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NASA NTRSDate not supplied

Agent-based modeling of microbes in space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal microgravity; however, much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER results agree with experimental data indicating that indirect effects of radiation (reactive oxygen species generation, metabolic impairment) have a greater impact on microorganisms than direct effects (DNA damage).

Jessica A Lee↗
NASA NTRS2022

Agent-Based Modeling of Microbes in Space

Space is tough on organisms. Microorganisms traveling to space experience stress from environmental features such as ionizing radiation and lack of normal gravity, and much remains unknown about the mechanisms by which those environmental features affect microbial physiology. Microbes experience changes in gravity not directly but rather through changes in their fluid environment, and deep-space particle radiation causes cell damage that is complex but rare. Computational modeling at the single-cell level (agent-based modeling) can allow us to probe the spatially heterogeneous processes that characterize space stresses, to gain insight into the relationships of microbial cells with their environments and with each other. Here we present two software packages for simulating microbial population dynamics in space conditions: CAMDLES and AMMPER. Microbes growing in liquid culture medium in the microgravity of an orbital space station experience a quiescent, poorly-mixed fluid environment. CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) simultaneously simulates biological, chemical, and mechanical processes to predict microbial ecological dynamics in microgravity, and in the rotating culture vessels used to create an artificial microgravity environment in the lab. Initial results demonstrate that the growth of a cross-feeding microbial consortium, dependent on the exchange of soluble metabolites, is sensitive to the initial spatial distribution of cells, and grows differently in real versus artificial microgravity. Microbial populations exposed to deep-space radiation experience spatially and temporally heterogeneous damage from the traversal of high-energy particles. AMMPER (Agent-Based Model for Microbial Populations Exposed to Radiation) pairs a 3d model of energy deposition along a radiation particle track with a microbial population growth and damage model to predict the effects of localized radiation damage on population-level responses. It includes a user-friendly graphical interface. AMMPER growth curves recapitulate experimental results, and allow comparison between direct effects (DNA damage) and indirect effects (reactive oxygen species generation, metabolic impairment) of radiation.

microbiology↗
NASA NTRSDate not supplied

Increasing Cognitive Ability/Reserve Using Software – Pilot (ICARUS-Pilot)

BACKGROUND This research study was competitively awarded under the 2022 JSC Innovation Charge Account (ICA) program administered by NASA Johnson Space Center’s Joint Technology Working Group. Study period of performance was May through September 2022, with a maximum allowed procurement budget of $10K. The study sought to quantify and assess the potential benefit of using commercial-off-the-shelf (COTS) cognitive training software to improve cognitive performance in an astronaut-like terrestrial population. METHODS Five volunteer research participants were recruited from the JSC employee population to mimic certain demographic characteristics of the NASA astronaut population (age, education/discipline). Participant cognitive performance was assessed before and after executing eighteen sessions of remote cognitive training executed nominally three times per week using six exercises within an adaptive app-based COTS software package (BrainHQ, Posit Science) on study-provided tablets. Pre- and post-training cognitive performance was measured using internal assessments in BrainHQ as well as Cognition Test Battery (CTB) version ISS B01 v3 (3.0.9-201710021500), an independent software test developed specifically for NASA and used currently in research studies on astronauts. BrainHQ exercises were posited to map well or partially to several CTB sub-tests. Participants provided feedback on their study experience formally via semi-structured interview at the conclusion of testing and informally throughout the study if they encountered issues. RESULTS The enrolled ICARUS-Pilot study participants generally matched Artemis crew demographic characteristics. Four of five participants have completed study training and assessment activities as of the writing of this abstract. These test participants complied well with desired training session frequency and duration yielding an average cumulative active training duration of 15 hours over an average of 45 days; participants showed 78% average improvement in metric performance for the six trained exercises, with an associated overall 33%ile ranking increase against performance of the entire BrainHQ subscribing population for internal pre/post assessment, agreeing with post-study survey self-reported performance increases. CTB overall feedback scoring, not corrected for learning effects, showed an average of 19% performance improvement across its 10 performance measures over the training period for the completed participants. Detailed analyses will be conducted once participant data collection for the study is complete and the resulting dataset is fully populated. DISCUSSION These preliminary results provide a positive trend for the effectiveness of the training approach, but further analysis will be needed to establish significance, investigate far transfer, and suggest the needed participant pool size for subsequent efforts to achieve statistically significant outcomes given similar results. The pilot study has already been helpful by allowing the study team to learn a great deal about the capabilities and limitations of the COTS software package that will be reflected in future proposals along with revised timelines for study execution and test participant management. From participant feedback, one common thread regarding the COTS training was that it felt overly repetitive – future proposals should reassess overall training duration, available levels for each trained exercise, and the behavior of the BrainHQ internal scheduler in determining which exercises should be trained and for how long. If the final analysis of this feasibility study ultimately supports it, the study team will recommend further investigation to fully evaluate this potential countermeasure and optimize its implementation. Future proposals would cite this feasibility study’s outcome and would seek to refine the training protocol and obtain statistically significant results for cognitive performance increases as well as retention data.

cognitive training↗
NASA NTRSDate not supplied

Increasing Cognitive Ability/Reserve Using Software – Pilot (ICARUS-Pilot)

Background: This research study was competitively awarded under the 2022 JSC Innovation Charge Account (ICA) program administered by NASA Johnson Space Center’s Joint Technology Working Group. Study period of performance was May through September 2022, with a maximum allowed procurement budget of $10K. The study sought to quantify and assess the potential benefit of using commercial-off-the-shelf (COTS) cognitive training software to improve cognitive performance in an astronaut-like terrestrial population. Methods: Five volunteer research participants were recruited from the JSC employee population to mimic certain demographic characteristics of the NASA astronaut population (age, education/discipline). Participant cognitive performance was assessed before and after executing eighteen sessions of remote cognitive training executed nominally three times per week using six exercises within an adaptive app-based COTS software package (BrainHQ, Posit Science) on study-provided tablets. Pre- and post-training cognitive performance was measured using internal assessments in BrainHQ as well as Cognition Test Battery (CTB) version ISS B01 v3 (3.0.9-201710021500), an independent software test developed specifically for NASA and used currently in research studies on astronauts. BrainHQ exercises were posited to map well or partially to several CTB sub-tests. Participants provided feedback on their study experience formally via semi-structured interview at the conclusion of testing and informally throughout the study if they encountered issues. Results: The enrolled ICARUS-Pilot study participants generally matched Artemis crew demographic characteristics. Four of five participants have completed study training and assessment activities as of the writing of this abstract. These test participants complied well with desired training session frequency and duration yielding an average cumulative active training duration of 15 hours over an average of 45 days; participants showed 78% average improvement in metric performance for the six trained exercises, with an associated overall 33%ile ranking increase against performance of the entire BrainHQ subscribing population for internal pre/post assessment, agreeing with post-study survey self-reported performance increases. CTB overall feedback scoring, not corrected for learning effects, showed an average of 19% performance improvement across its 10 performance measures over the training period for the completed participants. Detailed analyses will be conducted once participant data collection for the study is complete and the resulting dataset is fully populated. Discussion: These preliminary results provide a positive trend for the effectiveness of the training approach, but further analysis will be needed to establish significance, investigate far transfer, and suggest the needed participant pool size for subsequent efforts to achieve statistically significant outcomes given similar results. The pilot study has already been helpful by allowing the study team to learn a great deal about the capabilities and limitations of the COTS software package that will be reflected in future proposals along with revised timelines for study execution and test participant management. From participant feedback, one common thread regarding the COTS training was that it felt overly repetitive – future proposals should reassess overall training duration, available levels for each trained exercise, and the behavior of the BrainHQ internal scheduler in determining which exercises should be trained and for how long. If the final analysis of this feasibility study ultimately supports it, the study team will recommend further investigation to fully evaluate this potential countermeasure and optimize its implementation. Future proposals would cite this feasibility study’s outcome and would seek to refine the training protocol and obtain statistically significant results for cognitive performance increases as well as retention data.

cognitive training↗
NASA NTRS2022

A Deep and Wide Twilight Survey for Asteroids Interior to Earth and Venus

We are conducting a survey using twilight time on the Dark Energy Camera with the Blanco 4 m telescope in Chile to look for objects interior to Earth's and Venus' orbits. To date we have discovered two rare Atira/Apohele asteroids, 2021 LJ4 and 2021 PH27, which have orbits completely interior to Earth's orbit. We also discovered one new Apollo-type Near Earth Object (NEO) that crosses Earth's orbit, 2022 AP7. Two of the discoveries have diameters ≳1 km. 2022 AP7 is likely the largest Potentially Hazardous Asteroid (PHA) discovered in about eight years. To date we have covered 624 square degrees of sky near to and interior to the orbit of Venus. The average images go to 21.3 mag in the *r* band, with the best images near 22nd mag. Our new discovery 2021 PH27 has the smallest semimajor axis known for an asteroid, 0.4617 au, and the largest general relativistic effects (53 arcsec/century) known for any body in the solar system. The survey has detected ∼15% of all known Atira NEOs. We put strong constraints on any stable population of Venus co-orbital resonance objects existing, as well as the Atira and Vatira asteroid classes. These interior asteroid populations are important to complete the census of asteroids near Earth, including some of the most likely Earth impactors that cannot easily be discovered in other surveys. Comparing the actual population of asteroids found interior to Earth and Venus with those predicted to exist by extrapolating from the known population exterior to Earth is important to better understand the origin, composition, and structure of the NEO population.

Scott S. Sheppard↗
NASA NTRS2024

Applications of Remote Sensing for Land Use Planning Scenarios with Suitability Analysis

In regions undergoing rapid urbanization, such as West Africa, land use planning (LUP) is vital to accommodate growing population and manage natural resources. Suitability analysis modeling is a widely used tool in LUP to determine the extent to which a land area is suitable for a designated purpose, but there is a gap in the integration of remote sensing time series data into land use decisions. The goal of this study was to incorporate remote sensing time series information with suitability analyses to inform LUP decisions in urban areas. In the study area of Kumasi, Ghana, land cover trends and land surface temperature (LST) from 2000 to 2019 were used to understand climate change trends. Suitability analyses determined the fitness of land areas for predetermined uses. These background processes informed a genetic algorithm to project plausible futures for three land use scenarios. One scenario represented current land use planning practices for addressing population growth, another scenario prioritized minimizing climate change impacts while also accommodating population growth, and the final scenario focused on both of these climate and population goals in addition to high density urban development. Each of these scenarios was successful in achieving population accommodation and respective climate change mitigation goals. The results for these scenarios provide insight into plausible land use distributions in 2050 based on different planning approaches. The genetic algorithm was able to effectively develop results for each scenario through the integration of remotely sensed trends and suitability models, providing a novel approach to land use decision-making.

remote sensing time series↗
DOE OSTI2020

A ``Tail" of Two Cities: Fatality-based Modeling of COVID-19 Evolution in New York City and Cook County, IL

I describe $SIR$ modeling of the COVID-19 pandemic in two U.S. urban environments, New York City (NYC) and Cook County, IL, from onset through the month of June, 2020. Since testing was not widespread early in the pandemic in the U.S., I do not use data on confirmed cases and rely solely on public fatality data to estimate model parameters. Fits to the first 20 days of data determine a degenerate combination of the basic reproduction number, $R_0$, and the mean time to removal from the infectious population, $\gamma^{-1}$, with $\gamma (R_0-1) = 0.25 (0.21)$ inverse days for NYC (Cook County). Equivalently, the initial doubling time was $t_d = 2.8 (3.4)$ days for NYC (Cook). The early fatality data suggest that both locations had infections in early February. I model the mitigation measures implemented in mid-March in both locations (distancing, quarantine, isolation, etc) via a time-dependent reproduction number $R_t$ that declines monotonically from $R_0$ to a sma ller asymptotic value, with a parameterized functional form. The timing (mid-March) and duration (several days) of the transitions in $R_t$ appear well determined by the data. However, the fatality data determine only a degenerate combination of the parameters $R_0$, the percentage reduction in social contact due to mitigation measures, $X$, and the infection fatality rate (IFR), $f$. With flat priors, based on simulations the NYC model parameters have 95.45\% credible intervals of $R_0 = 3.0-5.4$, $X= 80-99.9\%$ and $f=2-6\%$, with $5-13\%$ of the population asymptotically infected. A strong external prior indicating a lower value of $f$ or of $\gamma^{-1}$ would imply lower values of $R_0$ and $X$ and higher percentage infection of the population. For Cook County, the evolution was qualitatively different: after mitigation measures were implemented, the daily fatality counts reached a plateau for about a month before tailing off. This is consistent with an $SIR$ model that exhibits ``critical slowing-down", in which $R_t$ plateaus ! at a value just above unity. For Cook County, the 95.45\% credible intervals for the model parameters are much broader and shifted downward, $R_0=1.4-4.7$, $X=26-54\%$, and $f=0.1-0.6\%$ with $15-88\%$ of the population asymptotically infected. Despite the apparently lower efficacy of its social contact reduction measures, Cook County has had significantly fewer fatalities per population than NYC, $D_\infty/N=100$ vs. 270 per 100,000. In the model, this is attributed to the lower inferred IFR for Cook; an external prior pointing to similar values of the IFR for the two locations would instead chalk up the difference in $D/N$ to differences in the relative growth rate of the disease. I derive a model-dependent threshold, $X^{crit}_e$, for `safe' re-opening, that is, for easing of contact reduction that would not trigger a second wave; for NYC, the models predict that increasing social contact by more than 20\% from post-mitigation levels will lead to renewed spread, while for Cook County the threshold value is very uncertain, given the parameter degeneracies. The timing of 2nd-wave growth will depend on the amplitude of contact increase relative to $X^{crit}_e$ and on the asymptotic growth rate, and the impact in terms of fatalities will depend on the parameter $f$.

Frieman, Joshua↗
DOE OSTI2020

Million Worker Study

Radiation health issues have been an important aspect of DOE's Worker Safety and Health programs. The goal is to ensure that workers are adequately protected from the various radiological hazards associated with DOE sites and operations. Since the early 1940’s DOE has supported the conduct of epidemiologic studies of practically every DOE (AEC) facility and collected these data, now managed by the Oak Ridge Associated Universities (ORAU), in remarkable detail. In the early 2000s, the Office of Health, Safety and Security authorized access to specific DOE worker datasets. Shortly thereafter, the DOE Office of Science provided funds for a pilot study that confirmed the feasibility of the Million Worker Study (MWS), and then additional resources were provided (with other agencies) to extend the follow-up of many populations, not just DOE workers, but also atomic veterans, industrial radiographers, nuclear power plant workers and medical radiation workers (the Million Persons Study (MPS)). This proposal was a continuation of support provided by DOE, specifically to extend the follow-up of the worker populations at the Mallinckrodt Chemical Works (MCW) and Los Alamos National Laboratory (LANL). The work addresses DOE’s interest in clarifying the health risks of their workers as well as contributing knowledge on radiation risks that is relevant today with regard to compensation schemes. The findings are also important for the US public in light of the increased population exposure to medical imaging, environmental circumstances such as hydraulic fracturing, increased exposures during high altitude flights, and with regard to nuclear accidents such as Fukushima and possible terrorist events. Furthermore, it is important to consider reducing the uncertainty in current risk estimates by developing risk coefficients based on healthy American workers who are more representative of U.S. workers and the general public than 1945 Japanese survivors of the atomic bombs living in a war-torn country which experienced deprivation, malnourishment, and increased rates of infections and other diseases. But more importantly, it is important to learn whether radiation exposures received gradually over time (e.g., years) are more or less effective in causing health effects, cancer in particular, than if the radiation dose is received all at once in a fraction of a second as experienced by the Japanese atomic bomb survivors. Finally, the ability to evaluate and combine large populations with intakes of radionuclides such as uranium, radium, plutonium, americium and polonium will provide new quantitative knowledge on human health effects that hitherto has not been possible. This cost-efficient study has built on the investments made and foundations laid by investigators and government agencies, including DOE, over the past 30-40 years, which have established early worker cohorts that can now provide answers to questions on the lifetime human health risks associated with low-level radiation exposures. Collaborating institutions included: International Epidemiology Institute, Oak Ridge Associated Universities, Oak Ridge National Laboratory, Los Alamos National Laboratory, Landauer, Inc., and Vanderbilt University. Follow-up of these two populations and the integration of them with the many other cohorts (now a total of 31) in the MPS continues under a separate DOE grant (DE-AU0000046).

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2023

An Interpretable Index of Social Vulnerability to Environmental Hazards

Index-based measures of social vulnerability to environmental hazards are commonly modeled from composites of population-level risk factors. These models overlook individual context in communities' experiences of environmental hazards, producing metrics that may hinder spatial decision support for mitigating and responding to hazards. This paper introduces an interpretable, high-resolution model for generating an individual-oriented social vulnerability index (IOSVI) for the United States built on synthetic populations that couples individual and social determinants of vulnerability. The IOSVI combines an individual vulnerability index (IVI) that ranks individuals in an area’s synthetic population based on intersecting risk factors, with a social vulnerability index (SVI) based on the population’s cumulative distribution of IVI scores. Interpretability of the IOSVI procedure is demonstrated through examples of national, metropolitan, and neighborhood (census tract) level spatial variation in index scores and IVI themes, as well as an exploratory analysis examining risk factors affecting a specific sub-population (military veterans) in areas of high social and environmental vulnerability.

Tuccillo, Joe↗
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 OSTI2021

A time-varying vulnerability index for COVID-19 in New Mexico, USA using generalized propensity scores

The coronavirus disease (COVID-19) pandemic has highlighted systemic inequities in the United States and resulted in a larger burden of negative social outcomes for marginalized communities. New Mexico, a state in the southwestern US, has a unique population with a large racial minority population and a high rate of poverty that may make communities more vulnerable to negative social outcomes from COVID-19. To identify which communities may be at the highest relative risk, we created a county-level vulnerability index. After the first COVID-19 case was reported in New Mexico on March 11, 2020, we fit a generalized propensity score model that incorporates sociodemographic factors to predict county-level viral exposure and thus, the generic risk to negative social outcomes such as unemployment or mental health impacts. We used four static sociodemographic covariates important for the state of New Mexico—population, poverty, household size, and minority population—and weekly cumulative case counts to iteratively run our model each week and normalize the exposure score to create a time-varying vulnerability index. We found the relative vulnerability between counties varied in the first eight weeks from the initial COVID-19 case before stabilizing. This framework for creating a location-specific vulnerability index in response to an ongoing disaster may be used as a quick, deployable metric to inform health policy decisions such as allocating state resources to the county level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. In this work, we observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Additionally, mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Video frame prediction of microbial growth with a recurrent neural network

The recent explosion of interest and advances in machine learning technologies has opened the door to new analytical capabilities in microbiology. Using experimental data such as images or videos, machine learning, in particular deep learning with neural networks, can be harnessed to provide insights and predictions for microbial populations. This paper presents such an application in which a Recurrent Neural Network (RNN) was used to perform prediction of microbial growth for a population of two Pseudomonas aeruginosa mutants. The RNN was trained on videos that were acquired previously using fluorescence microscopy and microfluidics. Of the 20 frames that make up each video, 10 were used as inputs to the network which outputs a prediction for the next 10 frames of the video. The accuracy of the network was evaluated by comparing the predicted frames to the original frames, as well as population curves and the number and size of individual colonies extracted from these frames. Overall, the growth predictions are found to be accurate in metrics such as image comparison, colony size, and total population. Yet, limitations exist due to the scarcity of available and comparable data in the literature, indicating a need for more studies. Both the successes and challenges of our approach are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Gravitational Microlensing Event Statistics for the Zwicky Transient Facility

Microlensing surveys have discovered thousands of events, with almost all events discovered within the Galactic bulge or toward the Magellanic Clouds. The Zwicky Transient Facility (ZTF), while not designed to be a microlensing campaign, is an optical time-domain survey that observes the entire northern sky, including the Galactic plane, every few nights. The ZTF observes ~10 9 stars in the g and r bands and can significantly contribute to the observed microlensing population. In this paper, we predict that the ZTF will observe ~1100 microlensing events in 3 yr of observing within 10° latitude of the Galactic plane, with ~500 events in the outer Galaxy (ℓ ≥ 10°). This yield increases to ~1400 (~800) events by combining every three ZTF exposures, ~1800 (~900) events if the ZTF observes for a total of 5 yr, and ~2400 (~1300) events for a 5 yr survey with postprocessing image stacking. Using the microlensing modeling software PopSyCLE, we compare the microlensing populations in the Galactic bulge and the outer Galaxy. We also present an analysis of the microlensing event ZTF18abhxjmj to demonstrate how to leverage these population statistics in event modeling. The ZTF will constrain Galactic structure, stellar populations, and primordial black holes through photometric microlensing.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2016

Towards a Global Water Scarcity Risk Assessment Framework: Incorporation of Probability Distributions and Hydro-Climatic Variability

Changing hydro-climatic and socioeconomic conditions increasingly put pressure on fresh water resources and are expected to aggravate water scarcity conditions towards the future. Despite numerous calls for risk-based water scarcity assessments, a global-scale framework that includes UNISDR's definition of risk does not yet exist. This study provides a first step towards such a risk based assessment, applying a Gamma distribution to estimate water scarcity conditions at the global scale under historic and future conditions, using multiple climate change and population growth scenarios. Our study highlights that water scarcity risk, expressed in terms of expected annual exposed population, increases given all future scenarios, up to greater than 56.2% of the global population in 2080. Looking at the drivers of risk, we find that population growth outweigh the impacts of climate change at global and regional scales. Using a risk-based method to assess water scarcity, we show the results to be less sensitive than traditional water scarcity assessments to the use of fixed threshold to represent different levels of water scarcity. This becomes especially important when moving from global to local scales, whereby deviations increase up to 50% of estimated risk levels.

Populations↗
NASA NTRS2022

Sea Level Rise and City-Level Climate Action

Background: Climate change is the greatest threat to global health in the 21st century. Rising sea levels are one particularly concerning manifestation of this and many of the world’s largest cities are vulnerable to sea level rise (SLR). Thus, urban climate adaptation and mitigation policies are increasingly important to protect population health. Objectives: This study aimed to determine whether being at risk of SLR was associated with city-level climate action. It also aimed to assess the wider drivers of climate action in cities, in order to guide ongoing efforts to motivate climate action, assess public health preparedness and identify research gaps. Methods: This is an ecological cross-sectional study using secondary data from CDP, the Urban Climate Change Research Network (UCCRN), World Bank, United Nations Cities and EM-DAT (Emergency Events Database). The study population consisted of 517 cities who participated in CDP’s 2019 Cities Survey. Multivariable logistic regression was utilized to assess the relationship between risk of SLR and city-level climate action, and secondly, to assess the wider determinants of city-level climate action. Results: There was evidence of crude associations between risk of SLR and three outcome variables representing city-level climate action. However, after adjusting for confounding variables, these crude associations disappeared. World region, national income status and urban population were shown to be stronger predictors of city-level climate action. Conclusion: It is concerning for population health that there is no association demonstrated between risk of SLR and climate action. This could indicate a lack of awareness of the risks posed by SLR within urban governance. To fulfil their health protection responsibilities, it is essential that public health professionals take a leading role in advocating for climate action.

sea level rise↗
DOE OSTI2021

Distribution, Ecology, Life History, and Conservation Status of the Berry Cave Salamander (Gyrinophilus gulolineatus)

The Berry Cave Salamander (Gyrinophilus gulolineatus) is a neotenic, stygobitic salamander endemic to eight cave systems and an isolated surface record in the Appalachian Valley and Ridge of eastern Tennessee. We conducted surveys for G. gulolineatus from 2017–2019 to assess the status of the species, locate new populations, and address knowledge gaps related to life history and population ecology required for conservation assessment. We confirmed G. gulolineatus presence at four historical sites, but we did not observe the species at any additional caves. At the three known sites with greatest abundance, visual counts per survey ranged 0–19 salamanders in 2017–2019. There was no apparent trend in abundance at Berry Cave. Visual counts declined 65% since the mid-2000s at Meads Quarry Cave and 80% since the early 1980s at Mudflats Cave. Mark-recapture studies in 160-m of cave stream at Berry Cave in 2017–2018 and 900-m of cave stream at Meads Quarry Cave in 2008 yielded population size estimates that ranged from 34–78 and 15–65 individuals, respectively. We identified 13 existing or potential threats to populations. Habitat degradation and groundwater contamination (associated with urbanization of the Knoxville metropolitan area and past mining operations) represent the most evident threats to long-term viability. Based on our conservation assessments, we recommend a rank of Endangered under IUCN Red List criteria and Critically Imperiled–Imperiled (G1G2) under NatureServe criteria. In opposition to the recent U.S. Fish & Wildlife Service decision, we advocate that, at minimum, G. gulolineatus remain a Candidate Species. Given the identified threats and these ranks, we offer several recommendations for research, conservation, and management of this rare salamander.

59 BASIC BIOLOGICAL SCIENCES↗