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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.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dynamic enhancer landscapes in human craniofacial development

The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Single‐Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human‐Derived Microglia

Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mammalian Chromosome Analysis and Sorting by Flow Cytometry

The analysis of chromosomes by flow cytometry is termed flow cytogenetics, and it involves the analysis and sorting of single mitotic chromosomes in suspension. The study of flow karyograms provides insight into chromosome number and structure to provide information on chromosomal DNA content and can enable the detection of deletions, translocations, or any forms of aneuploidy. Beyond its clinical applications, flow cytogenetics greatly contributed to the Human Genome Project through the ability to sort pure populations of chromosomes for gene mapping, cloning, and the construction of DNA libraries. Maximizing the potential of these important applications of flow cytogenetics relies on precise instrument setup and optimal sample processing, both of which impact the accuracy and quality of the data that are generated. This article is a compilation of the existing protocols that describe the stepwise methodology of accumulating, isolating, and staining metaphase chromosomes to prepare single-chromosome suspensions for flow cytometric analysis and sorting. Although the chromosome preparation protocols have remained largely unchanged, cytometer technology has advanced dramatically since these protocols were originally developed. Advances in cytometry technologies offer new and exciting approaches for understanding and monitoring chromosomal aberrations, but the hallmark of these protocols remains their simplicity in methodologies and reagent requirements and the accuracy of data resolvable to every chromosome of the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CMIP6 skill at predicting interannual to multi-decadal summer monsoon precipitation variability

Monsoons affect the economy, agriculture, and human health of two thirds of the world’s population. Therefore, predicting variations in monsoon precipitation is societally important. We explore the ability of climate models from the sixth phase of the Climate Model Intercomparison Project to predict summer monsoon precipitation variability by using hindcasts from the Decadal Climate Prediction Project (Component A). The multi-model ensemble-mean shows significant skill at predicting summer monsoon precipitation from one year to 6–9 years ahead. However, this skill is dependent on the model, monsoon domain, and lead-time. In general, the skill of the multi-model ensemble-mean prediction is low in year 1 but increases for longer-lead times and is largely consistent with externally forced changes. The best captured region is northern Africa for the 2–5 and 6–9 year forecast lead times. In contrast, there is no significant skill using the ensemble-mean over East and South Asia and, furthermore, there is significant spread in skill among models for these domains. By sub-sampling the ensemble we show that the difference in skill between models is tied to the simulation of the externally forced response over East and South Asia, with models with a more skilful forced response capable of better predictions. A further contribution is from skilful prediction of Pacific Ocean temperatures for the South Asian summer monsoon at longer lead-times. Therefore, these results indicate that predictions of the East and South Asian monsoons could be significantly improved.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dose Coefficient Calculation for Use in Dosimetry Assessment of a Fission-Based Weapon

In the event of a fission-based weapon or improvised nuclear device (IND) detonation, dose coefficients can be harnessed to provide dose assessments for defense, emergency preparedness, and consequence management, as well as to prospectively inform the assessment of radiation biomarkers and development of medical prophylaxis countermeasures for defense and homeland security stakeholders and decision-makers. Although dose coefficients have previously been calculated for this group, they would apply specifically to the studied population, the 1945 Japanese cohort, after which their anthropomorphic computational phantoms were modeled. For this reason, applications to other populations may be limited, and instead, an assessment of a more standardized population is desired. We employed a series of computational human phantoms representing international reference individuals: UF/NCI voxel phantom series containing newborn, 1-, 5-, 10-, 15-, and 35-year-old males and females. Irradiation of the phantoms was simulated using the Monte Carlo N-Particle transport code to determine organ dose coefficients under four idealized irradiation geometries at three distances from the detonation hypocenter at Hiroshima and Nagasaki using DS02 free-in-air prompt neutron and photon fluence spectra. Through these simulations, age-specific dose coefficients were determined for individual organs. Various articulated PIMAL stylized phantoms were simulated as well to estimate the effect of body posture on dose coefficients and determine the effect of posture on dosimetric estimation and reconstruction. Results additionally demonstrate that 137 Cs and the Watt fission spectra are not ideal general surrogate sources for fission weapons, which may be considered for experimental testing of medical countermeasures. Supplementary data provided tabulates the compilation of organ dose-rate coefficients in this study.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
DOE OSTI2019

Conceptual Design of an Electron Accelerator for Bio-Solid Waste Treatment.

Several studies have identified electron beam (EB) irradiation of municipal wastewater and bio-solids as an effective and promising approach to the environmental remediation of the enormous quantities of human waste created by a growing world-wide population and increased urbanization. However, despite the technical success of experimental and pilot programs over the last several decades, the technique is still not in commercial use anywhere in the world. In addition, the report also identifies the need for “Financial and infrastructure participation from a utility for demonstration project” and “Education and awareness of safety of utilizing electron beam technology” as two additional roadblocks preventing technology adoption of EB treatment for bio-solids. In this concept design, we begin to address these barriers by working with Metropolitan Water Reclamation District of Greater Chicago (MWRD) and by the applying the latest accelerator technologies developed at Fermilab and within the DOE Office of Science laboratory complex.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Fencing affects movement patterns of two large carnivores in Southern Africa

The erection of peripheral fences around protected areas has been shown to adversely affect the movement behavior, genetic connectivity and long-term viability of animal populations. However, fencing is also used extensively to reduce human encroachment, limit poaching activities, and mitigate human–wildlife conflicts. Limited information on the movement behavior of carnivores is available along the periphery of protected areas, particularly in semi-arid environments. To quantify the potential effects of the 824 km perimeter fence surrounding the Etosha National Park (Etosha, Namibia) on the movement and space use of carnivores, we collected GPS movement data from 36 lions (Panthera leo) and seven spotted hyenas (Crocuta crocuta) over a 14-year period. For these two apex carnivores, we measured the impact of the Etosha fence on their movements (step lengths and path straightness), calculated the likelihood of fence crossings, and evaluated the spatial–temporal characteristics of these crossings. Our results indicated that lions and hyenas moved faster (longer step lengths) when closer to the fence. Lions showed no variation in path straightness with respect to the fence but hyenas had straighter movement paths when closer to the fence. When moving within the vicinity of the fence, lions had a 9% likelihood of crossing the fence, while hyenas were much more likely (18%) to do so, which suggests that the Etosha fence was more permeable for hyenas than for lions. Fence crossings predominantly occurred at night for both species. Lions were more likely to cross the fence during the cold dry season (May–August) whereas hyenas crossed more often during the warm wet season (December–April). Female and adult lions had a higher probability of crossing the fence than males and subadults. These findings could be useful in the development of appropriate strategies to mitigate human–carnivore conflicts and thus promote the conservation of carnivores in multiple-use areas along the periphery of the park. Further research is needed to better elucidate the impact of perimeter fences on a broader suite of carnivores and other large mammals, including species-specific variation in the response to fences, as well as the economic benefits of fencing provided to local communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mapping Human Dynamics

Researchers at Oak Ridge National Laboratory are mapping the global footprints of human activity with unprecedented spatiotemporal resolution. With a global population now approaching 8 billion people, this herculean effort demands advanced machine learning, artificial intelligence, and one of the world’s fastest supercomputers.

Rose, Amy↗
DOE OSTI2022

Vaccine-Associated Enhanced Respiratory Disease following Influenza Virus Infection in Ferrets Recapitulates the Model in Pigs

Influenza A virus (IAV) causes respiratory disease in swine and humans. Vaccines are used to prevent influenza illness in both populations but must be frequently updated due to rapidly evolving strains. Mismatch between the circulating strains and the strains contained in vaccines may cause loss of efficacy. Whole inactivated virus (WIV) vaccines with adjuvant, utilized by the swine industry, are effective against antigenically similar viruses; however, vaccine-associated enhanced respiratory disease (VAERD) may happen when the WIV is antigenically mismatched with the infecting virus. VAERD is a repeatable model in pigs, but had yet to be experimentally demonstrated in other mammalian species. We recapitulated VAERD in ferrets, a standard benchmark animal model for studying human influenza infection, in a direct comparison to VAERD in pigs. Both species were vaccinated with WIV with oil-in-water adjuvant containing a d -1 H1N2 (1B.2.2) derived from the pre-2009 human seasonal lineage, then challenged with a 2009 pandemic H1N1 (H1N1pdm09, 1A.3.3.2) 5 weeks after vaccination. Nonvaccinated and challenged groups showed typical signs of influenza disease, but the mismatched vaccinated and challenged pigs and ferrets showed elevated clinical signs, despite similar viral loads. VAERD-affected pigs exhibited a 2-fold increase in lung lesions, while VAERDaffected ferrets showed a 4-fold increase. Similar to pigs, antibodies from VAERD-affected ferrets preferentially bound to the HA2 domain of the H1N1pdm09 challenge strain. These results indicate that VAERD is not limited to pigs, as demonstrated here in ferrets, and the need to consider VAERD when evaluating new vaccine platforms and strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Here, using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential

The 2009 H1N1 pandemic (pdm09) lineage of influenza A virus (IAV) crosses interspecies barriers with frequent human-to-swine spillovers each year. These spillovers reassort and drift within swine populations, leading to genetically and antigenically novel IAV that represent a zoonotic threat. We quantified interspecies transmission of the pdm09 lineage, persistence in swine, and identified how evolution in swine impacted zoonotic risk. Human and swine pdm09 case counts between 2010 and 2020 were correlated and human pdm09 burden and circulation directly impacted the detection of pdm09 in pigs. However, there was a relative absence of pdm09 circulation in humans during the 2020–21 season that was not reflected in swine. During the 2020–21 season, most swine pdm09 detections originated from human-to-swine spillovers from the 2018–19 and 2019–20 seasons that persisted in swine. We identified contemporary swine pdm09 representatives of each persistent spillover and quantified cross-reactivity between human seasonal H1 vaccine strains and the swine strains using a panel of monovalent ferret antisera in hemagglutination inhibition (HI) assays. The swine pdm09s had variable antigenic reactivity to vaccine antisera, but each swine pdm09 clade exhibited significant reduction in cross-reactivity to one or more of the human seasonal vaccine strains. Further supporting zoonotic risk, we showed phylogenetic evidence for 17 swine-to-human transmission events of pdm09 from 2010 to 2021, 11 of which were not previously classified as variants, with each of the zoonotic cases associated with persistent circulation of pdm09 in pigs. These data demonstrate that reverse-zoonoses and evolution of pdm09 in swine results in viruses that are capable of zoonotic transmission and represent a potential pandemic threat.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A template of information needs for decision-making about delaying remediation on contaminated lands to protect human health

The contamination legacy of industrialization, militarization, and nuclear arms race poses current or future risks to populations and the environment. Responsible parties and regulators make decisions regarding which sites to clean up, how, how much, and when. This study aimed to provide an information needs template to evaluate and reduce risks to human health when considering whether to initiate or delay remediation. This investigation focused on four aspects of timing and prioritization: 1) management, planning and implementation, 2) source terms, pathways, and exposures, 3) risks and receptors, and 4) external drivers. Within each type, issues were identified and described. Management class included personnel, health and safety data, funding, equipment, and structural integrity. Source term included contaminant sources, pathways, initiating events, and barriers to exposure. Risk included types and exposures to workers and general public. External drivers included regulatory framework, stakeholders, Congressional mandates, and economic and social contexts. Risk may increase over time as contamination spreads, enters aquifers, and reaches receptors, and may decline as radionuclides decay, and plumes dissipate. The overall objective was to provide a template of information that is useful to managers and regulators, and might be used by the public to understand the risks and benefits of re-prioritization cleanup.

Environmental Sciences & Ecology↗
DOE OSTI2020

Repatriated Desert Bighorn Sheep Population on the Nevada National Security Site

Ecological studies have been conducted on the Nevada National Security Site (NNSS) since the 1960s. Desert bighorn sheep (Ovis canadensis nelsoni) were considered rare visitors on the NNSS, with only 9 recorded observations between 1963 and 2009, all of which were males. Females and young were not documented definitively until winter 2011, when several were killed by a radio-collared female mountain lion (Puma concolor). Following these observations, we initiated a study of desert bighorn sheep on the NNSS to better understand their movements/interactions with other populations, prevalence of disease, population size, origin, radionuclide burdens and potential radiological dose to humans that may consume harvested animals away from the NNSS. We captured and radio-collared 6 sheep (2 females, 4 males) in November 2015, and 15 (7 females, 8 males) in November 2016. We sampled blood for genetic and disease testing and collected nasal swabs for respiratory disease testing. Sheep from the NNSS spent most of their time around Shoshone Mountain, Fortymile Canyon, and Yucca Mountain but also moved to Bare Mountain, Thirsty Canyon, and Black Mountain. Females greatly expanded their core and overall home ranges during spring, whereas males expanded their home ranges during summer. Of 18 sheep sampled for disease, 12 showed an immune response to Mycoplasma ovipneumoniae, and 5 had the bacteria present. Genetic testing revealed that the ancestry of NNSS sheep is from the Bare Mountain (1991-1995, within 24 km of our study area), Specter Range (1990-1995, within 32 km of our study area), and Stonewall Mountain (1975-1983, within 72 km of our study area) reintroduced populations. Radionuclide burden in NNSS sheep was minimal with no significant difference from sheep captured on the Nevada Test and Training Range and northern Nevada. One marked adult male was legally harvested off the NNSS north of Bare Mountain. Finally, this recently colonized reproducing population of sheep on the NNSS warrants further monitoring, protection, and inclusion in resource management plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Scalable Generation of High-fidelity Synthetic Population Ensembles

Used within social simulations, synthetic population ensembles enable uncertainty quantification (UQ) methods for obtaining more robust model inference and prediction. A synthetic population ensemble is a series of plausible virtual reconstructions of an area’s population at the granularity of people and residences, generated stochastically to preserve privacy of the source population survey’s respondents. In this paper, we demonstrate the production of large synthetic population ensembles for the U.S. via Oak Ridge National Laboratory’s UrbanPop framework to support modeling of high spatial resolution energy affordability metrics from nationwide social surveys in collaboration with the fusionACS project. The study involves two scenarios: creating ensembles for (1) 17 U.S. metropolitan areas in 2019 and (2) full U.S. Census Divisions in 2023, with each scenario consisting of 41 population instances (a base realization and 40 replicates). To accomplish this task at scale, we configured an integrated system within a research cloud, comprised of virtual containerizations, GPU-enhanced functionality, and orchestrated deployments of UrbanPop’s maturing Likeness Python ecosystem. Results demonstrate we maintained high-fidelity approximations of residential totals by areas of interest and the demographic characteristics of neighborhoods while reducing manual workflow burdens. Finally, we discuss plans to fine-tune and further develop our automated workflows for truly distributed job orchestration to increase computational efficiency, as well as provide an outlook for broadening applications of the ensembles.

Cluster computing↗
DOE OSTI2021

Understanding collective human movement dynamics during large-scale events using big geosocial data analytics

Conventional approaches for modeling human mobility pattern often focus on human activity and movement dynamics in their regular daily lives and cannot capture changes in human movement dynamics in response to large-scale events. With the rapid advancement of information and communication technologies, many researchers have adopted alternative data sources (e.g., cell phone records, GPS trajectory data) from private data vendors to study human movement dynamics in response to large-scale natural or societal events. Big geosocial data such as georeferenced tweets are publicly available and dynamically evolving as real-world events are happening, making it more likely to capture the real-time sentiments and responses of populations. However, precisely-geolocated geosocial data is scarce and biased toward urban population centers. In this research, we developed a big geosocial data analytical framework for extracting human movement dynamics in response to large-scale events from publicly available georeferenced tweets. The framework includes a two-stage data collection module that collects data in a more targeted fashion in order to mitigate the data scarcity issue of georeferenced tweets; in addition, a variable bandwidth kernel density estimation(VB-KDE) approach was adopted to fuse georeference information at different spatial scales, further augmenting the signals of human movement dynamics contained in georeferenced tweets. To correct for the sampling bias of georeferenced tweets, we adjusted the number of tweets for different spatial units (e.g., county, state) by population. To demonstrate the performance of the proposed analytic framework, we chose an astronomical event that occurred nationwide across the United States, i.e., the 2017 Great American Eclipse, as an example event and studied the human movement dynamics in response to this event. Finally, this analytic framework can easily be applied to other types of large-scale events such as hurricanes or earthquakes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Photon to plate: A holistic view of photosynthetic and anthropogenic energy fluxes

Modern agriculture couples photosynthetic energy with human-applied energy supplements (e.g., fertilizers, labor, cultivation) to feed a growing population. These energy supplements usually come from fossil fuels, presenting an opportunity to decrease fossil fuel required per calorie by improving photosynthetic efficiency. To quantify how improving photosynthetic efficiency would decrease the supplemental energy needed per calorie, we present a “photon to plate” life cycle analysis of energy flows (photosynthetic and human-applied) needed to produce fresh-cut fries. Our results show that photosynthetic inefficiencies require ~80 times the energy used to cultivate, harvest, transport and prepare fries for consumption and that improvements to photosynthesis could reduce the energy applied by humans per calorie by almost 40%. This study highlights the magnitude of energy used during photosynthesis and the potential for photosynthetic improvements to increase agricultural sustainability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Global population structures and demographic history of Suillus luteus, a pine co‐introduced ectomycorrhizal fungus associated with exotic forestry and invasion

Human colonization since the 19th century has resulted in the global spread of pines beyond their original northern boreal distribution. Although the introduction history of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal (ECM) fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, whole genomes of 208 individuals collected across native and introduced ranges were sequenced to reveal the introduction history of pine co-introduced ECM fungi. Population genomics analyses showed that all introductions originated from Europe. With the exception of North America, introduced populations were genetically differentiated from the European population, with varying magnitudes of population expansion in different introduced regions. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial-genetic patterns of native vs exotic habitats. The spread of S. luteus is mediated by human activities accompanying pine introductions, with its demographic history linked to forestry practices. The spatial, temporal, and demographic patterns observed in S. luteus offer insight into the population genetics of a widely introduced ECM fungus and are likely applicable to other pine co-introduced ECM fungi.

Ke, Yi‐Hong↗