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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Sizing ice hydrometeor populations using the dual-wavelength radar ratio

Dual-wavelength (3.2 and 0.32 cm, i.e., X- and W-radar bands) radar ratio (DWR) measurements in ice clouds and precipitation using Canada's National Research Council Institute for Aerospace Research airborne radar are compared to closely collocated particle microphysical in situ sampling data in order to develop relations between DWR and characteristic hydrometeor size. This study uses the radar and in situ data sets collected during the In-Cloud ICing and Large-drop Experiment (ICICLE) campaign in midlatitude frontal clouds. Since atmospheric particle scattering at X band is predominantly in the Rayleigh regime and the W-band frequency is the highest frequency usually used for hydrometeor remote sensing, the X–W-band combination provides a relatively strong dual-wavelength reflectivity difference. This study considers radar and in situ measurements conducted in relatively homogeneous cloud and precipitation conditions. Measurements show that under these conditions, the difference between the X-band radar reflectivities observed with vertical and horizontal pointing of the radar beam are generally small and often negligible. However, W-band reflectivities at vertical beam pointing are, on average, larger than those for horizontal beam pointing by about 4 dB, which is a non-Rayleigh scattering effect from preferentially oriented non-spherical particles. A horizontal radar beam DWR–mean volume particle size relation, D v , provides robust estimates of this characteristic size for populations of particles with different habits. Uncertainties of D v retrievals using DWR are around 0.6 mm when D v is greater than approximately 1 mm. Size estimates using vertical radar beam DWRs have larger uncertainties due to smaller dual-wavelength signals and stronger influences of hydrometeor habits and orientations at this geometry of beam pointing. Mean relations among different characteristic sizes, which describe the entire particle size distribution (PSD), such as D v , and other sizes used in various applications (e.g., the mean, effective, and median sizes) are derived, so the results of this study can be used for estimating different PSD characteristic sizes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity

High-throughput and computational tools provide a new opportunity to calculate combined bioactivity of exposure to diverse chemicals acting through a common mechanism. We used high throughput in vitro bioactivity data and exposure predictions from the U.S. EPA’s Toxicity and Exposure Forecaster (ToxCast and ExpoCast) to estimate combined estrogen receptor (ER) agonist activity of non-pharmaceutical chemical exposures for the general U.S. population. High-throughput toxicokinetic (HTTK) data provide conversion factors that relate bioactive concentrations measured in vitro (µM), to predicted population geometric mean exposure rates (mg/kg/day). These data were available for 22 chemicals with ER agonist activity and were estimated for other ER bioactive chemicals based on the geometric mean of HTTK values across chemicals. For each chemical, ER bioactivity across ToxCast assays was compared to predicted population geometric mean exposure at different levels of in vitro potency and model certainty. Dose additivity was assumed in calculating a Combined Exposure-Bioactivity Index (CEBI), the sum of exposure/bioactivity ratios. Combined estrogen bioactivity was also calculated in terms of the percent maximum bioactivity of chemical mixtures in human plasma using a concentration-addition model. Estimated CEBIs vary greatly depending on assumptions used for exposure and bioactivity. In general, CEBI values were <1 when using median of the estimated general population chemical intake rates, while CEBI were ≥1 when using the upper 95th confidence bound for those same intake rates for all chemicals. Concentration-addition model predictions of mixture bioactivity yield comparable results. Based on current in vitro bioactivity data, HTTK methods, and exposure models, combined exposure scenarios sufficient to influence estrogen bioactivity in the general population cannot be ruled out. Future improvements in screening methods and computational models could reduce uncertainty and better inform the potential combined effects of estrogenic chemicals.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Long-term trends in urban NO 2 concentrations and associated paediatric asthma incidence: estimates from global datasets

Combustion-related nitrogen dioxide (NO 2 ) air pollution is associated with paediatric asthma incidence. We aimed to estimate global surface NO 2 concentrations consistent with the Global Burden of Disease study for 1990-2019 at a 1 km resolution, and the concentrations and attributable paediatric asthma incidence trends in 13 189 cities from 2000 to 2019. We scaled an existing annual average NO 2 concentration dataset for 2010-12 from a land use regression model (based on 5220 NO 2 monitors in 58 countries and land use variables) to other years using NO 2 column densities from satellite and reanalysis datasets. We applied these concentrations in an epidemiologically derived concentration-response function with population and baseline asthma rates to estimate NO 2 -attributable paediatric asthma incidence. We estimated that 1.85 million (95% uncertainty interval [UI] 0.93-2.80 million) new paediatric asthma cases were attributable to NO 2 globally in 2019, two thirds of which occurred in urban areas (1.22 million cases; 95% UI 0.60-1.8 million). The proportion of paediatric asthma incidence that is attributable to NO 2 in urban areas declined from 19.8% (1.22 million attributable cases of 6.14 million total cases) in 2000 to 16.0% (1.24 million attributable cases of 7.73 million total cases) in 2019. Urban attributable fractions dropped in high-income countries (-41%), Latin America and the Caribbean (-16%), central Europe, eastern Europe, and central Asia (-13%), and southeast Asia, east Asia, and Oceania (-6%), and rose in south Asia (+23%), sub-Saharan Africa (+11%), and north Africa and the Middle East (+5%). The contribution of NO 2 concentrations, paediatric population size, and asthma incidence rates to the change in NO 2 -attributable paediatric asthma incidence differed regionally. Despite improvements in some regions, combustion-related NO 2 pollution continues to be an important contributor to paediatric asthma incidence globally, particularly in cities. Mitigating air pollution should be a crucial element of public health strategies for children.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A GALAH view of the chemical homogeneity and ages of stellar strings identified in Gaia

ABSTRACT The advent of Gaia has led to the discovery of nearly 300 elongated stellar associations (called ‘strings’) spanning hundreds of parsecs in length and mere tens of parsecs in width. These newfound populations present an excellent laboratory for studying the assembly process of the Milky Way thin disc. In this work, we use data from GALAH DR3 to investigate the chemical distributions and ages of 18 newfound stellar populations, 10 of which are strings and 8 of which are compact in morphology. We estimate the intrinsic abundance dispersions in [X/H] of each population and compare them with those of both their local fields and the open cluster (OC) M 67. We find that all but one of these groups are more chemically homogeneous than their local fields. Furthermore, half of the strings, namely Theias 139, 169, 216, 303, and 309, have intrinsic [X/H] dispersions that range between 0.01 and 0.07 dex in most elements, equivalent to those of many OCs. These results provide important new observational constraints on star formation and the chemical homogeneity of the local interstellar medium (ISM). We investigate each population’s Li and chemical clock abundances (e.g. [Sc/Ba], [Ca/Ba], [Ti/Ba], and [Mg/Y]) and find that the ages suggested by chemistry generally support the isochronal ages in all but six structures. This work highlights the unique advantages that chemistry holds in the study of kinematically related stellar groups.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Pre-screening to guide coronary artery calcium scoring for early identification of high-risk individuals in the general population

Abstract Aims To evaluate the ability of Systematic COronary Risk Estimation 2 (SCORE2) and other pre-screening methods to identify individuals with high coronary artery calcium score (CACS) in the general population. Methods and results Computed tomography-based CACS quantification was performed in 6530 individuals aged 45 years or older from the general population. Various pre-screening methods to guide referral for CACS were evaluated. Miss rates for high CACS (CACS ≥300 and ≥100) were evaluated for various pre-screening methods: moderate (≥5%) and high (≥10%) SCORE2 risk, any traditional coronary artery disease (CAD) risk factor, any Risk Or Benefit IN Screening for CArdiovascular Disease (ROBINSCA) risk factor, and moderately (>3 mg/24 h) increased urine albumin excretion (UAE). Out of 6530 participants, 643 (9.8%) had CACS ≥300 and 1236 (18.9%) had CACS ≥100. For CACS ≥300 and CACS ≥100, miss rate was 32 and 41% for pre-screening by moderate (≥5%) SCORE2 risk and 81 and 87% for high (≥10%) SCORE2 risk, respectively. For CACS ≥300 and CACS ≥100, miss rate was 8 and 11% for pre-screening by at least one CAD risk factor, 24 and 25% for at least one ROBINSCA risk factor, and 67 and 67% for moderately increased UAE, respectively. Conclusion Many individuals with high CACS in the general population are left unidentified when only performing CACS in case of at least moderate (≥5%) SCORE2, which closely resembles current clinical practice. Less stringent pre-screening by presence of at least one CAD risk factor to guide CACS identifies more individuals with high CACS and could improve CAD prevention.

Ties, Daan (ORCID:0000000164729886)↗
DOE OSTI2026

Heat metrics and thresholds reshape population exposure and inequality signals

Extreme heat is intensifying worldwide, yet estimates of heat hazard and exposure inequality depend on both the heat metric and how extreme days are defined. Using summer 2022 across the Mediterranean, we quantify population heat exposure with four metrics—land surface temperature (LST), air temperature (Ta), heat index (HI), and wet-bulb globe temperature (WBGT)—under absolute (fixed-value) and relative (anomaly-based) thresholds. Under absolute thresholds, total heat exposure differs by more than two orders of magnitude across metrics (31.3 billion person-days for Ta vs 0.3 billion for HI). Geographic hotspots also diverge: WBGT concentrates in humid coastal North Africa (e.g. the Nile Delta), whereas Ta and LST are more widespread. Under relative thresholds, exposure totals converge and cross-metric hotspot agreement increases (e.g. Ta–WBGT top-tercile overlap increases from 10.7% to 29.0%), shifting hotspots toward densely populated southern Europe. Crucially, the exposure–deprivation relationship also reverses across threshold frameworks: absolute thresholds concentrate exposure in more deprived North Africa and the Middle East, whereas relative thresholds shift the burden toward less-deprived European cities. This sensitivity is decision-relevant: city rankings based on WBGT exposure duration are almost completely reordered when switching threshold frameworks. Threshold choice therefore systematically reshapes hotspot patterns and inequality signals. Reporting both absolute and relative exposures can reveal hidden hotspots and support more targeted heat-risk monitoring and intervention planning.

Mediterranean↗
DOE OSTI2025

Plasma GFAP for populational enrichment of clinical trials in preclinical Alzheimer's disease

Abstract INTRODUCTION Cognitively unimpaired (CU) amyloid beta (Aβ)+ individuals with elevated plasma glial fibrillary acidic protein (GFAP) have an increased risk of Alzheimer's disease (AD)‐related progression. We tested the utility of plasma GFAP for population enrichment CU populations in clinical trials. METHODS We estimated longitudinal progression, effect size, and costs of hypothetical clinical trials designed to test an estimated 25% drug effect on reducing tau positron emission tomography (PET) accumulation in the medial temporal lobe (MTL) and temporal neocortical region (NEO‐T). RESULTS CU GFAP+/Aβ+ individuals present an increased annual rate of change and effect size in tau PET MTL and tau PET NEO‐T compared to the other groups. An enrichment strategy selecting CU GFAP+/Aβ+ individuals would require a smaller sample size (≈ 57% reduction) and fewer Aβ PET scans (≈ 74% reduction) than trials enriched with Aβ PET alone, reducing total clinical trial costs by up to 64%. DISCUSSION Our results suggest that clinical trials focusing on preclinical AD recruiting Aβ+ individuals with elevated GFAP levels would improve cost effectiveness. Highlights Cognitively unimpaired (CU) glial fibrillary acidic protein (GFAP)+/amyloid beta (Aβ)+ shows increased changes in tau positron emission tomography (PET) . CU GFAP+/Aβ+ enriched clinical trials require a reduced sample size compared to Aβ+ only. CU GFAP+/Aβ+ enrichment reduces Aβ PET scans required and costs. CU GFAP+/Aβ+ enrichment allows the selection of individuals at early stages of the Alzheimer's disease continuum.

Neurosciences & Neurology↗
DOE OSTI2024

Probabilistic Discrete‐Time Models for Spreading Processes in Complex Networks: A Review

Abstract Research into network dynamics of spreading processes typically employs both discrete and continuous time methodologies. Although each approach offers distinct insights, integrating them can be challenging, particularly when maintaining coherence across different time scales. This review focuses on the Microscopic Markov Chain Approach (MMCA), a probabilistic f ramework originally designed for epidemic modeling. MMCA uses discrete dynamics to compute the probabilities of individuals transitioning between epidemiological states. By treating each time step—usually a day—as a discrete event, the approach captures multiple concurrent changes within this time frame. The approach allows to estimate the likelihood of individuals or populations being in specific states, which correspond to distinct epidemiological compartments. This review synthesizes key findings from the application of this approach, providing a comprehensive overview of its utility in understanding epidemic spread.

Granell, Clara↗
DOE OSTI2025

Comparison of removal and spatial mark‐resight models for estimating wild pig density

Density estimation is critical to effectively manage invasive species and elucidate areas of highest concern. For wild pigs (Sus scrofa), the ability to estimate density is complicated because of their variable home range sizes and social structure. Common methods for estimating density (e.g., mark-recapture) may be unsuitable in management applications because additional data needs to be collected before and after management. Removal models offer a suitable alternative to estimate density changes following management and can be applied broadly across areas where management of wild pigs is ongoing. We collected wild pig removal and camera trap data from 25 private properties ranging in size from approximately 0.5 km 2 to 95 km 2 across 3 ecoregions in South Carolina, USA, from 2020–2023. We compared factors affecting consistency and precision of property-level density estimates between removal and spatial mark-resight (SMR) models. In general, excluding 1 large outlier, density estimates from removal models were between 0.60 and 15.85 wild pigs/km 2 (median = 5.34) with a median coefficient of variation (CV) of 0.76 and 95% confidence intervals for the CV between 0.70 and 0.94. Similarly, excluding 1 large outlier, density estimates from SMR were between 0.22 and 30.97 wild pigs/km 2 (median = 5.48) with a median CV of 0.39 and 95% confidence intervals for the CV between 0.38 and 1.20. We found the precision of removal models was affected primarily by the number of wild pigs dispatched in the removal period (3 months) and the ecoregion in which they were removed. None of the covariates, including the number of recaptures (a corresponding measure of sample size), influenced precision of the SMR models, although recaptures did influence the density estimates. At the individual property level, density estimates from our 2 estimators were dissimilar from each other in approximately 80% of instances, although none of the covariates we examined influenced dissimilarity. Our results provide unique insight into how sample size affects density estimates using 2 common methods and into novel SMR models that incorporate both marked and unmarked detections. In addition, the density estimates in this study can be used as a reference for wild pig densities in common land cover types throughout the southeastern United States.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Public Health Response and Medical Management of Internal Contamination in Past Radiological or Nuclear Incidents: A Review

Following a radiological or nuclear emergency, workers, responders and the public may be internally contaminated with radionuclides. Screening, monitoring and assessing any internal contamination and providing necessary medical treatment, especially when a large number of individuals are involved, is challenging. Experience gained and lessons learned from the management of previous incidents would help to identify gaps in knowledge and capabilities on preparedness for and response to radiation emergencies. In this paper, eight largescale and five workplace radiological and nuclear incidents are reviewed cross 14 technical areas, under the broader topics of emergency preparedness, emergency response and recovery processes. The review findings suggest that 1) new strategies, algorithms and technologies are explored for rapid screening of large populations; 2) exposure assessment and dose estimation in emergency response and dose reconstruction in recovery process are supported by complementary sources of information, including ‘citizen science’; 3) surge capacity for monitoring and dose assessment is coordinated through national and international laboratory networks; 4) evidence-based guidelines for medical management and follow-up of internal contamination are urgently needed; 5) mechanisms for international and regional access to medical countermeasures are investigated and implemented; 6) long-term health and medical follow up programs are designed and justified; and 7) capabilities and capacity developed for emergency response are sustained through adequate resource allocation, routine nonemergency use of technical skills in regular exercises, training, and continuous improvement.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2022

Neutralization titer biomarker for antibody-mediated prevention of HIV-1 acquisition

The Antibody Mediated Prevention trials showed that the broadly neutralizing antibody (bnAb) VRC01 prevented acquisition of human immunodeficiency virus-1 (HIV-1) sensitive to VRC01. Using AMP trial data, here we show that the predicted serum neutralization 80% inhibitory dilution titer (PT 80 ) biomarker—which quantifies the neutralization potency of antibodies in an individual’s serum against an HIV-1 isolate—can be used to predict HIV-1 prevention efficacy. Similar to the results of nonhuman primate studies, an average PT 80 of 200 (meaning a bnAb concentration 200-fold higher than that required to reduce infection by 80% in vitro) against a population of probable exposing viruses was estimated to be required for 90% prevention efficacy against acquisition of these viruses. Based on this result, we suggest that the goal of sustained PT 80 <200 against 90% of circulating viruses can be achieved by promising bnAb regimens engineered for long half-lives. We propose the PT 80 biomarker as a surrogate endpoint for evaluatinon of bnAb regimens, and as a tool for benchmarking candidate bnAb-inducing vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The eROSITA Final Equatorial-Depth Survey (eFEDS)

The eROSITA Final Equatorial Depth Survey (eFEDS), completed in survey mode during the calibration and performance verification phase of the eROSITA instrument on Spectrum Roentgen Gamma, delivers data at and beyond the final depth of the 4-yr eROSITA all-sky survey (eRASS:8), f 0.5–2 keV = 1.1 × 10 –14 erg s –1 cm –2 , over 140 deg 2 . It provides the first view of normal galaxy X-ray emission from X-ray binaries (XRBs) and the hot interstellar medium at the full depth of eRASS:8. We used the Heraklion Extragalactic Catalogue (HECATE) of galaxies to correlate with eFEDS X-ray sources and identify X-ray detected normal galaxies. This flux-limited X-ray survey is relatively free from selection effects and enables the study of integrated normal galaxy X-ray emission and its relation to galaxy parameters such as the stellar mass, star formation rate (SFR), and metallicity. We cross-correlated 32 646 eFEDS X-ray sources to 1181 HECATE normal galaxies and obtained 94 matches. We classified galaxies as star-forming, early-type, composite, and active galactic nuclei (AGN) using Sloan Digital Sky Survey (SDSS) and Six-degree Field (6dF) optical spectroscopy. The eFEDS field harbours 37 normal galaxies: 36 late-type (star-forming) galaxies and one early-type galaxy. There are 1.9 times as many normal galaxies as predicted by scaling relations via simulations, with an overabundance of late-type galaxies and a dearth of early-type galaxies. When compared with empirical relations, eFEDS dwarf galaxies with a high specific SFR have elevated L X /SFR at a fixed specific SFR and metallicity, indicating an increase in XRB emission due to low metallicity. We expect that eRASS:8 will detect 12 500 normal galaxies, the majority of which will be star-forming, with the caveat that there are unclassified sources in eFEDS and galaxy catalogue incompleteness issues that could increase the actual number of detected galaxies over these current estimates. eFEDS observations detected a rare population of galaxies – the metal-poor dwarf starbursts – that do not follow known scaling relations. eRASS is expected to discover significant numbers of these high-redshift analogues, which are important for studying the heating of the intergalactic medium at high redshift. Further investigation of the hot gas emission from normal galaxies and stochastic effects in the dwarf galaxy population are required to constrain their X-ray output.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Tick bite frequency, prevention practices and Lyme disease diagnoses among U.S. Hispanic survey respondents

Abstract Tick bite prevention practices, knowledge of Lyme disease (LD) symptoms and transmission, and patterns of LD diagnoses among Hispanic persons have been reported but not comprehensively evaluated. In 2014, CDC examined questions from a prospective nationwide survey of U.S. Hispanic adults conducted via the Offerwise QueOpinas panel regarding ticks and LD. From October to November, a total of 2,649 surveys were released and 1,006 completed surveys returned. Overall, 44% of respondents reported routinely practising at least one form of personal protection against tick bites, and wearing repellent was the most commonly reported method (29%). Approximately 6% of respondents reported a tick bite for either themselves or someone in their household during the previous 12 months. An individual or household diagnosis of LD in the previous year was reported by 2% of respondents, with the highest proportion of diagnoses reported by respondents from high LD incidence states. The annual incidence of healthcare provider‐diagnosed LD in the survey population was higher than national surveillance estimates for reported LD among U.S. Hispanic persons during 2000–2013. As annual incidence of LD continues to increase, it is important to ensure equitable access to information about LD, including disease transmission, manifestations, and prevention recommendations. Results from this survey can help inform public health outreach focused on effective tick bite prevention methods and early recognition of LD.

Beck, Alyssa↗
DOE OSTI2020

The Relation of the Alpha Persei Star Cluster with the Nearby Stellar Stream

A map of 100° on a side extracted from Gaia DR2 and centered on Alpha Persei reveals two distinct structures—the Alpha Persei star cluster and a conspicuous stellar stream, as widely documented in recent literature. In this work we employ DBSCAN to assess individual stars’ membership and attempt at separating stars belonging to the cluster and to the stream from the general field. In turn, we characterize the stream and investigate its relation with the cluster. The stream population turned out to be significantly older (5 ± 1 Gyr) than the cluster, and to be positioned ∼90 pc away from the cluster, in its background. The stream exhibits a sizeable thickness of ∼180 pc in the direction of the line of view. Finally, the stream harbors a prominent population of white dwarf stars. We estimated an upper limit of the stream mass of ∼6000M {sub ⊙}. The stream would therefore be the leftover of a relatively massive old cluster. The surface density map of Alpha Persei indicates the presence of tidal tails. While it is tempting to ascribe their presence to the interaction with the disrupting old star cluster, we prefer to believe, conservatively, they are of Galactic origin.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Quantifying health benefits of sustainable aviation fuels: Modeling decreased ultrafine particle emissions and associated impacts on communities near the Seattle-Tacoma International Airport

Exposure to ultrafine particles (UFP, ≤100 nm) is an emerging health concern linked to premature mortality, with jet fuel combustion identified as a significant source of UFPs near airports. Sustainable aviation fuel (SAF) adoption has the potential to reduce aviation-related UFPs and may particularly benefit populations who reside nearby. However, assessing aviation-specific impacts on health remains challenging due to the lack of tools capable of addressing: fine-scale exposure evaluation, novel ambient pollutants, and groups with increased exposure or susceptibility. We develop and apply a method to estimate reductions in mortality associated with aviation-related UFP reductions at the Seattle-Tacoma (SEA-TAC) International Airport under SAF adoption scenarios, with a focus on near-airport communities. Using UFP exposure surfaces generated from AERMOD modeling, flight count data, and UFP measurements, we evaluated UFP reductions under various control scenarios. We estimated mortality reductions by combining this with population data, baseline mortality, and a hazard ratio of 1.012 (95 % confidence interval: 1.010, 1.015) per interquartile range increment of 2723 particles/cm 3 . Our analysis included 412 census tracts representing almost 1.5 million adults. Baseline aviation-related UFP exposures averaged 1145 (SD: 277) particles/cm 3 . The highest baseline concentrations and subsequent reductions under SAF scenarios were near SEA-TAC. Mortality case reductions averaged between 3.1 (95 % range: 2.5–3.7) for a 5 % UFP reduction to 31.0 (24.6–37.4) for a 50 % reduction, with corresponding mortality rate reductions of 0.2 (0.2–0.3) to 2.1 (1.7–2.5) cases per 100,000 people per year. Mortality rate reductions were larger among populations residing closer to SEA-TAC, including those that were Hispanic or Latino, below-poverty, and did not identify as White. Reducing aviation-related UFPs through SAF adoption could lead to lower mortality, particularly in near-airport communities. This reproducible approach can be adapted to other settings to evaluate health benefits from aviation-related UFP reductions.

Aviation-related air pollution↗
DOE OSTI2024

Improving precision and accuracy of genetic mapping with genotyping‐by‐sequencing data in outcrossing species

Abstract Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Survival of Immature Gopher Tortoises Recruited into a Translocated Population

Population manipulations such as translocation and head-starting are increasingly used as recovery tools for chelonians. However, evaluating success of individual projects can require decades of monitoring to detect population trends in these long-lived species. Furthermore, there are often few benchmarks from stable, unmanipulated populations against which to compare demographic rates, particularly for the immature stages. Here, we used 8 years of mark-recapture data to estimate apparent survival of immature gopher tortoises recruited into an introduced population of gopher tortoises (Gopherus polyphemus) first established on St. Catherines Island, Georgia, USA in 1987. During 2006 29 -2013, we conducted targeted trapping of immature gopher tortoises and compared survival of the hatchling, juvenile and subadult stages among treatments: 1) individuals released shortly after hatching from eggs obtained from gravid female founders (‘direct releases’); 2) individuals reared in captivity for 6-9 months following hatching (‘head-starts’); and 3) individuals first encountered as free-ranging, wild-recruited offspring (‘wild recruits’). Among the candidate models we examined, the best fit model included additive effects of tortoise stage and treatment, however, overlapping 95% credible intervals among treatments (CI) suggested that survival did not vary significantly among treatments. Annual apparent survival increased over the immature period, highlighting the importance of calculating separate estimates for the different immature stages. Across all treatments, the additive model estimated annual apparent survival probability to be 0.37 (CI: 0.25 40 – 0.48) for hatchlings, 0.71 (CI: 0.61 – 0.81) for juveniles, and 0.83 (CI: 0.74 – 0.94) for subadults. Our study, in combination with previous monitoring efforts at St. Catherines Island, provides strong evidence that the translocation and subsequent population augmentation efforts have been successful in establishing a robust population of gopher tortoises. Additionally, our results provide estimates of demographic rates for life stages that are poorly understood but critical to understanding population dynamics of this imperiled species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Swift and extensive Omicron outbreak in China after sudden exit from ‘zero-COVID’ policy

In late 2022, China transitioned from a strict ‘zero-COVID’ policy to rapidly abandoning nearly all interventions and data reporting. This raised great concern about the presumably-rapid but unreported spread of the SARS-CoV-2 Omicron variant in a very large population of very low pre-existing immunity. By modeling a combination of case count and survey data, we show that Omicron spread extremely rapidly, at a rate of 0.42/day (95% credibility interval: [0.35, 0.51]/day), translating to an epidemic doubling time of 1.6 days ([1.6, 2.0] days) after the full exit from zero-COVID on Dec. 7, 2022. Consequently, we estimate that the vast majority of the population (97% [95%, 99%], sensitivity analysis lower limit of 90%) was infected during December, with the nation-wide epidemic peaking on Dec. 23. Overall, our results highlight the extremely high transmissibility of the variant and the importance of proper design of intervention exit strategies to avoid large infection waves.

60 APPLIED LIFE SCIENCES↗