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PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)
The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.
PNNL Superfund Research Program Analytics (srpAnalytics Data Release v.1.0)
The OSU/PNNL superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. The PNNL Superfund have implemented a dose-response modelling pipeline to calculate benchmark dose parameters that enable the comparison of potency across chemicals and phenotypes. Our portal provides public access to this dataset and an interactive web site designed to enable exploration and re-use of this data by the scientific community at http://srp.pnnl.gov.
Application of physiologically based pharmacokinetic modeling for sertraline dosing recommendations in pregnancy
Pregnancy is a period of significant change that impacts physiological and metabolic status leading to alterations in the disposition of drugs. Uncertainty in drug dosing in pregnancy can lead to suboptimal therapy, which can contribute to disease exacerbation. A few studies show there are increased dosing requirements for antidepressants in late pregnancy; however, the quantitative data to guide dose adjustments are sparse. We aimed to develop a physiologically based pharmacokinetic (PBPK) model that allows gestational-age dependent prediction of sertraline dosing in pregnancy. A minimal physiological model with defined gut, liver, plasma, and lumped placental-fetal compartments was constructed using the ordinary differential equation solver package, ‘mrgsolve’, in R. We extracted data from the literature to parameterize the model, including sertraline physicochemical properties, in vitro metabolism studies, disposition in nonpregnant women, and physiological changes during pregnancy. The model predicted the pharmacokinetic parameters from a clinical study with eight subjects for the second trimester and six subjects for the third trimester. Based on the model, gestational-dependent changes in physiology and metabolism account for increased clearance of sertraline (up to 143% at 40 weeks gestational age), potentially leading to under-dosing of pregnant women when nonpregnancy doses are used. The PBPK model was converted to a prototype web-based interactive dosing tool to demonstrate how the output of a PBPK model may translate into optimal sertraline dosing in pregnancy. Quantitative prediction of drug exposure using PBPK modeling in pregnancy will support clinically appropriate dosing and increase the therapeutic benefit for pregnant women.
Effectiveness of street trees in reducing air temperature and outdoor heat exposure in Las Vegas
Urban greening and especially tree planting strategies are being widely planned and implemented to mitigate urban overheating and thermal stress in many urban areas. However, the effectiveness of these strategies depends on multiple factors, including urban morphology, environmental conditions, and tree characteristics. This study investigates the effects of street tree planting strategies on air temperature and outdoor heat exposure in Las Vegas by combining an urbanized mesoscale climate model coupled to a multi-layer street tree model (Weather Research and Forecasting-BEP-Tree; Δ x = 900 m) with a microscale pedestrian heat exposure model (Temperatures of Urban Facets for Pedestrian; Δ x = 1 m). A series of simulations are conducted for July and August 2022. Large city-wide increases of a drought tolerant tree species cool air temperature mainly during the nighttime (up to 1.5 °C), with daytime effects being limited due to leaves shedding sensible instead of latent heat as stomata close in response to high vapor pressure deficits. Increased evaporative cooling is achieved with a different tree species (double at night, and reaching 0.4 °C during the day), but water requirements increase threefold. Despite their relatively small effect on air temperature during the day, trees provide significant shade by intercepting solar radiation, reducing mean radiant temperature (up to 16 °C) and enhancing outdoor thermal comfort, a major benefit of street trees in hot arid climates. The nighttime cooling of trees and the daytime reduction of radiant loading show potential to reduce the heat-related health impacts. Our results highlight the need to evaluate the effects of street trees on a case-by-case basis.
Developmental Ethanol Exposure Impacts Purkinje Cells but Not Microglia in the Young Adult Cerebellum
Fetal alcohol spectrum disorders (FASD) caused by developmental ethanol exposure lead to cerebellar impairments, including motor problems, decreased cerebellar weight, and cell death. Alterations in the sole output of the cerebellar cortex, Purkinje cells, and central nervous system immune cells, microglia, have been reported in animal models of FASD. To determine how developmental ethanol exposure affects adult cerebellar microglia and Purkinje cells, we used a human third-trimester binge exposure model in which mice received ethanol or saline from postnatal (P) days 4–9. In adolescence, cerebellar cranial windows were implanted and mice were aged to young adulthood for examination of microglia and Purkinje cells in vivo with two-photon imaging or in fixed tissue. Ethanol had no effect on microglia density, morphology, dynamics, or injury response. However, Purkinje cell linear frequency was reduced by ethanol. Microglia–Purkinje cell interactions in the Purkinje Cell Layer were altered in females compared to males. Overall, developmental ethanol exposure had few effects on cerebellar microglia in young adulthood and Purkinje cells appeared to be more susceptible to its effects.
Quantifying mean, variability, and uncertainty in indoor radon exposure in Pennsylvania using random forest and quantile regression forest models
Radon is a naturally occurring radioactive gas that poses a serious health risk as the primary cause of lung cancer in non-smokers. Despite the well-known adverse association with health outcomes, current radon exposure assessments are limited to county-level or average-level estimates, which fail to capture regional variability. This study uses Machine Learning models, including Random Forest (RF) and Quantile Regression Forest (QRF), to estimate the indoor radon concentrations at the ZCTA (Zip code tabulation area)-level and characterize uncertainties in model estimates. Incorporating geological, meteorological, and building-specific data, the models aim to improve radon risk assessment by capturing mean exposure, variability, and extreme concentration levels. Processed radon test data (n = 718,111) were analyzed using average, variability, and quantile prediction methods. Models that estimate the average radon exposure at the ZCTA-level can yield promising model-fit results, but they do not capture the underlying variability of indoor radon exposure within a ZCTA. We utilize volatility analyses to identify characteristics indicative of high variability of indoor radon exposure. We also show that a QRF model can be used to estimate upper quantiles of residential radon exposure, thereby uncovering localized areas of elevated exposure that were not apparent in mean estimates. The results highlighted the need for a deep characterization of exposure risk and show that regions with moderate average exposure levels could still harbor extreme outliers with implications for evaluating health risks. Utilizing multiple radon exposure models allows for a deeper characterization of radon risk within a geographic area and can better identify high-risk areas. The results from this study provide a foundation for developing mitigation strategies and examining associations between radon exposure and health outcomes at fine scales. Future research should extend the geographic scope and incorporate additional environmental risk factors to establish a comprehensive framework for risk assessment.
Simulated Microgravity Alters Gene Regulation Linked to Immunity and Cardiovascular Disease
Microgravity exposure induces a cephalad fluid shift and an overall reduction in physical activity levels which can lead to cardiovascular deconditioning in the absence of countermeasures. Future spaceflight missions will expose crew to extended periods of microgravity among other stressors, the effects of which on cardiovascular health are not fully known. In this study, we determined cardiac responses to extended microgravity exposure using the rat hindlimb unloading (HU) model. We hypothesized that exposure to prolonged simulated microgravity and subsequent recovery would lead to increased oxidative damage and altered expression of genes involved in the oxidative response. To test this hypothesis, we examined hearts of male (three and nine months of age) and female (3 months of age) Long–Evans rats that underwent HU for various durations up to 90 days and reambulated up to 90 days post-HU. Results indicate sex-dependent changes in oxidative damage marker 8-hydroxydeoxyguanosine (8-OHdG) and antioxidant gene expression in left ventricular tissue. Three-month-old females displayed elevated 8-OHdG levels after 14 days of HU while age-matched males did not. In nine-month-old males, there were no differences in 8-OHdG levels between HU and normally loaded control males at any of the timepoints tested following HU. RNAseq analysis of left ventricular tissue from nine-month-old males after 14 days of HU revealed upregulation of pathways involved in pro-inflammatory signaling, immune cell activation and differential expression of genes associated with cardiovascular disease progression. Taken together, these findings provide a rationale for targeting antioxidant and immune pathways and that sex differences should be taken into account in the development of countermeasures to maintain cardiovascular health in space.
Helicon edge heating in Proto-MPEX: Azimuthally resolved RF modeling
The Material Plasma Exposure eXperiment (MPEX) is a linear device under construction at ORNL. MPEX employs a variety of heating systems, including a helicon antenna, which is the subject of this work. Lacking a resonant absorption mechanism, as tokamaks have, modeling the RF power absorption in such antennas requires detailed consideration of cold collisional physics. Previous modeling of the heating in this antenna was done exclusively in 2D, assuming axisymmetry and a single azimuthal mode number m = 1. In this study, we introduce a fully 3D model. By including the full 3D physics, with its self-consistent geometry-imposed azimuthal spectrum, we are able to reproduce the experimentally observed transition from edge heating to core heating.
The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes
The OSU/PNNL Superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 10 zebrafish-specific phenotypes. Our portal provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov.
Modeling the mechanisms of conifer mortality under seawater exposure
Summary Relative sea level rise (SLR) increasingly impacts coastal ecosystems through the formation of ghost forests. To predict the future of coastal ecosystems under SLR and changing climate, it is important to understand the physiological mechanisms underlying coastal tree mortality and to integrate this knowledge into dynamic vegetation models. We incorporate the physiological effect of salinity and hypoxia in a dynamic vegetation model in the Earth system land model, and used the model to investigate the mechanisms of mortality of conifer forests on the west and east coast sites of USA, where trees experience different form of sea water exposure. Simulations suggest similar physiological mechanisms can result in different mortality patterns. At the east coast site that experienced severe increases in seawater exposure, trees loose photosynthetic capacity and roots rapidly, and both storage carbon and hydraulic conductance decrease significantly within a year. Over time, further consumption of storage carbon that leads to carbon starvation dominates mortality. At the west coast site that gradually exposed to seawater through SLR, hydraulic failure dominates mortality because root loss impacts on conductance are greater than the degree of storage carbon depletion. Measurements and modeling focused on understanding the physiological mechanisms of mortality is critical to reducing predictive uncertainty.
Validation of earthquake ground-motion models in southern California, USA, using precariously balanced rocks
Accurate estimates of earthquake ground shaking rely on uncertain ground-motion models derived from limited instrumental recordings of historical earthquakes. A critical issue is that there is currently no method to empirically validate the resultant ground-motion estimates of these models at the timescale of rare, large earthquakes; this lack of validation causes great uncertainty in ground-motion estimates. Here, we address this issue and validate ground-motion estimates for southern California utilizing the unexceeded ground motions recorded by 20 precariously balanced rocks. We used cosmogenic 10Be exposure dating to model the age of the precariously balanced rocks, which ranged from ca. 1 ka to ca. 50 ka, and calculated their probability of toppling at different ground-motion levels. With this rock data, we then validated the earthquake ground motions estimated by the Uniform California Earthquake Rupture Forecast, Version 3 (UCERF3) seismic-source characterization and the Next Generation Attenuation (NGA)-West2 ground-motion models. We found that no ground-motion model estimated levels of earthquake ground shaking consistent with the observed continued existence of all 20 precariously balanced rocks. The ground-motion model I14 estimated ground-motion levels that were inconsistent with the most rocks; therefore, I14 was invalidated and removed. At a 2475 year mean return period, the removal of this invalid ground-motion model resulted in a 2−7% reduction in the mean and a 10−36% reduction in the 5th−95th fractile uncertainty of the ground-motion estimates. Our findings demonstrate the value of empirical data from precariously balanced rocks as a validation tool for removing invalid ground-motion models and, in turn, reducing the uncertainty in earthquake ground-motion estimates.
Hypothesis on the dust-borne atmospheric transport of Coccidioides , causative fungal pathogen for coccidioidomycosis (Valley fever)
For many decades, the fungal pathogen (Coccidioides spp.) that causes coccidioidomycosis (Valley fever) has been associated with dust exposure. However, the mechanism of atmospheric transport of arthroconidia has yet to be defined. As such, it is unclear whether the association between dust exposure and Coccidioides is coincidental or not: do soil-disturbing events simultaneously cause both free-floating Coccidioides conidia and dust particles (i.e., particulate matter) to become entrained in the atmosphere, or is Coccidioides attached to dust particles and they are jointly suspended? In this short article, we propose the dust-borne atmospheric transport hypothesis: Coccidioides conidia are transported in the atmosphere attached to dust particles, which protect the fungi from harsh environmental conditions like desiccation and UV exposure, allowing them to travel far while remaining viable in comparison to free-floating aerial transport. If true, the dust-borne atmospheric transport hypothesis provides a means for mechanistically modeling the transport and exposure risk of Coccidioides via atmospheric dispersion modeling and suggests health implications from simultaneous exposure to dust and a fungal pathogen.
Oxidation Lifetime Modeling of 625 and 120 Foils After Long-term Exposure in Flowing Air + 10% ${\hbox {H}_2\hbox {O}}$ at 700 and 800 $^\circ$C
A model describing oxidation kinetics considering simultaneous oxidation and volatilization of external oxide scales was integrated with a CALPHAD-based coupled thermodynamic and kinetic approach to predict the oxidation-induced lifetime of foils of alloys 625 and 120. Long-term exposures in flowing air +10% H 2 O at 700 and 800 °C under two flow velocities were used to validate the modeling results. The time to a critical Cr concentration of 10 wt% at the oxide/alloy interface, t 10 , was shown to correlate with the breakdown of the Cr 2 O 3 scale for the studied experimental conditions. Finally, the modeling approach was extended to consider time-dependent oxidation and volatilization rate constants to develop a more appropriate lifetime criterion for microturbine recuperator foils.
Molecular imaging of plant-microbe interactions on the Brachypodium seed surface
Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and with-in plant tissues, however the mechanism(s) by which plants associate with PGPR to elicit such beneficial effects needs further study. Here, we present high mass resolution time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25::GFP (P.) and Gram-positive Arthrobacter chlorophenolicus A6::GFP (A.). Delayed image extraction was used to image PGPB-treated seed sections to reveal morphological changes. ToF-SIMS spectral compari-son, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite prod-ucts and biomarkers, such as flavonoids, phenolic com-pounds, fatty acids, and indole-3-acetic acid (IAA), were ob-served on the PGPR-treated seed surfaces. These compounds had different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicited distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interac-tions and to provide insightful information with submicrome-ter lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.
Phase field modeling of hydrogen release in nitrile-butadiene rubber composites after high-pressure hydrogen exposure
Experimental data showed that a simple diffusion model doesn’t suffice to explain the hydrogen (H 2 ) release kinetics in nitrile butadiene rubber (NBR) composites (one with no filler or plasticizer, one with plasticizer only, one with fillers and plasticizer, and one with fillers only) after exposed to hydrogen gas at a pressure of 27.6 MPa. In this work, we developed a phase field model that considers the effect of H 2 gas bubble evolution on H 2 release kinetics. With the model, we simulated the effect of thermodynamic and kinetics properties on the nucleation, growth, and shrinkage of gas bubbles and H 2 release kinetics during and after decompression. Here, the results demonstrated that 1) the model built upon certain thermodynamic and kinetics properties of a given material can well describe its H 2 release kinetics measured in experiments, and 2) the model can predict the gas bubble evolution, which is associated with the material property degradation and failures, with accurate thermodynamic and kinetics properties or H 2 release data from experiments.
Biota Modeling in EPA’s Preliminary Remediation Goal and Dose Compliance Concentration Calculators for Use in EPA Superfund Risk Assessment: Explanation of Intake Rate Derivation, Transfer Factor Compilation, and Mass Loading Factor Sources
The Preliminary Remediation Goal (PRG) and Dose Compliance Concentration (DCC) calculators are screening level risk assessment tools that set forth the Environmental Protection Agency’s (EPA) recommended approaches and currently available risk assessment guidance for response actions at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites, commonly known as Superfund. The environmental screening levels derived by the PRG and DCC calculators are used to identify isotopes contributing the highest risk and dose as well as establish preliminary remediation goals. Each calculator has residential gardening and subsistence farmer exposure scenarios that model transfer of contaminants from soil and water into various types of biota (crops and animal products). New publications of human intake rates of biota; farm animal intakes of water, soil, and fodder; and soil to plant interactions require updates be implemented into the PRG and DCC calculators. Recent improvements in the biota modeling for these calculators include newly derived biota intake rates, enhanced soil mass loading factors (MLFs), and more comprehensive soil to plant transfer factors (BV’s) and soil to tissue transfer factors (TFs) for animals. New biota have been added in both the produce and animal products categories that greatly improve the accuracy and utility of the PRG and DCC calculators and encompass greater geographic diversity on a national and international scale.