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At least 55 records · Page 3

Status Report on the Molten Salt Thermodynamic Database (MSTDB) Development (FY20)

The current status of the Molten Salt Thermodynamic Database (MSTDB) is reported. While a series of informational exchange meetings with Moten Salt Reactor (MSR) developers has given the NEAMS program insight into the systems of interest, the current effort is devoted to mining data already available in the literature for continued development of MSTDB. Many relevant systems have not been previously studied. Therefore, once the data from the literature is completely reviewed, curated, and used as inputs for MSTDB, new thermodynamic values will need to be generated using computational and experimental approaches.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Text-mined dataset of gold nanoparticle synthesis procedures, morphologies, and size entities

Abstract Gold nanoparticles are highly desired for a range of technological applications due to their tunable properties, which are dictated by the size and shape of the constituent particles. Many heuristic methods for controlling the morphological characteristics of gold nanoparticles are well known. However, the underlying mechanisms controlling their size and shape remain poorly understood, partly due to the immense range of possible combinations of synthesis parameters. Data-driven methods can offer insight to help guide understanding of these underlying mechanisms, so long as sufficient synthesis data are available. To facilitate data mining in this direction, we have constructed and made publicly available a dataset of codified gold nanoparticle synthesis protocols and outcomes extracted directly from the nanoparticle materials science literature using natural language processing and text-mining techniques. This dataset contains 5,154 data records, each representing a single gold nanoparticle synthesis article, filtered from a database of 4,973,165 publications. Each record contains codified synthesis protocols and extracted morphological information from a total of 7,608 experimental and 12,519 characterization paragraphs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

59 BASIC BIOLOGICAL SCIENCES↗

High Performance EVA Glove Collaboration: Glove Injury Data Mining Effort

Human hands play a significant role during Extravehicular Activity (EVA) missions and Neutral Buoyancy Lab (NBL) training events, as they are needed for translating and performing tasks in the weightless environment. Because of this high frequency usage, hand and arm related injuries are known to occur during EVA and EVA training in the NBL. The primary objectives of this investigation were to: 1) document all known EVA glove related injuries and circumstances of these incidents, 2) determine likely risk factors, and 3) recommend interventions where possible that could be implemented in the current and future glove designs. METHODS: The investigation focused on the discomforts and injuries of U.S. crewmembers who had worn the pressurized Extravehicular Mobility Unit (EMU) spacesuit and experienced 4000 Series or Phase VI glove related incidents during 1981 to 2010 for either EVA ground training or in-orbit flight. We conducted an observational retrospective case-control investigation using 1) a literature review of known injuries, 2) data mining of crew injury, glove sizing, and hand anthropometry databases, 3) descriptive statistical analyses, and finally 4) statistical risk correlation and predictor analyses to better understand injury prevalence and potential causation. Specific predictor statistical analyses included use of principal component analyses (PCA), multiple logistic regression, and survival analyses (Cox proportional hazards regression). Results of these analyses were computed risk variables in the forms of odds ratios (likelihood of an injury occurring given the magnitude of a risk variable) and hazard ratios (likelihood of time to injury occurrence). Due to the exploratory nature of this investigation, we selected predictor variables significant at p≤0.15. RESULTS: Through 2010, there have been a total of 330 NASA crewmembers, from which 96 crewmembers performed 322 EVAs during 1981-2010, resulting in 50 crewmembers being injured inflight and 44 injured during 11,704 ground EVA training events. Of the 196 glove related injury incidents, 106 related to EVA and 90 to EVA training. Over these 196 incidents, 277 total injuries (126 flight; 151 training) were reported and were then grouped into 23 types of injuries. Of EVA flight injuries, 65% were commonly reported to the hand (in general), metacarpophalangeal (MCP) joint, and finger (not including thumb) with fatigue, abrasion, and paresthesia being the most common injury types (44% of total flight injuries). Training injuries totaled to more than 70% being distributed to the fingernail, MCP joint, and finger crotch with 88% of the specific injuries listed as pain, erythema, and onycholysis. Of these training injuries, when reporting pain or erythema, the most common location was the index finger, but when reporting onycholysis, it was the middle finger. Predictor variables specific to increased risk of onycholysis included: female sex (OR=2.622), older age (OR=1.065), increased duration in hours of the flight or training event (OR=1.570), middle finger length differences in inches between the finger and the EVA glove (OR=7.709), and use of the Phase VI glove (OR=8.535). Differentiation between training and flight and injury reporting during 2002-2004 were significant control variables. For likelihood of time to first onycholysis injury, there was a 24% reduction in rate of reporting for each year increase in age. Also, more experienced crewmembers, based on number of EVA flight or training events completed, were less likely to report an onycholysis injury (3% less for every event). Longer duration events also found reporting rates to occur 2.37 times faster for every hour of length. Crewmembers with larger hand size reported onycholysis 23% faster than those with smaller hand size. Finally, for every 1/10th of an inch increase in difference between the middle finger length and the glove, the rate of reporting increased by 60%. DISCUSSION: One key finding was that the Series 4000 glove had a lower injury risk than the Phase VI, which provides a platform for further evaluation. General interventions that reduce hand overexertion and repetitive use exposure through tool development, procedural changes and shorter exposures may be one mitigation path, but due to the way the training event times were reported, we cannot provide a guideline for a specific event duration change. When the finger length was different from the glove length, the risk of injury increased indicating that the use of larger finger take-ups could be contributing to injury and therefore may not be recommended. Prior to this investigation, there was one previous investigation indicating hand anthropometry may be related to onycholysis. We found different hand anthropometry variables indicated by this investigation as compared to the prior, specifically differences in middle finger length compared to glove finger length, which point more towards a sizing issue than a specific anthropometry issue. Additionally, although this investigation has identified sizing as an issue, the force and environmental-related variables of the EVA glove that could also cause injury were not accounted for.

Reid, C. R.↗

Toward the design of ultrahigh-entropy alloys via mining six million texts

Abstract It has long been a norm that researchers extract knowledge from literature to design materials. However, the avalanche of publications makes the norm challenging to follow. Text mining (TM) is efficient in extracting information from corpora. Still, it cannot discover materials not present in the corpora, hindering its broader applications in exploring novel materials, such as high-entropy alloys (HEAs). Here we introduce a concept of “context similarity" for selecting chemical elements for HEAs, based on TM models that analyze the abstracts of 6.4 million papers. The method captures the similarity of chemical elements in the context used by scientists. It overcomes the limitations of TM and identifies the Cantor and Senkov HEAs. We demonstrate its screening capability for six- and seven-component lightweight HEAs by finding nearly 500 promising alloys out of 2.6 million candidates. The method thus brings an approach to the development of ultrahigh-entropy alloys and multicomponent materials.

36 MATERIALS SCIENCE↗

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗

Exaflops Biomedical Knowledge Graph Analytics

We are motivated by newly proposed methods for mining large-scale corpora of scholarly publications (e.g., full biomedical literature), which consists of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover relationships among concepts. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as an all-pairs shortest paths (APSP) and validate connective paths against curated biomedical knowledge graphs (e.g., Spoke). In this context, we present Coast (Exascale Communication-Optimized All-Pairs Shortest Path) and demonstrate 1.004 EF/s on 9,200 Frontier nodes (73,600 GCDs). We develop hyperbolic performance models (HYPERMOD), which guide optimizations and parametric tuning. The proposed Coast algorithm achieved the memory constant parallel efficiency of 99% in the single-precision tropical semiring. Looking forward, Coast will enable the integration of scholarly corpora like PubMed into the Spoke biomedical knowledge graph.

Kannan, Ramakrishnan {ramki}↗

Deep Learning and Photogrammetric Reconstruction for Automated Crack Detection and Dimensional Measurement in Mining Operations

Surface crack detection and dimensional measurement at active mining sites present significant safety and operational challenges. Manual inspection methods are labor-intensive, spatially incomplete, and expose personnel to hazardous environments, while existing automated approaches have been developed primarily for concrete civil infrastructure and have not been validated on the complex, variable surfaces characteristic of mining environments. This dissertation presents an automated pipeline that integrates deep learning semantic segmentation with Structure-from-Motion photogrammetry to detect surface cracks and measure their aperture, length, and vertical displacement from standard RGB imagery acquired during routine Uncrewed Aerial Vehicle (UAV) survey operations, without requiring additional sensor hardware or manual measurement. The pipeline combines a U-Net architecture with an EfficientNet-B0 encoder, pretrained on the SDNET2018 concrete crack dataset and fine-tuned on a mining-specific dataset spanning laboratory concrete specimens, coal refuse impoundment embankments, and post-blast limestone quarry benches. Photogrammetric reconstruction is performed using COLMAP Structure-from-Motion and Multi-View Stereo, with crack segmentation masks projected into the reconstructed point cloud to enable three-dimensional vertical displacement measurement through local plane fitting and bimodal surface detection. The pipeline was validated across 36 controlled laboratory specimens at three imaging distances and four vertical displacement levels, achieving aperture measurement RMSE of 0.047 cm and R² of 0.954, and vertical displacement RMSE of 0.140 cm and R² of 0.966, against independent caliper measurements. Field application at a coal refuse impoundment in southwestern Pennsylvania detected 71 crack components across the embankment crest, with a dominant longitudinal crack exhibiting aperture values reaching 28 cm and a 95th percentile vertical displacement of 35.53 cm, consistent in magnitude and spatial distribution with simultaneously acquired LiDAR-derived estimates. Application across four post-blast limestone quarry bench datasets in California successfully characterized blast-induced fracture networks at ground sampling distances ranging from 0.59 to 1.23 cm/pixel, with detected crack geometries physically consistent with observable surface conditions at each site. The results demonstrate that deep learning-based crack detection and photogrammetric measurement can be integrated into routine UAV inspection workflows at mining sites, providing repeatable, scalable, and quantitative crack characterization across surface types, crack scales, and displacement magnitudes not previously addressed in the literature. The pipeline requires no dedicated surveying equipment beyond the UAV platforms already deployed at mine sites for survey and monitoring purposes, supporting practical adoption within existing operational workflows.

Crack detection, Dimensional Measurement↗

Sustainable recovery of Rare Earth Elements (REEs) from coal and coal ash through urban mining: A Nature Based Solution (NBS) for circular economy

The demand for rare earth elements (REEs) has surged in recent years, driven by their crucial role in various industrial applications and their uneven geological distribution. As a result, urban mining from secondary resources, particularly coal and coal ash, has gained traction as a sustainable solution within a circular economy framework. This study highlights the significant presence of REEs in coal and coal ash, revealing that certain samples contain REE concentrations that rival traditional ores. Notably, coal ash has the potential to yield approximately 312,000 tons of REEs annually, far exceeding global demand. The research delves into advanced techniques for analyzing REEs, including elemental, isotopic, and mineralogical studies. Additionally, it explores innovative extraction methods such as the use of green solvents, nature-based solutions, and bioleaching and biosorption. By leveraging coal and its byproducts as secondary resources, this study underscores the opportunity to reduce dependence on conventional mining, enhancing the sustainability of REE recovery. Here, a comprehensive literature review was conducted to highlight technological advancements and emerging opportunities that can address current challenges in this field.

Circular economy↗

Scalable Knowledge Graph Analytics at 136 Petaflop/s

We are motivated by newly proposed methods for data mining large-scale corpora of scholarly publications, such as the full biomedical literature, which may consist of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover how concepts relate to one another. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as one of computing all-pairs shortest paths (APSP), which becomes a significant bottleneck. In this context, we present a new high-performance algorithm and implementation of the Floyd-Warshall algorithm for distributed-memory parallel computers accelerated by GPUs, which we call DSNAPSHOT (Distributed Accelerated Semiring All-Pairs Shortest Path). For our largest experiments, we ran DSNAPSHOT on a connected input graph with millions of vertices using 4, 096nodes (24,576GPUs) of the Oak Ridge National Laboratory's Summit supercomputer system. We find DSNAPSHOT achieves a sustained performance of 136×1015 floating-point operations per second (136petaflop/s) at a parallel efficiency of 90% under weak scaling and, in absolute speed, 70% of the best possible performance given our computation (in the single-precision tropical semiring or “min-plus” algebra). Looking forward, we believe this novel capability will enable the mining of scholarly knowledge corpora when embedded and integrated into artificial intelligence-driven natural language processing workflows at scale.

Kannan, Ramakrishnan {ramki}↗

Remote Sensing Applications to the Pennsylvania Abandoned Mine Reclamation Program

Pennsylvania Abandoned Mine Land Inventory demonstrated the effective use of remote sensing techniques within the context of the Surface Mining Control and Reclamation Act of 1977. The inventory combined data from field work, a literature search, and photointerpretation to fulfill both State and Federal requirements. A primary project objective was to accurately identify and map all surface features and disturbances from abandoned surface and underground mining. Black-and-white aerial photographs were used to record pits, contour benches, highwalls, spoil material, graded and recontoured areas, impounded water, and serious erosion and slide prone areas. In addition, vegetation cover estimates and surrounding land uses were noted. The inventory data base provides Pennsylvania with a valuable resource management tool that should be systematically updated. The utilization of remotely sensed data from SPOT or LANDSAT-D satellites may prove valuable in the anticipated updating and monitoring of the Pennsylvania AML inventory over the next several years.

Clemens, E.↗

Comprehensive Study of the Potential of Extracting and Processing Critical Minerals from Coal-Based Resources - Phase I

The Phase I report prepared for the Department of Energy addresses U.S. Executive Order 13817 titled A Federal Strategy to Ensure Secure and Reliable Supplies of Critical Minerals, issued on December 20, 2017, that lists 35 critical minerals that are vulnerable to supply disruption. A comprehensive review of each of the minerals was conducted to determine the criticality based primarily on extractability from coal-based resources. Several other factors were also considered such as gaps in supply and demand, use in current technology, and the existence of viable substitutes. It was determined that the critical minerals that show highest potential for extraction from coal-based resources are lithium, rare earth elements (REEs), cobalt, and manganese. All four of the critical minerals listed serve an important role in the technology industry, have few substitutes, and have a heavy import reliance. Most notably are lithium, which is widely used in the electric vehicle industry, and the REEs which can be found in virtually all electronic devices. The research of critical mineral extraction from coal-based resources was completed using a combination of literature review from public sources as well as cooperation from coal mines and power plants across the United States. Samples collected from six different geographical locations across the U.S. were subjected to sample preparation (i.e., pH measurement, moisture content, particle size analysis) and characterization studies using Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) and Scanning Electron Microscopy, Energy Dispersive X-Ray Spectroscopy (SEM-EDX) instruments. 27 samples of coal waste materials such as refuse, sludge, and fly ash were tested to characterize the rare earth element concentration by total rare earth elements (TREEs), heavy rare earth elements (HREEs), and light rare earth elements (LREEs). Of the 27 samples tested, 22 contained a TREE concentration higher than the threshold of 300 ppm, which is considered a viable feedstock material. 3 samples contained less than 300 ppm of TREEs; however, they were within 20 ppm of the threshold, and could potentially be considered viable sources in the future pending the advancement of more efficient extraction technologies. 2 of the 27 samples had significantly low TREE concentrations, which does not imply any potential for being a source for REEs. For the minerals identified as most critical in the literature review, a conceptual process flow diagram (PFD) was developed for their extraction from different coal-based feedstocks. The process targets selective recovery of one commodity (i.e., rare earths, lithium, cobalt, and manganese) via several hydrometallurgical separation methods. By identifying potentially extractable coal-based critical mineral resources, a study of the current and future market environments for each critical mineral, and a review of current processing methodologies for critical mineral extraction from coal-based resources, the foundation has been laid to further characterize and explore new resources and extraction techniques. As reliance on technologies in industries such as the production of electronic devices, batteries, and alloys containing critical minerals utilizing critical minerals continues to increase, a sound understanding of our nation’s dependence on and even the global criticality of certain critical minerals, will serve as a catalyst for innovation in virtually all fields of science.

01 COAL, LIGNITE, AND PEAT↗

Utilization of lunar ilmenite: Basalt or regolith?

A critical discussion of whether lunar basalt or regolith should be used as a resource for mineral processing schemes on the lunar surface, with pros and cons for each argument is presented. A literature review has shown that the majority of authors feel that mining the lunar basalt, crushing it, and then processing to remove the desired minerals, would be the route to take. The argument that this method would not be a sound mineral processing practice is presented. Mining and crushing are difficult propositions even on Earth; to attempt such processes in the hostile lunar environment would be a phenomenal task. It would be better to start with a simpler scheme, such as processing the regolith, which can be adapted to the multitude of unknowns facing the first lunar production plant. If, however, the lunar mining trend is followed, it must be kept in mind that mining and processing technology which is radically different from what is currently available and used on Earth will have to be developed. Podnieks and Roepke (1987) and Lindroth and Podnieks (1987) have summarized the new technology that may be applicable, but this technology is very similar to the current, 99 percent inefficient technology used on Earth. One such possible technique is sodium vapor fragmentation of basalt. Initial testwork was conducted at Michigan Technological University on terrestrial basalt with extremely promising results, though much time and effort will be needed to fully develop this process.

Kawatra, S. K.↗

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗

Technology pathways for energy- and water-efficient controlled environment agriculture: A review of technologies, implementation pathways, and regional use cases

Controlled Environment Agriculture (CEA) offers high-yield, climate-resilient food production, but high energy and resource demands challenge its sustainability. This paper synthesizes technologies that can improve outcomes across six categories—energy, CO 2 utilization, building envelope, hardware, water, and process—plus colocation strategies. We evaluate 80 technologies and define ten implementation pathways bundling complementary technologies to reduce energy use, optimize water consumption, and minimize emissions. Regional application is demonstrated through five U.S. case studies spanning different climates. A logic framework guides pathway selection for case studies based on climate, infrastructure, and regulatory context, informing context-sensitive technology deployment. Results show energy intensity reductions of 3–55 %, ranging from energy management programs to comprehensive lighting retrofits; water savings of 20–40 % through closed-loop recirculation; and emissions reductions of 3–100 %, with strategic energy management achieving 3–5 % and renewable electricity paired with electrified heating achieving up to 100 %. Text mining revealed that energy, hardware, and process technologies account for 91 % of literature coverage. Water, building envelope, and CO 2 utilization remain underexplored, indicating priorities for future research. This integrative approach to technology assessment supports growers, developers, and policymakers in aligning CEA system design with local conditions, improving resource efficiency and addressing gaps in cross-domain technology coverage.

Controlled environment agriculture↗

A High-Throughput Computing Infrastructure to Generate Custom, Open Community Geothermal Datasets

The most significant challenge facing geothermal research, development, and deployment is a lack of comprehensive datasets describing the geological and economical properties of North America. Automated knowledge base construction, the process of designing algorithms to analyze text and images to programmatically build new datasets, is one possible solution to this problem. The xDD library of full-text scientific articles (https://xdd.wisc.edu) is one of the largest collections of open and controlled-access scientific documents available for knowledge base construction in the world, but it has been underutilized by experts in geothermal research. The xDD development team attributed the lack of engagement by software developers and geothermal researchers to two perceived shortcomings of the system. First, the workflow for obtaining data from xDD for local development and testing of data mining applications was unnecessarily abstruse and required significant manual intervention by xDD systems administrators. Second, although xDD already held articles from a broad cross-section of scientific literature with an emphasis on the geosciences, it did not have an explicit set of geothermal research documents that could serve as the nucleus of a geothermal data mining application. To address these issues, the Automated Data Extraction PlaTform (ADEPT) was proposed to extend the data distribution capabilities of the xDD system. The ADEPT extension added the following four key features to xDD: 1) integration of National Geothermal Data System (NGDS) documents into the xDD library to provide an explicitly geothermally-themed collection; 2) improved RESTful (i.e., https-protocol driven) web services for external partners to access xDD data for machine learning application development; 3) a web platform for end-users and xDD administrators to coordinate the development of data mining applications from the initial step of browsing available documents to the final stage of deploying a production-quality machine learning application on high-throughput computing infrastructure; and 4) the development of demonstration data mining applications to illustrate the new workflow to potential collaborators. A total of 21,674 geothermal documents from NGDS were fully ingested into the xDD library and the associated metadata is publicly available through the xDD web services; furthermore, the ADEPT web platform is now publicly accessible and fully live at https://xdd.wisc.edu/adept/.

15 GEOTHERMAL ENERGY↗