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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperform the baseline model across forecast weeks and locations in 2021–22 and 12 out of 18 models in 2022–23. Averaging across all forecast targets, the FluSight ensemble is the 2nd most accurate model measured by WIS in 2021–22 and the 5th most accurate in the 2022–23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degrade over longer forecast horizons. In this work we demonstrate that while the FluSight ensemble was a robust predictor, even ensembles face challenges during periods of rapid change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

Shigellosis is a gastrointestinal infection caused by species of Shigella . A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico between May 2021 and November 2023 that involved humans and non-human primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexican isolates as well as 15 closely related isolates from other states, and four from NHP. The outbreak was initially detected within men who have sex with men but then predominantly affected people experiencing homelessness. Nearly 70% of cases were hospitalized and there was one human death. The outbreak extended into Albuquerque’s BioPark Zoo, causing high morbidity and six deaths in NHPs. All isolates were multidrug-resistant, including towards fluoroquinolones, a first line treatment option which led to treatment failures in human and NHP populations. We show the circulation of the same S. flexneri strain in humans and NHPs, causing fatalities in both populations. This study demonstrates the threat of antimicrobial resistant organisms to vulnerable human and NHP populations and emphasizes the value of genomic surveillance within a One Health framework.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Risk of hematological malignancies from CT radiation exposure in children, adolescents and young adults

Over one million European children undergo computed tomography (CT) scans annually. Although moderate- to high-dose ionizing radiation exposure is an established risk factor for hematological malignancies, risks at CT examination dose levels remain uncertain. Here we followed up a multinational cohort (EPI-CT) of 948,174 individuals who underwent CT examinations before age 22 years in nine European countries. Radiation doses to the active bone marrow were estimated on the basis of body part scanned, patient characteristics, time period and inferred CT technical parameters. We found an association between cumulative dose and risk of all hematological malignancies, with an excess relative risk of 1.96 (95% confidence interval 1.10 to 3.12) per 100 mGy (790 cases). Similar estimates were obtained for lymphoid and myeloid malignancies. Results suggest that for every 10,000 children examined today (mean dose 8 mGy), 1–2 persons are expected to develop a hematological malignancy attributable to radiation exposure in the subsequent 12 years. Our results strengthen the body of evidence of increased cancer risk at low radiation doses and highlight the need for continued justification of pediatric CT examinations and optimization of doses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients in the DRC enrolled from 2017 to 2018

Rapid diagnostic tests (RDTs) detecting histidine-rich protein 2 (HRP2) and HRP3 are widely used throughout sub-Saharan Africa (SSA) to diagnose Plasmodium falciparum malaria. However, multiple SSA countries have reported pfhrp2 and pfhrp3 ( pfhrp2/3 ) gene deletions. Blood samples (n = 1109) collected from patients with P. falciparum infection from six health facilities throughout the Democratic Republic of the Congo (DRC) from March 2017 to January 2018 were evaluated for pfhrp 2/3 deletions. Samples were assayed for HRP2, pan- Plasmodium LDH (pLDH) and aldolase (pAldolase) antigens by bead-based multiplex antigen assay. Samples with low HRP2 concentration compared to pLDH and pAldolase antigens were selected for further pfhrp2/3 genotyping PCRs. The majority of blood samples (93.3%, 1035/1109) had high concentrations of the HRP2 antigen. Single deletions of pfhrp2 were identified in 0.27% (3/1109) of screened samples, with one sample from each of the Kapolowe, Mikalayi, and Rutshuru study sites. A pfhrp3 single deletion (0.09%, 1/1109) was found in the Kapolowe site. Dual pfhrp2 and pfhrp3 deletions were not observed. Due to, the low numbers of pfhrp2 deletions and the sporadic locations of these deletions, the use of HRP2-based RDTs appears to still be appropriate for these locations in DRC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Assessing the impact of human mobility to predict regional excess death in Ecuador

Abstract COVID-19 outbreaks have had high mortality in low- and middle-income countries such as Ecuador. Human mobility is an important factor influencing the spread of diseases possibly leading to a high burden of disease at the country level. Drastic control measures, such as complete lockdown, are effective epidemic controls, yet in practice one hopes that a partial shutdown would suffice. It is an open problem to determine how much mobility can be allowed while controlling an outbreak. In this paper, we use statistical models to relate human mobility to the excess death in Ecuador while controlling for demographic factors. The mobility index provided by GRANDATA, based on mobile phone users, represents the change of number of out-of-home events with respect to a benchmark date (March 2nd, 2020). The study confirms the global trend that more men are dying than expected compared to women, and that people under 30 show less deaths than expected, particularly individuals younger than 20 with a death rate reduction between 22 and 27%. The weekly median mobility time series shows a sharp decrease in human mobility immediately after a national lockdown was declared on March 17, 2020 and a progressive increase towards the pre-lockdown level within two months. Relating median mobility to excess deaths shows a lag in its effect: first, a decrease in mobility in the previous two to three weeks decreases excess death and, more novel, we found an increase of mobility variability four weeks prior increases the number of excess deaths.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Transmission history of SARS-CoV-2 in humans and white-tailed deer

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer ( Odocoileus virginianus ) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Inappropriate antibiotic access practices at the community level in Eastern Ethiopia

Access to antibiotic medications is critical to achieving the Sustainable Development Goal for good health and well-being. However, non-prescribed and informal sources are implicated as the most common causes of inappropriate antibiotic access practices, resulting in untargeted therapy, which leads to antibiotic resistance. Hence, knowing antibiotic access practices at the community level is essential to target misuse sources. In this study, 2256 household representatives were surveyed between July and September 2023 to examine their antibiotic access practices. Of 1245 household members who received antibiotics, 45.6% did so inappropriately. Non-prescribed antibiotic access was more common among urban residents and individuals not enrolled in health insurance schemes. This means of antibiotic access was also more common among individuals concerned about distance, drug availability, and healthcare convenience at public facilities. In addition, women and rural individuals were more likely to get antibiotics from unauthorized sources. Unrestricted antibiotic dispensing practices in urban areas enabled their non-prescribed access, while unlicensed providers prevailed with this access practice in rural areas. In this regard, personal behaviors and healthcare-related gaps such as the lack of health insurance, inconvenience, and drug unavailability have led community members to seek antibiotics from unofficial and non-prescribed sources. Targeting the identified behavioral and institutional factors can enhance antibiotic access through prescriptions, hence reducing antibiotic resistance.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Simulating nationwide coupled disease and fear spread in an agent-based model

Human cognitive responses, behavioral responses, and disease dynamics co-evolve over the course of any disease outbreak, and can result in complex feedbacks. We present a dynamic agent-based model that explicitly couples the spread of disease with the spread of fear surrounding the disease, implemented within the EpiCast simulation framework. EpiCast models transmission within a realistic synthetic population, capturing individual-level interactions. In our model, fear propagates through both in-person contact and broadcast media, prompting individuals to adopt protective behaviors that reduce disease spread. In order to better understand these coupled dynamics, we create and compare a range of compartmental models to ensure that introducing additional disease states does not prevent the emergence of multiple waves in these simpler models. Additionally, we compare a range of behavioral scenarios within EpiCast, varying the level and intensity of fear and behavior change. Our results show that the addition of asymptomatic, exposed, and pre-symptomatic disease states can impact both the rate at which an outbreak progresses and its overall trajectory in compartmental models. In EpiCast, the combination of non-local fear spread via broadcasters and strong behavioral responses by fearful individuals generally leads to multiple epidemic waves, an outcome that occurs only within a narrow parameter range when fear spreads purely through local contact. Accounting for the coupled spread of fear and disease is critical for understanding disease dynamics and designing timely, targeted responses to emerging infectious threats.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Enhancing fire emissions inventories for acute health effects studies: integrating high spatial and temporal resolution data

Daily fire progression information is crucial for public health studies that examine the relationship between population-level smoke exposures and subsequent health events. Issues with remote sensing used in fire emissions inventories (FEI) lead to the possibility of missed exposures that impact the results of acute health effects studies. This paper provides a method for improving an FEI dataset with readily available information to create a more robust dataset with daily fire progression. High temporal and spatial resolution burned area information from two FEI products are combined into a single dataset, and a linear regression model fills gaps in daily fire progression. The combined dataset provides up to 71% more PM 2.5 emissions, 69% more burned area, and 367% more fire days per year than using a single source of burned area information. The FEI combination method results in improved FEI information with no gaps in daily fire emissions estimates. The combined dataset provides a functional improvement to FEI data that can be achieved with currently available data.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Mortality among workers at the Los Alamos National Laboratory, 1943–2017

During World War II (WWII), the Manhattan Engineering District established a secret laboratory in the mountains of northern New Mexico. The mission was to design, construct and test the first atomic weapon, nicknamed ‘The Gadget’ that was detonated at the TRINITY site in Alamogordo, NM. After WWII, nuclear weapons research continued, and the laboratory became the Los Alamos National Laboratory (LANL). The mortality experience of 26,328 workers first employed between 1943 and 1980 at LANL was determined through 2017. Included were 6157 contract workers employed by the ZIA Company. Organ dose estimates for each worker considered all sources of exposure, notably photons, neutrons, tritium, 238Pu and 239Pu. Vital status determination included searches within the National Death Index, Social Security Administration and New Mexico State Mortality Files. Standardized Mortality Ratios (SMR) and Cox regression models were used in the analyses. Most workers (55%) were hired before 1960, 38% had a college degree, 25% were female, 81% white, 13% Hispanic and 60% had died. Vital status was complete, with only 0.1% lost to follow-up. The mean dose to the lung for the 17,053 workers monitored for radiation was 28.6 weighted-mGy (maximum 16.8 weighted-Gy) assuming a Dose Weighting Factor of 20 for alpha particle dose to lung. The Excess Relative Risk (ERR) at 100 weighted-mGy was 0.01 (95%CI -0.02, 0.03; n = 839) for lung cancer. The ERR at 100 mGy was -0.43 (95%CI -1.11, 0.24; n = 160) for leukemia other than chronic lymphocytic leukemia (CLL), -0.06 (95%CI -0.16, 0.04; n = 3043) for ischemic heart disease (IHD), and 0.29 (95%CI 0.02, 0.55; n = 106) for esophageal cancer. Among the 6499 workers with measurable intakes of plutonium, an increase in bone cancer (SMR 2.44; 95%CI 0.98, 5.03; n = 7) was related to dose. The SMR for berylliosis was significantly high, based on 4 deaths. SMRs for Hispanic workers were significantly high for cancers of the stomach and liver, cirrhosis of the liver, nonmalignant kidney disease and diabetes, but the excesses were not related to radiation dose. There was little evidence that radiation increased the risk of lung cancer or leukemia. Esophageal cancer was associated with radiation, and plutonium intakes were linked to an increase of bone cancer. IHD was not associated with radiation dose. More precise evaluations will await the pooled analysis of workers with similar exposures such as at Rocky Flats, Savannah River and Hanford.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2022

Mortality among Tennessee Eastman Corporation (TEC) uranium processing workers, 1943–2019

Background: There are few occupational studies of women exposed to ionizing radiation. During World War II, the Tennessee Eastman Corporation (TEC) operated an electromagnetic field separation facility of 1152 calutrons to obtain enriched uranium (235U) used for the Hiroshima atomic bomb. Thousands of women were involved in these operations. Materials and methods: We report a new study was conducted of 13,951 women and 12,699 men employed at TEC between 1943 and 1947 for at least 90 days. Comprehensive dose reconstruction techniques were used to estimate lung doses from the inhalation of uranium dust based on airborne measurements. Vital status through 2018/2019 was obtained from the National Death Index, Social Security Death Index, Tennessee death records and online public record databases. Analyses included standardized mortality ratios (SMRs) and Cox proportional hazards models. Results: Most workers were hourly (77.7%), white (95.6%), born before 1920 (58.3%), worked in dusty environments (57.0%), and had died (94.9%). Vital status was confirmed for 97.4% of the workers. Women were younger than men when first employed: mean ages 25.0 years and 33.0 years, respectively. The estimated mean absorbed dose to the lung was 32.7 mGy (max 1048 mGy) for women and 18.9 mGy (max 501 mGy) for men. The mean dose to thoracic lymph nodes (TLNs) was 127 mGy. Statistically significant SMRs were observed for lung cancer (SMR 1.25; 95% CI 1.19, 1.31; n = 1654), nonmalignant respiratory diseases (NMRDs) (1.23; 95% CI 1.19, 1.28; n = 2585), and cerebrovascular disease (CeVD) (1.13; 95% CI 1.08, 1.18; n = 1945). For lung cancer, the excess relative rate (ERR) at 100 mGy (95% CI) was 0.01 (–0.10, 0.12; n = 652) among women, and –0.15 (–0.38, 0.07; n = 1002) among men based on a preferred model for men with lung doses <300 mGy. NMRD and non-Hodgkin lymphoma were not associated with estimated absorbed dose to the lung or TLN. Conclusions: There was little evidence that radiation increased the risk of lung cancer, suggesting that inhalation of uranium dust and the associated high-LET alpha particle exposure to lung tissue experienced over a few years is less effective in causing lung cancer than other types of exposures. There was no statistically significant difference in the lung cancer risk estimates between men and women. The elevation of certain causes of death such as CeVD is unexplained and will require additional scrutiny of workplace or lifestyle factors given that radiation is an unlikely contributor since only the lung and lymph nodes received appreciable dose.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2022

Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

Prospective molecular studies of HIV-1 pol region (2253–5250 in HXB2 genome) sequences from sequenced samples of 269 HIV-1-infected patients in Cyprus (2017–2021) revealed a transmission cluster of 14 unknown HIV-1 recombinants that were not classified as previously established CRFs. The earliest recombinant was collected in September 2017, and the transmission cluster continued to grow until November 2020. Near full-length HIV-1 genome sequences of the 11 of the 14 recombinants were successfully obtained (790–8795 in HXB2 genome) and aligned against a reference dataset of HIV-1 subtypes and CRFs. We employed MEGAX for maximum-likelihood tree construction (GTR model, 1000 bootstrap replicates), Cluster-Picker for phylogenetic clustering analysis (genetic distance ≤0.045, bootstrap support value ≥70%), and REGA-3.0 for subtype determination. Bootscan and similarity plot analyses (sliding window of 400 nucleotides overlapped by 40 nucleotides) were conducted using SimPlot-v3.5.1, and subregion confirmatory neighbour-joining tree analyses were conducted using MEGAX (Kimura two-parameter model, 1000 bootstrap replicates, ≥70% bootstrap-support value). Exclusive clustering of the HIV-1 recombinants revealed their uniqueness. The recombination analyses illustrated the same unique mosaic pattern with six putative intersubtype recombination breakpoints, seven fragments of subtypes CRF02_AG, G, J and an unclassified fragment. We conclusively characterized the mosaic structure of the novel HIV-1 CRF, named CRF91_cpx, by the Los Alamos HIV Sequence Database. Additionally, we identified a URF of CRF91_cpx with two additional recombination sites, generated by a recombination event between subtype B and CRF91_cpx. Since the identification of CRF91_cpx, two additional patient samples have been entered into the CRF91_cpx transmission cluster, demonstrating active growth.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Archival records housed at USTUR support radium dial worker dosimetry

The American radium dial worker (RDW) cohort of over 3200 persons is being revisited as part of the Million Person Study (MPS) to include a modern approach to RDW dosimetry. An exceptional source of data and contextualization in this project is an extensive collection of electronic records (digitized from existing microfilm and microfiche) housed at the United States Transuranium and Uranium Registries (USTUR). Although the type, extent, and quality (e.g. legibility) of record(s) varies between individuals, the remarkable occupational, medical and demographic data include in vivo radiation measurements (e.g. radon breath, whole body counts), autopsy results, medical records (including copies of radiographs), interviews over the years, and correspondence. Of particular dosimetric interest are the details of radiation measurements. For example, there are some instances where hand-written and transcribed values are both available, along with notes providing context for why a particular measurement in a series of measurements was chosen to assign an intake, or if there were concerns about a particular measurement. Born prior to 1935, RDW have nearly all passed away. Thus, the updated dosimetry, especially for the skeletal tissues, will allow the correlation of lifetime cumulative dose with radiation risk. Here we review typical information available in this collection of historical records and highlight some interesting finds. Additionally, we discuss the relevance to current and ongoing work related to updating the dosimetry of the RDW in the MPS, including providing an example of the usefulness of information contained in these records. The RDW cohort provides a unique historical perspective on occupational exposure to radium, making it a valuable dataset for understanding long-term health effects and improving current radiation protection standards.

Million Person Study↗
DOE OSTI2021

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes

Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research community have expended considerable capital and effort tracking the evolution and spread of AMR by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing (AST). For the last several years, we have been capturing these efforts by curating data from the literature and data resources and building a set of assembled bacterial genome sequences that are paired with laboratory-derived AST data. This collection currently contains AST data for over 67 000 genomes encompassing approximately 40 genera and over 100 species. In this paper, we describe the characteristics of this collection, highlighting areas where sampling is comparatively deep or shallow, and showing areas where attention is needed from the research community to improve sampling and tracking efforts. In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. Further, we demonstrate this by describing two machine learning models that are built from the entire dataset to show where the predictive power is comparatively high or low.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel

In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.

59 BASIC BIOLOGICAL SCIENCES↗