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At least 469 records · Page 26

PAVplotR

PAVplotR is an R package that accepts as input a haploid VCF and, for a user-specified bin size, calculates proportional presence-absence variation (PAV). First, all variants in the file are considered to calculate an expanded coordinate system that accounts for insertions relative to the reference sequence. Next, for each sample in the VCF, proportional PAV is summarized per bin in the expanded coordinate system and finally, PAV is plotted such that rows are samples and columns are bins with the x-axis (chromosome position) labeled according to the reference haplotype's original coordinate system.

Harder, Avril↗

SCALE Input and Result Files Supporting SCALE Inventory and Reactivity Analysis as Part of the Hermes 2021 PSAR Review

This dataset contains input and result files of computational simulations with the SCALE code system. The simulations cover radionuclide inventory and reactivity analyses of a fluoride salt-cooled high temperature pebble-bed reactor (PB-FHR), specifically the Hermes low-power PB-FHR demonstration reactor. Users wanting to reproduce results from this dataset are required to obtain a license to the SCALE code system for which details on the distribution can be found here: https://www.ornl.gov/scale/releases

equilibrium core↗

SCALE Input and Result Files Supporting SCALE Inventory and Reactivity Analysis of the gFHR

This dataset contains input and result files of computational simulations with the SCALE code system. The simulations cover radionuclide inventory and reactivity analyses of a fluoride salt-cooled high temperature pebble-bed reactor (PB-FHR), specifically the generic FHR benchmark. Users wanting to reproduce results from this dataset are required to obtain a license to the SCALE code system for which details on the distribution can be found here: https://www.ornl.gov/scale/releases

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Dynamically Downscaled (WRF) 1km, Hourly Meteorological Conditions 1987-2020. East/Taylor Watersheds

This dataset contains meteorological output from the Weather Research and Forecasting (WRF) version 3.8.1. This dataset has been created to 1) investigate hydrometeorological processes impacting the East River and water-delivery to the Critical Zone, and 2) provide meteorological forcing data for distributed Earth-science modeling applications in the East River watershed. Variables have a 1 kilometer spatial resolution and hourly temporal resolution and encompass a rectangular region encompassing the East and Taylor River watersheds, Colorado, near the town of Crested Butte. WRF was forced using Climate Forecast System Reanalysis (CFSR) lateral boundary conditions. Each .zip file contains one "water year" of data (October 1 -- September 30; i.e. water year 2017 starts October 1, 2016 and ends September 30, 2017). Each zip folder contains 12 netcdf (.nc) files containing one month of hourly data each and are approximately 250mb. Model timestamps are in UTC time.The files contain the following data variables:EAST_MASK: binary mask of the watershed regionTAYLOR_MASK: binary mask of the watershed regionGLW downwelling longwave radiation (w/m2)HR_PRCP: Hourly Precipitation Rate (mm/hr). Includes all hydrometeors (solid+liquid). HFX NoahMP LSM total grid-cell modelled sensible heat flux (w/m2) [positive towards atmosphere]LH NoahMP LSM total grid-cell modelled latent heat flux (w/m2) [positive towards atmosphere; can be converted to ET]PSFC Surface Barometric Pressure (hPa)Q2 Two-meter specific humidity (kg/kg)SWDOWN Downwelling shortwave solar radiation (w/m2)SWNORM Terrain-normal downwelling shortwave radiation (w/m2)T2 Two-meter air temperature (deg K)U10 10-m U-component of wind velocity (m/s)V10 10m V-component of wind velocity (m/s)XLAT Latitude of grid-center point XLONG Longitude of grid-center point XTIME Model timestamp, **in UTC**

54 ENVIRONMENTAL SCIENCES↗

CHESS 2025: Location data for field observations and sampling

This dataset represents geolocation data associated with field observations and sampling from the Colorado Headwaters Ecological Spectroscopy Study (CHESS) during June and July of 2025. Location data were collected using Trimble DA2 Global Navigation Satellite System (GNSS) receivers with Trimble Catalyst 2 centimeter (cm) positioning service and the Environmental Systems Research Institute (Esri) Field Maps mobile app. Files in this data package include meadow site polygons, shrub site polygons, tree site polygons and stem point locations, and Leaf Area Index (LAI) plot polygons (.geojson). The geojson files can be opened with open-source GIS software (e.g, QGIS). A csv file is also provided with point coordinates for all locations. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking (FY2020 Progress Report)

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g. height, color and grayscale values; all as functions of a location in a plane projection). It is the objective of this project to produce a user-friendly interface that incorporated all operations needed to perform surface examination. For this reason, a Matlab-based Graphical User Interface (GUI) was created to integrate data input with software developed for processing and evaluation. In summary, the GUI permits selective downloading of binary data, interrogation of attributes, data labeling, flagging of significant features, execution of Machine Learning (ML) algorithms, output of parameters for trained ML algorithms, reports of ML model accuracy with respect to labeled data, and generation of graphical representations of various analyses.

3013 corrosion↗

FY21 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g., height, color and grayscale values; all as functions of a location in a plane projection). A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data, flag significant features, execute Machine Learning (ML) algorithms, output parameters for trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Features can be called out by user-specified thresholds, manual labeling or machine learning algorithms when they have been completed. The ability to rapidly label data is important because of the volume of data required for training machine learning algorithms. The GUI has the flexibility to allow addition of improved ML algorithms, methods for data visualization, and statistical computations. Statistical analyses via the GUI include areas of pits within a defined range of pit depths, correlations between Red-Green-Blue (RGB) or grayscale intensity and relative surface height, covariances between values associated with features, and feature histograms. The development of supervised machine learning algorithms, however, has been hindered by a lack of training data. The machine learning algorithms for crack identification are being refined but require improvements to the true positive rate for crack detection. This shortcoming is an artifact of the limited training data currently available, perhaps more so than the structure of the neural networks. At present, the best results are had from a consensus over an ensemble of randomly generated Deep Neural Network (DNN) or Convolutional Neural Network (CNN) algorithms. Although the consensus accuracy method has yielded optimum true positive and true negative rates in excess of 80%, additional validation testing is necessary. In addition to the suite of LCM data that was initially used, and which represents the majority of the work presented in this report, WAMS image data was also reviewed at a preliminary level. The review included a comparison between image resolution and dynamic range for each method. WAMS (ZON file) image data was found to have a pixel pitch of 3.69μm compared to 1 μm for the LCM (vk4 file) data, which implies a lower resolution for the WAMS images. Conversely, the ratio of dynamic range of the WAMS data to the LCM data was approximately 41:20 for height data, suggesting that information from WAMS should more accurately determine the depth of pits. At present, the significance of the greater dynamic range of the WAMS data relative to the LCM data has not yet been evaluated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Development of an Automated J-R Curve Analysis Software Based on the ASTM E1820-18 Normalization Method

The J-integral versus crack-growth resistance curve (J-R curve) is a useful tool for evaluating material fracture toughness in the ductile region. A widely accepted practice for conducting J-R curve testing is ASTM standard E1820, which introduces the normalization method. This method does not require compliance measurements during testing, significantly simplifying J-R curve testing compared with the conventional elastic unloading compliance (EUC) method. Despite the advantage in testing, analysis procedures for the normalization method are very complicated. Also, there is no open source software currently available to perform such analysis.The authors developed an open source automated J-R curve-analysis software based on the normalization method in ASTM E1820-18. Source codes were written in MATLAB and the compiled software, in the form of a stand-alone executable, has a user-friendly graphic interface and is readily compatible with modern Windows operating systems. Both source codes and the compiled executable file are available for download at https://code.ornl.gov/xc8/ANJR.git. Comparisons between resulting J-R curves from the software and manual analysis procedures show essentially identical results, indicating the suitability of applying the automated software for J-R curve analysis.

36 MATERIALS SCIENCE↗

Bufferless communication for redundant multithreading using register permutation

Systems, apparatuses, and methods for implementing bufferless communication for redundant multithreading applications using register permutation are disclosed. In one embodiment, a system includes a parallel processing unit, a register file, and a scheduler. The scheduler is configured to cause execution of a plurality of threads to be performed in lockstep on the parallel processing unit. The plurality of threads include a first thread and a second thread executing on adjacent first and second lanes, respectively, of the parallel processing unit. The second thread is configured to perform a register permute operation from a first register location to a second register location in a first instruction cycle, with the second register location associated with the second processing lane. The second thread is configured to read from the second register location in a second instruction cycle, wherein the first and second instruction cycles are successive instruction cycles.

97 MATHEMATICS AND COMPUTING↗

California Publicly-Owned Utilities (POUs) – LBNL ‘Beyond Widgets’ Project. Task: ambient lighting and occupancy-based plug load control. System Program Manual

This program manual contains detailed technical information for implementing an incentive program for task-ambient lighting and occupancy-based plug load control. This manual was developed by Lawrence Berkeley National Laboratory, in collaboration with the California Publicly-Owned Utilities (CA POUs) as a partner in the ‘Beyond Widgets’ program funded by the U.S. Department of Energy Building Technologies Office. The primary audience for this manual is the program staff of the various CA POUs. It may also be used by other utility incentive programs to help develop similar programs. It is anticipated that the content of this manual be utilized by the CA POU staff for developing related documents such as the Technical Resource Manual and other filings pertaining to the rollout of an energy systems-based rebate incentive program.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

USACE FUSRAP Records Management Challenges in the Digital Age - 20242

In late 2016, the U.S. Army Corps of Engineers (USACE) implemented a Headquarters-supported nationwide records management initiative managed by the USACE-New England District to address the digitization and organization of Formerly Utilized Sites Remedial Action Program (FUSRAP) project files. This initiative will prepare USACE FUSRAP for moving toward a fully electronic system of records management. Additionally, the records management initiative streamlines the process and prepares the Administrative Record (AR) and Permanent Record (PR) file for transfer from USACE to the U.S. Department of Energy (DOE)-Office of Legacy Management (LM) following project closeout. Over the past couple of years, USACE and DOE-LM have been working to finalize a joint guidance document to assist in the FUSRAP records transition process. However, there remain key records management topics that require further discussion and development. Specifically, these topics include the implementation, process, and procedure for the capture of social media records and compliance with Section 508 of the Rehabilitation Act of 1973 (29 USC 794d), as amended. Due to advances in technology and the ease of communication it provides, USACE is using social media more often to interface with the public than 5, 10 or 15 years ago. The identification and capture of these records are challenging because it requires each USACE district or producer of a record to track what has been released through social media so that it can be captured as part of the AR or PR. USACE is currently evaluating processes and procedures for social media records capture. This paper explores how social media is being used by USACE across FUSRAP projects and best practices for the capture of social media records. Public accessibility to the project AR is required under the Comprehensive Environmental Response, Compensation, and Liability Act, which USACE FUSRAP must follow. As USACE FUSRAP ARs are converted to a digital format, greater accessibility to the files can be provided through web sites or other electronic media. However, Section 508 of the Rehabilitation Act must be considered when releasing electronic files to the public. Under Section 508, government agencies must ensure that information is made available to the public in a format that provides equal access to persons with disabilities. This paper discusses the electronic records requirements under Section 508 and addresses broad implementation of compliance across large digital records sets. Records management challenges are presented in the context of the FUSRAP records management program; however, these records management considerations and best practices are applicable across all Federal agency records management programs. Examples presented will further aid in understanding electronic records requirements that may be included on new USACE FUSRAP contracts as well as upcoming National Archives Records Administration requirements that will move us toward an electronic government. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Database Management Module Framework for Dynamic Contingency Analysis and Visualization

The Dynamic Contingency Analysis Tool (DCAT) is being developed to mimic the response of generation dynamics, protection, and load components to extreme contingencies in power systems. Currently, DCAT generates a huge data set, with the analysis results stored in multiple subfolders using a great many files in different formats (power flow cases, time series, figures, spreadsheets). To help power system engineers thoroughly understand and analyze system behavior under many scenarios and contingencies, we developed a database management module (DBM) that enables future integration of DCAT with industry-grade Big Data analytical and interactive visualization platforms. In this paper, we demonstrate the DBM framework with interactive analytics and visualization for DCAT on the synthetic South Carolina 500-bus power system model using hurricane contingencies that capture possibilities for an extreme contingency. DCAT’s advanced data management and interactive visualization can help planning engineers to visually explore and analyze system behavior, all in one view.

Cascading, dynamic simulations, database managemen↗

SU-D-201-03: During-Treatment Delivery Monitoring System for TomoTherapy

Purpose: Multiple error pathways can lead to delivery errors during the treatment course that cannot be caught with pre-treatment QA. While in vivo solutions are being developed for linacs, no such solution exists for tomotherapy. The purpose of this study is to develop a near real-time system for tomotherapy that can monitor the delivery and dose accumulation process during the treatment-delivery, which enable the user to assess the impact of delivery variations and/or errors and to interrupt the treatment if necessary. Methods: A program running on a tomotherapy planning station fetches the raw DAS data during treatment. Exit detector data is extracted as well as output, gantry angle, and other machine parameters. For each sample, the MLC open-close state is determined. The delivered plan is compared with the original plan via a Monte Carlo dose engine which transports fluence deviations from a pre-treatment Monte Carlo run. A report containing the difference in fluence, dose and DVH statistics is created in html format. This process is repeated until the treatment is completed. Results: Since we only need to compute the dose for the difference in fluence for a few projections each time, dose with 2% statistical uncertainty can be computed in less than 1 second on a 4-core cpu. However, the current bottleneck in this near real-time system is the repeated fetching and processing the growing DAS data file throughout the delivery. The frame rate drops from 10Hz at the beginning of treatment to 5Hz after 3 minutes and to 2Hz after 10 minutes. Conclusion: A during-treatment delivery monitor system has been built to monitor tomotherapy treatments. The system improves patient safety by allowing operators to assess the delivery variations and errors during treatment delivery and adopt appropriate actions.

60 APPLIED LIFE SCIENCES↗

GADRAS Batch Inject Tool User Guide

Gamma Detector Response and Analysis Software (GADRAS) is used by the radiation detection and emergency response community to perform modeling and spectral analysis for gamma detector systems. Built into GADRAS is the ability to define a detector, geometry, background characteristics and source composition to generate synthetic spectra for drills and exercises (injects). Consequence Management is currently in development of a sample result data simulator tool in which a deposition model is probed for source conditions at moments in time and locations in space. These values are used to generate realistic sample results for use in drills and exercises. In addition to sample results, there is a need to simulate the actual spectra that would be observed in the field by downlooking HPGe instruments given a deposition activity. This way, the FRMAC Gamma Spectroscopist can practice their process of generating quantified results from spectra on realistic data as well. Recognizing the decades of work done in GADRAS to accurately generate synthetic spectra, this team decided to build a link between the new simulator and GADRAS to generate these spectra quickly and easily. The simulator tool will generate a file that specifies the name of the spectra, its location, date/time of measurement, duration of measurement, height off the ground, and the deposition activity and age for every radionuclide in the simulation. Then, a new tool within the Inject Tab of GADRAS was developed to read in this file given a detector selection and generate In-Situ spectra for each row in the file in any file format the user chooses. This way, simulation cell staff can take these files and then upload them to the appropriate data system (RAMS or RadResponder) for use during drills and exercises. An advanced feature of this tool allows for generating any spectra given an appropriate model and mapping of source to model layer in the batch inject tool. This way, spectra from field sample counts, mobile laboratories, or even fixed laboratories can be generated in bulk given an estimate of the radioactivity concentration or total radioactivity in an import file. This expands the capabilities of this tool a great deal and will make it a more useful tool for CM and others to help estimate detector response for nearly any situation. This user guide will explain the steps needed to perform a batch inject file generation.

61 RADIATION PROTECTION AND DOSIMETRY↗

Lignin Forcefield Source Datafiles

Three archives are provided here comprising the development of a CHARMM36-compatible lignin forcefield suitable for use in biomolecular simulations. One archive parameters.zip contains the output topology and parameter files in CHARMM format suitable for use in constructing simulation systems. The remaining two hold the logic of the parameterization featuring scripts that do the optimization including the source for the GPU-accelerated objective function evaluation and target data creation scripts.zip as well as minimal outputs needed to recreate the work datafiles.zip. Due to licensing restrictions Gaussian log files that created the target data are not provided here. Instead only binary-formatted parsed target data as well as the input decks used to create the target data are provided in datafiles.zip. Readme files for individual directories created within the directory structure are contained within scripts.zip.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of a mobile toolmark characterization/comparison system [Development of a mobile, automated toolmark characterization/comparison system]

Since the development of the striagraph, various attempts have been made to enhance forensic investigation through the use of measuring and imaging equipment. This study describes the development of a prototype system employing an easy-to-use software interface designed to provide forensic examiners with the ability to measure topography of a toolmarked surface and then conduct various comparisons using a statistical algorithm. Acquisition of the data is carried out using a portable 3D optical profilometer, and comparison of the resulting data files is made using software named “MANTIS” (Mark and Tool Inspection Suite). The system has been tested on laboratory-produced markings that include fully striated marks (e.g., screwdriver markings), quasistriated markings produced by shear-cut pliers, impression marks left by chisels, rifling marks on bullets, and cut marks produced by knives. Using the system, an examiner has the potential to (i) visually compare two toolmarked surfaces in a manner similar to a comparison microscope and (ii) use the quantitative information embedded within the acquired data to obtain an objective statistical comparison of the data files. Finally, this study shows that, based on the results from laboratory samples, the system has great potential for aiding examiners in conducting comparisons of toolmarks.

47 OTHER INSTRUMENTATION↗

RAVEN User Manual

RAVEN is a generic software framework to perform parametric and probabilistic analy- sis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncer- tainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by inputs files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused to- ward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN has started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is in- terested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for an important process such as peak pressure in a pipe) is exceeded under certain conditions. The initial development of RAVEN has been focused on providing dynamic risk assess- ment capability to RELAP-7, currently under develop-ment at the INL and, likely, future replacement of the RELAP5-3D code. Most the capabilities that have been implemented having RELAP-7 as principal focus are easily deployable for other system codes. For this reason, several side activates are currently ongoing for coupling RAVEN with soft- ware such as RELAP5-3D, etc. The aim of this document is the explaination of the input requirements, focalizing on the input structure.

97 MATHEMATICS AND COMPUTING↗