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Artificial Intelligence (AI) Methods for Augmenting the IMPACT Tool Evidence Library

Development of the Evidence Library for use with the IMPACT probability risk assessment tool took several years and involved a staggering amount of effort from a multi-disciplinary team. A very significant amount of the labor effort to collect, assess and finalize the Clinical Finding Form (CliFF) for each of the 119 medical conditions was provided by physician subject matter experts from the Exploration Medical Capability (ExMC) Element Clinical and Science Team. Many AI tools such as ChatGPT are excellent at summarizing large amounts of information and the current project was initiated to determine how such tools might streamline laborious processes, e.g., review and summarization of many scientific research publications, to execute key steps more efficiently in the process of developing CliFFs. The process for collecting the evidence which is found in the CliFFs is well documented in the Evidence Library Methods document (ELM; HRP-48036*). Using ELM and the CliFF development instructions as a guideline, a team of developers is leveraging Microsoft Azure AI tools and services along with open-source frameworks, to construct an AI-assisted automated pipeline. This pipeline is designed to search, retrieve, and process the necessary data sources, and ultimately help generate the final version of a CliFF. Currently, the large language model evaluates the relevance of each source material to spaceflights, either as direct evidence or as an analog. Additionally, the model assists in extracting keywords and generating brief summaries to enhance augmented retrieval and search processes in later stages of CliFF development. Once the data is ready, the model can perform semantic search and retrieval, generating and extracting valuable information for the CliFF. For instance, it can handle epidemiological statistical data, such as incidence rates and the likelihood of best or worst-case scenarios. The steps that required reading and summarizing articles were viewed as providing the greatest return on investment since large language models are very efficient and accurate in summarizing large amounts of text. Since labor effort to complete the original CliFF was not recorded with sufficient granularity, comparisons with an AI tool-generated CliFF will provide merely an approximation of time saved. Upon completion of the process, the CliFF for the medical condition “appendicitis” generated with the support of AI-based methods will serve as a proof-of-concept and will be compared to the original appendicitis CliFF to determine if use of the tools resulted in content and conclusory similarity. Based upon the results from face validation of the two CliFFs, modifications to the process will be made if necessary and additional condition CliFFs will be evaluated. Ultimately, CliFFs for the entire set of medical conditions will be created with the assistance of AI tools. Depending on the cost savings realized, CliFFs for additional medical conditions can be created to expand the Evidence Library. Future direction includes specifying the characteristics of the reviewer (prompting the AI tools to generate output assuming the reviewer is a sub-specialist physician, or nurse or EMT/medic) to determine if the effects on AI-generated output are different based on knowledge, skills and abilities. *Exploration Medical Capability Evidence Library Methods, HRP-48036 Rev A, July 2022.

Ali Al↗

DOE OSTI2015

SU-E-T-354: Efficient and Enhanced QA Testing of Linear Accelerators Using a Real-Time Beam Monitor

Purpose: To investigate the feasibility of performing routine QA tests of linear accelerators (Linac) using the Integral Quality Monitoring (IQM) system. The system, consisting of a 1-D sensitivity gradient large area ion-chamber mounted at the collimator, allows automatic collection and analysis of beam data. Methods: The IQM was investigated to perform several QA constancy tests, similar to those recommended by AAPM TG142, of a Linac including: beam output, MLC calibration, beam symmetry, relative dose factor (RDF), dose linearity, output as a function of gantry angle and dose rate. All measurements by the IQM system accompanied a reference measurement using a conventional dosimetry system and were performed on an Elekta Infinity Linac with Agility MLC. The MLC calibration check is done using a Picket-Fence type 2×10cm{sup 2} field positioned at different off-axis locations along the chamber gradient. Beam symmetry constancy values are established by signals from an 4×4cm{sup 2} aperture located at various off-axis positions; the sensitivity of the test was determined by the changes in the signals in response to a tilt in the beam. The data for various square field sizes were used to develop a functional relationship with RDF. Results: The IQM tracked the beam output well within 1% of the reference ion-chamber readings. The Picket-Fence type field test detected a 1mm shift error of one MLC bank. The system was able to detect 2.5% or greater beam asymmetry. The IQM results for all other QA tests were found to agree with the reference values to within 0.5%. Conclusion: It was demonstrated that the IQM system can effectively monitor the Linac performance parameters for the purpose of routine QA constancy tests. With minimum user interactions a comprehensive set of tests can be performed efficiently, allowing frequent monitoring of the Linac. The presenting author’s salary is funded by the manufacturer of the QA device. All the other authors have financial interests with the commercialization of this QA device.

07 ISOTOPE AND RADIATION SOURCES↗

NASA NTRS1991

The first ANDES elements: 9-DOF plate bending triangles

New elements are derived to validate and assess the assumed natural deviatoric strain (ANDES) formulation. This is a brand new variant of the assumed natural strain (ANS) formulation of finite elements, which has recently attracted attention as an effective method for constructing high-performance elements for linear and nonlinear analysis. The ANDES formulation is based on an extended parametrized variational principle developed in recent publications. The key concept is that only the deviatoric part of the strains is assumed over the element whereas the mean strain part is discarded in favor of a constant stress assumption. Unlike conventional ANS elements, ANDES elements satisfy the individual element test (a stringent form of the patch test) a priori while retaining the favorable distortion-insensitivity properties of ANS elements. The first application of this formulation is the development of several Kirchhoff plate bending triangular elements with the standard nine degrees of freedom. Linear curvature variations are sampled along the three sides with the corners as gage reading points. These sample values are interpolated over the triangle using three schemes. Two schemes merge back to conventional ANS elements, one being identical to the Discrete Kirchhoff Triangle (DKT), whereas the third one produces two new ANDES elements. Numerical experiments indicate that one of the ANDES element is relatively insensitive to distortion compared to previously derived high-performance plate-bending elements, while retaining accuracy for nondistorted elements.

Militello, Carmelo↗

DOE OSTI2019

Gaussian mixture models as automated particle classifiers for fast neutron detectors

Pulse shape discrimination (PSD) is the task of classifying electronic pulse shapes for different particle types such as gamma rays and fast neutrons interacting in scintillators and read out by photo sensitive detectors. This field has been limited in its adoption of techniques found in the statistical learning community. Methods initially employed in the 1960s for analog electronic circuitry persist in the current PSD literature describing operations performed on digitized pulses, which are amenable to statistical rigor. Despite vast amounts of data collected at low energy levels, traditional PSD methods are unable to discriminate particles below a certain threshold. As such, in this work, Gaussian mixture models (GMMs) are used as a clustering technique for fast neutron detection in the absence of labeled data. GMMs yield improvements spanning the energy spectrum in a desirably efficient, unsupervised fashion. An extension, the Dirichlet Process GMM, provides further flexibility and classification improvement.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

Abstract Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost‐efficient genotyping using next‐generation sequencing. However, accurate genotype calling from next‐generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome‐wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype‐calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum , and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype‐calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost‐efficiently implement GWAS and genomic prediction in polyploid crops.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

The Mu2e calorimeter: Quality assurance of production crystals and SiPMs

Not Available

Atanov, N.↗

DOE OSTI2016

Picosecond wide-field time-correlated single photon counting fluorescence microscopy with a delay line anode detector

We perform wide-field time-correlated single photon counting-based fluorescence lifetime imaging (FLIM) with a crossed delay line anode image intensifier, where the pulse propagation time yields the photon position. This microchannel plate-based detector was read out with conventional fast timing electronics and mounted on a fluorescence microscope with total internal reflection (TIR) illumination. The picosecond time resolution of this detection system combines low illumination intensity of microwatts with wide-field data collection. This is ideal for fluorescence lifetime imaging of cell membranes using TIR. We show that fluorescence lifetime images of living HeLa cells stained with membrane dye di-4-ANEPPDHQ exhibit a reduced lifetime near the coverslip in TIR compared to epifluorescence FLIM.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2012

Improving I/O Throughput with PRIMACY: Preconditioning ID-Mapper for Compressing Incompressibility

The ability to efficiently handle massive amounts of data is necessary for the continuing development towards exascale scientific data-mining applications and database systems. Unfortunately, recent years have shown a growing gap between the size and complexity of data produced from scientific applications and the limited I/O bandwidth available on modern high-performance computing systems. Utilizing data compression in order to lower the degree of I/O activity offers a promising means to addressing this problem. However, the standard compression algorithms previously explored for such use offer limited gains on both the end-to-end throughput and storage fronts. In this paper, we introduce an in-situ compression scheme aimed at improving end-to-end I/O throughput as well as reduction of dataset size. Our technique, PRIMACY (Preconditioning Id-MApper for Compressing incompressibility), acts as a preconditioner for standard compression libraries by modifying representation of original floating-point scientific data to increase byte-level repeatability, allowing standard loss less compressors to take advantage of their entropy-based byte-level encoding schemes. We additionally present a theoretical model for compression efficiency in high-performance computing environments and evaluate the efficiency of our approach via comparative analysis. Based on our evaluations on 20 real-world scientific datasets, PRIMACY achieved up to 38% and 22% improvements upon standard end-to-end write and read throughputs respectively in addition to a 25% increase in compression ratios paired with 3-to-4-fold improvement in both compression and decompression throughput over general purpose compressors.

Computer Science↗

DOE OSTI2012

Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1

Cytomegaloviruses are highly host restricted resulting in co-speciation with their hosts. As a natural pathogen of rhesus macaques (RM), Rhesus Cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). To date, most in vivo experiments performed with RhCMV employed strain 68-1 cloned as bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV we re-evaluated the RhCMV 68-1 BAC-genome by whole genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By additionally comparing the RhCMV genome to that of several closely related Old World Monkey (OWM) CMVs we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis eliminated many genes previously characterized as RhCMV-specific while consolidating a high conservation of ORFs among OWM-CMVs and between RhCMV and HCMV. Moreover, virion proteomics independently validated the revised ORF predictions since only proteins encoded by predicted ORFs could be detected. Taken together these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes and OWMs than previously assumed. Remarkably, BAC-derived RhCMV is able to establish and maintain persistent infection despite the lack of multiple genes homologous to HCMV genes involved in tissue tropism.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2017

EnergyPlus™ [SWR-17-23]

Originally developed in 1999, an updated version 8.8.0 with bug fixes was released on September 30th, 2017. EnergyPlus™ is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings. EnergyPlus is a console-based program that reads input and writes output to text files. It ships with a number of utilities including IDF-Editor for creating input files using a simple spreadsheet-like interface, EP-Launch for managing input and output files and performing batch simulations, and EP-Compare for graphically comparing the results of two or more simulations. Several comprehensive graphical interfaces for EnergyPlus are also available. DOE does most of its work with EnergyPlus using the OpenStudio® software development kit and suite of applications. DOE releases major updates to EnergyPlus twice annually.

Source record↗

DOE OSTI2024

Genomic surveillance indicates clonal replacement of hypervirulent Klebsiella pneumoniae ST881 and ST29 lineage strains in vivo

The emergence of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat, particularly regarding its carriage in the healthy population. However, the genomic epidemiological characteristics and population dynamics of hvKp within a single patient across distinct infection episodes remain largely unknown. This study aimed to investigate the clonal replacement of hvKp K2-ST881 and K54-ST29 lineage strains in a single patient experiencing multiple-site infections during two independent episodes. Two strains, designated EDhvKp-1 and EDhvKp-2, were obtained from blood and cerebrospinal fluid during the first admission, and the strain isolated from blood on the second admission was named EDhvKp-3. Whole-genome sequencing, utilizing both short-read Illumina and long-read Oxford Nanopore platforms, was conducted. In silico multilocus sequence typing (MLST), identification of antimicrobial resistance and virulence genes, and the phylogenetic relationship between our strains and other K. pneumoniae ST881 and ST29 genomes retrieved from the public database were performed. Virulence potentials were assessed through a mouse lethality assay. Our study indicated that the strains were highly susceptible to multiple antimicrobial agents. Plasmid sequence analysis confirmed that both virulence plasmids, pEDhvKp-1 (166,008 bp) and pEDhvKp-3 (210,948 bp), belonged to IncFIB type. Multiple virulence genes, including rmpA , rmpA2 , rmpC , rmpD , iroBCDN , iucABCD , and iutA , were identified. EDhvKp-1 and EDhvKp-2 showed the closest relationship to strain 502 (differing by 51 SNPs), while EDhvKp-3 exhibited 69 SNPs differences compared to strain TAKPN-1, which all recovered from Chinese patients in 2020. In the mouse infection experiment, both ST881 EDhvKp-1 and ST29 EDhvKp-3 displayed similar virulence traits, causing 90 and 100% of the mice to die within 72 h after intraperitoneal infection, respectively. Our study expands the spectrum of hvKp lineages and highlights genomic alterations associated with clonal switching between two distinct lineages of hvKP that successively replaced each other in vivo . The development of novel strategies for the surveillance, diagnosis, and treatment of high-risk hvKp is urgently needed.

Liu, Ning↗

NASA NTRS1975

Modal test - Measurement and analysis requirements

Data from the Viking Orbiter Modal Test Program are used to illustrate modal test measurement and analysis requirements. The test was performed using a multiple shake dwell technique where data were acquired one channel at a time and recorded on paper tape. Up to ten shakers were used simultaneously, with a complete set of data consisting of 290 strain-gage readings and 125 accelerometer readings. The data analysis provided information sufficient to minimize errors in the data. The list of analyses in order of value is orthogonality, residual mass, frequency sweep, data checks to assure good test data, multilevel trends, global kinetic energy, and global strain energy.

Wada, B. K.↗

NASA NTRS1993

Flexible storage medium for write-once optical tape

A write-once data storage media was developed which is suitable for optical tape applications. The media is manufactured using a continuous film process to deposit a ternary alloy of tin, bismuth, and copper. This laser sensitive layer is sputter deposited onto commercial plastic web as a single-layer thin film. A second layer is sequentially deposited on top of the alloy to enhance the media performance and act as an abrasion resistant hard overcoat. The media was observed to have laser write sensitivities of less than 2.0 njoules/bit, carrier-to-noise levels of greater than 50dB's, modulation depths of approximately 100 percent, read-margins of greater than 35, uniform grain sizes of less than 200 Angstroms, and a media lifetime that exceeds 10 years. Prototype tape media was produced for use in the CREO drive system. The active and overcoat materials are first sputter deposited onto three mil PET film in a single pass through the vacuum coating system, and then converted down into multiple reels of 35mm x 880m tape. One mil PET film was also coated in this manner and then slit and packaged into 3480 tape cartridges.

Strandjord, Andrew J. G.↗

NASA NTRS2017

Giovanni in the Cloud: Earth Science Data Exploration in Amazon Web Services

Giovanni is an exploration tool at the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), providing 22 analysis and visualization services for over 1600 Earth Science data variables. Owing to its popularity, Giovanni has experienced a consistent growth in overall demand, with periodic usage spikes attributed to trainings by education organizations, extensive data analysis in response to natural disasters, preparations for science meetings, etc. Furthermore, the new generation of spaceborne sensors and high resolution models have resulted in an exponential growth in data volume with data distributed across the traditional boundaries of data centers. Seamless exploration of data (without users having to worry about data center boundaries) has been a key recommendation of the GES DISC User Working Group. These factors have required new strategies for delivering acceptable performance. The cloud-based Giovanni, built on Amazon Web Services (AWS), evaluates (1) AWS native solutions to provide a scalable, serverless architecture; (2) open standards for data storage in the Cloud; (3) a cost model for operations; and (4) end-user performance. Our preliminary findings indicate that the use of serverless architecture has a potential to significantly reduce development and operational cost of Giovanni. The combination of using AWS managed services, storage of data in open standards, and schema-on-read data access strategy simplifies data access and analytics, in addition to making data more accessible to the end users of Giovanni through popular programming languages.

Giovanni↗

NASA NTRS2018

Characterization of a Radiometer Window for Mars Aftbody Heating Including Ablation Product Deposition Using a Miniature Arc Jet

The Mars Entry, Descent, and Landing Instrumentation 2 (MEDLI2) sensor suite for the Mars 2020 mission includes a radiometer on the backshell to measure the radiative heating during entry into the Martian atmosphere. Thermal Protection System (TPS) ablation products may be deposited on the radiometer window which would degrade the transmission and thus alter the accuracy of the radiometer readings. Testing in NASA Ames Research Center's miniature arc jet (mARC) facility was conducted to deposit TPS ablation products on radiometer windows in an effort to characterize how the ablation products change the window transmission and thus alter radiometer performance. Heat flux and stagnation pressure characterization of the mARC facility in a 90 percent CO2, 10 percent N2 (by mass) Mars-like environment are presented. The spectral transmission of the radiometer windows before and after mARC testing are compared. Additionally, a discussion of how flight-like these test conditions were and future work to further characterize the effect of TPS ablation on radiometer performance are presented.

Miller, Ruth A.↗

DOE OSTI2016

A source-attractor approach to network detection of radiation sources

Radiation source detection using a network of detectors is an active field of research for homeland security and defense applications. We propose Source-attractor Radiation Detection (SRD) method to aggregate measurements from a network of detectors for radiation source detection. SRD method models a potential radiation source as a magnet -like attractor that pulls in pre-computed virtual points from the detector locations. A detection decision is made if a sufficient level of attraction, quantified by the increase in the clustering of the shifted virtual points, is observed. Compared with traditional methods, SRD has the following advantages: i) it does not require an accurate estimate of the source location from limited and noise-corrupted sensor readings, unlike the localizationbased methods, and ii) its virtual point shifting and clustering calculation involve simple arithmetic operations based on the number of detectors, avoiding the high computational complexity of grid-based likelihood estimation methods. We evaluate its detection performance using canonical datasets from Domestic Nuclear Detection Office s (DNDO) Intelligence Radiation Sensors Systems (IRSS) tests. SRD achieves both lower false alarm rate and false negative rate compared to three existing algorithms for network source detection.

Wu, Qishi↗

DOE OSTI2017

EnergyPlus™

Source record↗

DOE OSTI2015

241-AY-102 Leak detection pit drain line visual inspection - 15678

In October 2012, Washington River Protection Solutions LLC (WRPS) determined that waste had leaked into the annulus of Tank 241-AY-102. WRPS conducted an extensive review of Tank AY-102 and increased both inspection and monitoring of the tank; however, the precise cause and location of the leak could not be determined. In parallel with the leak in the primary tank, the Tank AY-102 leak detection pit (LDP) was accumulating water through the drain system external to the secondary tank liner. Liquid collecting in the LDP is suspected to be from water intrusion and collects at a rate such that the LDP must be pumped routinely. Following a routine pumping event on June 20, 2013, elevated radiation dose rates were noted on the transfer hose and surface contamination readings were found on the transfer pump when it was removed from the Tank AY-102 LDP. These two field readings suggested that tank waste from a secondary liner breach could be leaking into the LDP. As a result, WRPS initiated a plan to ascertain the integrity of the secondary tank liner including a robotic inspection of the LDP. To perform the robotic visual inspection, a custom robotic crawler with a deployment device was designed, built, and operated by IHI Southwest for WRPS to inspect the 6 in (152 mm) leak detection pit drain line. To ensure success when deployed in the field, the inspection equipment was demonstrated at both the IHI facility in Denver, Colorado, and the Hanford Site using full scale piping mockups. On November 20, 2013 WRPS inspected the 6 in (152 mm) diameter drain line. The deployment device successfully attached to the drain line, and the crawler entered the drain line and traversed to within approximately 7 ft (2.1 m) of the central sump located under the center of the tank before losing traction. Crawler performance was satisfactory, and the quality of the camera image and lighting provided sufficient detail to document the current condition of the visible regions of the pipe. The inspection showed that the majority of the drain line was dry. Two wet areas were observed, a portion of the line nearest the LDP and a portion near the center of the tank. The portion nearest the LDP was under water prior to pumping on November 14, 2013. Although sediment and debris were seen during the inspection, it is believed to be construction debris and corrosion products. No material was found in the inspection that looked like tank waste or the material seen in the Tank AY-102 annulus (i.e., no greenish or yellowish deposits or dark fluids, dried salt deposits, or crystalline material). The contamination levels seen on the crawler were consistent with past values seen on LDP pumping equipment. Sampling and analysis of the recovered residues from the crawlers did not find material consistent with tank waste. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗