AndreaBozzo/ceres-open-data-index huggingface dataset:
Year-round presence of neonicotinoid insecticides in tributaries to the Great Lakes, USA

To better understand the transport of neonicotinoid insecticides into the Great Lakes, monthly samples (October 2015-September 2016) were collected from 10 tributaries to the Great Lakes, USA. At least one neonicotinoid was detected in 74% of the monthly samples with up to three neonicotinoids detected in an individual sample (10% of all samples). The most frequently detected neonicotinoid was imidacloprid (53%) followed by clothianidin (44%), thiamethoxam (22%), acetamiprid (2%), and dinotefuran (1%). Thiacloprid was not detected in any samples. More spatially intensive samples from were collected in an agriculturally dominated area (Maumee River, Ohio) twice during spring 2016. Three neonicotinoids were ubiquitously detected (clothiandin, imidacloprid, thiamethoxam) in all water samples collected within this basin. 

This dataset is associated with the following publication:
Hladik, M., S. Corsi, D. Kolpin, A. Baldwin, B. Blackwell, and J. Cavallin. Year-round presence of neonicotinoid insecticides in tributaries to the Great Lakes, USA.   ENVIRONMENTAL POLLUTION. Elsevier Science Ltd, New York, NY, USA, 235: 102-1029, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, neonicotinoids, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Wilkin et al. (2017) As Se Co-contamination

The dataset includes groundwater information for: water stable isotopes, As concentrations, Se concentrations, and spectroscopic scans. 

This dataset is associated with the following publication:
Wilkin, R.T., T. Lee, D. Beak, R. Anderson, and B. Burns. Groundwater Co-Contaminant Behavior of Arsenic and Selenium at a Lead and Zinc Smelting Facility.   APPLIED GEOCHEMISTRY. Elsevier Science Ltd, New York, NY, USA, 89: 255-264, (2018).

Tags: arsenic, groundwater, metalloids, selenium
Organization: U.S. Environmental Protection Agency
Cao et al 20xx Data Set (Version 1)

HF183/BacR287 qPCR data from standard curves and coastal water samples used to seed simulations in study. 

This dataset is associated with the following publication:
Cao, Y., M. Sivaganesan, C. Kelty, D. Wang, A. Boehm, J. Griffith, S. Weisberg, and O. Shanks. A Human Fecal Contamination Score for Ranking Recreational Sites using the HF183/BacR287 Quantitative Real-Time PCR Method.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 128: 148-156, (2018).

Tags: human-fecal-pollution, microbial-source-tracking, qpcr, site-prioritization, water-quality
Organization: U.S. Environmental Protection Agency
Bioactive Contaminants of Emerging Concern in National Park Waters of the Northern Colorado Plateau, USA

Water and sediment was collected to assess the occurrence of contaminants of emerging concern (CECs) in National Park waters of the northern Colorado Plateau, USA. CEC presence in water and sediment is reported for 21 sites in eight U.S. national parks in the northern Colorado Plateau region. From 2012 to 2016, at least one PPCP and/or WWI was detected at most sites on over half of sampling visits, indicating that CECs are not uncommon even in isolated areas. Maximum concentrations in this study were generally below available water quality benchmarks, sediment quality guidelines, and concentrations known to induce biological activity in vitro. C occurrence patterns and similarities between continuous and isolated flow locations suggest that direct contamination from individual visitors may also occur. While the data indicate there is little aquatic health risk associated with CECs at our sites, results demonstrate the ubiquity of CECs on the landscape and a continued need for public outreach concerning resource-use ethics and the potential effects of upstream development. 

This dataset is associated with the following publication:
Weissinger, R., B. Blackwell, K. Keteles, W. Battaglin, and P. Bradley. Bioactive contaminants of emerging concern in national park waters of the northern Colorado plateau, USA.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 636: 910-918, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, contaminants-of-emerging-concern-cec, ecotoxicology, endocrine-disruption, exposure-activity-ratio, national-parks, northern-colorado-plateau, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Open source data summaries - Fish, Rat, and Goat Metabolism Studies

Public versions of EFSA DAR's - metabolism study summaries for the pesticides; Fluazinam, Halauxifen-methyl, Kresoxim-methyl, Mandestrobin, Tolclofos-methyl in fish (bluegill or rainbow trout), rat, and goat. 

This dataset is associated with the following publication:
Kolanczyk, R., J. Serrano, M. Tapper, and P. Schmieder. A comparison of fish pesticide metabolic pathways with those of the rat and goat.   REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 94: 124-143, (2018).

Tags: biotransformation, bluegill-sunfish, draft-assessment-report, efsa, goat, metabolic-map, metabolism, metapath, rainbow-trout, rat, risk-assessment, species-extrapolation
Organization: U.S. Environmental Protection Agency
All raw data used to generate results

This dataset contains all data used in this study, including site ID, latitude, longitude, watershed land cover, water chemistry, and carbon and nitrogen stable isotope ratios of periphyton, invertebrate functional feeding groups, and five most frequently observed invertebrate families. Also included is a list of all invertebrates collected in this study along with their functional feeding group and stable isotope ratios. 

This dataset is associated with the following publication:
Smucker, N., A. Kuhn, C. Cruz-Quinones, J. Serbst, and J. Lake. Stable isotopes of algae and macroinvertebrates in streams respond to watershed urbanization, inform management goals, and indicate food web relationships.   ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 90: 295-304, (2018).

Tags: algae, benthic-macroinvertebrates, food-webs, impervious-cover, land-cover, nitrogen, nutrients, urban, watersheds
Organization: U.S. Environmental Protection Agency
NEEAR Water Study

Epidemiological data from the NEEAR Water Study. This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: Request from Tim Wade- wade.tim@epa.gov. Format: Data are stored in comma-delimited databases. 

This dataset is associated with the following publications:
Wade, T., S. Augustine, S. Griffin, E. Sams, K. Oshima, A. Egorov, K. Simmons, T. Eason, and A. Dufour. Asymptomatic norovirus infection associated with swimming at a tropical beach: A prospective cohort study.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 13(3): e0195056, (2018).
Deflorio-Barker, S., B. Arnold, E. Sams, A. Dufour, J. Colford, S. Weisberg, K. Schiff, and T. Wade. Child environmental exposures to water and sand at the beach: Findings from studies of over 60,000 subjects at 12 beaches.   Journal of Exposure Science and Environmental Epidemiology. Nature Publishing Group, London,  UK, 28(2): 93-100, (2018).

Tags: beach-water-quality, diarrhea, swimming
Organization: U.S. Environmental Protection Agency
Metabolism of Diazinon in Rainbow Trout Liver Slices version 1 Tapper A-12jq 09122017

Understanding biotransformation pathways in aquatic species is an integral part of ecological risk assessment with respect to the potential bioactivation of chemicals to more toxic metabolites. The long-range goal is to gain sufficient understanding of fish metabolic transformation reactions to be able to accurately predict fish xenobiotic metabolism. While some metabolism data exist, there are few fish in vivo exposure studies where metabolites have been identified and the metabolic pathways proposed. Previous biotransformation work has focused on in vitro studies which have the advantage of high throughput but may have limited metabolic capabilities, and in vivo studies which have full metabolic capacity but are low throughput. An aquatic model system with full metabolic capacity in which a large number of chemicals could be tested would be a valuable tool. The current study evaluated the ex vivo rainbow trout liver slice model, which has the advantages of high throughput as found in vitro models and non-dedifferentiated cells and cell to cell communication found in in vivo systems. The pesticide diazinon, which has been previously tested both in vitro and in vivo in a number of mammalian and aquatic species including rainbow trout, was used to evaluate the ex vivo slice model as a tool to study biotransformation pathways. While somewhat limited by the analytical chemistry method employed, results of the liver slice model, mainly that hydroxypyrimidine was the major diazinon metabolite, are in line with the results of previous rainbow trout in vivo studies. Therefore, the rainbow trout liver slice model is a useful tool for the study of metabolism in aquatic species. 

This dataset is associated with the following publication:
Tapper, M., J. Serrano, P. Schmieder, D. Hammermeister, and R. Kolanczyk. Metabolism of diazinon in rainbow trout liver slices.   Applied In Vitro Toxicology. Mary Ann Liebert, Inc., Larchmont, NY, USA, 4(1): 13-23, (2018).

Tags: biotransformation, diazinon, liver-slices, metabolism, trout
Organization: U.S. Environmental Protection Agency
Linking terrestrial phosphorus inputs to riverine export across the US

Phosphorus inputs to the landscape from fertilizer and manure inputs, P surplus and P removal by crop harvest and hydrologic export.  The input layers are now available on EPA's EnviroAtlas under Pollutants: Nutrients and specifically the layers include 1) Phosphorus application as manure and 2) Phosphorus fertilizer application. 

This dataset is associated with the following publication:
Metson, G., J. Lin, J.A. Harrison, and J. Compton. Linking terrestrial phosphorus inputs to riverine export across the United States.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 124: 177-191, (2017).

Tags: algal-blooms, crop-harvest-p, fertilizer-p, legacies, manure, nutrients, phosphorus, surplus-p, water-quality
Organization: U.S. Environmental Protection Agency
A Nitrogen Physical Input-Output Model for Illinois

This file provides all the data that was used to estimate the physical input outputs for the State of Illinois.  The attached paper describes how the data was collected and provides all the metadata. 

This dataset is associated with the following publication:
Singh, S., J. Compton, T. Hawkins, D. Sobota, and E. Cooter. A Nitrogen Physical Input-Output Table (PIOT) Model for Illinois.   ECOLOGICAL MODELLING. Elsevier Science BV, Amsterdam,  NETHERLANDS, 360: 194-203, (2017).

Tags: illinois, input-output-data, life-cycle-assessment, nitrogen
Organization: U.S. Environmental Protection Agency
Metabolite profiles of repeatedly sampled urine from male fathead minnows (Pimephales promelas) contain unique lipid signatures following exposure to anti-androgens

The purpose of this study was twofold. First, we sought to identify candidate markers of exposure to antiandrogens
by analyzing endogenous metabolite profiles in the urine of male fathead minnows (mFHM,
Pimephales promelas). Based on earlier work, we hypothesized that unidentified lipids in the urine of mFHM
were selectively responsive to exposure to androgen receptor antagonists,which is otherwise difficult to confirm
using established fish toxicity assays. A second goal was to evaluate the feasibility of non-lethally and repeatedly
sampling urine from individual mFHMs over the time course of response to a chemical exposure. Accordingly, we
exposed mFHM to the model anti-androgens vinclozolin or flutamide. Urine was collected from each fish at
48 hour intervals over the course of a 14 day exposure. Parallel experiments were conducted with mFHM exposed
to bisphenol A or control water. The frequent handling/sampling regime did not cause apparent adverse
effects on the fish. Endogenous metabolite profiling was conducted with gas chromatography–mass spectrometry
(GC–MS), which exhibited lower variation for the urinary metabolome than was found in earlier work with
nuclear magnetic resonance (NMR) spectroscopy. Specifically, for inter- and intra-individual variations, the median
spectrum-wide relative standard deviation (RSD) was 32.6% and 33.3%, respectively, for GC–MS analysis of
urine from unexposed mFHM. These results compared favorably with similar measurements of urine from other
model species, including the Sprague Dawley rat. In addition, GC–MS allowed us to identify several lipids
(e.g., certain saturated fatty acids) in mFHM urine as candidate markers of exposure to androgen receptor
antagonists.
The dataset that is uploaded here is the complete processed data from GC-MS instrument. 

This dataset is associated with the following publication:
Collette , T., D. Skelton, J. Davis , J. Cavallin , K. Jensen , M. Kahl , G. Ankley , G. Ankley , D. Martinovic-Weigelt, and D. Ekman. Metabolite profiles of repeatedly sampled urine from male fathead minnows (Pimephales promelas) contain unique lipid signatures following exposure to anti-androgens.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY - PART D: GENOMICS AND PROTEOMICS. Elsevier BV, AMSTERDAM,  NETHERLANDS, 19: 190-198, (2016).

Tags: anti-androgens, metabolomics
Organization: U.S. Environmental Protection Agency
Linking Field-based Metabolomics and Chemical Analyses to Prioritize Contaminants of Emerging Concern in the Great Lakes Basin

Matrix of contaminant measurements and endogenous metabolite intensities (measured by NMR). 

This dataset is associated with the following publication:
Davis, J., D. Ekman, Q. Teng , G. Ankley , J. Berninger , J. Cavallin , K. Jensen , M. Kahl , A. Schroeder , D. Villeneuve , Z. Jorgenson, K. Lee, and T. Collette. Linking field-based metabolomics and chemical analyses to prioritize contaminants of emerging concern in the Great Lakes basin.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(10): 2493–2502, (2016).

Tags: chemicals-of-emerging-concern, fathead-minnows, great-lakes, metabolomics, nuclear-magnetic-resonance-spectroscopy
Organization: U.S. Environmental Protection Agency
Polypropylene-MWCNT degradation and Nanomaterials release

Degradation kinetics of nanocomposite in the environment.  Nano-polymer composites are exposed to sunlight and oxidizing conditions that cause weathering of the polymers, leading to degradation and the release of nanoparticles. 

This dataset is associated with the following publication:
Han, C., E. Sahle-Demessie, A. Zhao, T. Richardson, and J. Wang. Environmental aging and degradation of multiwalled carbon nanotube reinforced polypropylene.   CARBON. Pergamon Press Ltd., New York, NY, USA, 129: 137-151, (2018).

Tags: degradation, engineered-nanomaterials, environmental-degredation, multiwalled-carbon-nanotubes, nanocomposites, nanorelease
Organization: U.S. Environmental Protection Agency
Seasonal Variation of Natural Organic Matter influence on the fate and transport of engineered nanomaterials

This study characterized Ohio river natural organic matter (NOM) during winter and summer times, and demonstrated the effects of these NOM samples on stability and transport of ceria nanoparticles in saturated porous media. Ohio river NOM samples that were characterized by thermal analysis, spectroscopic method, solid state NMR spectrometer and elemental analysis showed to have structural and compositional differences from standard humic acid that is used for laboratory tests,  This study explored the effects of Ohio river NOM in enhancing the transport and breakthrough of ceria nanoparticles in moderate (1-10 mM) ionic strength solutions. The enhancement in stability and transport appear to be dominated by the altered electrokinetic properties of the ceria NPs. 

This dataset is associated with the following publication:
Li, Z., E. Sahle-Demessie, A. Aly Hassan, J. Pressman, C. Han, and G. Sorial. Effects of source and seasonal variations of natural organic matters on the fate and transport of CeO2 nanoparticles in the environment.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 609: 1616-1626, (2017).

Tags: ceo2, engineered-nanoparticles-np, nanoparticles, natural-organic-matter, ohio-river, packed-column-transport, ssnmr-ftir
Organization: U.S. Environmental Protection Agency
Biofiltration of trihalomethanes stripped from chlorinated drinking water

This study examined the removal of chloroform under two environmental conditions (anaerobic and aerobic), and in the presence of ethanol as co-metabolite.  Investigations of the biological community structure within the BTFs were also conducted. The use of aerobic fungi BTF under acidic condition successfully enhanced the biodegradation process of chloroform. The BTF provided more stable performance by having smaller standard deviation in the removal efficiency as compared to the anaerobic BTF. Hence, acidic aerobic BTF had achieved significant improvement in the removal of chloroform. 

This dataset is associated with the following publication:
Sahle-Demessie, E., J. Lu, B. Mezgebe, and G. Sorial. Performance of Anaerobic Biotrickling Filter and Its Microbial Diversity for the Removal of Stripped Disinfection By-products.   INTERNATIONAL JOURNAL OF ENVIRONMENTAL POLLUTION. Universidad Nacional Autonoma de Mexico,    228: 437, (2017).

Tags: aerobic, anaerobic, biofiltration, biotrickling-filter, choloform, disinfection-byproducts, microbial-diversity, trihalomethanes
Organization: U.S. Environmental Protection Agency
Supporting data for "Stuhldreher, M., Kargul, J., Barba, D., McDonald, J. et al. 2018. Benchmarking a 2016 Honda Civic 1.5-liter L15B7 Turbocharged Engine and Evaluating the Future Efficiency Potential of Turbocharged Engines, SAE 2018-01-0319" V1

A 2016 Honda Civic with a 4-cylinder 1.5-liter L15B7 turbocharged engine and continuously variable transmission (CVT) was benchmarked. The test method involved installing the engine and its CVT in an engine dynamometer test cell with the engine wiring harness tethered to its vehicle parked outside
the test cell. Engine and transmission torque, fuel flow, key engine temperatures and pressures, and onboard diagnostics
(OBD)/CAN bus data were recorded. The paper published as part of this work documents the test results for idle, low,
medium and high load engine operation, as well as motoring
torque, wide-open throttle torque and fuel consumption during transient operation using both EPA Tier 2 and Tier 3 test
fuels. Particular attention is given to characterizing enrichment
control during high load engine operation. Results have been used to create complete engine fuel consumption and efficiency maps and estimate CO2 emissions using EPA’s ALPHA full vehicle simulation model, over regulatory drive cycles. Within the published paper, the design and performance of the 1.5-liter Honda engine are compared to several other past, present, and future downsized-boosted engines and potential advancements were evaluated. 

This dataset is associated with the following publication:
Dekraker, P., S. Bohac, J. McDonald, J. Kargul, and D. Barba. Benchmarking a 2016 Honda Civic 1.5L Turbo Engine and Evaluating the Future Efficiency Potential of Turbocharged Engines.   SAE Technical Paper Series. SAE International, Warrendale, PA, USA,  34, (2018).

Tags: air-quality, electric-vehicles, energy-demand, ghg, hybrid-electric-vehicles, internal-combustion-engines, light-duty-vehicles
Organization: U.S. Environmental Protection Agency
Determining Pathogen and Indicator Levels in Class B Municipal Organic Residuals Used for Land Application

Biosolids are nutrient rich organic residuals that are currently used to amend soils for food production.  Treatment requirements to inactivate pathogens for production of Class A biosolids are energy intensive.  One less energy intensive alternative is to treat biosolids to Class B standards, but it could result in higher pathogen loads.  Quantitative microbial risk assessments models have been developed on land application of Class B biosolids, but contain many uncertainties because of limited data on specific pathogen densities and the use of fecal indicator organisms as accurate surrogates of pathogen loads.   To address this gap, a 12-month study of the levels and relationships between Cryptosporidium, Giardia, and human adenovirus (HAdV) with fecal coliform, somatic and F-RNA coliphage levels in Class B biosolids from nine wastewater treatment plants throughout the United States was conducted.  Results revealed that fecal coliform, somatic, and F-RNA coliphage densities were consistent throughout the year.  More importantly, results revealed that HAdV (=2.5x103 genome copies/dry g) and Giardia (=4.14 x103 cysts/dry g) were in all biosolids samples regardless of treatment processes, location, or season.  Cryptosporidium oocysts were also detected (38 % positive; range: 0 -1.9 x 103 oocysts/dry g), albeit sporadically.  Positive correlations among three fecal indicator organisms and HAdV, but not protozoa, were also observed.  Overall, study reveals the high concentrations of enteric pathogens (e.g., Cryptosporidium, Giardia, and HAdV) are present in biosolids throughout the US.  Microbial densities found can further assist management and policy makers establish more accurate risk assessment models associated with land application of Class B biosolids. 

This dataset is associated with the following publication:
Rhodes , E., L. Boczek , M. Ware , M. McKay, J. Hoelle , M. Schoen, and E. Villegas. Determining pathogen and indicator levels in Class B municipal organic residuals used for land application.   JOURNAL OF ENVIRONMENTAL QUALITY. American Society of Agronomy, MADISON, WI, USA, 44(1): 265-274, (2015).

Tags: biosolids, cryptosporidium, fecal-indicator-bacteria, giardia, occurrence, organic-residual, wastewater
Organization: U.S. Environmental Protection Agency
Zebrafish Locomotor Responses Reveal Irritant Effects of Fine PM Extracts and a Role for TRPA1

This dataset contains 60-min locomotor response data for all control, chemical and particulate-extract-treated zebrafish. 

This dataset is associated with the following publication:
Stevens, J., S. Padilla, D. DeMarini, D. Hunter, K. Martin, L. Thompson, I. Gilmour, M. Hazari, and A. Farraj. Zebrafish Locomotor Responses Reveal Irritant Effects of Fine Particulate Matter Extracts and a Role for TRPA1.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  161(2): 290-299, (2018).

Tags: air-pollution, behavior, diesel-exhaust, health, irritant-responses, locomotor, organic-extracts, particulate-matter, trpa1, zebrafish
Organization: U.S. Environmental Protection Agency
The mouse thermoregulatory system: Its impact on translating biomedical data to humans

Ambient temperature vs.Core temperature. 

This dataset is associated with the following publication:
Gordon, C. THE MOUSE THERMOREGULATORY SYSTEM:
ITS IMPACT ON TRANSLATING BIOMEDICAL DATA TO HUMANS.   Physiology & Behavior. Elsevier B.V., Amsterdam,  NETHERLANDS,  55-66, (2017).

Tags: behavior, core-temperature, extrapolation, hypothermia, metabolic-rate, preferred-temperature, thermal-conductance
Organization: U.S. Environmental Protection Agency