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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

NuclPred v1

This tool takes a genome assembly as input and predicts per-site nucleosome occupancy as output. Trained on physical maps of nucleosome binding preferences across the fungal kingdom, NuclPred can be applied broadly across fungi (and other eukaryotes). This breadth, combined with its accuracy, means it could have both basic and applied biological implications, for example in understanding eukaryotic gene regulation and genetic engineering. Almost universally across eukaryotes, nucleosomes - each wrapping ~150 base pairs of DNA - serve to package DNA inside the nucleus, with major consequences on DNA access, gene activity and DNA integration. NuclPred was generated using a supervised deep learning approach combining convolutional and recurrent neural networks to take DNA features (nucleotides, GC content and structural information) as input, then use that information to predict the physical attractiveness DNA sequences might have for forming nucleosomes. With this information at hand, researchers can design more efficient CRISPR constructs, explore the interplay between DNA signatures and other regulators impact nucleosome locations, predict expression patterns, etc. This tool will be published as part of a manuscript currently under revision at iScience (draft attached).

Mondo, Stephen↗
DOE OSTI2026

lumicap v0.1

Automated HDR luminance imaging system designed for daylighting research and building science. It controls a fisheye-lens camera to capture time-lapse bracket sequences, merges them into calibrated HDR images, and runs a full post-processing pipeline — all unattended. Features: - Scheduled LDR bracket capture via gphoto2 - HDR merging with vignetting, ND filter, and fisheye projection corrections - Illuminance and luminance meter integration (Konica Minolta T-10A, LS-100/150) - Daylight glare probability (DGP) and solar position computation - Automated false-color rendering, JPEG thumbnails, and daily time-lapse video - CSV data logging per timestep Uses: - Long-term monitoring of daylight conditions in buildings - Glare analysis for occupant comfort research - Solar irradiance and sky luminance studies Advantages: - End-to-end automation — capture, calibration, analysis, and archiving run without manual intervention - Built on the proven Radiance toolchain, ensuring photometrically accurate HDR output - Hardware-agnostic meter support via serial auto-detection - Lightweight — no GUI overhead, deployable on a headless Raspberry Pi or similar embedded system

Wang, Taoning [Lawrence Berkeley National Laborato↗
DOE OSTI2023

Curb Allocation and Pick-Up Drop-Off Aggregation for a Shared Autonomous Vehicle Fleet

Advances in information technologies and vehicle automation have birthed new transportation services, including shared autonomous vehicles (SAVs). Shared autonomous vehicles are on-demand self-driving taxis, with flexible routes and schedules, able to replace personal vehicles for many trips in the near future. The siting and density of pick-up and drop-off (PUDO) points for SAVs, much like bus stops, can be key in planning SAV fleet operations, since PUDOs impact SAV demand, route choices, passenger wait times, and network congestion. Unlike traditional human-driven taxis and ride-hailing vehicles like Lyft and Uber, SAVs are unlikely to engage in quasi-legal procedures, like double parking or fire hydrant pick-ups. In congested settings, like central business districts (CBD) or airport curbs, SAVs and others will not be allowed to pick up and drop off passengers wherever they like. This paper uses an agent-based simulation to model the impact of different PUDO locations and densities in the Austin, Texas CBD, where land values are highest and curb spaces are coveted. In this paper 18 scenarios were tested, varying PUDO density, fleet size and fare price. The results show that for a given fare price and fleet size, PUDO spacing (e.g., one block vs. three blocks) has significant impact on ridership, vehicle-miles travelled, vehicle occupancy, and revenue. A good fleet size to serve the region’s 80 core square miles is 4000 SAVs, charging a $1 fare per mile of travel distance, and with PUDOs spaced three blocks of distance apart from each other in the CBD.

Hunter, Christian B.↗
DOE OSTI2020

Factors Influencing Willingness to Pool in Ride-Hailing Trips

In the past decade, transportation network companies (TNCs) such as Uber, Lyft, and Via have established themselves as a viable transportation alternative to other modes. However, the popularity of these services has come with a fair share of criticism for their negative externalities such as increasing vehicle miles traveled and congestion in cities. Pooled ride-hailing trips, in which all or a part of two individual (or group) trips are combined in and served by a single vehicle, have the potential to reduce these externalities. Pooling of rides is an effective solution to reduce congestion and travel cost, but pooled rides still represent a small percentage of the total trips served (and miles driven) by TNCs relative to single-occupancy (and without customer) vehicle miles. Both TNCs and cities alike will benefit from understanding what factors encourage or deter pooling a ride-hailing trip. In this study, newly available Chicago transportation network provider data were explored to identify the extent to which different socioeconomic, spatiotemporal, and trip characteristics affect willingness to pool (WTP) in ride-hailing trips. Furthermore, multivariate linear regression and machine-learning models were employed to understand and predict WTP based on location, time, and trip factors. The results show intuitive trends, with income level at drop-off and pickup locations and airport trips as the most important predictors of WTP. Results from this study can help TNCs and cities devise strategies that increase pooled ride-hailing, thereby reducing adverse transportation and energy impacts from ride-hailing modes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Use of Shared Automated Vehicles for First-Mile Last-Mile Service: Micro-Simulation of Rail-Transit Connections in Austin, Texas

Shared fleets of fully automated vehicles (SAVs) coupled with real-time ride-sharing to and from transit stations are of interest to cities and nations in delivering more sustainable transportation systems. By providing first-mile last-mile (FMLM) connections to key transit stations, SAVs can replace walk-to-transit, drive-to-transit, and drive-only trips. Using the SUMO (Simulation of Urban MObility) toolkit, this paper examines mode splits, wait times, and other system features by micro-simulating two fleets of SAVs providing an FMLM ride-sharing service to 10% of central Austin’s trip-makers near five light-rail transit stations. These trips either start or end within two geofenced areas (called automated mobility districts [AMDs]), and travel time and wait time feedbacks affect mode choices. With rail service headways of 15?min, and 15 SAVs serving FMLM connections to and from each AMD, simulations predict that 3.7% of the person-trip-making will shift from driving alone to transit use in a 3?mi?×?6?mi central Austin area. During a 3-h morning peak, 30 SAVs serve about 10 person-trips each (to or from the stations), with 3.4?min average wait time for SAVs, and an average vehicle occupancy of 0.74 persons (per SAV mile-traveled), as a result of empty SAV driving between riders. Sensitivity analysis of transit headways (from 5 to 20?min) and fleet sizes (from 5 to 20 vehicles in each AMD) shows an increase in FMLM mode share with more frequent transit service and larger fleet size, but total travel time served as the biggest determinant in trip-makers’ mode share.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Centrifugal Generation of Droplet-Based 3D Cell Cultures

Quickly and easily producing uniform populations of microsphere-based 3D cell cultures using droplet-based templating methods has the potential to enable widespread use of such platforms in drug discovery or cancer research. Here, we advance the design of centrifuge-based droplet generation devices, describe the use of this platform for droplet generation with controlled cell occupancy, and demonstrate weeklong culture duration. Using simple-to-construct devices and easily implemented protocols, the initial concentration of encapsulated cells is adjustable up to hundreds of cells per microsphere. This work demonstrates the first instance of using centrifugal droplet-generating devices to produce large numbers of cell-encapsulating microspheres. Applications of this versatile methodology include the rapid formation of templated 3D cell culture populations suitable for suspension culture or large batch bioreactor studies that require uniform populations.

Biochemistry & Molecular Biology↗
DOE OSTI2026

DLK1 is a GATA1s-driven dependency and therapeutic target in Down syndrome–associated myeloid leukemia

Children with Down syndrome have a markedly increased risk of developing myeloid leukemia. Although having an excellent prognosis, 10% to 20% develop relapsed or refractory disease with poor survival, highlighting the need for new targeted approaches. The pathogenesis of myeloid leukemia of Down syndrome (ML-DS) is tightly linked to fetal hematopoiesis and mutations in GATA1, generating the truncated GATA1 short (GATA1s) isoform. We identified Delta-like noncanonical Notch ligand 1 (DLK1) as a direct GATA1s target. DLK1, a paternally imprinted transmembrane protein, is highly expressed in fetal liver CD34 + cells but absent in adult hematopoiesis, making it an attractive immunotherapeutic target. Chromatin profiling revealed GATA1s occupancy at a distal enhancer within the DLK1-DIO3 locus, driving aberrant DLK1 upregulation in ML-DS. Functional studies demonstrated that DLK1 is a leukemia dependency, as its genetic ablation impaired proliferation and engraftment, induced apoptosis, and altered Notch and β-catenin signaling. Therapeutically, a DLK1-directed antibody-drug conjugate–induced selective cytotoxicity, abrogated colony formation, and significantly prolonged survival in refractory ML-DS patient-derived xenograft (PDX) models, achieving durable remissions at higher doses. These findings establish DLK1 as a leukemia-specific vulnerability and provide preclinical proof-of-concept for DLK1-targeted therapies in ML-DS and other leukemias with fetal-like expression programs.

Biological and medical sciences↗
DOE OSTI2024

The human plasma lipidome response to exertional heat tolerance testing

The year of 2023 displayed the highest average global temperatures recorded in history— the duration and severity of extreme heat are projected to increase. Rising global temperatures represent a major public health threat, especially to occupations exposed to hot environments, such as construction and agricultural workers, and first responders. Despite efforts of the scientific community, there is still a need to characterize the pathophysiological processes leading to heat related illness and develop biomarkers that can predict its onset. Here, we performed a plasma lipidomic analysis on male and female subjects who underwent heat tolerance testing (HTT), consisting of a 2-h treadmill walk at 5 km/h with 2% inclination at a controlled temperature of 40oC. We identified 995 lipids from 27 classes, with nearly half of all detected lipids being responsive to HTT. Lipid classes related to substrate utilization were predominantly affected by HTT, with a downregulation of triacylglycerols and upregulation of free fatty acids and acyl-carnitines. We additionally examined correlations between changes in plasma lipids by using the even chain acyl-carnitines is physiological strain index (PSI). Here, even chain acyl-carnitines, bi-products of incomplete beta oxidation, and diacylglycerols displayed the highest correlation to PSI. PSI did not correlate with plasma lactate levels, which suggests that correlations with related to metabolic efficiency versus physical exertion. Overall, our results show that HTT has a strong impact on the plasma lipidome and that incomplete beta oxidation may underlie heat intolerance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Disruption of histone acetylation homeostasis reveals multilayered chromatin regulation for transcriptional resiliency

Background Epigenetic modifications, nucleosome occupancy, and three-dimensional chromatin architecture collectively create a multi-layered, highly interactive regulatory system for controlling genomic functionality. Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states. Therapies focused on epigenetic modulation can alter gene expression to correct dysfunction, though the perpetuation of these states and the relationships among chromatin regulatory layers is not well understood. Results Here, we investigated global and local chromatin structural and functional responses after acute histone deacetylase inhibitor treatment (suberoylanilide hydroxamic acid) in lung cancer cells across time. Treatment substantially increased global histone acetylation resulting in a pervasive but not distinctive signature. The spread of acetylation did not significantly impact global chromatin accessibility, and nucleosome remodeling largely occurred at finer scales in functionally relevant genomic regions. Indeed, both H 3 K 4 trimethylation, a mark of active transcription, and gene expression changes were altered in a controlled locus-specific manner, suggesting aberrant acetylation indirectly leads to balanced and bidirectional gene expression profiles from tighter regulation of other chromatin features. HDACi treatment induced (13%) genomic rearrangement in chromatin compartmentalization and moderate weakening of topologically associating domains. Conclusions Continuous wavelet analysis of these features demonstrates that scale-dependent, locus-specific factors influence the relationship between chromatin architecture and functional output, suggesting that regulation of transcription and nucleosome remodeling is not entirely (nor linearly) dependent upon large scale compartment exchange. Structural and functional responses are most pronounced early after treatment with partial persistence of differential local chromatin features and expression later in time; this highlights the plasticity of chromatin regulation, which may have implications for the efficacy of epigenetic treatments. These results demonstrate the effectiveness of multi-layered regulation of transcription: in resilient systems, disruption of one chromatin feature does not distort the regulation of other features in supporting a transcriptional program that allows for survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Elucidating regulatory processes of intense physical activity by multi-omics analysis

Abstract Background Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. Methods To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student’s t -test followed by pathway analysis and comparison between the different omics modalities. Results Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. Conclusion This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Seroprevalence of Brucella spp. and Rift Valley fever virus among slaughterhouse workers in Isiolo County, northern Kenya

Brucella spp. and Rift Valley fever virus (RVFV) are classified as priority zoonotic agents in Kenya, based on their public health and socioeconomic impact on the country. Data on the pathogen-specific and co-exposure levels is scarce due to limited active surveillance. This study investigated seroprevalence and co-exposure of Brucella spp. and RVFV and associated risk factors among slaughterhouse workers in Isiolo County, northern Kenya. A cross-sectional serosurvey was done in all 19 slaughterhouses in Isiolo County, enrolling 378 participants into the study. The overall seroprevalences for Brucella spp. and RVFV were 40.2% (95% CI: 35.2–45.4) and 18.3% (95% CI: 14.5–22.5), respectively while 10.3% (95% CI 7.4%-13.8%) of individuals were positive for antibodies against both Brucella spp. and RVFV. Virus neutralisation tests (VNT) confirmed anti-RVFV antibodies in 85% of ELISA-positive samples. Our seroprevalence results were comparable to community-level seroprevalences previously reported in the area. Since most of the study participants were not from livestock-keeping households, our findings attribute most of the detected infections to occupational exposure. The high exposure levels indicate slaughterhouse workers are the most at-risk population and there is need for infection, prevention, and control programs among this high-risk group. This is the first VNT confirmation of virus-neutralising antibodies among slaughterhouse workers in Isiolo County and corroborates reports of the area being a high-risk RVFV area as occasioned by previously reported outbreaks. This necessitates sensitization campaigns to enhance awareness of the risks involved and appropriate mitigation measures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Analysis of mobility data to build contact networks for COVID-19

As social distancing policies and recommendations went into effect in response to COVID-19, people made rapid changes to the places they visit. These changes are clearly seen in mobility data, which records foot traffic using location trackers in cell phones. While mobility data is often used to extract the number of customers that visit a particular business or business type, it is the frequency and duration of concurrent occupancy at those sites that governs transmission. Understanding the way people interact at different locations can help target policies and inform contact tracing and prevention strategies. This paper outlines methods to extract interactions from mobility data and build networks that can be used in epidemiological models. Several measures of interaction are extracted: interactions between people, the cumulative interactions for a single person, and cumulative interactions that occur at particular businesses. Network metrics are computed to identify structural trends which show clear changes based on the timing of stay-at-home orders. Measures of interaction and structural trends in the resulting networks can be used to better understand potential spreading events, the percent of interactions that can be classified as close contacts, and the impact of policy choices to control transmission.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

High throughput embryonic zebrafish test with automated dechorionation to evaluate nanomaterial toxicity

Engineered nanomaterials pose occupational health and environmental concerns as they possess unique physical and chemical properties that can contribute to toxicity. High throughput toxicity screening methods are needed to address the increasing number of nanomaterials in production. Here we used a zebrafish photomotor response (PMR) test to evaluate a set of fifteen nanomaterials with military relevance. Automated dechorionation of zebrafish embryos was used to enhance nanomaterials bioavailability. Optimal PMR activity in zebrafish embryos was found at 30–31 hours post-fertilization (hpf). Behavioral and toxicological responses were measured at 30 and 120 hpf; behavioral responses were found for thirteen of the fifteen nanomaterials and acute toxicity (LC50) levels for nine of the fifteen nanomaterials below the maximum test concentration of 500 μg/ml. Physico-chemical characterization of the nanomaterials detected endotoxin and bacterial contamination in two of the tested samples, which may have contributed to observed toxicity and reinforces the need for physical and chemical characterization of nanomaterials use in toxicity testing. The zebrafish PMR test, together with automated dechorionation, provides an initial rapid assessment of the behavioral effects and toxicity of engineered nanomaterials that can be followed up by physico-chemical characterization if toxicity is detected, reducing the amount of time and monetary constraints of physico-chemical testing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Misclassification of causes of death among a small all-autopsied group of former nuclear workers: Death certificates vs. autopsy reports

The U.S. Transuranium and Uranium Registries performs autopsies on each of its deceased Registrants as a part of its mission to follow up occupationally-exposed individuals. This provides a unique opportunity to explore death certificate misclassification errors, and the factors that influence them, among this small population of former nuclear workers. Underlying causes of death from death certificates and autopsy reports were coded using the 10 th revision of the International Classification of Diseases (ICD-10). These codes were then used to quantify misclassification rates among 268 individuals for whom both full autopsy reports and death certificates with legible underlying causes of death were available. When underlying causes of death were compared between death certificates and autopsy reports, death certificates correctly identified the underlying cause of death’s ICD-10 disease chapter in 74.6% of cases. The remaining 25.4% of misclassified cases resulted in over-classification rates that ranged from 1.2% for external causes of mortality to 12.2% for circulatory disease, and under-classification rates that ranged from 7.7% for external causes of mortality to 47.4% for respiratory disease. Neoplasms had generally lower misclassification rates with 4.3% over-classification and 13.3% under-classification. A logistic regression revealed that the odds of a match were 2.8 times higher when clinical history was mentioned on the autopsy report than when it was not. Similarly, the odds of a match were 3.4 times higher when death certificates were completed using autopsy findings than when autopsy findings were not used. This analysis excluded cases where it could not be determined if autopsy findings were used to complete death certificates. The findings of this study are useful to investigate the impact of death certificate misclassification errors on radiation risk estimates and, therefore, improve the reliability of epidemiological studies.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2026

2011 Seattle Tolling Impact Survey

The 2011 Tolling Impact Survey measured the impact of tolling on travel behavior in Seattle, Washington. The Volpe Center conducted the survey on behalf of the U.S. Department of Transportation and the Urban Partnership Agreement. The population surveyed included drivers, public transportation users, carpoolers, and vanpoolers using the SR-520 corridor in Seattle. The survey was conducted in two phases—before and after toll implementation—to evaluate related attitude changes. The survey assessed route changes, trip timing, trip purpose, and travel mode (i.e., single-occupancy vehicle, carpool, or public transportation).

1Hz data↗
DOE OSTI2026

2011 Atlanta Tolling Impact Survey

The 2011 Tolling Impact Survey measured the impact of tolling on travel behavior in Atlanta, Georgia. The Volpe Center conducted the survey on behalf of the U.S. Department of Transportation and the Urban Partnership Agreement. The population surveyed included drivers, public transportation users, carpoolers, and vanpoolers using the I-85 corridor in Atlanta, Georgia. The survey was conducted in two phases—before and after toll implementation—to evaluate related attitude changes. The survey assessed route changes, trip timing, trip purpose, and travel mode (i.e., single-occupancy vehicle, carpool, or public transportation).

1Hz data↗
DOE OSTI2026

2000-2001 California Statewide Household Travel Survey

The 2000-2001 California Statewide Household Travel Survey, conducted under the auspices of the California Department of Transportation, was conducted between October 2000 and December 2001 among households located in each of California's 58 counties. The purpose of the study was to update the statewide database of household socioeconomic and travel information and helped to refine travel estimates, models, and forecasts throughout California. The survey was an essential element in determining statewide and regional travel patterns. A total of 17,040 households participated in the survey, contributing household socioeconomic and travel data. Travel variables collected include trip times, mode, activity at location, origin and destination, and vehicle occupancy, among other travel-related data from 134,173 trips. Residents completed diary records of their daily travel over a 24-hour (weekday) or 48-hour period (Friday/Saturday or Sunday/Monday pair).

1Hz data↗