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DOE OSTI2023

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1992

A system for verifying models and classification maps by extraction of information from a variety of data sources

Recent updates to a geographical information system (GIS) called VICAR (Video Image Communication and Retrieval)/IBIS are described. The system is designed to handle data from many different formats (vector, raster, tabular) and many different sources (models, radar images, ground truth surveys, optical images). All the data are referenced to a single georeference plane, and average or typical values for parameters defined within a polygonal region are stored in a tabular file, called an info file. The info file format allows tracking of data in time, maintenance of links between component data sets and the georeference image, conversion of pixel values to `actual' values (e.g., radar cross-section, luminance, temperature), graph plotting, data manipulation, generation of training vectors for classification algorithms, and comparison between actual measurements and model predictions (with ground truth data as input).

Norikane, L.↗

DOE OSTI2019

A Barrierless Pathway Accessing the C9H9 and C9H8 Potential Energy Surfaces via the Elementary Reaction of Benzene with 1-Propynyl

Abstract The crossed molecular beams reactions of the 1-propynyl radical (CH 3 CC; X 2 A 1 ) with benzene (C 6 H 6 ; X 1 A 1g ) and D6-benzene (C 6 D 6 ; X 1 A 1g ) were conducted to explore the formation of C 9 H 8 isomers under single-collision conditions. The underlying reaction mechanisms were unravelled through the combination of the experimental data with electronic structure and statistical RRKM calculations. These data suggest the formation of 1-phenyl-1-propyne (C 6 H 5 CCCH 3 ) via the barrierless addition of 1-propynyl to benzene forming a low-lying doublet C 9 H 9 intermediate that dissociates by hydrogen atom emission via a tight transition state. In accordance with our experiments, RRKM calculations predict that the thermodynamically most stable isomer – the polycyclic aromatic hydrocarbon (PAH) indene – is not formed via this reaction. With all barriers lying below the energy of the reactants, this reaction is viable in the cold interstellar medium where several methyl-substituted molecules have been detected. Its underlying mechanism therefore advances our understanding of how methyl-substituted hydrocarbons can be formed under extreme conditions such as those found in the molecular cloud TMC-1. Implications for the chemistry of the 1-propynyl radical in astrophysical environments are also discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2019

PoPsCpp

A new format for storing particle information (i.e., mass, spin, parity) has been developed. The format is a subset of the Generalized Nuclear Data Structure (GNDS) developed for storing nuclear reaction data. A C++ library dubbed "Property of Particles" (PoPs) has been developed to read particle data in the GNDS format. The PoPs library provides functions for reading in a GNDS particle database as well as for accessing a particle and its properties.

Beck, Bret↗

DOE OSTI2021

Example on how to (intelligently) augment the nuclear-data pipeline with machine learning [Slides]

The presentation discusses how machine learning has helped the Los Alamos National Laboratory (LANL) nuclear-data pipeline. It also discusses the strengths of machine learning as it finds trends in large amounts of data where human brains are overwhelmed and that this information may be crucial to improve our nuclear data. It does stress, however, that machine learning is no "silver bullet" and that it is critical to feed it expert knowledge and use physics intuition to interpret the results. The presentation discusses the need to develop infrastructure and tools to provide data in an easily readable and unambiguously interpretable format (e.g., EXFOR format), to develop experimental data and theory to solve physics questions, and that statisticians and nuclear-data experts must be brought together to correctly interpret the results. The presentation concludes by stating that machine learning is a great tool and that LANL needs to use the algorithms along with developing physics data, tools and infrastructure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

C-HER Metadata Overview: Approach, Standards, and Rigor for the Centralized Health and Exposomic Resource

The Centralized Health and Exposomic Resource (C-HER) unifies environmental, demographic, geographic, and health-related data for exposomic research. The source data differ in format, geographic coverage, time period, resolution, terminology, and documentation. We use a common metadata framework to describe those differences and to record how each data resource has been processed, documented, and ingested. This document relates only to the C-HER metadata framework. It explains the information that is recorded for each resource, the standards used to organize that information, the conditions for metadata completeness, and the relationship between metadata and quality review. It is intended for those who need to understand what C-HER metadata communicates and how it supports appropriate use of the data. It is not an implementation specification or procedure. It does not document the database schema, source code, deployment configuration, transformation algorithms, or dataset-specific QA/QC thresholds. Those materials are maintained separately.

MacFarland, Midgie [ORNL] (ORCID:0009000807354078)↗

NASA NTRS1973

The thermal and mechanical properties of a low density elastomeric ablation material

Thermal and mechanical properties data were obtained for a low density elastomeric resin based ablation material with phenolic-glass honeycomb reinforcement. Data were obtained for the material in the charred and uncharred state. Ablation material specimens were charred in a laboratory furnace at temperatures in the range from 600 K to 1700 K to obtain char specimens representative of the ablation char layer formed during reentry. These specimens were then used to obtain effective thermal conductivity, heat capacity, porosity, and permeability data at the char formation temperature. This provided a boxing of the data which enables the prediction of the transient response of the material during ablation. Limited comparisons were made between the furnace charred specimens and specimens which had been exposed to simulated reentry conditions.

Engelke, W. T.↗

NASA NTRS1974

Application of remote sensing techniques in land-use planning: Flood-plain delineation

The delineation of areas subject to inundation by means of remotely-sensed data acquisition represents a considerable saving in personnel time. Repeated input from aerial sensor sources provides the planner with a potent tool for the formation of a data base and for the monitoring of land use patterns over a period of time. The primary output of this project was a set of base map overlays at a scale of 1:62,500 delineating areas which require special regulations when proposed for land use involving human habitation or certain classes of storage. A secondary product of the study was county-wide maps of watershed configurations and of soil hydrologic groups. Further research is anticipated to extend the mapping of watershed areas outside the political boundaries of Cochise County, which will provide data for subsequent rainfall-runoff relationship studies in the area. All of the data provided will be incorporated into the Cochise County composite computer mapping project now operational. Results of this project have improved the pool of information available to the planning staff of Cochise County.

Altenstadter, J.↗

NASA NTRS1977

Telemetry and data relay for manned space programs

Previously and currently planned methods of transferring or relaying telemetered information from a remote receiving station to the Mission Control Center, at the National Aeronautics and Space Administration Lyndon B. Johnson Space Center, are discussed. The data flow techniques of the Apollo Program (fixed formats), the Skylab Program (data compression), and the Space Shuttle Program (data throughput) are defined and analyzed according to their advantages and deficiencies from an operations viewpoint. Excluded from the data flow technique discussions are command data, tracking data, television data, and Teletype and Datafax messages. Voice transmissions are addressed in the Space Shuttle Program discussion because they form a part of the telemetry data stream. The tradeoffs between actual data flow requirements and existing communications limitations are addressed for each of these programs. Finally, a short discussion of current problem areas in the planned ground data transmission system for the Space Shuttle Program is presented.

Anson, K. W.↗

NASA NTRS1979

Type U CAMAC crate controller for the Spacelab multi-crate, multi-processor system

A set of standard CAMAC modules for Spacelab payloads is being developed by NASA. A crate controller, a processor module, memory modules and a databus to connect them are being developed at the Goddard Space Flight Center. These components will provide for the implementation of CAMAC data systems ranging in complexity from fixed-format, single-crate data collection systems not requiring a processor to a multi-crate data system, including several computers (processors). The Spacelab CAMAC data system is introduced with the role of the crate controller described. The implementation and operation of the crate controller is described. The instruction set of the crate controller is also presented.

Baker, R. G.↗

NASA NTRS1982

Programs for transferring data between a relational data base and a finite element structural analysis program

An interface system for passing data between a relational information management (RIM) data base complex and engineering analysis language (EAL), a finite element structural analysis program is documented. The interface system, implemented on a CDC Cyber computer, is composed of two FORTRAN programs called RIM2EAL and EAL2RIM. The RIM2EAL reads model definition data from RIM and creates a file of EAL commands to define the model. The EAL2RIM reads model definition and EAL generated analysis data from EAL's data library and stores these data dirctly in a RIM data base. These two interface programs and the format for the RIM data complex are described.

Johnson, S. C.↗

NASA NTRS1991

Large angle transient dynamics (LATDYN) documentation. Post-processor manual

The post processor program was developed to view Large Angle Transient Dynamics (LATDYN) output data in predefined, predetermined formats. The post processor is used for plotting data, creating and maintaining a data base of plotting requests, comparing and manipulating data sets in the data base, and the preparing plots for documentation.

Mitchum, Maria V.↗

NASA NTRS1991

A unified approach for composite cost reporting and prediction in the ACT program

The Structures Technology Program Office (STPO) at NASA Langley Research Center has held two workshops with representatives from the commercial airframe companies to establish a plan for development of a standard cost reporting format and a cost prediction tool for conceptual and preliminary designers. This paper reviews the findings of the workshop representatives with a plan for implementation of their recommendations. The recommendations of the cost tracking and reporting committee will be implemented by reinstituting the collection of composite part fabrication data in a format similar to the DoD/NASA Structural Composites Fabrication Guide. The process of data collection will be automated by taking advantage of current technology with user friendly computer interfaces and electronic data transmission. Development of a conceptual and preliminary designers' cost prediction model will be initiated. The model will provide a technically sound method for evaluating the relative cost of different composite structural designs, fabrication processes, and assembly methods that can be compared to equivalent metallic parts or assemblies. The feasibility of developing cost prediction software in a modular form for interfacing with state of the art preliminary design tools and computer aided design (CAD) programs is assessed.

Freeman, W. Tom↗

NASA NTRS1992

A program of correlated observations using the EGRET instrument on GRO and the IMB neutrino detector

A reliable, real-time supernova monitoring system was devised using the IMB neutrino detector to serve as an 'early-warning' system for EGRET and other instruments on GRO. New methods and software were developed to allow the IMB monitoring computer in Cleveland to: recognize that a trigger burst had occurred; make a judgement on whether the burst was spurrious or an actual supernova; prepare brief summary files and 'quick-look' data so that a final disposition could be made by a trained scientist; and contact the 'watch' scientist via personal beeper in Baton Rouge. This system ran from Dec. 1990 to Apr. 1991, when the neutrino detector failed for unrelated reasons. In addition to the supernova system, high-energy neutrino data was prepared and formatted for comparison with EGRET gamma-ray data.

Svoboda, Robert C.↗

NASA NTRS2005

The Optimization of Trained and Untrained Image Classification Algorithms for Use on Large Spatial Datasets

The HARVIST project seeks to automatically provide an accurate, interactive interface to predict crop yield over the entire United States. In order to accomplish this goal, large images must be quickly and automatically classified by crop type. Current trained and untrained classification algorithms, while accurate, are highly inefficient when operating on large datasets. This project sought to develop new variants of two standard trained and untrained classification algorithms that are optimized to take advantage of the spatial nature of image data. The first algorithm, harvist-cluster, utilizes divide-and-conquer techniques to precluster an image in the hopes of increasing overall clustering speed. The second algorithm, harvistSVM, utilizes support vector machines (SVMs), a type of trained classifier. It seeks to increase classification speed by applying a "meta-SVM" to a quick (but inaccurate) SVM to approximate a slower, yet more accurate, SVM. Speedups were achieved by tuning the algorithm to quickly identify when the quick SVM was incorrect, and then reclassifying low-confidence pixels as necessary. Comparing the classification speeds of both algorithms to known baselines showed a slight speedup for large values of k (the number of clusters) for harvist-cluster, and a significant speedup for harvistSVM. Future work aims to automate the parameter tuning process required for harvistSVM, and further improve classification accuracy and speed. Additionally, this research will move documents created in Canvas into ArcGIS. The launch of the Mars Reconnaissance Orbiter (MRO) will provide a wealth of image data such as global maps of Martian weather and high resolution global images of Mars. The ability to store this new data in a georeferenced format will support future Mars missions by providing data for landing site selection and the search for water on Mars.

Kocurek, Michael J.↗

NASA NTRS2008

Using NASA's Giovanni Web Portal to Access and Visualize Satellite-based Earth Science Data in the Classroom

One of the biggest obstacles for the average Earth science student today is locating and obtaining satellite-based remote sensing data sets in a format that is accessible and optimal for their data analysis needs. At the Goddard Earth Sciences Data and Information Services Center (GES-DISC) alone, on the order of hundreds of Terabytes of data are available for distribution to scientists, students and the general public. The single biggest and time-consuming hurdle for most students when they begin their study of the various datasets is how to slog through this mountain of data to arrive at a properly sub-setted and manageable data set to answer their science question(s). The GES DISC provides a number of tools for data access and visualization, including the Google-like Mirador search engine and the powerful GES-DISC Interactive Online Visualization ANd aNalysis Infrastructure (Giovanni) web interface.

Lloyd, Steven↗

NASA NTRS2016

Availability of Previously Unprocessed ALSEP Raw Instrument Data, Derivative Data, and Metadata Products

In year 2010, 440 original data archival tapes for the Apollo Lunar Science Experiment Package (ALSEP) experiments were found at the Washington National Records Center. These tapes hold raw instrument data received from the Moon for all the ALSEP instruments for the period of April through June 1975. We have recently completed extraction of binary files from these tapes, and we have delivered them to the NASA Space Science Data Cordinated Archive (NSSDCA). We are currently processing the raw data into higher order data products in file formats more readily usable by contemporary researchers. These data products will fill a number of gaps in the current ALSEP data collection at NSSDCA. In addition, we have estabilished a digital, searcheable archive of ALSEP document and metadata as part of the web portal of the Lunar and Planetary Institute. It currently holds approx. 700 documents totaling approx. 40,000 pages

ALSEP↗

DOE OSTI2024

Characterization of Soil and Rock Magnetic Properties along Multiple Hillslope Transects at Teller Road Site, Seward Peninsula, Alaska, 2018 and 2023

The magnetometer data was collected in multiple directions across the watershed hillslope at the NGEE Arctic Teller Road site at mile marker 27 (TL_MM27) on the Seward Peninsula, Alaska over multiple years in March 2018 and April 2023. The magnetic data were collected using a Geometrics Inc. G-858 gradiometer and G-857 base station in 2018 and the G-864 gradiometer and G857 base station in 2023. The data was collected (in all instances) by towing the gradiometer behind a snow machine around the watershed with the two sensors in a vertical profile with constant spacing during the continuous survey in that specific year. Magnetic total field measurements were collected by gradiometer and base station, and the data processing was performed in Geometrics MagMap2000 software. The processing steps were limited to removal of data spikes (despiking), reading dropouts, and correction/removal of bad GPS points. All offsets between sensors and GPS are stated within the data files and metadata, alongwith the processed and raw data. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).In this data submission there are two sets of raw magnetic data (.bin and .stn for 2018 and base for 2023; raw rover mag for 2023 is in .csv) inside two .zip files that identify the year the mag data was collected. The data are proprietary format to Geometrics and can be opened and processed with MagMap2000 which can be downloaded for free at Geometrics website. There are also two processed data files *.csv for each year and two metadata files *.csv.

54 ENVIRONMENTAL SCIENCES↗