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At least 1,063 records · Page 59

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DOE OSTI2022

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↗

DOE OSTI2022

Warning Signs of Potential Black Swan Outbreaks in Infectious Disease

Black swan events in infectious disease describe rare but devastatingly large outbreaks. While experts are skeptical that such events are predictable, it might be possible to identify the warning signs of a black swan event. Specifically, following the initiation of an outbreak, key differentiating features could serve as alerts. Such features could be derived from meta-analyses of large outbreaks for multiple infectious diseases. We hypothesized there may be common features among the pathogen, environment, and host epidemiological triad that characterize an infectious disease black swan event. Using Los Alamos National Laboratory’s tool, Analytics for Investigation of Disease Outbreaks, we investigated historical disease outbreak information and anomalous events for several infectious diseases. By studying 32 different infectious diseases and global outbreaks, we observed that in the past 20–30 years, there have been potential black swan events in the majority of infectious diseases analyzed. Importantly, these potential black swan events cannot be attributed to the first introduction of the disease to a susceptible host population. This paper describes our observations and perspectives and illustrates the value of broad analysis of data across the infectious disease realm, providing insights that may not be possible when we focus on singular infectious agents or diseases. Data analytics could be developed to warn health authorities at the beginning of an outbreak of an impending black swan event. Such tools could complement traditional epidemiological modeling to help forecast future large outbreaks and facilitate timely warning and effective, targeted resource allocation for mitigation efforts.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

MFA-DVR: direct volume rendering of MFA models

3D volume rendering is widely used to reveal insightful intrinsic patterns of volumetric datasets across many domains. However, the complex structures and varying scales of volumetric data can make efficiently generating high-quality volume rendering results a challenging task. Multivariate functional approximation (MFA) is a new data model that addresses some of the critical challenges: high-order evaluation of both value and derivative anywhere in the spatial domain, compact representation for large-scale volumetric data, and uniform representation of both structured and unstructured data. Here, in this paper, we present MFA-DVR, the first direct volume rendering pipeline utilizing the MFA model, for both structured and unstructured volumetric datasets. We demonstrate improved rendering quality using MFA-DVR on both synthetic and real datasets through a comparative study. We show that MFA-DVR not only generates more faithful volume rendering than using local filters but also performs faster on high-order interpolations on structured and unstructured datasets. MFA-DVR is implemented in the existing volume rendering pipeline of the Visualization Toolkit (VTK) to be accessible by the scientific visualization community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Deep learning approaches for instantaneous laser absorptance prediction in additive manufacturing

Abstract The quantification of absorbed light is essential for understanding laser-material interactions and melt pool dynamics in order to minimize defects in additively manufactured metal components. The geometry of a vapor depression formed during laser melting is closely related to laser energy absorption. This relationship has been observed by the state-of-the-art in situ high-speed synchrotron X-ray visualization and integrating sphere radiometry. These two techniques create a temporally resolved dataset consisting of vapor depression images and corresponding laser absorptance. In this work, we propose two different approaches to predict instantaneous laser absorptance. The end-to-end approach uses deep convolutional neural networks to learn implicit features of X-ray images automatically and predict the laser energy absorptance. The two-stage approach uses a semantic segmentation model to engineer geometric features and predict absorptance using classical regression models. While having distinct advantages, both approaches achieved a consistently low mean absolute error of less than 3.3%.

Chemistry↗

DOE OSTI2024

Streamlining latent spaces in machine learning using moment pooling

Many machine learning applications involve learning a latent representation of data, which is often high-dimensional and difficult to directly interpret. In this work, we propose “moment pooling,” a natural extension of deep sets networks which drastically decreases the latent space dimensionality of these networks while maintaining or even improving performance. Moment pooling generalizes the summation in deep sets to arbitrary multivariate moments, which enables the model to achieve a much higher effective latent dimensionality for a fixed learned latent space dimension. We demonstrate moment pooling on the collider physics task of quark/gluon jet classification by extending energy flow networks (EFNs) to moment EFNs. We find that moment EFNs with latent dimensions as small as 1 perform similarly to ordinary EFNs with higher latent dimension. This small latent dimension allows for the internal representation to be directly visualized and interpreted, which in turn enables the learned internal jet representation to be extracted in closed form. Published by the American Physical Society 2024

Gambhir, Rikab (ORCID:0000000251080448)↗

DOE OSTI2026

Impacts of Electric Space Heating in Multifamily Apartments in Juneau, Alaska [Slides]

The study objective was to understand the change in electrical consumption and cost after the addition of a ductless mini-split air-source heat pump (ASHP) across rental apartments heated by electrical resistance heating systems in multifamily buildings in Juneau, Alaska. Alaska Electric Light and Power Company (AELP), the utility in Juneau, Alaska, funded installation of 19 heat pumps across four buildings. Using electrical meter interval data, including the total apartment consumption and submeter data for each heating appliance (electric resistance baseboard and heat pump), the National Laboratory of the Rockies (NLR) calculated energy use metrics before and after heat pump installation and visualized results. Through this research, NLR compares electrical use (total and specific to heating appliances), adjusted for weather and apartment size, and electrical demand in the year before and after installation of an ASHP across study units. The results will inform the utility and residents of documented energy and cost savings from transitioning building heating systems to a higher-efficiency electricity-based appliance, deliver a basis for building energy modeling across other multifamily housing dwellings, and enable estimates of potential electricity savings to AELP grid under widespread adoption scenarios.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Measurement and analysis of GPU-accelerated applications with HPCToolkit

To address the challenge of performance analysis on the US DOE’s forthcoming exascale supercomputers, Rice University has been extending its HPCToolkit performance tools to support measurement and analysis of GPU-accelerated applications. To help developers understand the performance of accelerated applications as a whole, HPCToolkit’s measurement and analysis tools attribute metrics to calling contexts that span both CPUs and GPUs. To measure GPU-accelerated applications efficiently, HPCToolkit employs a novel wait-free data structure to coordinate monitoring and attribution of GPU performance. To help developers understand the performance of complex GPU code generated from high-level programming models, HPCToolkit constructs sophisticated approximations of call path profiles for GPU computations. To support fine-grained analysis and tuning, HPCToolkit uses PC sampling and instrumentation to measure and attribute GPU performance metrics to source lines, loops, and inlined code. To supplement fine-grained measurements, HPCToolkit can measure GPU kernel executions using hardware performance counters. To provide a view of how an execution evolves over time, HPCToolkit can collect, analyze, and visualize call path traces within and across nodes. Finally, on NVIDIA GPUs, HPCToolkit can derive and attribute a collection of useful performance metrics based on measurements using GPU PC samples. Here, we illustrate HPCToolkit’s new capabilities for analyzing GPU-accelerated applications with several codes developed as part of the Exascale Computing Project.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Integrative illustration of a JCVI-syn3A minimal cell

Abstract Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell.

Goodsell, David S.↗

DOE OSTI2025

Unrolled Video Super-Resolution Network with Autoregressive Prior for the Case of Known Motion

Real-time detection and classification of distant objects is necessary for many national security applications. However, when objects are far from the sensor, they occupy only a small number of pixels in the captured video, limiting the amount of visual detail available for recognition. State-of-the-art classification methods typically rely on high-resolution (HR) video streams to capture characteristic object features, but obtaining such detail is challenging for distant objects that occupy only a few pixels. This motivates the development of video super-resolution (VSR) methods that enhance object classification by recovering fine details from low-pixel representations. Current VSR methods rely either on model-based optimization, which is interpretable but computationally expensive, or on learning-based approaches, which are efficient and high-performing but often lack flexibility and interpretability. In this report, we propose an end-to-end trainable unrolled VSR network, UVSRNet, which super-resolves each frame in a video by exploiting sub-pixel motion between neighboring low-resolution (LR) frames as well as incorporating high-frequency detail from previously super-resolved frames. In particular, by unrolling a plug-and-play (PnP) half-quadratic splitting (HQS) algorithm, we leverage a model-based data-fitting module alongside a learning-based autoregressive prior module. This combination yields a method that maintains the flexibility and interpretability of model-based methods while achieving the performance advantages of learning-based methods.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2022

Designing Unmanned Aerial Survey Monitoring Program to Assess Floating Litter Contamination

Monitoring marine contamination by floating litter can be particularly challenging since debris are continuously moving over a large spatial extent pushed by currents, waves, and winds. Floating litter contamination have mostly relied on opportunistic surveys from vessels, modeling and, more recently, remote sensing with spectral analysis. This study explores how a low-cost commercial unmanned aircraft system equipped with a high-resolution RGB camera can be used as an alternative to conduct floating litter surveys in coastal waters or from vessels. The study compares different processing and analytical strategies and discusses operational constraints. Collected UAS images were analyzed using three different approaches: (i) manual counting (MC), using visual inspection and image annotation with object counts as a baseline; (ii) pixel-based detection, an automated color analysis process to assess overall contamination; and (iii) machine learning (ML), automated object detection and identification using state-of-the-art convolutional neural network (CNNs). Our findings illustrate that MC still remains the most precise method for classifying different floating objects. ML still has a heterogeneous performance in correctly identifying different classes of floating litter; however, it demonstrates promising results in detecting floating items, which can be leveraged to scale up monitoring efforts and be used in automated analysis of large sets of imagery to assess relative floating litter contamination.

Almeida, Sílvia (ORCID:0000000320636826)↗

DOE OSTI2024

Mapping microhabitats of lignocellulose decomposition by a microbial consortium

The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

The evolution of HCO + in molecular clouds using a novel chemical post-processing algorithm

Modelling the chemistry of molecular clouds is critical to accurately simulating their evolution. To reduce computational cost, 3D simulations generally restrict their chemistry to species with strong heating and cooling effects. Time-dependent information about the evolution of other species is therefore often neglected. We address this gap by post-processing tracer particles in the SILCC-Zoom molecular cloud simulations. Using a chemical network of 39 species and 301 reactions (including freeze-out of CO and H 2 O) and a novel algorithm to reconstruct a density grid from sparse tracer particle data, we produce time-dependent density distributions for various species. We focus upon the evolution of HCO + , which is a critical formation reactant of CO but is not typically modelled on the fly. We find that ∼ 90 per cent of the HCO + content of the cold molecular gas forms in situ around n HCO + ∼ 10 3 –10 4 cm −3 , over a time-scale of approximately 1 Myr. The remaining ∼ 10 per cent forms at high extinction sites, with minimal turbulent mixing out into the less dense gas. We further show that the dominant HCO + formation pathway is dependent on the visual extinction, with the reaction H 3 + + CO contributing 90 per cent of the total HCO + production above A V, 3D = 3. We produce the very first maps of the HCO + column density, N(HCO + ), and show that it reaches values as high as 10 15 cm −2 . We find that 50 per cent of the HCO + mass is located within AV ∼ 10–30 in a density range of 10 3.5 –10 4.5 cm −3 . Our maps of N(HCO + ) are shown to be in good agreement with recent observations of the W49A star-forming region.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Few-shot Learning for Post-disaster Structure Damage Assessment

Automating post-disaster damage assessment with remote sensing data is critical for faster surveys of structures impacted by natural disasters. One significant obstacle to training state-of-the-art deep neural networks to support this automation is that large quantities of labelled data are often required. However, obtaining those labels is particularly unrealistic to support post-disaster damage assessment in a timely manner. Few-shot learning methods could help to mitigate this by reducing the amount of labelled data required to successfully train a model while achieving satisfactory results. To this end, we explore a feature reweighting method to the YOLOv3 object detection architecture to achieve few-shot learning of damage assessment models on the xBD dataset. Our results show that the feature reweighting approach yield improved mAP over the baseline with significantly fewer labelled samples. In addition, we use t-SNE to analyze the class-specific reweighting vectors generated by the reweighting module in order to evaluate their inter-class and intra-class similarity. We find that the vectors form clusters based on class, and that these clusters overlap with visually similar classes. Those results show the potential to employ this few-shot learning strategy for rapid damage assessment with post-event remote sensing images.

Bowman, Jordan↗

DOE OSTI2026

Data From: "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater"

This repository contains the data and code associated with the paper titled "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater," published in Nature Geoscience, 2026. This study seeks to answer how various ages of groundwater interact with mountainous streamflow in mountainous headwaters such as the East River. It includes various model-data processing scripts, primarily for ParFlow-CLM analysis of simulated water years 2015-2021, and two numerical warming experiments (+2.5 and +4.0 degrees C), including run scripts, forcing scripts, and post-processing, as well as comparison to observation datasets, detailed below. This data requires the use of R (.r, .rmd), Python (.py), Jupyter Notebook or Jupyter Lab (.ipynb), ParFLOW-CLM, EcoSLIM. Further information on the use of all file formats mentioned below (e.g. .tff. .nc) are provided within the associated scripts and directory where the files are located. Contents & Usage ASO/: Contains the bash and python scripts used to convert airborne snow observatory (ASO) data (ASO, 2023) in various data formats (georeferenced tiff file, NetCDF, UTM, and to latitude/longitude) then regrided to the ParFlow equivalent grid. Output data are in regrid_regll_data.zip and subsequently visualized and analyzed in plot_and_compare.py for Supplementary Figures A14 and A15. The wksht_ASO_comparison.xlsx spreadsheet is used to calculate the data for Supplementary Figure A16. EcoSLIM/: Contains the scripts and input files to run the EcoSLIM particle tracking simulations (/run_scripts) and the post-processing python script (/plot_scripts/eco_agedist_plots.ipynb). Jasechko et al./: Contains the jupyter notebook (Extract_Elevation.ipynb) to determine the outlet elevations of the 260 watersheds used in Jasechko et al. (2016), and the corresponding table, Table_S1_Watersheds_alt.csv. Used to create Supplementary Information Figure A2. PLM_Wells/: Contains the QA/QC-ed groundwater level time series of the PLM-1 and PLM-6 Monitoring Wells from Faybishenko et al. (2023), reformatted to water years used for Supplementary Figures A19 and and A20. ParFlow/: Contains the input files and run scripts to run ParFlow-CLM (/run_scripts), the python and tool command language (Tcl) scripts to create and distribute the ParFlow forcing simulation files (/forcing), and various scripts and intermediary files to analyze the model outputs (/post_process). SQUIRE/: Contains the processing scripts and intermediary files for the Surface QUantitatIve pRecipitation Estimation (SQUIRE) data (Grover, 2023) used to generate Supplementary Figure A18. USGS_Streamflow/: Contains the raw and gap-filled United States Geological Survey streamflow data (U.S. Geological Survey, 2026) used at the Almont station (site number 09112500). Gap-filling is performed in the R script with data from the Taylor station (site number 09110000). (/USGS_09112500_EAST_RIVER_AT_ALMONT_GAP_FILLED/code_almont_streamflow_gap_fill.Rmd). discharge/: Contains the gap-filled discharge data at the Watershed Function SFA East River pumphouse site (Newcomer et al., 2022) used to generate Supplementary Figure A13 and to compute hourly Nash-Sutcliffe model efficiency coefficients (NSE) in Table A4. snotel_and_flux_tower/: Contains the snow telemetry data (U.S. Department of Agriculture, 2024) from the Butte (site ID 380) and Schofield (site ID 737) stations, reformatted by water year, accessed with the snotelr R package. Used to create Supplementary Figure A17. Also contains the flux tower observational data (FluxTower_Pumphouse_ESS-DIVE.ET_only.h.txt) from Ryken et al. (2022) and sap flux transpiration data (MaxB_Transpiration_5Sites.daily_sums.h.txt) from Ryken (2021), used to create Supplementary Figures A22 and A23, respectively. Raw EcoSLIM model outputs are in excess of 24TB, and are stored on National Energy Research Scientific Computing Center (NERSC) and publicly available via the external link provided in the paper.

atmospheric warming↗

DOE OSTI2026

Energy Consumption, Performance, and Cost Estimates for Medium and Heavy-Duty Vehicles Based on 2022 Assumptions

Assumptions for this work was collected and the analysis was completed in FY22. This contains information for more than 20 types of medium and heavy duty vehicles. Vehicles with various levels of hybridization, electric and fuel cell powertrains are considered in this work. More details are available in the report published by Argonne accessible from https://vms.taps.anl.gov/research-highlights/u-s-doe-vto-hfto-r-d-benefits/. TechScape, a convenient data visualization tool is also provided by Argonne for this data, accessible from [TechScape Web](https://vms.taps.anl.gov/data/techscape-web-2023/).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

Resolving atomic transport through iron oxide under irradiation using isotopic tracers

Structural materials in nuclear environments are exposed to complex and harsh conditions, including high temperatures, corrosive solutions, and irradiation. Material stability and likewise degradation are fundamentally controlled by atomic transport mechanisms. Here, we investigate the influence of radiation-induced, non-equilibrium point defect populations on mass transport within model oxide systems using isotopic tracers and atom probe tomography. An isotopically labelled hematite (a-Fe2O3) film was synthesized with 16O- and 18O-rich layers (>30nm and 10 nm, respectively) sequentially deposited via molecular beam epitaxy. One region of the film was proton irradiated to ~0.1 dpa at 450°C, and regions outside the beam spot provided a non-irradiated control of thermal annealing only. 3D APT was used to directly visualize the elemental and O-isotopic redistribution following both thermal and combined thermal and irradiation conditions. Complementary scanning transmission electron microscopy (STEM) was also employed to study the microstructural evolution. Error function fits of the 18O-concentration profiles enabled quantification of diffusion coefficients.

isotopic tracers, diffusion, proton irradiation, h↗

DOE OSTI2026

Nanocrystal Geometry Governs Phase Transformation Pathways in Palladium Hydride

Pathways and structural dynamics of phase transformations impact performance of materials in energy and information storage technologies. Palladium hydride (PdH x ) nanocrystals are an ideal model system for studying solute-induced phase transformations, where elastic energy from lattice mismatch between α-PdH x and β-PdH x phases is often considered a key to determining the transformation pathways. α/β-PdH x interfacial elastic energy is affected by the confined geometry of a nanocrystal. However, how nanocrystal geometry influences phase transformation pathways is largely unknown. Using in situ liquid phase transmission electron microscopy, we directly visualize hydrogenation in Pd nanocrystals with two geometries, a nanocube and a hexagonal nanoplate. Both follow similar sequences of an initially curved nucleus, interface flattening, and reverse-stage nucleation; however, their evolving α/β-PdH x interfaces exhibit geometry-dependent crystallographic alignments. In nanocubes, {100}-aligned configurations conform to static elastic energy ordering, representing a pathway that maintains a local mechanical equilibrium, whereas nanoplates display both {110}- and {211}-aligned interfaces. Theoretical simulations show that geometry determines the accessibility of alternative phase transformation pathways as the system is driven far from equilibrium during hydrogenation. In conclusion, these findings identify geometry as a fundamental parameter for directing phase transformation pathways, offering design principles for accessing atypical configurations and improving properties of intercalation-based devices.

Lee, Daewon [Lawrence Berkeley National Laboratory↗

DOE OSTI2021

A Confidence-Guided Technique for Tracking Time-Varying Features

Application scientists often employ feature tracking algorithms to capture the temporal evolution of various features in their simulation data. However, as the complexity of the scientific features is increasing with the advanced simulation modeling techniques, quantification of reliability of the feature tracking algorithms is becoming important. One of the desired requirements for any robust feature tracking algorithm is to estimate its confidence during each tracking step so that the results obtained can be interpreted without any ambiguity. To address this, we develop a confidence-guided feature tracking algorithm that allows reliable tracking of user-selected features and presents the tracking dynamics using a graph-based visualization along with the spatial visualization of the tracked feature. Here, the efficacy of the proposed method is demonstrated by applying it to two scientific datasets containing different types of time-varying features.

97 MATHEMATICS AND COMPUTING↗