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DOE OSTI2023

Juvenile life history diversity is associated with lifetime individual heterogeneity in a migratory fish

Abstract Differences in the life history pathways (LHPs) of juvenile animals are often associated with differences in demographic rates in later life stages. For migratory animals, different LHPs often result in animals from the same population occupying distinct habitats subjected to different environmental drivers. Understanding how demographic rates differ among animals expressing different LHPs may reveal fitness trade‐offs that drive the expression of alternative LHPs and enable better prediction of population dynamics in a changing environment. To understand how demographic outcomes and their relationships with environmental variables differ among animals with different LHPs, we analyzed a long‐term (2006–2021) mark–recapture dataset for Chinook salmon ( Oncorhynchus tshawytscha ) from the Wenatchee River, Washington, USA. Distinct LHPs represented in this population include either remaining in the natal stream until emigrating to the ocean as a 1‐year‐old (natal‐reach rearing) or emigrating from the natal stream and rearing in downstream habitats for several months before completing the emigration to the ocean as a 1‐year‐old (downstream rearing). We found that downstream‐rearing fish emigrated to the ocean 19 days earlier on average and returned as adults from the ocean at higher rates. We detected a positive correlation between rate of return from the ocean by downstream‐rearing fish and coastal upwelling in their spring of outmigration, whereas for natal‐reach‐rearing fish we detected a positive correlation with sea surface temperature during their first marine summer. Different responses to environmental variability should lead to asynchrony in adult abundance among juvenile LHPs. A higher proportion of downstream‐rearing fish returned at younger ages compared with natal‐reach‐rearing fish, which contributed to variability in age at reproduction and greater mixing across generations. Our results demonstrate how diversity in juvenile LHPs is associated with heterogeneity in demographic rates during subsequent life stages, which can in turn affect variance in aggregate population abundance and response to environmental change. Our findings underscore the importance of considering life history diversity in demographic analyses and provide insights into the effects of life history diversity on population dynamics and trade‐offs that contribute to the maintenance of life history diversity.

Sorel, Mark H.↗

NASA NTRSDate not supplied

Diversity and Inclusion in Spacecraft Science Teams: What Do We Know and What Can We Do About It?

Introduction: Not only does the planetary science community lack diversity [1-3], the subset of the community that participates on spacecraft science team is even less diverse than the community as a whole [1, 4]. Results of 2020 Workforce Survey: Previous studies of the diversity of members of spacecraft science teams made incorrect assumptions about the nature of the data before collecting the data. Those analyses assumed a binary gender and ignored the existence of planetary scientists who are neither men nor women [4-6]. We present here results where demographic data was collected without assumptions; each individual surveyed supplied their own answers to demographic questions. The April 2020 survey of Planetary Scientists, which was conducted by the Statistical Research Center of the American Institute of Physics (AIP) and funded by the American Astronomical Society (AAS)’s Division of Planetary Science (DPS) asked participants their gender with 4 possible responses: Woman, Man, Another identify (please specify if you wish), and Prefer not to answer. 32% of respondents chose Woman, 67% chose Man and 1% chose Another gender identity [1]. The survey also asked demographic questions on race, ethnicity, LGBTQ+ identity, and disability. For a full list of questions, see https://dps.aas.org/sites/dps.aas.org/files/reports/2020/survey2020_questionnaire.pdf. In addition to demographic questions, the 2020 Workforce survey asked how many times respondents had been involved in Mission proposals as a Principal Investigator (PI) and, separately, as a Co-Investigator (CoI) [1]. Answers to questions about mission involvement were correlated with answers to demographic questions and the results show that members of historically underrepresented groups (non-white scientists, women, members of the LGBTQ+ community, and disabled scientists) were less likely to be involved in spacecraft mission proposals than were members of historically overrepresented groups [1]. The figures below show the correlated responses for four different axes of underrepresentation [1]. Note that while the figure on gender shows only Women and Men (due to the small percentage of folks answering “Another gender”), non-binary respondents are included in the LGBTQ+ community figure. Conclusion: Being part of a spacecraft science team is a goal for many planetary scientists. With it comes brand new data, more stable funding, and a sense of awe and exploration. It can lead to a cascade of opportunities from conference and public presentations, to membership in subsequent mission teams, and prestige in the community [4]. As a result, participation in spacecraft teams can be used a measure of success within the field. From the survey results, we see that members of historically excluded groups, even after they have overcome barriers to participating in the field, are still experiencing barriers to success within the field itself. Why?: The diminishing percentage of members of underrepresented groups as a career progresses has been referred to as a “leaky pipeline”. However, this fails to adequately capture the experiences of the members of these underrepresented groups as it implies a passive process. In order to capture the active processes (bias, discrimination, harassment, and other exclusionary behaviors) that contribute to low retention in the workforce, the term “Hostile Obstacle Course” is more useful [7,8]. It is these processes that need to be addressed in order to retain valued members of our community. Moving Forward: In order to broaden participation in planetary science, particularly mission science teams, we need to address conditions that create hostile workplace climates. What can mission teams and other groups do to address these conditions? First, each group/team needs to evaluate their own members to determine what specific barriers exist in their own interactions. One tool to accomplish this would be an anonymous survey designed to understand how team members feel about working within the group. Working with professionals who know how to create and analyze such surveys (often called “climate surveys” when applied to University students, for example) would ensure that the survey meets its goals and does not make assumptions that counter the meaningfulness of the results. Such professionals in EDIA (Equity, Diversity, Inclusion, and Accessibility) and workplace culture can make suggestions for policy changes that would eliminate hostile workplace conditions. Policy changes that are often suggested include instituting professional EDIA training for the team and/or for team leadership, instituting and following a code of conduct [9], including more interactive group activities in group meetings, etc. Training and information on EDIA is available for all members of the planetary science community. The first place to look would be in your University or Institution’s EDIA or human resources offices. Bystander Intervention is often offered as part of other meetings [10]. A newer offering is a Workshop on EDIA for Leaders in Planetary Science led by Julie Rathbun (first author of this abstract) and JA Grier (https://edialps.psi.edu/). This 3-day workshop gives participants the tools they need to enact positive change in their personal and professional spheres. The first workshop was help in November 2022 and another workshop will take place in the late spring 2023 with exact dates to be announced soon.

J. A. Rathbun↗

DOE OSTI2026

Estimating the Benefits of Sustainable Aviation Fuel Usage at Chicago O’Hare International Airport on Ultrafine Particle Exposure and Mortalities Reductions

The expanding commercial aviation sector necessitates diverse energy sources, and sustainable aviation fuels (SAFs) have emerged as a promising option. Widespread SAF adoption can help meet transportation fuel demand and offer health benefits for people residing near airports or along airport landing and takeoff (LTO) pathways, where elevated levels of aircraft-derived air pollution often exist. Blending SAF with traditional jet fuels can reduce ultrafine particle (UFP) emissions, which may improve health of near airport population. We analyzed a population of about 8 million people in 1925 census tracts around the Chicago O’Hare International Airport (ORD). We conducted a risk assessment to estimate anticipated UFP reductions for three adoption scenarios using blends of traditional jet fuels with 5, 25, and 50% SAF across all flights landing and taking off from ORD. We calculated baseline estimates of UFP emissions using ORD flight data, a dispersion model, and a calibration function derived from mobile monitoring data. We used this baseline UFP emission profile across the study area to estimate population-weighted UFP, as well as the attributable case reductions (ACRs) and attributable mortality rate reductions (AMRRs) across the demographic distribution around the airport, based on the SAF blending scenarios. We found a positive association of SAF blending with UFP reductions, particularly near the airport and along LTO flight pathways. Our study showed that the population-weighted UFP across different demographics was similar. ACRs were largely dependent on individual demographic populations, while AMRRs for all populations were relatively similar, with an estimated 0.3 (95% range: 0.2−0.3), 1.1 (0.9−1.4), and 1.8 (1.5−2.2) fewer mortalities per 100,000 people per year expected with the adoption of 5, 25, and 50% SAF blends, respectively. This study indicates that communities near ORD, across a range of demographics, may benefit similarly from SAF adoption, thus highlighting how SAF adoption may offer an opportunity to improve health outcomes like aviation UFP-related mortalities around airports.

10 SYNTHETIC FUELS↗

DOE OSTI2024

Large Divergence of Projected High Latitude Vegetation Composition and Productivity Due To Functional Trait Uncertainty

Abstract Vegetation distribution and composition are expected to change in northern high latitudes under rapid warming, which regulates ecosystem functions but remains challenging to predict. Vegetation change arises from the interplay of chronic climate trends such as warming and transient demographic processes of recruitment, growth, competition, and mortality. Most predictive models overlooked the role of demographic dynamics controlled by plant traits. Here, we simulate vegetation dynamics at the Kougarok Hillslope site in Alaska under historical and future climates using the E3SM Land Model coupled to the Functionally Assembled Terrestrial Simulator (ELM‐FATES). To evaluate the roles of plant traits, we parameterize the model with 5,265 trait configurations representing diverse physiological and demographic strategies. Results show current modeled biomass, composition, and productivity are most sensitive to traits controlling photosynthetic capacity, carbon allocation, allometry, and phenology. Among all trait configurations, ∼5% reproduce in situ biomass and plant functional type (PFT) composition measured in 2016, that are indistinguishable from these two observed ecosystem states. Notably, these same trait configurations produce diverging biomass, composition, and productivity under future climate, where the uncertainty attributable to traits is twice the change attributable to climate change. The variation of projected productivity arises from emerging PFT composition under novel climate regimes, primarily explained by traits controlling cold‐induced mortality, recruitment, and allometry. Our findings highlight the importance and uncertainty of demographic dynamics and its interaction with climate change in shaping Arctic vegetation change. Improved model predictions will likely benefit from explicit consideration of vegetation demography and better constraints of critical traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗

DOE OSTI2025

Expanding Activity Allocation Models to Daily Activities: Tracking Simulated Agent Trips to Exercise Locations in Clarksville, TN

Exercise facilities have been proven to have numerous physical, mental, and psychological benefits, yet exercise facilities are still inaccessible to a large portion of the population. This study serves to explore the accessibility of fitness centres through geographical, demographic, and temporal lenses through an expansion of the UrbanPop framework that seeks to allocate simulated agents to fitness centres in the Clarksville metro to explore the effects of travel distances on different demographics throughout the week. Findings indicate that senior and retired demographics consistently travel longer distances to exercise in the larger Clarksville area, likely due to tendencies to live further from the center of the metropolitan area. Furthermore, all demographics tend to travel further distances to exercise on the weekends rather than the weekdays, indicating that travel distance can affect likelihood of agents to travel, especially on weekdays when many agents are in the workforce or participating in schooling.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Improving Medication Regimen Recommendation for Parkinson’s Disease Using Sensor Technology

Parkinson’s disease medication treatment planning is generally based on subjective data obtained through clinical, physician-patient interactions. The Personal KinetiGraph™ (PKG) and similar wearable sensors have shown promise in enabling objective, continuous remote health monitoring for Parkinson’s patients. In this proof-of-concept study, we propose to use objective sensor data from the PKG and apply machine learning to cluster patients based on levodopa regimens and response. The resulting clusters are then used to enhance treatment planning by providing improved initial treatment estimates to supplement a physician’s initial assessment. We apply k-means clustering to a dataset of within-subject Parkinson’s medication changes—clinically assessed by the MDS-Unified Parkinson’s Disease Rating Scale-III (MDS-UPDRS-III) and the PKG sensor for movement staging. A random forest classification model was then used to predict patients’ cluster allocation based on their respective demographic information, MDS-UPDRS-III scores, and PKG time-series data. Clinically relevant clusters were partitioned by levodopa dose, medication administration frequency, and total levodopa equivalent daily dose—with the PKG providing similar symptomatic assessments to physician MDS-UPDRS-III scores. A random forest classifier trained on demographic information, MDS-UPDRS-III scores, and PKG time-series data was able to accurately classify subjects of the two most demographically similar clusters with an accuracy of 86.9%, an F1 score of 90.7%, and an AUC of 0.871. A model that relied solely on demographic information and PKG time-series data provided the next best performance with an accuracy of 83.8%, an F1 score of 88.5%, and an AUC of 0.831, hence further enabling fully remote assessments. These computational methods demonstrate the feasibility of using sensor-based data to cluster patients based on their medication responses with further potential to assist with medication recommendations.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2006

Beyond Population and Environment: Household Life Cycle Demography and Land Use Allocation among Small Farm Colonists in the Amazon

Most research featuring demographic factors in environmental change has focused on processes operating at the level of national or global populations. This paper focuses on household-level demographic life cycles among colonists in the Amazon, and evaluates the impacts on land use allocation. The analysis goes beyond prior research by including a broader suite of demographic variables, and by simultaneously assessing their impacts on multiple land uses with different economic and ecological implications. We estimate a system of structural equations that accounts for endogeneity among land uses, and the findings indicate stronger demographic effects than previous work. These findings bear implications for modeling land use, and the place of demography in environmental research.

Perz, Stephen G.↗

DOE OSTI2022

Forest regeneration within Earth system models: current process representations and ways forward

Earth system models must predict forest responses to global change in order to simulate future global climate, hydrology, and ecosystem dynamics. These models are increasingly adopting vegetation demographic approaches that explicitly represent tree growth, mortality, and recruitment, enabling advances in the projection of forest vulnerability and resilience, as well as evaluation with field data. To date, simulation of regeneration processes has received far less attention than simulation of processes that affect growth and mortality, in spite of their critical role maintaining forest structure, facilitating turnover in forest composition over space and time, enabling recovery from disturbance, and regulating climate-driven range shifts. Here, our critical review of regeneration process representations within current Earth system vegetation demographic models reveals the need to improve parameter values and algorithms for reproductive allocation, dispersal, seed survival and germination, environmental filtering in the seedling layer, and tree regeneration strategies adapted to wind, fire, and anthropogenic disturbance regimes. These improvements require synthesis of existing data, specific field data-collection protocols, and novel model algorithms compatible with global-scale simulations. Vegetation demographic models offer the opportunity to more fully integrate ecological understanding into Earth system prediction; regeneration processes need to be a critical part of the effort.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Climate warming threatens the persistence of a community of disturbance-adapted native annual plants

With ongoing climate change, populations are expected to exhibit shifts in demographic performance that will alter where a species can persist. This presents unique challenges for managing plant populations and may require ongoing interventions, including in situ management or introduction into new locations. However, few studies have examined how climate change may affect plant demographic performance for a suite of species, or how effective management actions could be in mitigating climate change effects. Over the course of two experiments spanning 6 yr and four sites across a latitudinal gradient in the Pacific Northwest, United States, here we manipulated temperature, precipitation, and disturbance intensity, and quantified effects on the demography of eight native annual prairie species. Each year we planted seeds and monitored germination, survival, and reproduction. We found that disturbance strongly influenced demographic performance and that seven of the eight species had increasingly poor performance with warmer conditions. Across species and sites, we observed 11% recruitment (the proportion of seeds planted that survived to reproduction) following high disturbance, but just 3.9% and 2.3% under intermediate and low disturbance, respectively. Moreover, mean seed production following high disturbance was often more than tenfold greater than under intermediate and low disturbance. Importantly, most species exhibited precipitous declines in their population growth rates (λ) under warmer-than-ambient experimental conditions and may require more frequent disturbance intervention to sustain populations. Aristida oligantha, a C4 grass, was the only species to have λ increase with warmer conditions. These results suggest that rising temperatures may cause many native annual plant species to decline, highlighting the urgency for adaptive management practices that facilitate their restoration or introduction to newly suitable locations. Frequent and intense disturbances are critical to reduce competitors and promote native annuals’ persistence, but even such efforts may prove futile under future climate regimes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Hierarchical semi-Markov models with duration-aware dynamics for activity sequences

Residential electricity demand at granular scales is driven by what people do and for how long. Accurately forecasting this demand for applications like microgrid management and demand response therefore requires generative models for activities that can produce realistic daily activity sequences, capturing both the timing and duration of human behavior. This paper develops a generative model of human activity sequences using nationally representative time-use diaries at a 10-min resolution. We use this model to quantify which demographic factors are most critical for improving predictive performance. We propose a hierarchical semi-Markov framework that addresses two key modeling challenges. First, a time-inhomogeneous Markov router learns the patterns of “which activity comes next.” Second, a semi-Markov hazard component explicitly models activity durations, capturing “how long” activities realistically last. To ensure statistical stability when data are sparse, the model pools information across related demographic groups and time blocks. The entire framework is trained and evaluated using survey design weights to ensure our findings are representative of the U.S. population. On a held-out test set, we demonstrate that explicitly modeling durations with the hazard component provides a substantial and statistically significant improvement over purely Markovian models. Furthermore, our analysis reveals a clear hierarchy of demographic factors: Sex, Day-Type, and Household Size provide the largest predictive gains, while Region and Season, though important for energy calculations, contribute little to predicting the activity sequence itself. The result is an interpretable and robust generator of synthetic activity traces, providing a high-fidelity foundation for downstream energy systems modeling.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Investigating the Global Biogeophysical Impact of Area and Mass Based Wood Harvest in a Vegetation Demography Model

Wood harvesting alters land surface properties and energy redistribution, but there is a lack of studies estimating these changes on a global scale. We coupled a vegetation demographic model, the Functionally Assembled Terrestrial Ecosystem Simulator, with the E3SM land model to perform offline model simulation to investigate the land biogeophysical responses, including canopy coverage, leaf area index, albedo, surface roughness length, and energy fluxes, to historical wood harvest on the global scale. In this study, we found 50% less harvested carbon (C) when choosing the area-based harvest rate as driving data that has not been spatially harmonized, compared to reharmonized mass-based harvesting. By considering the uncertainty from reconstruction of historical wood harvest time series and the choice of wood harvest approach in the model, continuous wood harvest (1850–2015) results in 5%–10% of canopy coverage loss, contributing 0.5%–1% increase of albedo over disturbed land, which is much stronger than a non-demographic land surface model. Changes in energy flux from the wood harvest are negligible (<1%), but the responses of land surface properties vary (up to 30%) due to differences in model structure between the single canopy, sun-shade leaf model and vegetation demographic model.

Shu, Shijie [Lawrence Berkeley National Laboratory↗

DOE OSTI2024

Divergent urban land trajectories under alternative population projections within the Shared Socioeconomic Pathways

Population change is a main driver behind global environmental change, including urban land expansion. In future scenario modeling, assumptions regarding how populations will change locally, despite identical global constraints of Shared Socioeconomic Pathways (SSPs), can have dramatic effects on subsequent regional urbanization. Using a spatial modeling experiment at high resolution (1 km), this study compared how two alternative US population projections, varying in the spatially explicit nature of demographic patterns and migration, affect urban land dynamics simulated by the Spatially Explicit, Long-term, Empirical City development (SELECT) model for SSP2, SSP3, and SSP5. The population projections included: (1) newer downscaled state-specific population (SP) projections inclusive of updated international and domestic migration estimates, and (2) prevailing downscaled national-level projections (NP) agnostic to localized demographic processes. Our work shows that alternative population inputs, even those under the same SSP, can lead to dramatic and complex differences in urban land outcomes. Under the SP projection, urbanization displays more of an extensification pattern compared to the NP projection. This suggests that recent demographic information supports more extreme urban extensification and land pressures on existing rural areas in the US than previously anticipated. Urban land outcomes to population inputs were spatially variable where areas in close spatial proximity showed divergent patterns, reflective of the spatially complex urbanization processes that can be accommodated in SELECT. Although different population projections and assumptions led to divergent outcomes, urban land development is not a linear product of population change but the result of complex relationships between population, dynamic urbanization processes, stages of urban development maturity, and feedback mechanisms. These findings highlight the importance of accounting for spatial variations in the population projections, but also urbanization process to accurately project long-term urban land patterns.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Factors associated with emerging multimodal transportation behavior in the San Francisco Bay Area

Abstract This paper identifies the influence of demographic, local transportation environment, and individual preferences for transportation attributes on multimodal transportation behavior in an urban environment with emergent transportation mode availability. Multimodality is the use of more than one mode of transportation during a given timeframe. Multimodality has been considered a key component of sustainable and efficient transportation systems, as this travel behavior can represent a shift away from personal vehicle use to more sustainable transportation modes, especially in urban environments with diverse transportation systems and emergent shared transportation alternatives (e.g., carsharing, ridehailing, bike sharing). However, it is unclear what factors contribute towards people being more likely to exhibit multimodal transportation behavior in modern urban environments. We assessed commuting behavior based on a survey administered in the San Francisco Bay Area according to whether residents commuted (i) exclusively by vehicle, (ii) by a mix of vehicle and non-vehicle modes, or (iii) exclusively by non-vehicle modes. A classification tree approach identified correlations between commuting classes and demographic variables, preferences for transportation attributes, and location-based information. The characterization of commuting styles could inform regional transportation policy and design that aims to reduce vehicle use by identifying the demographic, preference, and location-based considerations correlated with each commuting style.

McAuliffe Wells, Emily↗

DOE OSTI2024

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994–2018) and four hyperendemic Lake Victoria fishing communities (2011–2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

pyFLANK, a graph neural network based null distribution inference model for F ST outlier detection

Detecting genomic regions under selection is essential for understanding how populations adapt to different environments, yet it remains challenging due to the confounding effects of demographic history and linkage disequilibrium (LD). Fixation index (F ST ) is a widely used statistic to identify genomic regions under adaptation. However, identifying genes under selection by defining F ST outliers often remains challenging, owing to confounding effects of underlying demographic history. Traditional methods assume independence among loci and rely on simple demographic models, while newer models perform much better but are computationally expensive and not easily scalable. Here, we present pyFLANK, an open-source and automated Python implementation which detects F ST outliers using a null distribution inferred from quasi-independent loci. Our tool integrates three approaches to identify loci obeying a null distribution: graph neural network (GNN) inference, linkage disequilibrium (LD)-based inference, and user-defined input. Because pyFLANK uses GNN-based inference of quasi-independent loci, it yields a more accurate null model with less need for user parameter input. In simulation experiments, pyFLANK achieved lower false positive rates than current methods while maintaining comparable detection power, indicating that its refined null model better distinguishes true adaptive loci from background variation. The GNN-based model, in particular, detected additional loci associated with phenotypic variance that were not identified by existing methods. Assessments of simulation and real data from different species demonstrate that pyFLANK achieves lower false positive rates compared with other commonly used F ST outlier detectors, while maintaining comparable detection power and excellent computational performance, providing a robust and user-friendly tool for identifying loci under divergent selection. It extends existing F ST outlier frameworks by incorporating explicit LD-aware strategies for null model calibration. The method is intended as a practical and scalable complement to existing genome scan approaches.

FST↗

DOE OSTI2026

Mitigating Algorithmic Bias in Cancer Site Classification Models

Purpose Integrating artificial intelligence in cancer diagnostics has improved tumor classification beyond rule-based systems. Despite these advancements, these models may still encode demographic biases. We conducted a large-scale, applied bias-probing study of a deep learning–based cancer site classifier to quantify race information encoded in document embeddings. We then evaluated how performance changes when race-correlated embedding dimensions are removed in a post-training sensitivity analysis. Methods The cancer site classifier was trained using 3.5 million electronic cancer pathology reports from six of the National Cancer Institute's SEER registries. We trained a hierarchical self-attention network to generate 400-dimensional document embeddings. These embeddings were used to train two downstream, gradient-boosted decision tree classifiers: one to classify the cancer sites and another to predict racial categories. We identified overlapping features by intersecting the top 50 feature-importance rankings from the site and race models and computed their cumulative feature importance in each model. As a post hoc sensitivity analysis, we progressively pruned these overlapping dimensions, retrained the site model, and compared overall macro-F1 and accuracy, race-stratified macro-F1, and group fairness metrics on the basis of demographic parity and equalized odds before and after pruning. Results The analysis revealed minimal feature overlap between the cancer site and race prediction models, and the cumulative importance scores indicated a negligible influence of racial information on clinical predictions. Post-training pruning of overlapping features did not compromise the models' diagnostic accuracy, with a 0.07% loss in accuracy. Conclusion Our findings demonstrate that HiSAN-generated embeddings from SEER data can be used effectively in cancer site classification without significant demographic bias influencing the outcomes. Post-training pruning therefore functions as a practical audit and sensitivity check.

Shivanna, Abhishek [ORNL] (ORCID:0009000665228593)↗

DOE OSTI2026

1990 Seattle Household Travel Survey Wave 2

The Seattle Household Travel Survey Wave 2, conducted in 1990, was the second wave in a 10-part longitudinal panel survey of the travel patterns of households in the Puget Sound region of Washington state. The survey series was initiated in 1989 by the Puget Sound Regional Council. Data collection for the second wave took place in the fall of 1990, which included full interviews and travel diaries, as well as some panel refreshment. Demographic and work trip data updates, but no travel diaries, were gathered for 2,023 households in four counties in the Seattle area. The survey relied on the willingness of study area residents to 1) provide demographic information about their household, its members, and its vehicles; 2) document all travel for each household member, aged 15 years or older, for an assigned two-day period; and 3) agree to participate in additional survey waves. After an initial telephone screening, survey participants received mailed travel diaries to aid in documenting travel information for the two-day assessment period. Respondents were instructed to record their mode of transportation, trip purpose, number of passengers, departure and arrival times, ride fare, and parking costs. Demographic information for this study includes age, gender, education, employment status, and household income.

1Hz data↗