl lipid metabolism has been reported. This review provides a brief background and history on identification of mutants in acyl lipid metabolism, an analysis of the distribution of mutants in different areas of acyl lipid metabolism and presents an annotated database (ARALIPmutantDB) of these mutants. The database provides information on the phenotypes of mutants, pathways and enzymes/proteins associated with the mutants, and allows rapid access via hyperlinks to summaries of information about each mutant and to literature that provides information on the lipid composition of the mutants. Mutants for at least 30 % of the genes in the database have multiple names, which have been compiled here to reduce ambiguities in searches for information. Furthermore, the database should also provide a tool for exploring the relationships between mutants in acyl lipid-related genes and their lipid phenotypes and point to opportunities for further research.

59 BASIC BIOLOGICAL SCIENCES↗

A harmonized longitudinal biomarkers and cognition database for assessing the natural history of preclinical Alzheimer's disease from young adulthood and for designing prevention trials

Abstract Introduction Large longitudinal biomarkers database focusing on middle age is needed for Alzheimer's disease (AD) prevention. Methods Data for cerebrospinal fluid analytes, molecular imaging of cerebral fibrillar β‐amyloid with positron emission tomography, magnetic resonance imaging–based brain structures, and clinical/cognitive outcomes were harmonized across eight AD biomarker studies. Statistical power was estimated. Results The harmonized database included 7779 participants with clinical/cognitive data: 3542 were 18∼65 years at the baseline, 5865 had longitudinal cognitive data for a median of 4.7 years, 2473 participated in the cerebrospinal fluid studies (906 had longitudinal data), 2496 participated in the magnetic resonance imaging studies (1283 had longitudinal data), and 1498 participated in the positron emission tomography amyloid studies (849 had longitudinal data). The database provides adequate power for detecting early biomarker changes, and demonstrates the feasibility of AD prevention trials on middle‐aged individuals. Discussion The harmonized database is an optimum resource to design AD prevention trials decades before symptomatic onset.

Xiong, Chengjie↗

A database of ultrastable MOFs reassembled from stable fragments with machine learning models

High-throughput screening of hypothetical metal-organic framework (MOF) databases can uncover new materials, but their stability in real-world applications is often unknown. We leverage community knowledge and machine learning (ML) models to identify MOFs that are thermally stable and stable upon activation. We separate these MOFs into their building blocks and recombine them to make a new hypothetical MOF database of over 50,000 structures with orders of magnitude more (1) connectivity nets and (2) inorganic building blocks than were present in prior databases. Further, this database shows a 10-fold enrichment of ultrastable MOF structures that are stable upon activation and more than 1 standard deviation more thermally stable than the average experimentally characterized MOF. For nearly 10,000 ultrastable MOFs, we compute elastic moduli to confirm that these materials have good mechanical stability, and we report methane deliverable capacities. We identify privileged metal nodes in ultrastable MOFs that optimize gas storage and mechanical stability simultaneously.

36 MATERIALS SCIENCE↗

FIPD: The SFR metallic fuels irradiation & physics database

The DOE Advanced Reactor Technology (ART) program has supported efforts to recover and preserve metallic fuel data generated throughout the US sodium-cooled fast reactor (SFR) program. Those efforts have been focused on establishing databases of the experimental data that were mainly generated during the Integral Fast Reactor (IFR) program including data generated at Experimental Breeder Reactor-II (EBR-II), Fast Flux Test Facility (FFTF), and Transient Reactor Test Facility (TREAT) reactors, as well as out of pile data. The data is essential for future licensing activities of metallic fuel based advanced fast reactors. This paper describes the development of the SFR Metallic Fuels Irradiation & Physics Database (FIPD) and covers the scientific knowledge available in the database. Furthermore, the architecture of the FIPD is described by showing the available reactor operation data, fabrication, and post-irradiation examination (PIE) data, and other documents. The applications of the fuel database are also discussed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Initial demonstration of automated fuel performance modeling with 1977 EBR-II metallic fuel pins using BISON code with FIPD and IMIS databases

Using the BISON fuel performance code, simulations were conducted using an automated process to read initial and operating conditions from the Fuels Irradiation and Physics Database (FIPD) and Integral Fast Reactor materials information system (IMIS) database, which contains metallic fuel data from the Experimental Breeder Reactor-II (EBR-II). This work demonstrates use of an integrated framework to access the vast majority of EBR-II experimental fuel pin data to support rapid development of fuel performance models for next-generation metallic fuel systems. With this capability, validation for fuel qualification can be performed rapidly. Between IMIS and FIPD, there is enough information to conduct 1977 unique EBR-II metallic fuel pin histories from 24 different experiments, at varying levels of detail between the two databases. Each of these histories includes a high-resolution power history, flux history, coolant channel flow rates, and coolant channel temperatures. Fission gas release (FGR), cumulative damage fraction (CDF), fuel axial swelling, cladding profilometry, and burnup were all simulated in BISON. The results were compared to post-irradiation examination (PIE) results for the initial demonstration of automated BISON modeling. BISON simulations conducted with IMIS and FIPD were in rough agreement with PIE measurements and calculations. Cladding profilometry, FGR, and fuel axial swelling were found to be in rough agreement with PIE measurements, depending on the physics used within the BISON input files. Here, the mechanical contact solver chosen was found to significantly impact axial fuel swelling and cladding strain predictions. CDF values were assessed to see whether pin failure may have been predicted (CDF ≥ 1). This work suggests that continued development of an automated tool for BISON should focus on inclusion of the Fast Flux Test Facility (FFTF) experimental data for a larger database for metallic fuel, improved physical models to better capture fuel performance, such as fuel-cladding interactions, and a more detailed comparison with available PIE data to further the BISON model development.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Current nonclinical testing paradigm enables safe entry to First-In-Human clinical trials: The IQ consortium nonclinical to clinical translational database

The contribution of animal testing in drug development has been widely debated and challenged. An industry-wide nonclinical to clinical translational database was created to determine how safety assessments in animal models translate to First-In-Human clinical risk. The blinded database was composed of 182 molecules and contained animal toxicology data coupled with clinical observations from phase I human studies. Animal and clinical data were categorized by organ system and correlations determined. The 2 × 2 contingency table (true positive, false positive, true negative, false negative) was used for statistical analysis. Sensitivity was 48% with a 43% positive predictive value (PPV). The nonhuman primate had the strongest performance in predicting adverse effects, especially for gastrointestinal and nervous system categories. When the same target organ was identified in both the rodent and nonrodent, the PPV increased. Specificity was 84% with an 86% negative predictive value (NPV). The beagle dog had the strongest performance in predicting an absence of clinical adverse effects. If no target organ toxicity was observed in either test species, the NPV increased. While nonclinical studies can demonstrate great value in the PPV for certain species and organ categories, the NPV was the stronger predictive performance measure across test species and target organs indicating that an absence of toxicity in animal studies strongly predicts a similar outcome in the clinic. These results support the current regulatory paradigm of animal testing in supporting safe entry to clinical trials and provide context for emerging alternate models. - Highlights: • Translational database created to determine animal to human safety concordance. • 182 molecules with animal and clinical data; concordance parameters determined • Positive predictive value of 43%; Negative predictive value of 86% • Absence of toxicity in animal study strongly predicts similar outcome in the clinic. • Database supports animal testing to ensure human safety in the clinic.

60 APPLIED LIFE SCIENCES↗

Building a Consistent and Reproducible Database for Adsorption Evaluation in Covalent–Organic Frameworks

We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal's postcombustion flue gases. This workflow is applied to a database of 324 covalent-organic frameworks (COFs) reported in the literature, to characterize their CO 2 adsorption properties using the following steps: (1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory, (2) fitting atomic point charges based on the electron density, (3) characterizing the pore geometry of the structures before and after optimization, (4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally, (5) assessing the CO 2 parasitic energy via process modeling. The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The northeast materials database for magnetic materials

The discovery of magnetic materials with high operating temperature ranges and optimized performance is essential for advanced applications. Current data-driven approaches are limited by the lack of accurate, comprehensive, and feature-rich databases. This study aims to address this challenge by using Large Language Models (LLMs) to create a comprehensive, experiment-based, magnetic materials database named the Northeast Materials Database (NEMAD), which consists of 67,573 magnetic materials entries (www.nemad.org). The database incorporates chemical composition, magnetic phase transition temperatures, structural details, and magnetic properties. Enabled by NEMAD, we trained machine learning models to classify materials and predict transition temperatures. Our classification model achieved an accuracy of 90% in categorizing materials as ferromagnetic (FM), antiferromagnetic (AFM), and non-magnetic (NM). The regression models predict Curie (Néel) temperature with a coefficient of determination (R 2 ) of 0.87 (0.83) and a mean absolute error (MAE) of 56K (38K). These models identified 25 (13) FM (AFM) candidates with a predicted Curie (Néel) temperature above 500K (100K) from the Materials Project. This work shows the feasibility of combining LLMs for automated data extraction and machine learning models to accelerate the discovery of magnetic materials.

Ferromagnetism↗

A database of battery materials auto-generated using ChemDataExtractor

A database of battery materials is presented which comprises a total of 292,313 data records, with 214,617 unique chemical-property data relations between 17,354 unique chemicals and up to five material properties: capacity, voltage, conductivity, Coulombic efficiency and energy. 117,403 data are multivariate on a property where it is the dependent variable in part of a data series. The database was auto-generated by mining text from 229,061 academic papers using the chemistry-aware natural language processing toolkit, ChemDataExtractor version 1.5, which was modified for the specific domain of batteries. The collected data can be used as a representative overview of battery material information that is contained within text of scientific papers. Public availability of these data will also enable battery materials design and prediction via data-science methods. To the best of our knowledge, this is the first auto-generated database of battery materials extracted from a relatively large number of scientific papers. We also provide a Graphical User Interface (GUI) to aid the use of this database.

25 ENERGY STORAGE↗

A thermoelectric materials database auto-generated from the scientific literature using ChemDataExtractor

An auto-generated thermoelectric-materials database is presented, containing 22,805 data records, automatically generated from the scientific literature, spanning 10,641 unique extracted chemical names. Each record contains a chemical entity and one of the seminal thermoelectric properties: thermoelectric figure of merit, ZT; thermal conductivity, κ; Seebeck coefficient, S; electrical conductivity, σ; power factor, PF; each linked to their corresponding recorded temperature, T. The database was auto-generated using the automatic sentence-parsing capabilities of the chemistry-aware, natural language processing toolkit, ChemDataExtractor 2.0, adapted for application in the thermoelectric-materials domain, following a rule-based sentence-simplification step. Data were mined from the text of 60,843 scientific papers that were sourced from three scientific publishers: Elsevier, the Royal Society of Chemistry, and Springer. To the best of our knowledge, this is the first automatically-generated database of thermoelectric materials and their properties from existing literature. The database was evaluated to have a precision of 82.25% and has been made publicly available to facilitate the application of data science in the thermoelectric-materials domain, for analysis, design, and prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulated sulfur K-edge X-ray absorption spectroscopy database of lithium thiophosphate solid electrolytes

X-ray absorption spectroscopy (XAS) is a premier technique for materials characterization, providing key information about the local chemical environment of the absorber atom. In this work, we develop a database of sulfur K-edge XAS spectra of crystalline and amorphous lithium thiophosphate materials based on the atomic structures reported in Chem. Mater., 34, 6702 (2022). The XAS database is based on simulations using the excited electron and core-hole pseudopotential approach implemented in the Vienna Ab initio Simulation Package. Our database contains 2681 S K-edge XAS spectra for 66 crystalline and glassy structure models, making it the largest collection of first-principles computational XAS spectra for glass/ceramic lithium thiophosphates to date. This database can be used to correlate S spectral features with distinct S species based on their local coordination and short-range ordering in sulfide-based solid electrolytes. The data is openly distributed via the Materials Cloud, allowing researchers to access it for free and use it for further analysis, such as spectral fingerprinting, matching with experiments, and developing machine learning models.

36 MATERIALS SCIENCE↗