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At least 937 records · Page 52

Towards a Comparative Assessment of Data-Driven Process Models in Health Information Technology

Process mining for conformance analysis focuses on comparing a reference process model against a data-driven process model that is generated via log files from information technology systems. While this approach is helpful when there is an existing process model in an organization, it leaves the question of what to do in the absence of a complete reference process model unanswered. In this paper, we present a comparative assessment approach that combines process mining, process mapping for dimensionality reduction, and statistical analysis. Our goal is to find similarities and dissimilarities in data-driven process models among U.S. Veterans Health Administration (VHA) facilities to assess process conformance among different healthcare facilities, which can help assess the standardization of care. We illustrate our approach by applying it to two clinical radiology order process models generated by two similar facilities. Our results demonstrate statistical similarities in the standardization of care among those two facilities.

Klasky, Hilda↗

Multi-Resolution UAV Path Replanning for Inspection of Tailings Dams

Autonomous inspection of large and complex structures with a commercial unmanned aerial vehicle (UAV) is a challenging problem that has been addressed in recent years. In this paper, we address the global motion planning problem of creating autonomous inspection missions for UAVs considering photogrammetry constraints. We focus on the inspection of large tailings dams, which are dam structures used to store waste byproducts of mining. Our method uses a prior sparse point cloud of the dam to generate a voxel grid, where paths satisfying photogrammetry constraints are tested for collisions. We then apply the A* algorithm as a local planner to avoid obstacles within the global mission. Moreover, we address the problem of changing routes online by using octree-based multi-resolution grids for efficient and fast pathfinding. Our results, obtained using tridimensional maps of an actual coal mine tailings dam, show that using octrees for multi-resolution motion planning is faster than using a fixed voxel grid in online missions while inspecting large structures.

42 ENGINEERING↗

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}↗

Resiliency-Driven Proactive Distribution System Reconfiguration With Synchrophasor Data

Measuring and enabling resiliency of electric distribution systems with increasing weather and cyber events are important. Some of the extreme events (e.g. Earthquakes, Hurricanes) and associated paths are predicted and monitored closely in advance and allow to take pre-event proactive control actions. The Distribution Phasor Measurement Units (D-PMUs) provide new opportunities and supporting such proactive actions. Here, a synchrophasor based resiliency driven pre-event reconfiguration can ensure minimizing impact of the expected event on the power distribution system and associated performance. However, the D-PMUs will also face challenges in terms of data quality similar to the transmission PMUs. The focus of this paper is to provide data mining approaches for anomaly detection in D-PMUs and proposing resiliency-driven pre-event reconfiguration with islanding as a proactive mechanisms to minimize the impact of adverse events on system using processed synchrophasors data. Results are validated for real industrial feeders and test cases with satisfactory response

controlled islanding↗

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

ABSTRACT Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions. IMPORTANCE Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.

59 BASIC BIOLOGICAL SCIENCES↗

A shift between mineral and nonmineral sources of iron and sulfur causes proteome-wide changes in Methanosarcina barkeri

ABSTRACT Iron (Fe) and sulfur (S) are required elements for life, and changes in their availability can limit the ecological distribution and function of microorganisms. In anoxic environments, soluble Fe typically exists as ferrous iron [Fe(II)] and S as sulfide (HS − ). These species exhibit a strong affinity that ultimately drives the formation of sedimentary pyrite (FeS 2 ). Recently, paradigm-shifting studies indicate that Fe and S in FeS 2 can be made bioavailable by methanogens through a reductive dissolution process. However, the impact of the utilization of FeS 2 , as opposed to canonical Fe and S sources, on the phenotype of cells is not fully understood. Here, shotgun proteomics was utilized to measure changes in the phenotype of Methanosarcina barkeri MS grown with FeS 2 , Fe(II)/HS − , or Fe(II)/cysteine. Shotgun proteomics tracked 1,019 proteins overall, with 307 observed to change between growth conditions. Functional characterization and pathway analyses revealed these changes to be systemic and largely tangential to Fe/S metabolism. As a final step, the proteomics data were viewed with respect to previously collected transcriptomics data to deepen the analysis. Presented here is evidence that M. barkeri adopts distinct phenotypes to exploit specific sources of Fe and S in its environment. This is supported by observed protein abundance changes across broad categories of cellular biology. DNA adjacent metabolism, central carbon metabolism methanogenesis, metal trafficking, quorum sensing, and porphyrin biosynthesis pathways are all features in the phenotypic differentiation. Differences in trace metal availability attributed to complexation with HS − , either as a component of the growth medium [Fe(II)/HS − ] or generated through reduction of FeS 2 , were likely a major factor underpinning these phenotypic differences. IMPORTANCE The methanogenic archaeon Methanosarcina barkeri holds great potential for industrial bio-mining and energy generation technologies. Much of the biochemistry of this microbe is poorly understood, and its characterization will provide a glimpse into biological processes that evolved close to life’s origin. The discovery of its ability to extract iron and sulfur from bulk, solid-phase minerals shifted a longstanding paradigm that these elements were inaccessible to biological systems. The full elucidation of this process has the potential to help scientists and engineers extract valuable metals from low-grade ore and mine waste generating energy in the form of methane while doing so.

59 BASIC BIOLOGICAL SCIENCES↗

Interpretation of hydrothermal conditions, production-injection induced effects, and evidence for enhanced geothermal system-type heat exchange in response to >30 years of production at Roosevelt Hot Springs, Utah, USA

The Roosevelt Hot Springs hydrothermal system is located at the base of the Mineral Mountains in southwestern Utah on the eastern side of the Basin and Range. Hydrothermal activity is related to relatively recent bimodal magmatism, and the system is hosted in coarsely crystalline rock made of Oligocene–Miocene granitoids and Precambrian gneiss. The hydrothermal plume covers ~5 km 2 , with a maximum temperature of 268 °C at ~750 m depth, and a vertically extensive fault-fracture mesh east of the Opal Mound fault controls the upflow of hydrothermal fluids. Power generation (currently 38 MWe gross) began in 1984, and up through 2016, four wells were used for fluid production, and three wells were used for edge-field injection. Chemical analyses of produced fluids show that modern reservoir fluid compositions are similar to but more concentrated than those at the start of production, having near-neutral pH, total dissolved solids of 7000–10,000 mg/kg, and ionic ratios of Cl/HCO 3 ~50–100, Cl/SO4 ~50–100, and Na/K ~4–5. Chemical geothermometers indicate equilibration temperatures that mainly range between 240° and 300 °C. Early production induced a steep drop in pressure (~3.0–3.5 MPa), which was accompanied by a 250–300 m lowering of piezometric levels in wells and development of a shallow steam zone across the system. Hydrothermal fluid compositions evolved continuously in response to production-related steam-loss and injection breakthrough, which is reflected by gradual increases in chloride of up to 35% and stable isotope ratios of up to ~2‰δ 18 O and ~10‰δD. Simple mixing model calculations suggest that there has been a significant amount, ~10–20 MW th , of sustained multi-decadal heat mining and enhanced geothermal system (EGS)–type heat transfer by the injectate as it returns to the production zone. Overall, the two factors that have sustained long-term power production (currently 38 MWe gross) are the increased upflow of deep chloride water and, to a lesser extent, the mining of heat at <1 km depth.

58 GEOSCIENCES↗

Provenance infrastructure for multimodal x-ray experiments and reproducible analysis

Exploring relationships between material structures and desired properties for material discovery and synthesis requires mining machine-readable databases and linking experimental data with sufficiently rich annotations. There are vast gaps both in these data sources and in the connections between them. We present a provenance-based data management and analysis framework that enables capturing, persisting, and reanalyzing experimental data from the BNL National Synchrotron Light Source II (NSLS-II). Our system leverages NSLS-II Bluesky for experimental data acquisition, captures analysis parameters, and enriches the search space with results from the scientific literature. We describe in detail the challenges and benefits of data-driven approaches when comparing computational and experimental data, such as the multiple possible scenarios of interest in often ill-posed inverse problems and missing data. Our infrastructure utilizes the NSLS-II event model and includes discovery mechanisms across multiple beamlines. A text and data mining module using natural language processing classification techniques extracts relevant information from the literature that is added to data sources. We describe a provenance acquisition and analysis rerun workflow based on a directed acyclic graph that keeps track of process and data provenance and allows to replay analysis.

97 MATHEMATICS AND COMPUTING↗

SANSMIC v.1.0

SAND2024-01036O The updated Sandia Solution Mining Code (SANSMIC) modeling software models the dissolution of underground salt cavern walls due to raw-water injection (leaching), assuming an oil blanket. A previous version of this software modeled the impacts of leaching at the Strategic Petroleum Reserve and has been used in research for several decades, but the source code was not available. The new version will enhance current research as additional subsurface storage of energy in solution-mined caverns increases. It will also allow research reproducibility by making the software available to the wider research community. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Hart, David↗

EGS Collab Testbed 2: Laser Scanned 4100 L Drift Map

The EGS Collab project is evaluating a site for Experiment 2 (hydraulic fracturing/shearing) at a depth of 1.25 km in the Sanford Underground Research Facility (SURF) on the 4100 Level. Two early test holes were drilled in an alcove (formerly known as Battery Charging Station) near Yates Shaft. Recently, we conducted a laser survey around the Testbed 2 to capture the details of the drift. This submission package includes the laser scanned drift map around the Testbed 2. The drift map data are presented in AutoCAD (*dxf), Leapfrog mesh (*.msh), and point cloud (*.csv) file formats. Note: The coordinate system used is local Homestake Mine Coordinate (HMC) system from an old gold mine that was in operation for over 100 years.

15 GEOTHERMAL ENERGY↗

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↗

Toward a least-effort principle for evaluating prices of elements as indicators of sustainability

In this article, we explore simplifying mechanisms in materials economics for conceptionally organizing the flows of chemical elements into society. We use the concept of rank, which plays a crucial role in information theory where power laws are involved, and is a useful measure for seeking extremal principles. Borrowing from an analogy to Zipf’s law leads to a power-law relationship between abundance and rank that—pressing the Zipf’s law analogy further—may suggest that the price paid for elemental materials optimizes efficient utilization. Factors such as weight, volume, and moles in the earth's crust or in global mining production of elements are used in our analysis. For this research, 42 elements with price and production data for the year 2010 (a relatively typical year) were considered. We observe that the role of the volume from global mining production dominates in materials economics and indicate that elements such as Te and He should be sold at prices at leas ~ 100–1000 times more than their present price for efficient utilization.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

AmeriFlux FLUXNET-1F US-GLE GLEES

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-GLE GLEES. This is the FLUXNET version of the carbon flux data for the site US-GLE GLEES produced by applying the standard ONEFlux (1F) software. Site Description - The Glacier Lakes Ecosystem Experiments Site (GLEES) site is located on land owned by the U.S. government and managed by US Forest Service as part of the Medicine Bow National Forest. Many of the trees in the immediate vicinity of the site are older than 400 years, inter-dispersed among trees much younger in age. This widespread age distribution is most likely a derivation of one of two scenarios: 1) A widespread stand replacement about 400 years ago followed by a slow replacement; 2) Intermittent random disturbances over the past 400 years (Bradford et al. 2008). A decade long spruce beetle outbreak that peaked in 2008 resulted in the mortality of 85% of the forested basal area. There are a few private land holdings in the area, with scattered uncorked mining claims. Following the establishment of the National Forest, mining was banned and grazing was closed in the early 1990's in the upper portion of the GLEES site. Recreation in the winter, when snow can remain in patches into the summer months, snow mobiling and cross country skiing are popular. During the limited summer, hiking, camping and fishing are common activities. The site is accessible by vehicle only during the summer on Forest Road FDR 317, and in the winter, the tower is only reachable via snowmobile.

Frank, John↗

The Effects of Assumed Source Depth and Shear-Wave Velocity on Moment Tensors Estimated for Small, Contained Chemical Explosions in Granite

ABSTRACT The Source Phenomenology Experiment (SPE-Arizona) included of a series of chemical explosions detonated within a copper mine in Arizona. This study focuses on ground motions from detonations in the copper mine, which are analyzed to assess the uniqueness of the resulting source representation when the source region propagation characteristics have a range of possible models. P-wave velocities are well constrained by refraction data with less constraint of the S-wave velocities. The effects of explosion source depth and VS are assessed with Green’s functions for a range of models in which VP is held constant. Propagation models with a Poisson’s value of 0.25 and a source depth 30–60 m most accurately replicate the data. The explosion was detonated at a centroid depth of 30 m, so trade-offs in depth are demonstrated. The compensated linear vector dipole and explosion components of the Green’s functions convolved with a Mueller–Murphy source function are compared. Both produce significant energy in the 2–12 Hz band, due to surface-wave contributions with no clear depth dependencies above 20 Hz. The range of propagation models is used with the observational data to invert for the frequency-domain moment tensor. Fits to the data from these inversions have cross-correlation values of 0.64, demonstrating effectiveness in replicating the observations with the assumed propagation path effects and resulting source function. Inversions produce horizontal dipoles (Mxx and Myy), roughly half the maximum amplitude of Mzz, consistent with a compensated linear vector dipole source, which is frequency dependent. Denny and Johnson, Mueller–Murphy, Walter and Ford, and the revised Mueller–Murphy source models, parameterized for granite, are compared to the moment tensors. Despite a nonisotropic moment tensor source, the revised Mueller–Murphy isotropic source model best replicates the long-period moments, overshoot, and corner frequency.

Geochemistry & Geophysics↗

Hydroxylpyromorphite, a mineral important to lead remediation: Modern description and characterization

Abstract Hydroxylpyromorphite, Pb5(PO4)3(OH), has been documented in the literature as a synthetic and naturally occurring phase for some time but has not previously been formally described as a mineral. It is fully described here for the first time using crystals collected underground in the Copps mine, Gogebic County, Michigan. Hydroxylpyromorphite occurs as aggregates of randomly oriented hexagonal prisms, primarily between about 20–35 μm in length and 6–10 μm in diameter. The mineral is colorless and translucent with vitreous luster and white streak. The Mohs hardness is ~3½–4; the tenacity is brittle, the fracture is irregular, and indistinct cleavage was observed on {001}. Electron microprobe analyses provided the empirical formula Pb4.97(PO4)3(OH0.69F0.33Cl0.06)Σ1.08. The calculated density using the measured composition is 7.32 g/cm3. Powder X-ray diffraction data for the type material is compared to data previously reported for hydroxylpyromorphite from the talc mine at Rabenwald, Austria, and from Whytes Cleuch, Wanlockhead, Scotland. Hydroxylpyromorphite is hexagonal, P63/m, at 100 K, a = 9.7872(14), c = 7.3070(10) Å, V = 606.16(19) Å3, and Z = 2. The structure [R1 = 0.0181 for 494 F>4σ(F) reflections] reveals that hydroxylpyromorphite adopts a column anion arrangement distinct from other members of the apatite supergroup due to the presence of fluorine and steric constraints imposed by stereoactive lone-pair electrons of Pb2+ cations. The F– anion sites are displaced slightly from hydroxyl oxygen anions, which allows for stronger hydrogen-bonding interactions that may in turn stabilize the observed column-anion arrangement and overall structure. Our modern characterization of hydroxylpyromorphite provides deeper understanding to a mineral useful for remediation of lead-contaminated water.

Geochemistry & Geophysics↗

Toward CO 2 Multimeasurement Geophysical Monitoring in the North Dakota CarbonSAFE Project

Paper presented at 16th International Conference on Greenhouse Gas Control Technologies (GHGT-16), October 23–27, 2022, Lyon, France. Overcoming data acquisition challenges associated with a lake in the study area, electrical infrastructure around the plant, noise from mine activities, complex near-surface conditions associated with reclaimed mine land, high wind speed, and extremely cold temperatures, data processing, modeling, and inversion of the baseline geophysical data demonstrated the importance of high-quality data for a CO 2 geophysical monitoring program. Implementing more advanced data acquisition and processing techniques in future monitoring surveys can further improve confidence in interpretations of geophysical survey data.

20 FOSSIL-FUELED POWER PLANTS↗

Argonne’s global critical materials agent-based model (GCMat)

Several studies have identified rare earths as critical materials. Although reasonably abundant in the Earth’s crust, rare earths typically occur in low concentrations of mined ores. Processes for recovering rare earth concentrates from these ores are complex and capital intensive. Further, lead times for deposit development, licensing, and construction are long, with reports of 10- 15 years. China is a major player in the rare earths supply chain, both in production capacity and technology innovation. In 2017, China supplied more than 80% of global rare earth oxide demand. Rare earth elements (REEs) have unique magnetic, catalytic, and phosphorescent properties that significantly improve performance of a wide range of technologies. These technologies span aerospace, energy, telecommunications, electronics, transportation, defense, and other diverse applications. Consequently, disruptions in rare earth supply can have a significant societal impact. Estimating that impact requires understanding of the dynamics across the supply chain, from rare earth oxide extraction to end use application. This report documents Argonne’s Global Critical Materials model (GCMat), first described by Riddle et al. 2015. GCMat provides capabilities to explore supply chain dynamics and uncertainty under scenarios of demand growth or shrinkage, technology adoption, supply disruptions, and trade policies and mitigation strategies of new supply sources, product substitution, consumer thrifting, and stockpiling. Supply chain participants from rare earth mining through final demand are modeled as interacting agents who make market decisions independently as time progresses. Since the version documented in Riddle et al. 2015, GCMat has been expanded to cover additional REEs, derived products and supply chains that use these REEs, and includes new agent behaviors and modeling capabilities. Section 2 provides a summary of the GCMat model design, including the structure of the model and key assumptions, section 3 summarizes methods used for model calibration and sensitivity analysis, and section 4 provides examples of model results.

36 MATERIALS SCIENCE↗

Economic Extraction, Recovery and Upgrading of Rare Earth Elements from Coal-Based Resources

The overall objective of this project is to produce a rare earth elements product with greater than 8% rare earth elements from coal-based resources using an economically viable and environmentally benign processing methodology. The objective of the coal processing work will be to acquire appropriate coal feed and produce a viable clean coal product, a concentrated REE feed stream, and a pyrite stream (where available) that can be used to enhance leaching. The objective of the bio-oxidation portion of the project is to utilize bacteria to oxidize sulfide minerals and ferrous ions to ferric ions to accelerate leaching and remove the sulfides to prevent future acid mine drainage and related liabilities. The objective of the solution conditioning work is to remove iron and control leaching solution conditions to facilitate extraction of REEs without significant thorium extraction. The objective of the column leaching work is to engineer/model and simulate heap leaching to demonstrate low-cost extraction of REEs from coal-based resources. The objective of the solvent extraction work is to selectively extract and recover through controlled stripping of REEs that are solubilized through leaching. The objective of the precipitation portion of the project is to recover the REEs from the solvent extraction stripping solutions and dry them to achieve the final product of rare earth elements that is > 8 % REEs. The objective of the technical, economic, and environmental analysis is to determine the overall viability of the processing approach that is demonstrated in this project. This project encompasses a range of technologies that are currently in industrial practice that are applied and engineered to produce rare earth element product from coal feed sources. The potential sources include large coal feed resources in active coal mines in addition to coal waste. This technology involves the utilization of advanced coal processing technology that can be used to deliver clean coal for the market as well as rare-earth-element-bearing non-coal rock that is of the correct size for heap leaching applications in addition to providing concentrated sulfide minerals (for mid to high sulfur coals) for cleaner coal and for enhanced bio-oxidation to accelerate leaching of REEs from the non-coal rock. The removal of the sulfide minerals cleans the coal, accelerates subsequent REEs extraction, and it removes the future potential for most acid-rock drainage. (For low sulfur coals some pyrite may be purchased if needed.) The processing method also utilizes bio-oxidation to enhance ferric ion production to enhance leaching, while also consuming the sulfide mineral and its associated environmental liability. The project includes a technical, economic, and environmental analysis to facilitate an appropriate assessment of commercial viability for this processing technology.

01 COAL, LIGNITE, AND PEAT↗