Showing papers by "United States Environmental Protection Agency published in 2017"

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Abstract: Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency’s (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA’s DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such as chemicals on the Toxic Substances Control Act listing, while providing the user community with a flexible and dynamic web-based platform for integration, processing, visualization and delivery of data and resources. The Dashboard provides support for a broad array of research and regulatory programs across the worldwide community of toxicologists and environmental scientists.

A mangrove forest map of China in 2015: analysis of time series Landsat 7/8 and Sentinel-1A imagery in Google Earth Engine cloud computing platform.

Abstract: Due to rapid losses of mangrove forests caused by anthropogenic disturbances and climate change, accurate and contemporary maps of mangrove forests are needed to understand how mangrove ecosystems are changing and establish plans for sustainable management. In this study, a new classification algorithm was developed using the biophysical characteristics of mangrove forests in China. More specifically, these forests were mapped by identifying: (1) greenness, canopy coverage, and tidal inundation from time series Landsat data, and (2) elevation, slope, and intersection-with-sea criterion. The annual mean Normalized Difference Vegetation Index (NDVI) was found to be a key variable in determining the classification thresholds of greenness, canopy coverage, and tidal inundation of mangrove forests, which are greatly affected by tide dynamics. In addition, the integration of Sentinel-1A VH band and modified Normalized Difference Water Index (mNDWI) shows great potential in identifying yearlong tidal and fresh water bodies, which is related to mangrove forests. This algorithm was developed using 6 typical Regions of Interest (ROIs) as algorithm training and was run on the Google Earth Engine (GEE) cloud computing platform to process 1941 Landsat images (25 Path/Row) and 586 Sentinel-1A images circa 2015. The resultant mangrove forest map of China at 30 m spatial resolution has an overall/users/producer’s accuracy greater than 95% when validated with ground reference data. In 2015, China’s mangrove forests had a total area of 20,303 ha, about 92% of which was in the Guangxi Zhuang Autonomous Region, Guangdong, and Hainan Provinces. This study has demonstrated the potential of using the GEE platform, time series Landsat and Sentine-1A SAR images to identify and map mangrove forests along the coastal zones. The resultant mangrove forest maps are likely to be useful for the sustainable management and ecological assessments of mangrove forests in China.

Considering sex as a biological variable in preclinical research

Abstract: In June 2015, the National Institutes of Health (NIH) released a Guide notice (NOT-OD-15-102) that highlighted the expectation of the NIH that the possible role of sex as a biologic variable be factored into research design, analyses, and reporting of vertebrate animal and human studies. Anticipating these guidelines, the NIH Office of Research on Women's Health, in October 2014, convened key stakeholders to discuss methods and techniques for integrating sex as a biologic variable in preclinical research. The workshop focused on practical methods, experimental design, and approaches to statistical analyses in the use of both male and female animals, cells, and tissues in preclinical research. Workshop participants also considered gender as a modifier of biology. This article builds on the workshop and is meant as a guide to preclinical investigators as they consider methods and techniques for inclusion of both sexes in preclinical research and is not intended to prescribe exhaustive/specific approaches for compliance with the new NIH policy.-Miller, L. R., Marks, C., Becker, J. B., Hurn, P. D., Chen, W.-J., Woodruff, T., McCarthy, M. M., Sohrabji, F., Schiebinger, L., Wetherington, C. L., Makris, S., Arnold, A. P., Einstein, G., Miller, V. M., Sandberg, K., Maier, S., Cornelison, T. L., Clayton, J. A. Considering sex as a biological variable in preclinical research.

Exposure to Perfluorinated Alkyl Substances and Health Outcomes in Children: A Systematic Review of the Epidemiologic Literature.

Abstract: Perfluoroalkyl substances (PFAS), chemicals used to make products stain and stick resistant, have been linked to health effects in adults and adverse birth outcomes. A growing body of literature also addresses health effects in children exposed to PFAS. This review summarizes the epidemiologic evidence for relationships between prenatal and/or childhood exposure to PFAS and health outcomes in children as well as to provide a risk of bias analysis of the literature. A systematic review was performed by searching PubMed for studies on PFAS and child health outcomes. We identified 64 studies for inclusion and performed risk of bias analysis on those studies. We determined that risk of bias across studies was low to moderate. Six categories of health outcomes emerged. These were: immunity/infection/asthma, cardio-metabolic, neurodevelopmental/attention, thyroid, renal, and puberty onset. While there are a limited number of studies for any one particular health outcome, there is evidence for positive associations between PFAS and dyslipidemia, immunity (including vaccine response and asthma), renal function, and age at menarche. One finding of note is that while PFASs are mixtures of multiple compounds few studies examine them as such, therefore the role of these compounds as complex mixtures remains largely unknown.

Impacts of 25 years of groundwater extraction on subsidence in the Mekong delta, Vietnam.

Abstract: Many major river deltas in the world are subsiding and consequently become increasingly vulnerable to flooding and storm surges, salinization and permanent inundation. For the Mekong Delta, annual subsidence rates up to several centimetres have been reported. Excessive groundwater extraction is suggested as the main driver. As groundwater levels drop, subsidence is induced through aquifer compaction. Over the past 25 years, groundwater exploitation has increased dramatically, transforming the delta from an almost undisturbed hydrogeological state to a situation with increasing aquifer depletion. Yet the exact contribution of groundwater exploitation to subsidence in the Mekong delta has remained unknown. In this study we deployed a delta-wide modelling approach, comprising a 3D hydrogeological model with an integrated subsidence module. This provides a quantitative spatially-explicit assessment of groundwater extraction-induced subsidence for the entire Mekong delta since the start of widespread overexploitation of the groundwater reserves. We find that subsidence related to groundwater extraction has gradually increased in the past decades with highest sinking rates at present. During the past 25 years, the delta sank on average ~18 cm as a consequence of groundwater withdrawal. Current average subsidence rates due to groundwater extraction in our best estimate model amount to 1.1 cm yr−1, with areas subsiding over 2.5 cm yr−1, outpacing global sea level rise almost by an order of magnitude. Given the increasing trends in groundwater demand in the delta, the current rates are likely to increase in the near future.

Tropospheric emissions: Monitoring of pollution (TEMPO)

Abstract: TEMPO was selected in 2012 by NASA as the first Earth Venture Instrument, for launch between 2018 and 2021. It will measure atmospheric pollution for greater North America from space using ultraviolet and visible spectroscopy. TEMPO observes from Mexico City, Cuba, and the Bahamas to the Canadian oil sands, and from the Atlantic to the Pacific, hourly and at high spatial resolution (~2.1 km N/S×4.4 km E/W at 36.5°N, 100°W). TEMPO provides a tropospheric measurement suite that includes the key elements of tropospheric air pollution chemistry, as well as contributing to carbon cycle knowledge. Measurements are made hourly from geostationary (GEO) orbit, to capture the high variability present in the diurnal cycle of emissions and chemistry that are unobservable from current low-Earth orbit (LEO) satellites that measure once per day. The small product spatial footprint resolves pollution sources at sub-urban scale. Together, this temporal and spatial resolution improves emission inventories, monitors population exposure, and enables effective emission-control strategies. TEMPO takes advantage of a commercial GEO host spacecraft to provide a modest cost mission that measures the spectra required to retrieve ozone (O3), nitrogen dioxide (NO2), sulfur dioxide (SO2), formaldehyde (H2CO), glyoxal (C2H2O2), bromine monoxide (BrO), IO (iodine monoxide),water vapor, aerosols, cloud parameters, ultraviolet radiation, and foliage properties. TEMPO thus measures the major elements, directly or by proxy, in the tropospheric O3 chemistry cycle. Multi-spectral observations provide sensitivity to O3 in the lowermost troposphere, substantially reducing uncertainty in air quality predictions. TEMPO quantifies and tracks the evolution of aerosol loading. It provides these near-real-time air quality products that will be made publicly available. TEMPO will launch at a prime time to be the North American component of the global geostationary constellation of pollution monitoring together with the European Sentinel-4 (S4) and Korean Geostationary Environment Monitoring Spectrometer (GEMS) instruments.

Developmental PBDE Exposure and IQ/ADHD in Childhood: A Systematic Review and Meta-analysis

Abstract: Background: In the United States, one in six children are affected by neurodevelopmental disorders, and polybrominated diphenyl ethers (PBDEs) in flame-retardant chemicals are measured ubiquitously...

Expanded Target-Chemical Analysis Reveals Extensive Mixed-Organic-Contaminant Exposure in U.S. Streams

Abstract: Surface water from 38 streams nationwide was assessed using 14 target-organic methods (719 compounds). Designed-bioactive anthropogenic contaminants (biocides, pharmaceuticals) comprised 57% of 406 organics detected at least once. The 10 most-frequently detected anthropogenic-organics included eight pesticides (desulfinylfipronil, AMPA, chlorpyrifos, dieldrin, metolachlor, atrazine, CIAT, glyphosate) and two pharmaceuticals (caffeine, metformin) with detection frequencies ranging 66–84% of all sites. Detected contaminant concentrations varied from less than 1 ng L–1 to greater than 10 μg L–1, with 77 and 278 having median detected concentrations greater than 100 ng L–1 and 10 ng L–1, respectively. Cumulative detections and concentrations ranged 4–161 compounds (median 70) and 8.5–102 847 ng L–1, respectively, and correlated significantly with wastewater discharge, watershed development, and toxic release inventory metrics. Log10 concentrations of widely monitored HHCB, triclosan, and carbamazepine explain...

Estimates of Present and Future Flood Risk in the Conterminous United States

Abstract: Past attempts to estimate rainfall-driven flood risk across the US either have incomplete coverage, coarse resolution or use overly simplified models of the flooding process. In this paper, we use a new 30 m resolution model of the entire conterminous US with a 2D representation of flood physics to produce estimates of flood hazard, which match to within 90% accuracy the skill of local models built with detailed data. These flood depths are combined with exposure datasets of commensurate resolution to calculate current and future flood risk. Our data show that the total US population exposed to serious flooding is 2.6–3.1 times higher than previous estimates, and that nearly 41 million Americans live within the 1% annual exceedance probability floodplain (compared to only 13 million when calculated using FEMA flood maps). We find that population and GDP growth alone are expected to lead to significant future increases in exposure, and this change may be exacerbated in the future by climate change.

Climate Change Impacts on Harmful Algal Blooms in U.S. Freshwaters: A Screening-Level Assessment

Abstract: Cyanobacterial harmful algal blooms (CyanoHABs) have serious adverse effects on human and environmental health. Herein, we developed a modeling framework that predicts the effect of climate change on cyanobacteria concentrations in large reservoirs in the contiguous U.S. The framework, which uses climate change projections from five global circulation models, two greenhouse gas emission scenarios, and two cyanobacterial growth scenarios, is unique in coupling climate projections with a hydrologic/water quality network model of the contiguous United States. Thus, it generates both regional and nationwide projections useful as a screening-level assessment of climate impacts on CyanoHAB prevalence as well as potential lost recreation days and associated economic value. Our projections indicate that CyanoHAB concentrations are likely to increase primarily due to water temperature increases tempered by increased nutrient levels resulting from changing demographics and climatic impacts on hydrology that drive n...

Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement.

Abstract: Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal-indicator bacteria are used; however, they cannot distinguish human fecal waste from other animal pollution sources. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based on initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against an animal fecal reference library, and crAssphage genetic markers were highly abundant in raw sewage and sewage-impacted water samples. In addition, CPQ_056 and CPQ_064 performance was compared to HF183/BacR287 and HumM2 assays in paired experiments. Findings confirm tha...

Tropospheric Ozone Assessment Report: Database and Metrics Data of Global Surface Ozone Observations

Abstract: In support of the first Tropospheric Ozone Assessment Report (TOAR) a relational database of global surface ozone observations has been developed and populated with hourly measurement data and enhanced metadata. A comprehensive suite of ozone data products including standard statistics, health and vegetation impact metrics, and trend information, are made available through a common data portal and a web interface. These data form the basis of the TOAR analyses focusing on human health, vegetation, and climate relevant ozone issues, which are part of this special feature. Cooperation among many data centers and individual researchers worldwide made it possible to build the world's largest collection of in-situ hourly surface ozone data covering the period from 1970 to 2015. By combining the data from almost 10,000 measurement sites around the world with global metadata information, new analyses of surface ozone have become possible, such as the first globally consistent characterisations of measurement sites as either urban or rural/remote. Exploitation of these global metadata allows for new insights into the global distribution, and seasonal and long-term changes of tropospheric ozone and they enable TOAR to perform the first, globally consistent analysis of present-day ozone concentrations and recent ozone changes with relevance to health, agriculture, and climate. Considerable effort was made to harmonize and synthesize data formats and metadata information from various networks and individual data submissions. Extensive quality control was applied to identify questionable and erroneous data, including changes in apparent instrument offsets or calibrations. Such data were excluded from TOAR data products. Limitations of a posteriori data quality assurance are discussed. As a result of the work presented here, global coverage of surface ozone data for scientific analysis has been significantly extended. Yet, large gaps remain in the surface observation network both in terms of regions without monitoring, and in terms of regions that have monitoring programs but no public access to the data archive. Therefore future improvements to the database will require not only improved data harmonization, but also expanded data sharing and increased monitoring in data-sparse regions.

Evaluating a Space-Based Indicator of Surface Ozone-NO x -VOC Sensitivity Over Midlatitude Source Regions and Application to Decadal Trends

Abstract: Determining effective strategies for mitigating surface ozone (O3) pollution requires knowledge of the relative ambient concentrations of its precursors, NOx, and VOCs. The space-based tropospheric column ratio of formaldehyde to NO2 (FNR) has been used as an indicator to identify NOx-limited versus NOx-saturated O3 formation regimes. Quantitative use of this indicator ratio is subject to three major uncertainties: (1) the split between NOx-limited and NOx-saturated conditions may shift in space and time, (2) the ratio of the vertically integrated column may not represent the near-surface environment, and (3) satellite products contain errors. We use the GEOS-Chem global chemical transport model to evaluate the quantitative utility of FNR observed from the Ozone Monitoring Instrument over three northern midlatitude source regions. We find that FNR in the model surface layer is a robust predictor of the simulated near-surface O3 production regime. Extending this surface-based predictor to a column-based FNR requires accounting for differences in the HCHO and NO2 vertical profiles. We compare four combinations of two OMI HCHO and NO2 retrievals with modeled FNR. The spatial and temporal correlations between the modeled and satellite-derived FNR vary with the choice of NO2 product, while the mean offset depends on the choice of HCHO product. Space-based FNR indicates that the spring transition to NOx-limited regimes has shifted at least a month earlier over major cities (e.g., New York, London, and Seoul) between 2005 and 2015. This increase in NOx sensitivity implies that NOx emission controls will improve O3 air quality more now than it would have a decade ago.

Effect of Therapeutic Hypothermia Initiated After 6 Hours of Age on Death or Disability Among Newborns With Hypoxic-Ischemic Encephalopathy: A Randomized Clinical Trial.

Abstract: Importance Hypothermia initiated at less than 6 hours after birth reduces death or disability for infants with hypoxic-ischemic encephalopathy at 36 weeks’ or later gestation. To our knowledge, hypothermia trials have not been performed in infants presenting after 6 hours. Objective To estimate the probability that hypothermia initiated at 6 to 24 hours after birth reduces the risk of death or disability at 18 months among infants with hypoxic-ischemic encephalopathy. Design, Setting, and Participants A randomized clinical trial was conducted between April 2008 and June 2016 among infants at 36 weeks’ or later gestation with moderate or severe hypoxic-ischemic encephalopathy enrolled at 6 to 24 hours after birth. Twenty-one US Neonatal Research Network centers participated. Bayesian analyses were prespecified given the anticipated limited sample size. Interventions Targeted esophageal temperature was used in 168 infants. Eighty-three hypothermic infants were maintained at 33.5°C (acceptable range, 33°C-34°C) for 96 hours and then rewarmed. Eighty-five noncooled infants were maintained at 37.0°C (acceptable range, 36.5°C-37.3°C). Main Outcomes and Measures The composite of death or disability (moderate or severe) at 18 to 22 months adjusted for level of encephalopathy and age at randomization. Results Hypothermic and noncooled infants were term (mean [SD], 39 [2] and 39 [1] weeks’ gestation, respectively), and 47 of 83 (57%) and 55 of 85 (65%) were male, respectively. Both groups were acidemic at birth, predominantly transferred to the treating center with moderate encephalopathy, and were randomized at a mean (SD) of 16 (5) and 15 (5) hours for hypothermic and noncooled groups, respectively. The primary outcome occurred in 19 of 78 hypothermic infants (24.4%) and 22 of 79 noncooled infants (27.9%) (absolute difference, 3.5%; 95% CI, −1% to 17%). Bayesian analysis using a neutral prior indicated a 76% posterior probability of reduced death or disability with hypothermia relative to the noncooled group (adjusted posterior risk ratio, 0.86; 95% credible interval, 0.58-1.29). The probability that death or disability in cooled infants was at least 1%, 2%, or 3% less than noncooled infants was 71%, 64%, and 56%, respectively. Conclusions and Relevance Among term infants with hypoxic-ischemic encephalopathy, hypothermia initiated at 6 to 24 hours after birth compared with noncooling resulted in a 76% probability of any reduction in death or disability, and a 64% probability of at least 2% less death or disability at 18 to 22 months. Hypothermia initiated at 6 to 24 hours after birth may have benefit but there is uncertainty in its effectiveness. Trial Registration clinicaltrials.gov Identifier:NCT00614744

httk: R Package for High-Throughput Toxicokinetics

Abstract: Thousands of chemicals have been profiled by high-throughput screening programs such as ToxCast and Tox21; these chemicals are tested in part because most of them have limited or no data on hazard, exposure, or toxicokinetics. Toxicokinetic models aid in predicting tissue concentrations resulting from chemical exposure, and a "reverse dosimetry" approach can be used to predict exposure doses sufficient to cause tissue concentrations that have been identified as bioactive by high-throughput screening. We have created four toxicokinetic models within the R software package httk. These models are designed to be parameterized using high-throughput in vitro data (plasma protein binding and hepatic clearance), as well as structure-derived physicochemical properties and species-specific physiological data. The package contains tools for Monte Carlo sampling and reverse dosimetry along with functions for the analysis of concentration vs. time simulations. The package can currently use human in vitro data to make predictions for 553 chemicals in humans, rats, mice, dogs, and rabbits, including 94 pharmaceuticals and 415 ToxCast chemicals. For 67 of these chemicals, the package includes rat-specific in vitro data. This package is structured to be augmented with additional chemical data as they become available. Package httk enables the inclusion of toxicokinetics in the statistical analysis of chemicals undergoing high-throughput screening.

Climate change damages to Alaska public infrastructure and the economics of proactive adaptation.

Abstract: Climate change in the circumpolar region is causing dramatic environmental change that is increasing the vulnerability of infrastructure. We quantified the economic impacts of climate change on Alaska public infrastructure under relatively high and low climate forcing scenarios [representative concentration pathway 8.5 (RCP8.5) and RCP4.5] using an infrastructure model modified to account for unique climate impacts at northern latitudes, including near-surface permafrost thaw. Additionally, we evaluated how proactive adaptation influenced economic impacts on select infrastructure types and developed first-order estimates of potential land losses associated with coastal erosion and lengthening of the coastal ice-free season for 12 communities. Cumulative estimated expenses from climate-related damage to infrastructure without adaptation measures (hereafter damages) from 2015 to 2099 totaled $5.5 billion (2015 dollars, 3% discount) for RCP8.5 and $4.2 billion for RCP4.5, suggesting that reducing greenhouse gas emissions could lessen damages by $1.3 billion this century. The distribution of damages varied across the state, with the largest damages projected for the interior and southcentral Alaska. The largest source of damages was road flooding caused by increased precipitation followed by damages to buildings associated with near-surface permafrost thaw. Smaller damages were observed for airports, railroads, and pipelines. Proactive adaptation reduced total projected cumulative expenditures to $2.9 billion for RCP8.5 and $2.3 billion for RCP4.5. For road flooding, adaptation provided an annual savings of 80-100% across four study eras. For nearly all infrastructure types and time periods evaluated, damages and adaptation costs were larger for RCP8.5 than RCP4.5. Estimated coastal erosion losses were also larger for RCP8.5.

Description and evaluation of the Community Multiscale Air Quality (CMAQ) modeling system version 5.1.

Abstract: The Community Multiscale Air Quality (CMAQ) model is a comprehensive multipollutant air quality modeling system developed and maintained by the US Environmental Protection Agency's (EPA) Office of Research and Development (ORD). Recently, version 5.1 of the CMAQ model (v5.1) was released to the public, incorporating a large number of science updates and extended capabilities over the previous release version of the model (v5.0.2). These updates include the following: improvements in the meteorological calculations in both CMAQ and the Weather Research and Forecast (WRF) model used to provide meteorological fields to CMAQ, updates to the gas and aerosol chemistry, revisions to the calculations of clouds and photolysis, and improvements to the dry and wet deposition in the model. Sensitivity simulations isolating several of the major updates to the modeling system show that changes to the meteorological calculations result in enhanced afternoon and early evening mixing in the model, periods when the model historically underestimates mixing. This enhanced mixing results in higher ozone (O3) mixing ratios on average due to reduced NO titration, and lower fine particulate matter (PM2.5) concentrations due to greater dilution of primary pollutants (e.g., elemental and organic carbon). Updates to the clouds and photolysis calculations greatly improve consistency between the WRF and CMAQ models and result in generally higher O3 mixing ratios, primarily due to reduced cloudiness and attenuation of photolysis in the model. Updates to the aerosol chemistry result in higher secondary organic aerosol (SOA) concentrations in the summer, thereby reducing summertime PM2.5 bias (PM2.5 is typically underestimated by CMAQ in the summer), while updates to the gas chemistry result in slightly higher O3 and PM2.5 on average in January and July. Overall, the seasonal variation in simulated PM2.5 generally improves in CMAQv5.1 (when considering all model updates), as simulated PM2.5 concentrations decrease in the winter (when PM2.5 is generally overestimated by CMAQ) and increase in the summer (when PM2.5 is generally underestimated by CMAQ). Ozone mixing ratios are higher on average with v5.1 vs. v5.0.2, resulting in higher O3 mean bias, as O3 tends to be overestimated by CMAQ throughout most of the year (especially at locations where the observed O3 is low); however, O3 correlation is largely improved with v5.1. Sensitivity simulations for several hypothetical emission reduction scenarios show that v5.1 tends to be slightly more responsive to reductions in NO x (NO + NO2), VOC and SO x (SO2 + SO4) emissions than v5.0.2, representing an improvement as previous studies have shown CMAQ to underestimate the observed reduction in O3 due to large, widespread reductions in observed emissions.