Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “life data analysis”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Endogeneity of pedestrian survival time and emergency medical service response time: Variations across disadvantaged and non-disadvantaged communities

The Vision Zero-Safe Systems Approach prioritizes fast access to Emergency Medical Services (EMS) to improve the survivability of road users in transportation crashes, especially concerning the recent increase in pedestrian-involved crashes. Pedestrian crashes resulting in immediate or early death are considerably more severe than those taking longer. The time gap between injury and fatality is known as survival time, and it heavily relies on EMS response time. The characteristics of the crash location may be associated with EMS response and survival time. A US Department of Transportation initiative identifies communities often facing challenges. Six disadvantaged community (DAC) indicators, including economy, environment, equity, health, resilience, and transportation access, enable an analysis of how survival and EMS response times vary across DACs and non-DACs. To this end, this study created a unique and comprehensive database by linking DACs data with 2017–2021 pedestrian-involved fatal crashes. This study utilizes two-stage residual inclusion models with segmentation for DACs and non-DACs accounting for the endogenous relationship between EMS response and pedestrian survival time. The results indicate that EMS response time is higher and pedestrian survival time is lower in DACs than in non-DACs. A delayed EMS response time is associated with a greater reduction in survival time in DACs compared to non-DACs. Factors, e.g., nighttime and interstate crashes, contribute to higher EMS response time, while pedestrian drugs, driver speeding, and hit-and-run behaviors are associated with a greater reduction in survival time in DACs than non-DACs. Finally, the implications of the findings are discussed in the paper.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Generating Co-expression Networks for Three Cyanobacteria: Synechococcus sp. PCC 7942, Synechococcus sp. PCC 7002, Synechocystis sp. PCC 6803

Cyanobacteria are photosynthetic organisms capable of high growth rate and represent a promising bioplatform for harnessing the sun’s energy to make biofuel. Additionally, the process of photosynthesis absorbs CO2 from the environment. Understanding the metabolic processes involved in photosynthesis could lead to solutions to the recent rise of CO2 concentration in Earth’s atmosphere and the associated climate change. More research on the transcriptional regulation of these cells is needed to learn how to harness the untapped potential of cyanobacteria for these applications. Transcriptional analysis via RNA-seq provides an understanding of how gene expression changes at the mRNA level under diverse growing conditions. I systematically collected and analyzed RNA-Seq data obtained under a variety of conditions and available on the NCBI database for three cyanobacteria model organisms: Synechococcus elongatus sp. PCC 7942, Synechococcus sp. PCC 7002, and Synechocystis sp. PCC 6803. For each organism, the data was mapped to a reference genome to characterize the RNA expression profile. Samples were checked for quality based on the number of reads and the correlation of the expression profile between labeled replicates. All samples were transformed into transcripts per million reads, followed by a log transformation to account for the wide range of sample sizes. Gene co-expression networks were generated and analyzed for each species using Cytoscape. These networks provide a base level of gene expression for each species. The network topology and high-betweeness nodes of these networks need to be analyzed further to provide insight on potential ways to harness cyanobacteria genetics. Additionally, these datasets can be used together to form a core genome network analysis- one that includes only the genes that are homologous between the three species. This project has prepared the way for a more in-depth study on photosynthetic microbes on a genetic level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cosmogenic 137 Xe Analysis of Alternatives for nEXO

Neutrinoless double-beta decay is a hypothetical nuclear decay in which two matter particles are produced without corresponding antimatter particles. Observation of neutrinoless double-beta decay would shed light on a potential explanation of matter-antimatter observed in the universe and also indicate the Majorana nature of neutrinos, meaning that the neutrino can act as its own antiparticle. The nEXO experiment is a proposed 5-ton liquid xenon time projection chamber detector with a projected 1.35 × 10 28 yr half-life sensitivity to neutrinoless double-beta decay in 136 Xe [J. Phys. G 49, 015104 (2022)]. While nEXO has a baseline location of SNOLAB, there are several other underground facilities in the world capable of hosting the experiment. The primary change at each site will be cosmogenic 137 Xe backgrounds, caused by varied cosmogenic muon activity at each site. This study finds that while there is a negligible increase in nEXO’s half-life sensitivity at 90% C.L. from improving the cosmogenic 137 Xe veto rejection procedure for SNOLAB, much higher daily muon rates at three other sites will have an adversely negative effect on nEXO’s sensitivity and would likely require further modifications to nEXO’s baseline design to reach nEXO’s scientific goals. Monte Carlo simulations of muons inducing 137 Xe backgrounds were conducted at four underground sites, SNOLAB, SURF, LNGS, and WIPP, each with roughly a factor of 10 times higher daily muon activity than the previous site. There were two primary inputs to these simulations. The first was sample data of cosmogenic muon flight through nEXO’s outer detector, a 12.8m tall and 12.3m wide cylindrical water tank lined with photomultiplier tubes to detect Cerenkov radiation, and all of the secondary interactions produced in the detector. The second input was a parametrization of 137 Xe* production tagging when 137 Xe de-excites and release prompt gammas, as well as accidental tagging caused by neutron capture on 63 Cu, 65 Cu, 19 F, and 1 H throughout the detector. Together, the number of backgrounds relative to the previous 2021 Sensitivity Paper [J. Phys. G 49, 015104 (2022)] was found at each of these four sites across three energy windows, from 400, 1400, and 2600 keV all up to 4600 keV, just above the end point of the prompt gamma spectrum for 137 Xe*. Using level curves for the sensitivity as 137 Xe backgrounds scale relative to baseline calculations, the half-life sensitivity at 90% C.L. for each of trial was found. Even with reduced 137 Xe backgrounds, the results for SNOLAB yielded neglible improvements in nEXO’s predicted sensitivity. On the contrary, the increased backgrounds for the three other considered sites yielded sensitivity estimates below nEXO’s previous projections. This study demonstrates that the shielding from cosmogenic muons at SNOLAB makes it highly preferred even amongst other world leading underground laboratories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia

Abstract This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, compares the entire expressed whole blood host transcriptome between Kenyan children (3-48 mos.) with non-SMA (Hb ≥ 6.0 g/dL, n = 39) and SMA ( n = 18). Differential expression analyses reveal 1403 up-regulated and 279 down-regulated transcripts in SMA, signifying impairments in host inflammasome activation, cell death, and innate immune and cellular stress responses. Immune cell profiling shows decreased memory responses, antigen presentation, and immediate pathogen clearance, suggesting an immature/improperly regulated immune response in SMA. Module repertoire analysis of blood-specific gene signatures identifies up-regulation of erythroid genes, enhanced neutrophil activation, and impaired inflammatory responses in SMA. Enrichment analyses converge on disruptions in cellular homeostasis and regulatory pathways for the ubiquitin-proteasome system, autophagy, and heme metabolism. Pathway analyses highlight activation in response to hypoxic conditions [Hypoxia Inducible Factor (HIF)−1 target and Reactive Oxygen Species (ROS) signaling] as a central theme in SMA. These signaling pathways are also top-ranking in protein abundance measures and a Ugandan SMA cohort with available transcriptomic data. Targeted RNA-Seq validation shows strong concordance with our entire expressed transcriptome data. These findings identify key molecular themes in SMA pathogenesis, offering potential targets for new malaria therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Using mixed methods to construct and analyze a participatory agent-based model of a complex Zimbabwean agro-pastoral system

Complex social-ecological systems can be difficult to study and manage. Simulation models can facilitate exploration of system behavior under novel conditions, and participatory modeling can involve stakeholders in developing appropriate management processes. Participatory modeling already typically involves qualitative structural validation of models with stakeholders, but with increased data and more sophisticated models, quantitative behavioral validation may be possible as well. In this study, we created a novel agent-basedmodel applied to a specific context: Zimbabwean non-governmental organization the Muonde Trust has been collecting data on their agro-pastoral system for the last 35 years and had concerns about land-use planning and the effectiveness of management interventions in the face of climate change. We collaboratively created an agent-based model of their system using their data archive, qualitatively calibrating it to the observed behavior of the real system without tuning any parameters to match specific quantitative outputs. We then behaviorally validated the model using quantitative community-based data and conducted a sensitivity analysis to determine the relative impact of underlying parameter assumptions, Indigenous management interventions, and different rainfall variation scenarios. We found that our process resulted in a model which was successfully structurally validated and sufficiently realistic to be useful for Muonde researchers as a discussion tool. The model was inconsistently behaviorally validated, however, with some model variables matching field data better than others. We observed increased model system instability due to increasing variability in underlying drivers (rainfall), and also due to management interventions that broke feedbacks between the components of the system. Interventions that smoothed year-to-year variation rather than exaggerating it tended to improve sustainability. The Muonde trust has used the model to successfully advocate to local leaders for changes in land-use planning policy that will increase the sustainability of their system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The Uniform Methods Project: Smart Thermostat Evaluation Protocol

A smart thermostat is an internet-connected device that controls home heating, ventilation, and air-conditioning (HVAC) equipment and can automatically adjust temperature set points to optimize performance and achieve energy savings. Smart thermostat features often include two way communication, occupancy detection (such as geofencing and occupancy sensors), schedule learning, and seasonal optimization algorithms. Smart thermostats can control most conventional HVAC systems, including central air conditioners, heat pumps, and forced air furnaces. Several types of residential utility programs offer smart thermostats as replacements measures. Working with smart thermostat vendors, utilities can offer separate optimization programs to produce energy savings beyond those achieved by installing a smart thermostat. From an evaluation perspective, smart thermostat programs have several noteworthy features. First, the energy savings from a smart thermostat may change over the life of the device. As a smart thermostat is connected to the internet, original equipment manufacturers can update the thermostat software to improve the thermostat's energy efficiency. Likewise, users can adjust the thermostat settings and schedules over time in response to changes in weather, thermal comfort, energy prices, or preferences for energy efficiency. Additionally, many thermostat manufacturers offer seasonal optimization programs that recommend changes or make minor, automated adjustments to the thermostat settings to improve energy efficiency. These opt-in programs are now standard offerings for many smart thermostat manufacturers and provided at no additional cost to users. The potential for software updates and continuous optimization and the evolving nature of user interactions mean future energy savings may differ from first-year savings and the energy savings of smart thermostats may need to be evaluated more than once. Second, smart thermostats often have small unit energy savings relative to a home's total energy consumption, especially in comparison to whole- home retrofit programs. This can make it difficult to detect the smart thermostat savings in billing or advanced metering infrastructure (AMI) meter consumption data. For example, as cooling loads in many regions average about 20% of annual electricity consumption, smart thermostat savings of 10% of cooling energy use would equate to a 2% reduction in home electricity consumption. Evaluators should use regression analysis of whole-home billing consumption or advanced metering infrastructure (AMI) meter consumption data to evaluate smart thermostat savings because, as explained at greater length below , these data are usually available to evaluators and regression can control for the impacts of weather and other potentially confounding factors on a home's energy consumption. Finally, as with other energy efficiency programs, participation in smart thermostat programs is self-selective. As discussed at greater length below , smart thermostat participants tend to be, among other things, younger, higher-income, and more likely to adopt electric vehicles (EVs) and internet connected devices than nonparticipants. These differences are often unobservable to the evaluator and correlated with a home's energy consumption, creating the potential for bias in estimating savings. Due to the small unit savings of thermostats, errors and biases from self-selection that may not be very consequential when evaluating a whole- home retrofits (e.g., ±2% of home electricity consumption) can have a major impact when evaluating the savings and cost-effectiveness of smart thermostat programs. A percentage point change in the estimated savings could affect the cost-effectiveness of a program. This means it is important for evaluators to assess and to minimize the potential for error from selection bias in estimating smart thermostat program savings. The Uniform Methods Project provides model protocols for determining energy savings and demand reductions that result from specific energy efficiency measures implemented through state and utility programs. In most cases, the measure protocols are based on a particular option identified by the International Performance Verification and Measurement Protocol ; however, this work provides a more detailed approach to implementing that option. Each chapter is written by technical experts in collaboration with their peers, reviewed by industry experts, and subject to public review and comment. The UMP protocols can be used by utilities, program administrators, public utility commissions, evaluators, and other stakeholders for both program planning and evaluation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

New constraint on the Np 237 ( n , γ ) Np 238 integral cross section using the Godiva-IV critical assembly

Accurate knowledge of the 237 Np(n, γ) 238 Np cross section at fast neutron energies is important for applied nuclear science. The presently available experimental data has large disagreements in the fast neutron region. Perform a model-independent measurement of the 237 Np(n, γ) 238 Np integral cross section using a well characterized fast neutron source and compare the result with previous measurements and current nuclear data evaluations. Provide an integral measurement that can be used as a benchmark for current evaluations. Multiple samples of 237 Np were irradiated in the Godiva-IV critical assembly. Following the irradiation, the samples placed in a γ-ray counting setup and the γ-rays emitted from the decay of 238 Np were measured over a time period of approximately 7 days. Multiple γ-ray decay branches of 238 Np were observed. The observed activity of 238 Np was used to calculate the amount of 238 Np produced during the irradiation via the 237 Np(n, γ) 238 Np reaction and an integral cross section of 342(11) mb was measured for the Godiva-IV neutron spectrum. Further, the 238 Np half-life has been measured with a result of 50.31(5) hours. The 237 Np(n, γ) 238 Np integral cross section measured in this work is in agreement with overlapping 1σ error bands to ENDF/B-VIII.0. However, the measured value is 3σ away from the calculated integral cross section using JENDL-5. This measurement offers a reliable benchmark for future 237 Np(n, γ) 238 Np cross section evaluations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

A Phenomenological Model for Cavitation

A phenomenological model of cavitation is presented, based on observations that both large relative negative pressures and large negative time derivatives of pressure are required for cavitation onset. We simulated two cavitation experiments to generate cavitation scaling parameters for relative pressure drop and rate of pressure drop. Our results show the model, while simple, is effective at reproducing results from laboratory experiments of cavitation. The parameters were then used in conjunction with a human surrogate computational model to predict, at any position within the head, the probability of intracranial cavitation caused by exposure to a blast event. The results suggest that the magnitude of blast overpressure observed in field data is sufficient to cause intracranial cavitation. Our analysis indicates that the helmeted head, when compared to the unhelmeted head configuration, results in a decrease but not elimination of cavitation exposure. When density functions of cavitation probability versus cumulative brain volume are combined with an injury severity model, the results show helmet efficacy at low and moderate risk levels. However, the convergence of unhelmeted and helmeted probability density functions at high-to-excessive risk thresholds indicates the helmet offers diminishing protection at elevated exposure levels, relative to the unhelmeted baseline. Future investigation and collaboration with neuroscience subject matter experts are needed to contextualize the current computational results. While the present work contributes specific and quantified predictions of intracranial cavitation location and severity, more research is required to apply our results to clinical settings with population-based brain injury subjects and controls. The relationship between our intracranial cavitation predictions with their anticipated clinical sequelae remains a topic in need of exploration.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

People who inject drugs in metropolitan Chicago: A meta-analysis of data from 1997-2017 to inform interventions and computational modeling toward hepatitis C microelimination

Progress toward hepatitis C virus (HCV) elimination in the United States is not on track to meet targets set by the World Health Organization, as the opioid crisis continues to drive both injection drug use and increasing HCV incidence. A pragmatic approach to achieving this is using a microelimination approach of focusing on high-risk populations such as people who inject drugs (PWID). Computational models are useful in understanding the complex interplay of individual, social, and structural level factors that might alter HCV incidence, prevalence, transmission, and treatment uptake to achieve HCV microelimination. However, these models need to be informed with realistic sociodemographic, risk behavior and network estimates on PWID. We conducted a meta-analysis of research studies spanning 20 years of research and interventions with PWID in metropolitan Chicago to produce parameters for a synthetic population for realistic computational models (e.g., agent-based models). We then fit an exponential random graph model (ERGM) using the network estimates from the meta-analysis in order to develop the network component of the synthetic population.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Towards verifiable cancer digital twins: tissue level modeling protocol for precision medicine

Cancer exhibits substantial heterogeneity, manifesting as distinct morphological and molecular variations across tumors, which frequently undermines the efficacy of conventional oncological treatments. Developments in multiomics and sequencing technologies have paved the way for unraveling this heterogeneity. Nevertheless, the complexity of the data gathered from these methods cannot be fully interpreted through multimodal data analysis alone. Mathematical modeling plays a crucial role in delineating the underlying mechanisms to explain sources of heterogeneity using patient-specific data. Intra-tumoral diversity necessitates the development of precision oncology therapies utilizing multiphysics, multiscale mathematical models for cancer. This review discusses recent advancements in computational methodologies for precision oncology, highlighting the potential of cancer digital twins to enhance patient-specific decision-making in clinical settings. We review computational efforts in building patient-informed cellular and tissue-level models for cancer and propose a computational framework that utilizes agent-based modeling as an effective conduit to integrate cancer systems models that encode signaling at the cellular scale with digital twin models that predict tissue-level response in a tumor microenvironment customized to patient information. Furthermore, we discuss machine learning approaches to building surrogates for these complex mathematical models. These surrogates can potentially be used to conduct sensitivity analysis, verification, validation, and uncertainty quantification, which is especially important for tumor studies due to their dynamic nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Relationships between Habitual Polyphenol Consumption and Gut Microbiota in the INCLD Health Cohort

While polyphenol consumption is often associated with an increased abundance of beneficial microbes and decreased opportunistic pathogens, these relationships are not completely described for polyphenols consumed via habitual diet, including culinary herb and spice consumption. This analysis of the International Cohort on Lifestyle Determinants of Health (INCLD Health) cohort uses a dietary questionnaire and 16s microbiome data to examine relationships between habitual polyphenol consumption and gut microbiota in healthy adults (n = 96). In this exploratory analysis, microbial taxa, but not diversity measures, differed by levels of dietary polyphenol consumption. Taxa identified as exploratory biomarkers of daily polyphenol consumption (mg/day) included Lactobacillus, Bacteroides, Enterococcus, Eubacterium ventriosum group, Ruminococcus torques group, and Sutterella. Taxa identified as exploratory biomarkers of the frequency of polyphenol-weighted herb and spice use included Lachnospiraceae UCG-001, Lachnospiraceae UCG-004, Methanobrevibacter, Lachnoclostridium, and Lachnotalea. Several of the differentiating taxa carry out activities important for human health, although out of these taxa, those with previously described pro-inflammatory qualities in certain contexts displayed inverse relationships with polyphenol consumption. Our results suggest that higher quantities of habitual polyphenol consumption may support an intestinal environment where opportunistic and pro-inflammatory bacteria are represented in a lower relative abundance compared to those with less potentially virulent qualities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Describing patterns of familial cancer risk in subfertile men using population pedigree data

STUDY QUESTION Can we simultaneously assess risk for multiple cancers to identify familial multicancer patterns in families of azoospermic and severely oligozoospermic men? SUMMARY ANSWER Here, distinct familial cancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in familial cancer risk by both type of subfertility and within subfertility type. WHAT IS KNOWN ALREADY Subfertile men and their relatives show increased risk for certain cancers including testicular, thyroid, and pediatric. STUDY DESIGN, SIZE, DURATION A retrospective cohort of subfertile men (N = 786) was identified and matched to fertile population controls (N = 5674). Family members out to third-degree relatives were identified for both subfertile men and fertile population controls (N = 337 754). The study period was 1966–2017. Individuals were censored at death or loss to follow-up, loss to follow-up occurred if they left Utah during the study period. PARTICIPANTS/MATERIALS, SETTING, METHODS Azoospermic (0 × 10 6 /mL) and severely oligozoospermic (<1.5 × 10 6 /mL) men were identified in the Subfertility Health and Assisted Reproduction and the Environment cohort (SHARE). Subfertile men were age- and sex-matched 5:1 to fertile population controls and family members out to third-degree relatives were identified using the Utah Population Database (UPDB). Cancer diagnoses were identified through the Utah Cancer Registry. Families containing ≥10 members with ≥1 year of follow-up 1966–2017 were included (azoospermic: N = 426 families, 21 361 individuals; oligozoospermic: N = 360 families, 18 818 individuals). Unsupervised clustering based on standardized incidence ratios for 34 cancer phenotypes in the families was used to identify familial multicancer patterns; azoospermia and severe oligospermia families were assessed separately. MAIN RESULTS AND THE ROLE OF CHANCE Compared to control families, significant increases in cancer risks were observed in the azoospermia cohort for five cancer types: bone and joint cancers hazard ratio (HR) = 2.56 (95% CI = 1.48–4.42), soft tissue cancers HR = 1.56 (95% CI = 1.01–2.39), uterine cancers HR = 1.27 (95% CI = 1.03–1.56), Hodgkin lymphomas HR = 1.60 (95% CI = 1.07–2.39), and thyroid cancer HR = 1.54 (95% CI = 1.21–1.97). Among severe oligozoospermia families, increased risk was seen for three cancer types: colon cancer HR = 1.16 (95% CI = 1.01–1.32), bone and joint cancers HR = 2.43 (95% CI = 1.30–4.54), and testis cancer HR = 2.34 (95% CI = 1.60–3.42) along with a significant decrease in esophageal cancer risk HR = 0.39 (95% CI = 0.16–0.97). Thirteen clusters of familial multicancer patterns were identified in families of azoospermic men, 66% of families in the azoospermia cohort showed population-level cancer risks, however, the remaining 12 clusters showed elevated risk for 2-7 cancer types. Several of the clusters with elevated cancer risks also showed increased odds of cancer diagnoses at young ages with six clusters showing increased odds of adolescent and young adult (AYA) diagnosis [odds ratio (OR) = 1.96–2.88] and two clusters showing increased odds of pediatric cancer diagnosis (OR = 3.64–12.63). Within the severe oligozoospermia cohort, 12 distinct familial multicancer clusters were identified. All 12 clusters showed elevated risk for 1–3 cancer types. An increase in odds of cancer diagnoses at young ages was also seen in five of the severe oligozoospermia familial multicancer clusters, three clusters showed increased odds of AYA diagnosis (OR = 2.19–2.78) with an additional two clusters showing increased odds of a pediatric diagnosis (OR = 3.84–9.32). LIMITATIONS, REASONS FOR CAUTION Although this study has many strengths, including population data for family structure, cancer diagnoses and subfertility, there are limitations. First, semen measures are not available for the sample of fertile men. Second, there is no information on medical comorbidities or lifestyle risk factors such as smoking status, BMI, or environmental exposures. Third, all of the subfertile men included in this study were seen at a fertility clinic for evaluation. These men were therefore a subset of the overall population experiencing fertility problems and likely represent those with the socioeconomic means for evaluation by a physician. WIDER IMPLICATIONS OF THE FINDINGS This analysis leveraged unique population-level data resources, SHARE and the UPDB, to describe novel multicancer clusters among the families of azoospermic and severely oligozoospermic men. Distinct overall multicancer risk and familial multicancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in cancer risk by type of subfertility and within subfertility type. Describing families with similar cancer risk patterns provides a new avenue to increase homogeneity for focused gene discovery and environmental risk factor studies. Such discoveries will lead to more accurate risk predictions and improved counseling for patients and their families. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by GEMS: Genomic approach to connecting Elevated germline Mutation rates with male infertility and Somatic health (Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD): R01 HD106112). The authors have no conflicts of interest relevant to this work.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Machine learning models for rat multigeneration reproductive toxicity prediction

Reproductive toxicity is one of the prominent endpoints in the risk assessment of environmental and industrial chemicals. Due to the complexity of the reproductive system, traditional reproductive toxicity testing in animals, especially guideline multigeneration reproductive toxicity studies, take a long time and are expensive. Therefore, machine learning, as a promising alternative approach, should be considered when evaluating the reproductive toxicity of chemicals. We curated rat multigeneration reproductive toxicity testing data of 275 chemicals from ToxRefDB (Toxicity Reference Database) and developed predictive models using seven machine learning algorithms (decision tree, decision forest, random forest, k-nearest neighbors, support vector machine, linear discriminant analysis, and logistic regression). A consensus model was built based on the seven individual models. An external validation set was curated from the COSMOS database and the literature. The performances of individual and consensus models were evaluated using 500 iterations of 5-fold cross-validations and the external validation data set. The balanced accuracy of the models ranged from 58% to 65% in the 5-fold cross-validations and 45%–61% in the external validations. Prediction confidence analysis was conducted to provide additional information for more appropriate applications of the developed models. The impact of our findings is in increasing confidence in machine learning models. We demonstrate the importance of using consensus models for harnessing the benefits of multiple machine learning models (i.e., using redundant systems to check validity of outcomes). While we continue to build upon the models to better characterize weak toxicants, there is current utility in saving resources by being able to screen out strong reproductive toxicants before investing in vivo testing. The modeling approach (machine learning models) is offered for assessing the rat multigeneration reproductive toxicity of chemicals. Our results suggest that machine learning may be a promising alternative approach to evaluate the potential reproductive toxicity of chemicals.

consensus model↗
DOE OSTI2024

Evaluation of partial volume correction and analysis of longitudinal [ 18 F]GTP1 tau PET imaging in Alzheimer's disease using linear mixed-effects models

Purpose: We evaluated the impact of partial volume correction (PVC) methods on the quantification of longitudinal [ 18 F]GTP1 tau positron-emission tomography (PET) in Alzheimer's disease and the suitability of describing the tau pathology burden temporal trajectories using linear mixed-effects models (LMEM). Methods: We applied van Cittert iterative deconvolution (VC), 2-compartment, and 3-compartment, and the geometric transfer matrix plus region-based voxelwise methods to data acquired in an Alzheimer's disease natural history study over 18 months at a single imaging site. We determined the optimal PVC method by comparing the standardized uptake value ratio change (%ΔSUVR) between diagnostic and tau burden–level groups and the longitudinal repeatability derived from the LMEM. The performance of LMEM analysis for calculating %ΔSUVR was evaluated in a natural history study and in a multisite clinical trial of semorinemab in prodromal to mild Alzheimer's disease by comparing results to traditional per-visit estimates. Results: The VC, 2-compartment, and 3-compartment PVC methods had similar performance, whereas region-based voxelwise overcorrected regions with a higher tau burden. The lowest within-subject variability and acceptable group separation scores were observed without PVC. The LMEM-derived %ΔSUVR values were similar to the per-visit estimates with lower variability. Conclusion: The results indicate that the tested PVC methods do not offer a clear advantage or improvement over non-PVC images for the quantification of longitudinal [ 18 F]GTP1 PET data. LMEM offers a robust framework for the longitudinal tau PET quantification with low longitudinal test–retest variability. Clinical trial registration: NCT02640092 and NCT03289143.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Application of multi-criteria decision analysis techniques and decision support framework for informing select agent designation for agricultural animal pathogens

The United States Department of Agriculture (USDA), Division of Agricultural Select Agents and Toxins (DASAT) established a list of biological agents and toxins (Select Agent List) that potentially threaten agricultural health and safety, the procedures governing the transfer of those agents, and training requirements for entities working with them. Every 2 years the USDA DASAT reviews the Select Agent List, using subject matter experts (SMEs) to perform an assessment and rank the agents. To assist the USDA DASAT biennial review process, we explored the applicability of multi-criteria decision analysis (MCDA) techniques and a Decision Support Framework (DSF) in a logic tree format to identify pathogens for consideration as select agents, applying the approach broadly to include non-select agents to evaluate its robustness and generality. We conducted a literature review of 41 pathogens against 21 criteria for assessing agricultural threat, economic impact, and bioterrorism risk and documented the findings to support this assessment. The most prominent data gaps were those for aerosol stability and animal infectious dose by inhalation and ingestion routes. Technical review of published data and associated scoring recommendations by pathogen-specific SMEs was found to be critical for accuracy, particularly for pathogens with very few known cases, or where proxy data (e.g., from animal models or similar organisms) were used to address data gaps. The MCDA analysis supported the intuitive sense that select agents should rank high on the relative risk scale when considering agricultural health consequences of a bioterrorism attack. However, comparing select agents with non-select agents indicated that there was not a clean break in scores to suggest thresholds for designating select agents, requiring subject matter expertise collectively to establish which analytical results were in good agreement to support the intended purpose in designating select agents. The DSF utilized a logic tree approach to identify pathogens that are of sufficiently low concern that they can be ruled out from consideration as a select agent. In contrast to the MCDA approach, the DSF rules out a pathogen if it fails to meet even one criteria threshold. Both the MCDA and DSF approaches arrived at similar conclusions, suggesting the value of employing the two analytical approaches to add robustness for decision making.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Plutonium in Manhattan Project workers: Using autopsy data to evaluate organ content and dose estimates based on urine bioassay with implications for radiation epidemiology

Purpose Radiation dose estimates in epidemiology typically rely on intake predictions based on urine bioassay measurements. The purpose of this article is to compare the conventional dosimetric estimates for radiation epidemiology with the estimates based on additional post-mortem tissue radiochemical analysis results. Methods The comparison was performed on a unique group of 11 former Manhattan Project nuclear workers, who worked with plutonium in the 1940s, and voluntarily donated their bodies to the United States Transuranium and Uranium Registries. Results Post-mortem organ activities were predicted using different sets of urine data and compared to measured activities. Use of urinalysis data collected during the exposure periods overestimated the systemic (liver+skeleton) deposition of 239 Pu by 155±134%, while the average bias from using post-exposure urinalyses was –4±50%. Committed effective doses estimated using early urine data differed from the best estimate by, on average, 196±193%; inclusion of follow-up urine measurements in analyses decreased the mean bias to 0.6±36.3%. Cumulative absorbed doses for the liver, red marrow, bone surface, and brain were calculated for the actual commitment period. Conclusion On average, post-exposure urine bioassay results were in good agreement with post-mortem tissue analyses and were more reliable than results of urine bioassays collected during the exposure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Predicting defects in laser powder bed fusion using in-situ thermal imaging data and machine learning

Variation in the local thermal history during the Laser Powder Bed Fusion (LPBF) process in Additive Manufacturing (AM) can cause micropore defects, which add to the uncertainty of the mechanical properties (e.g., fatigue life, tensile strength) of the built materials. In-situ sensing has been proposed for monitoring the AM process to minimize defects, but successful minimization requires establishing a quantitative relationship between the sensing data and the porosity, which is particularly challenging with a large number of variables (e.g., laser speed, power, scan path, powder property). Physics-based modeling can simulate such an in-situ sensing-porosity relationship, but it is computationally costly. In this work, we develop Machine Learning (ML) models that can use in-situ thermographic data to predict the micropore of LPBF stainless steel materials. This work considers two identified key features from the thermal histories: the time above the apparent melting threshold ($\tau$) and the maximum radiance ( T max ). These features are computed, stored for each voxel in the built material, and then used as inputs. The binary state of each voxel, either defective or normal, is the output. Different ML models are trained and tested for the binary classification task. In addition to using the thermal features of each voxel to predict its own state, the thermal features of neighboring voxels are also included as inputs. This is shown to improve the prediction accuracy, which is consistent with thermal transport physics around each voxel contributing to its final state. Among the models trained, the F1 scores on test sets reach above 0.96 for Random Forests. Feature importance analysis based on the ML models shows that T max is more important to the voxel state than $\tau$ . The analysis also finds that the thermal history of the voxels above the present voxel is more influential than those beneath it. Our study significantly extends the capability of using in-situ thermographic data to predict porosity in LPBF materials. Finally, since ML models are fast, they may play integral roles in the optimization and control of such AM technologies.

36 MATERIALS SCIENCE↗