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At least 379 records · Page 21

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study.

60 APPLIED LIFE SCIENCES↗

Data-driven analysis of neutron diffraction line profiles: application to plastically deformed Ta

Abstract Non-destructive evaluation of plastically deformed metals, particularly diffraction line profile analysis (DLPA), is valuable both to estimate dislocation densities and arrangements and to validate microstructure-aware constitutive models. To date, the interpretation of whole line diffraction profiles relies on the use of semi-analytical models such as the extended convolutional multiple whole profile (eCMWP) method. This study introduces and validates two data-driven DLPA models to extract dislocation densities from experimentally gathered whole line diffraction profiles. Using two distinct virtual diffraction models accounting for both strain and instrument induced broadening, a database of virtual diffraction whole line profiles of Ta single crystals is generated using discrete dislocation dynamics. The databases are mined to create Gaussian process regression-based surrogate models, allowing dislocation densities to be extracted from experimental profiles. The method is validated against 11 experimentally gathered whole line diffraction profiles from plastically deformed Ta polycrystals. The newly proposed model predicts dislocation densities consistent with estimates from eCMWP. Advantageously, this data driven LPA model can distinguish broadening originating from the instrument and from the dislocation content even at low dislocation densities. Finally, the data-driven model is used to explore the effect of heterogeneous dislocation densities in microstructures containing grains, which may lead to more accurate data-driven predictions of dislocation density in plastically deformed polycrystals.

36 MATERIALS SCIENCE↗

Muon flux measurement at China Jinping Underground Laboratory

China Jinping Underground Laboratory (CJPL) is ideal for studying solar, geo-, and supernova neutrinos. A precise measurement of the cosmic-ray background is essential in proceeding with R&D research for these MeV-scale neutrino experiments. Using a 1-ton prototype detector for the Jinping Neutrino Experiment (JNE), we detected 264 high-energy muon events from a 645.2-day dataset from the first phase of CJPL (CJPL-I), reconstructed their directions, and measured the cosmic-ray muon flux to be $(3.53\pm0.22_{\rm{stat.}}\pm0.07_{\rm{sys.}})\times10^{-10}$ cm $^{-2}$s $^{-1}$. The observed angular distributions indicate the leakage of cosmic-ray muon background and agree with simulation data accounting for Jinping mountain's terrain. A survey of muon fluxes at different laboratory locations, considering both those situated under mountains and those down mine shafts, indicates that the flux at the former is generally a factor of $(4\pm2)$ larger than at the latter, with the same vertical overburden. In conclusion, this study provides a convenient back-of-the-envelope estimation for the muon flux of an underground experiment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NEWTS Economic Data Dashboard: Critical Materials for Energy

The NEWTS Economic Data Dashboard: Critical Materials for Energy is an economic screening tool for assessing the concentration and potential value of the 18 critical materials for energy in fossil energy-related wastewater across the United States. Datasets used to develop the dashboard and complete economic calculations are available as supplementary downloads. These resources were developed primarily using geochemical composition and volume data from the NEWTS Integrated dataset (version 1.0). Energy-related wastewater types presented in the dashboard include produced water (PW), brackish groundwater (BW), acid mine drainage (AMD), coal combustion residual leachate (CCRL), power plant flue gas desulfurization wastewater (FGD), and geothermal fluids. The concentrations of the following critical minerals were included in the analysis, when available: Al, Co, Cu, Dy, F, Ga, Ge, C, Ir, Li, Mg, Mn, Nd, Ni, Pt, Pr, Si, Tb. This economic screening tool was built to support identification of promising critical mineral feedstocks and economic research targets.

Critical Minerals; Critical Minerals and Materials↗

Raman spectroscopic investigation of selected natural uranyl sulfate minerals

Uranyl sulfates are important constituents of uranium ores and represent a significant fraction of U(VI) minerals discovered in recent years owing to their propensity to form in mine tailings and legacy sites related to uranium exploration. Recently, we surveyed all published Raman spectra for uranium minerals and found significantly less easily accessible data available for uranyl sulfates relative to other groups of uranium minerals (Spano et al. 2023). In that work, we described average spectra for groups of uranyl minerals to understand common vibrational spectroscopic features attributable to similarities in oxyanion chemistry among U(VI) minerals, but only data for three uranyl sulfate minerals were included in the study. The present work reports on Raman spectra collected for 18 additional uranyl sulfate minerals. In conclusion, to better understand underlying structural and chemical features that give rise to spectroscopic observables, we relate differences in structural topology, charge-balancing cations, and locality of origin to features observed in the Raman spectra of selected natural uranyl sulfates.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

EGS Collab Experiment 2: Testbed Well Orientation Data

This dataset contains the north seeking gyro data for each of the 11 boreholes drilled at the Experiment 2 testbed on the 4100 foot level of the SURF (Sanford Underground Research Facility). Each gyro file is in individual folders for each well. A single folder called 'E2 All Well Trajectories' contains the trajectories for all the wells but in the mine coordinate system. An image of the well layout is provided in a PowerPoint.

15 GEOTHERMAL ENERGY↗

Predicting material microstructure evolution via data-driven machine learning

The recent rapid rise in data-driven practices in the materials science domain has led to the development of efficient, generalizable, and accurate approaches for several applications, including: material property prediction, mining (micro)structure- property and (micro)structure-processing relationships, and characterization of material microstructures. Central to the materials science domain is linking microstructure to properties and performance, and critical to building such linkages is understanding how microstructures evolve as a function of environmental exposure or processing conditions (e.g., time, temperature, applied stress or strain, irradiation). This preview article summarizes recent work on the development of recurrent neural networks for predicting spatio-temporal microstructure evolution detailed by Yang et al in their manuscript entitled 'Self-supervised Learning and Prediction of Microstructure Evolution with Recurrent Neural Networks'.

machine learning (ML), materials characterization↗

Dynamic Network Analysis of Nuclear Science Literature for Research Influence Assessment

Analyzing nuclear science literature via data-driven methods is a critical step for assessing research influence and technology advancements. Indicators of scholarly activities may be buried in large volumes of nuclear research publications and collaboration networks over time. Mining for relevant scholarly influence trends in large volumes of text can be computationally challenging; however, open-source information on research collaborations over time can offer opportunities to extract meaningful insights. While network centrality analysis of scholarly research provides topology-based insights, additional emphasis on dynamics associated with the diffusion of information through these networks is important. Here this paper represents a step in that direction through the development of a novel dynamic network analysis framework and computational engine to identify key entities and capabilities over time within global scholarly nuclear science collaboration networks. Network theoretic, stochastic simulation, and optimization methods are leveraged to address variability in scholarly interactions, influence propagation, and collaboration patterns via network connections. A topic-aware influence maximization algorithm is developed to address the goal of identifying key influential authors in diverse research topics over time. Efficient parallelized implementation of the algorithm is applied to reduce computational costs. A proof-of-concept case study using open-source Scopus data with 33,517 published nuclear research papers from 2000-2019 is presented and representative analytic insights are generated. Broad implications of these insights are discussed and future research directions are also identified.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Final Scientific/Technical Report: Real Time Particle Size and Settling Velocity for In-Situ Monitoring of Deep-Sea Polymetallic Nodule Mining

In the coming decade, it is anticipated that deep-sea mining activities will commence throughout the deep ocean, at depths around 4000-6000m where vast deposits of baseball-sized rocks called polymetallic nodules lay on the seabed. These nodules contain resources such as cobalt, copper and nickel which are needed to produce batteries for electric vehicles. Collector machines driving on the seabed and gathering these nodules will stir up clouds of sediment, and there is concern about how the resulting concentration of sediment in the near-bottom ocean water will affect deep and mid-ocean biology. There is currently no technology capable of comprehensively monitoring the concentrations and properties of stirred up sediment in the deep. This project addressed this critical gap by developing a deep-sea particle measurement system (Real-Time Size and Settling Velocity, RTSSV) that uses a multi-camera high-resolution video imaging system, with accompanying image processing, to measure the concentration, size distribution and settling speed of sediment. Importantly, these measurements are made in-situ, so that delicate sediment aggregates will not be disturbed, as is the case when collecting samples at depth to be measured in the lab. The instrument can be mounted on a variety of established deep-sea platforms such as moorings, AUVs and ROVs, providing data in near real time, where the key measurements need to be made—from the source of the sediment disturbance and throughout the resulting plume—vital for determining if deep-sea mining can be done in an environmentally responsible manner. The developed system (RTSSV) will possess the only such capability worldwide, giving a US-based group a substantial competitive advantage as this newly evolving global industry develops. As added value, the technology will also have widespread application to the offshore oil and gas industry, dredging industry, and to sediment science research.

47 OTHER INSTRUMENTATION↗

Verifiable Fuel Cycle Simulation

The Verifiable Fuel Cycle Simulation (VISION) is a system-dynamics model of the entire nuclear fuel cycle, from mining to disposal, using user-defined deployment scenarios, fuel recipes, and recycling parameters. It is written in the PowerSim simulation environment and utilized MS Excel to manage data inputs and outputs.

Hays, RossD (0000000184587539)↗

Graph identification of proteins in tomograms ( GRIP‐Tomo )

Abstract In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases for refinement. We hypothesized that the topological connectivity of protein structures is invariant, and they are distinctive for the purpose of protein identification from distorted data presented in volume densities. Three‐dimensional densities of a protein or a complex from simulated tomographic volumes were transformed into mathematical graphs as observables. We systematically introduced data distortion or defects such as missing fullness of data, the tumbling effect, and the missing wedge effect into the simulated volumes, and varied the distance cutoffs in pixels to capture the varying connectivity between the density cluster centroids in the presence of defects. A similarity score between the graphs from the simulated volumes and the graphs transformed from the physical protein structures in point data was calculated by comparing their network theory order parameters including node degrees, betweenness centrality, and graph densities. By capturing the essential topological features defining the heterogeneous morphologies of a network, we were able to accurately identify proteins and homo‐multimeric complexes from 10 topologically distinctive samples without realistic noise added. Our approach empowers future developments of tomogram processing by providing pattern mining with interpretability, to enable the classification of single‐domain protein native topologies as well as distinct single‐domain proteins from multimeric complexes within noisy volumes.

59 BASIC BIOLOGICAL SCIENCES↗

2018 Industrial Energy Data Book

The 2018 Industry Energy Data Book summarizes the status of, and it identifies the key trends in energy use and its underlying economic drivers across the four industrial subsectors: agriculture, construction, manufacturing, and mining.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

The EGS Collab Project – Stimulations at Two Depths

The EGS Collab project, supported by the US Department of Energy, is performing intensively monitored rock stimulation and flow tests at the 10-m scale in an underground research laboratory to address challenges in implementing enhanced geothermal systems (EGS). Data and observations from the field tests are compared to simulations to understand processes and build confidence in numerical modeling of the processes. We have completed Experiment 1 (of 3), which examined hydraulic fracturing in a well-characterized underground fractured phyllite test bed at a depth of approximately 1.5 km at the Sanford Underground Research Facility (SURF) in Lead, South Dakota. Testbed characterization included fracture mapping, borehole acoustic and optical televiewers, full waveform sonic, conductivity, resistivity, temperature, campaign p- and s-wave investigations and electrical resistance tomography. Borehole geophysical techniques including passive seismic, continuous active source seismic monitoring, electrical resistance tomography, fiber-based distributed strain, distributed temperature, and distributed acoustic monitoring, were used to carefully monitor stimulation events and flow tests. More than a dozen stimulations and nearly one year of flow tests were performed. Quality data and detailed observations were collected and analyzed during stimulation and water flow tests using ambient temperature and chilled water. We achieved adaptive control of the tests using real-time monitoring and rapid dissemination of data and near-real-time simulation. More detailed numerical simulation was performed to answer key experimental design questions, forecast fracture propagation trajectories and extents, and analyze and evaluate results. Data are freely available from the Geothermal Data Repository. Experiment 2 examines the potential for hydraulic shearing in amphibolite at a depth of about 1.25 km at SURF. This site has a different set of stress and fracture conditions than Experiment 1. The Experiment 2 testbed consists of nine subhorizontal boreholes configured in two fans of two boreholes which surround the testbed and contain grouted-in electrical resistance tomography, seismic sensors, active seismic sources and distributed fiber sensors. A “five-spot” set of test wells that extends from a custom mined alcove includes an injection well and four production/monitoring wells. The testbed was characterized geophysically and hydrologically, and three stimulations have been performed using the Step-Rate Injection Method for Fracture In-Situ Properties (SIMFIP) tool to measure strains, and a new strain quantifying tool (downhole robotic strain analysis tool -DORSA) was deployed in a monitoring hole during stimulation. Real-time data were broadcast during stimulations to allow real-time response to arising issues.

EGS Collab, Enhanced Geothermal Systems, EGS, fiel↗

UV-Vis spectrophotometric determination of rare earth elements (REE) speciation at near-neutral to alkaline pH. Part II: hydrolysis of Er from 25 to 75 °C

Aqueous speciation of rare earth elements (REE) controls their mobilization, fractionation, and enrichment in the natural waters. Geochemical modeling of their speciation is key to improve our understanding of the formation of economic mineral deposits, for developing mineral separation and mine tailing recovery technologies, and for characterizing the geochemistry of thermal water. However, our ability to predict the fate of REE in a wide pH and temperature range is limited by the scarcity of thermodynamic data for the REE hydroxyl complexes. In part I of this study (H. J. Han and A. P. Gysi, Dalton Trans., 2024, 53, 13129–13141), the optical properties of m-cresol purple (mCP) were determined using UV-Vis spectrophotometry between 25 and 75 °C in order to develop a method for deriving the hydrolysis constants of erbium (Er). Here, UV-Vis spectrophotometry experiments were conducted as a function of temperature between 35 and 75 °C to determine the hydrolysis of Er in near-neutral to alkaline solutions using mCP as an in situ pH color indicator. Here, the experiments were conducted with Er concentrations from 0 to ~0.253 mmol kg –1 in low ionic strength solutions (≤0.001 mol kg –1 ).

58 GEOSCIENCES↗

A New Method for High Resolution Surface Change Detection: Data Collection and Validation of Measurements from UAS at the Nevada National Security Site, Nevada, USA

The use of uncrewed aerial systems (UAS) increases the opportunities for detecting surface changes in remote areas and in challenging terrain. Detecting surface topographic changes offers an important constraint for understanding earthquake damage, groundwater depletion, effects of mining, and other events. For these purposes, changes on the order of 5–10 cm are readily detected, but sometimes it is necessary to detect smaller changes. An example is the surface changes that result from underground explosions, which can be as small as 3 cm. Previous studies that described change detection methodologies were generally not aimed at detecting sub-5-cm changes. Additionally, studies focused on high-fidelity accuracy were either computationally modeled or did not fully provide the necessary examples to highlight the usability of these workflows. Detecting changes at this threshold may be critical in certain applications, such as global security research and monitoring for high-consequence natural hazards, including landslides. Here we provide a detailed description of the methodology we used to detect 2–3 cm changes in an important applied research setting—surface changes related to underground explosions. This methodology improves the accuracy of change detection data collection and analysis through the optimization of pre-field planning, surveying, flight operations, and post-processing the collected data, all of which are critical to obtaining the highest output data resolution possible. We applied this methodology to a field study location, collecting 1.4 Tb of images over the course of 30 flights, and location data for 239 ground control points (GCPs). We independently verified changes with orthoimagery, and found that structure-from-motion, software-reported root mean square errors (RMSEs) for both control and check points underestimated the actual error. We found that 3 cm changes are detectable with this methodology, thereby improving our knowledge of a rock’s response to underground explosions.

47 OTHER INSTRUMENTATION↗

Estimating value of information for heliostat washing operations at solar thermal plants

Concentrating solar power (CSP) plants depend on thousands of heliostats whose reflectance declines as dust accumulates. Operators routinely measure reflectance to estimate soiling and, in turn, inform cleaning schedules, but the value of collecting more frequent or more accurate data has not been formally quantified. This study introduces a Monte Carlo discrete event simulation framework that integrates stochastic models of soiling, weather, and measurement error with a dynamic cleaning dispatch policy to estimate annual energy production and operations costs. Applied to two representative central-receiver field configurations, the results show that both the frequency and accuracy of reflectance measurements can meaningfully impact plant performance. In both case studies, reducing measurement intervals yields significant returns, with the energy gains greatly exceeding the cost of more frequent data collection. The simulation framework serves as a decision-support tool for CSP operators, allowing them to input site-specific soiling conditions, measurement accuracy, and survey frequency to evaluate the tradeoffs between data collection cost and energy recovery, and to identify measurement strategies that maximize plant profit.

14 SOLAR ENERGY↗