AndreaBozzo/ceres-open-data-index huggingface dataset:
Sediment Porewater Data Set

The data set contains a summary of all measurements that were collected at the cottage grove
reservoir over the time period of the study. 

This dataset is associated with the following publication:
Eckley, C., T. Luxton, J. Goetz, and J. McKernan. Water-level fluctuations influence sediment porewater chemistry and methylmercury production in a flood-control reservoir..  David Carpenter, and Eddy Zeng  ENVIRONMENTAL POLLUTION. Elsevier Science Ltd, New York, NY, USA, 222: 32-41, (2017).

Tags: dissolved-organic-carbon, mercury, mercury-methylation, methylmercury, porewater, reservoir
Organization: U.S. Environmental Protection Agency
Data Table for Figures

This excel file contains 7 tabs, each tabs contains the data for one specific figure in the paper. Description of the data and column names is also provided in each tab. 

This dataset is associated with the following publication:
Wang, J., D. Hallinger, A. Murr, A. Buckalew, S. Simmons, S. Laws, and T. Stoker. High-Throughput Screening and Quantitative Chemical Ranking for Sodium Iodide Symporter Inhibitors in ToxCast Phase 1 Chemical Library.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(9): 5417-5426, (2018).

Tags: endocrine-disruptor, high-throughput-in-vitro-screening-assay, sodium-iodide-symporter, thyroid
Organization: U.S. Environmental Protection Agency
HESI_Biocrates_TMT_2017

Biocrates metabolomics data for cerebrospinal fluid, serum, plasma, and urine from rats dosed with trimethyl tin at 2, 6, 10, or 14 days after treatmetn. 

This dataset is associated with the following publication:
Imam, S., Z. He, E. Cuevas, H. Rosas-Hernandez, S. Lantz, S. Sarkar, J. Raymick, B. Robinson, J. Hanig, D. Herr, D. MacMillan, A. Smith, S. Liachenko, S. Ferguson, J. O'Callaghan, D. Miller, C. Somps, I. Pardo, W. Slikker, J. Pierson, R. Roberts, B. Gong, W. Tong, M. Aschner, M.J. Kallman, D. Calligaro, and M. Paule. Changes in the metabolome and microRNA levels in biological fluids might represent biomarkers of neurotoxicity: A trimethyltin study.   Experimental Biology and Medicine. SAGE Publications, THOUSAND OAKS, CA, USA, 243(3): 228-236, (2018).

Tags: biocrates, biomarker, metabolomics, neurotoxicity, trimethyltin
Organization: U.S. Environmental Protection Agency
Cylindrospermopsin 90-day oral route toxicology study

General toxicology, clinical chemistry, complete blood counts, histopathology, gene expression. 

This dataset is associated with the following publication:
Chernoff, N., D. Hill, I. Chorus, D. Diggs, H. Huang, D. King, J. Lang, T. Le, J. Schmid, G. Travlos, E. Whitley, R. Wilson, and C. Wood. Cylindrospermopsin toxicity in mice following a 90-d oral exposure.   ENVIRONMENTAL TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, USA,  549-566, (2018).

Tags: 90-day-study, algal-toxin, cyanobacterial-toxin, cylindrospermopsin, kidney-toxicity, liver-toxicity, oral-exposure
Organization: U.S. Environmental Protection Agency
Fort Riley Tensiometer Data

Tensiometers were installed a various depths and distances to monitor soil moisture tension. The installation was used to monitor subsurface water flow patterns from the storage gallery under the permeable pavement site. 

This dataset is associated with the following publication:
Razzaghmanesh, M., and M. Borst. Monitoring the performance of urban green infrastructure using a tensiometer approach.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 651: 2535-2545, (2019).

Tags: exfiltration, permeable-pavement, sidewalls, stormwater-control, tensiometer
Organization: U.S. Environmental Protection Agency
Wanjugi et al 2016_Data Set

Decomposition data of bacterial and viral fecal indicators in common human pollution types. 

This dataset is associated with the following publication:
Wanjugi, P., M. Sivaganesan, A. Korajkic, C. Kelty, B. McMinn, R. Ulrich, V. Harwood, and O. Shanks. Differential Decomposition of Bacterial and Viral Fecal Indicators in Common Human Pollution Types.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 105: 591-601, (2016).

Tags: coliphage, human-fecal-pollution, microbial-source-tracking, qpcr, water-quality
Organization: U.S. Environmental Protection Agency
Using methods development efforts ongoing within NRMRL, NERL, and Regional labs, the concentrations of polyfluorinated chemicals

Concentrations of polyfluorinated chemicals in drinking water from homes. 

This dataset is associated with the following publication:
Dasu, K., S. Nakayama, M. Yoshikane, M. Mills, J.M. Wright, and S. Ehrlich. An Ultra-Sensitive Method for the Analysis of Perfluorinated Alkyl Acids in Drinking Water using a Column Switching High-Performance Liquid Chromatography Tandem Mass Spectrometry.  M.C. Breadmore, J.G. Dorsey, P. Dugo, S. Fanali  JOURNAL OF CHROMATOGRAPHY A. Elsevier Science Ltd, New York, NY, USA, 1494: 46-54, (2017).

Tags: column-switching-hplc, drinking-water, perfluorinated-alkyl-acids, solid-phase-extraction
Organization: U.S. Environmental Protection Agency
On-road Emissions and Chemical Transformation of Nitrogen Oxides

On-road chase and PEMS measurement data while following traffic.  Time-averaged to assess the emission rate of the followed vehicle, including the presence of a PEMS to measure direct tailpipe exhaust. 

This dataset is associated with the following publication:
Snow, R., J. Faircloth, R. Baldauf, B. Yand, M. Zhang, P. Deshmukh, and X. Zhang. On-road Emissions and Chemical Transformation of Nitrogen Oxides.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA,  22, (2017).

Tags: chase-measurement, emissions, nitrogen-oxides, on-road, pems, traffic
Organization: U.S. Environmental Protection Agency
Traffic Density Parameters

The complete data sets and programs used for data analysis were combined into one zip file. 

This dataset is associated with the following publication:
Liu , S., J. Burke , F. Chen , and J. Xue. Evaluation of Traffic Density Parameters as an Indicator of Vehicle Emission-Related Near-Road Air Pollution: A Case Study with NEXUS Measurement Data on Black Carbon.   International Journal of Environmental Research and Public Health. Molecular Diversity Preservation International, Basel,  SWITZERLAND, 14(12): 1581, (2017).

Tags: air-pollutant, black-carbon, exposure, near-road, nexus, traffic-density, vehicle-emission
Organization: U.S. Environmental Protection Agency
Environmental Monitoring and Assessment Program (1990-1998), National Coastal Assessment (2000-2006), National Aquatic Resource Surveys (2000-2015)

These data are from EPA's national coastal monitoring programs and include data from the water column, sediments, and biota, 1990-2015. 

This dataset is associated with the following publication:
Hale, S., H. Buffum, J. Kiddon, and M. Hughes. Subtidal Benthic Invertebrates Shifting Northward Along the U.S. Atlantic Coast.   Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA, 40(6): 1744-1756, (2017).

Tags: benthic-invertebrates, carolinian-biogeographic-province, species-range-shifts, u-s-atlantic-coast, virginian-biogeographic-province
Organization: U.S. Environmental Protection Agency
Data for a PPAR-alpha dependence of developmental effects of PFNA in mouse.

Perfluorononanoic acid (PFNA) is one of the perfluoroalkyl acids found in the environment and in tissues of humans and wildlife. Prenatal exposure to PFNA negatively impacts survival and development of mice and activates the mouse and human peroxisome proliferator-activated receptor-alpha (PPARα). In the current study, we used PPARα knockout (KO) and 129S1/SvlmJ wild-type (WT) mice to investigate the role of PPARα in mediating PFNA-induced in vivo effects. Pregnant KO and WT mice were dosed orally with water (vehicle control: 10 ml/kg), 0.83, 1.1, 1.5, or 2mg/kg PFNA on gestational days (GDs) 1−18 (day of sperm plug = GD 0). Maternal weight gain, implantation, litter size, and pup weight at birth were unaffected in either strain. PFNA exposure reduced the number of live pups at birth and survival of offspring to weaning in the 1.1 and 2 mg/kg groups in WT. Eye opening was delayed (mean delay 2.1 days) and pup weight at weaning was reduced inWT pups at 2mg/kg. These developmental endpoints were not affected in the KO. Relative liver weight was increased in a dose-dependent manner in dams and pups of theWT strain at all dose levels but only slightly increased in the highest dose group in the KO strain. In summary, PFNA altered liver weight of dams and pups, pup survival, body weight, and development in the WT, while only inducing a slight increase in relative liver weight of dams and pups at 2mg/kg in KO mice. These results suggest that PPARα is an essential mediator of PFNA-induced developmental toxicity in the mouse. 

This dataset is associated with the following publication:
Abbott, B., C. Wolf, J. Schmid, C. Lau, and R. Zehr. Developmental Effects of Perfluorononanoic Acid in the Mouse Are Dependent on Peroxisome Proliferator-Activated Receptor-alpha..   PPAR research. Hindawi Publishing Corporation, New York, NY, USA,  1-11, (2010).

Tags: developmental-toxicity, perfluoroalkyl-acids, pfaa, pfna, ppar-alpha
Organization: U.S. Environmental Protection Agency
Supplementary Material for "The Effects of Source Water Quality on Drinking Water Treatment Costs: A Review and Synthesis of Empirical Literature"

Characteristics of 24 studies that model drinking water treatment costs to source water quality. 

This dataset is associated with the following publication:
Price, J., and M. Heberling. The Effects of Source Water Quality on Drinking Water Treatment Costs: A Review and Synthesis of Empirical Literature - Ecological Economics.   ECOLOGICAL ECONOMICS. Elsevier Science Ltd, New York, NY, USA, 151: 195-209, (2018).

Tags: drinking-water, economics, literature-review, source-water-protection, treatment-costs
Organization: U.S. Environmental Protection Agency
HTMLS of Spatial Stream Network Modeling to Predict Total Phosphorus Concentration in the East Fork of the Little Miami River, Ohio

These files contain data for relating stream total phosphorus concentration, a nutrient, to land cover and land use variables in the East Fork of the Little Miami River watershed near Cincinnati, Ohio.  Water quality grab samples were collected from June 26, 2012 to September 11, 2012, and total phosphorus concentrations were measured on those samples.  The files in the jawr12543-sup-002-R_code_and outputs folder are htmls, which can be opened with any browser to view the data and work flow of the data analysis.  The files in the jawr12543-sup-003-SSN_file_objects contains the dataset as an R object, which can be opened in the open-source R software. 

This dataset is associated with the following publication:
Scown, M., M. McManus, J. Carson, and C. Nietch. Improving predictive models of in-stream phosphorus based on nationally-available spatial data coverages in a Southwestern Ohio watershed.   JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION. American Water Resources Association, Middleburg, VA, USA, 53(4): 944-960, (2017).

Tags: phosphorus, spatial-autocorrelation, spatial-data, spatial-statistical-network-model, stream-networks
Organization: U.S. Environmental Protection Agency
Integrated cell culture RT quantitative PCR and UV disinfection dataset

This dataset includes the standard curves for ICCRTqPCR to convert the assay quantities to the concentrations of infectious viruses and all the calculations on inactivation rate constants. Also, all the figures used in the manuscripts are presented. 

This dataset is associated with the following publication:
Ryu, H., K. Schrantz, N. Brinkman, and L. Boczek. Applicability of integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) for the simultaneous detection of the four human enteric enterovirus species in disinfection studies.   JOURNAL OF VIROLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 258: 35-40, (2018).

Tags: enteroviruses, multiplex-integrated-cell-culture-quantitative-pcr, uv-disinfection
Organization: U.S. Environmental Protection Agency
Taxonomic summary tables for illumina sequences from MEC study on influence of electrical conductivity by microbial activity in biofilm anode

This study assessed the conductivity of a Geobacter-enriched biofilm anode along with biofilm activity in a microbial electrochemical cell (MxC) equipped with two gold anodes (25 mM acetate medium), as different proton gradients were built throughout the biofilm. There was no pH gradient across the biofilm anode at 100 mM phosphate buffer (current density 2.38 A/m2) and biofilm conductivity (Kbio) was as high as 0.87 mS/cm. In comparison, an inner biofilm became acidic at 2.5 mM phosphate buffer in which approximately 80 μm of the inner biofilm anode was metabolically inactive. At this low phosphate buffer, Kbio significantly decreased by 0.27 mS/cm, together with declined current density of 0.64 A/m2. This work demonstrates that biofilm conductivity depends on metabolic activity of Geobacter in the conductive biofilm anode. The decreased Kbio at acidic environment implies the presence of multiple conduction-EET pathways in the biofilm anode. 

This dataset is associated with the following publication:
Dhar, B., J. Sim, H. Ryu, H. Ren, J. Santodomingo, J. Chae, and H. Lee. Microbial Activity Influences Electrical Conductivity of Biofilm Anode.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 127: 230-238, (2017).

Tags: biofilm-anode, electrical-conductivity, geobacter, microbial-electrochemical-cell
Organization: U.S. Environmental Protection Agency
Self-Cleaning Carbon Nanotube Membranes for Water Purification-confocal microscope pitures and slide preparation procedures

The pictures in the power point file were taken using a confocal microscope with green and red filters which represent viable and dead bacteria cells, respectively. Additionally, we provided the detailed procedures of bacteria propagation and viability staining in a MS word file. The data may provide background/supporting information for other researchers who are planning to perform for microscopic bacteria viability assays. 

This dataset is associated with the following publication:
Alvarez, N., R. Noga, S. Chae, G. Sorial, H. Ryu, and V. Shanov. Heatable carbon nanotube composite membranes for sustainable recovery from biofouling.   Biofouling. Taylor & Francis Group, London,  UK, 33(10): 847-854, (2017).

Tags: biofouling, carbon-nanotubes, drawable-and-spinnable-cnt, escherichia-coli, membranes, ohmic-heating, water-and-wastewater-treatment
Organization: U.S. Environmental Protection Agency
Adverse Outcome Pathway Networks II: Network Analytics

The data set provides a set of txt files and cytoscape files that were used to construct the example AOP networks included in the paper. Additionally, a supplementary table file provides all the network statistics discussed in the manuscript (e.g., node degree calculations, betweenness centrality, eccentricity, etc.). 

This dataset is associated with the following publication:
Villeneuve, D., M. Angrish, M. Fortin, I. Katsiadaki, M. Leonard, L. Margiotta-Casaluci, S. Munn, J. O'Brien, N. Pollesch, C. Smith, X. Zhang, and D. Knapen. Adverse outcome pathway networks II: Network analytics.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(6): 1734-1748, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Adverse Outcome Pathway Networks I: Development and Applications

In September, 2015, a water sample was collected downstream of a major metropolitan waste water treatment plant that discharges to the South Platte River, Colorado, USA. The grab sample, 1L, was collected just below the water surface, directly into a pre-cleaned, organic-free, amber glass bottle. The water sample was extracted by solid phase extraction using an Oasis-HLB glass catridge. Cartidges were conditioned sequentially using 5mL each of ethyl acetate, 50:50 methanol (MeOH):dichloromethane (DCM), MeOH, and water. The extract in DMSO was tested in the Attagene cis- and trans-FactorialTM assays (http://www.attagene.com/technology.php; Martin and others 2010; Romanov and others 2008). Data were analyzed using an established analysis pipeline for analyzing ToxCast™ high throughput screening data (Filer and others 2017). "Active hits" in the Attagene assay are included in the data table. 

This dataset is associated with the following publication:
Knapen, D., M. Angrish, M. Fortin, I. Katsiadaki, M. Leonard, L. Mariotta-Casaluci, S. Munn, J. O'Brien, N. Pollesch, L.C. Smith, X. Zhang, and D. Villeneuve. Adverse outcome pathway networks I: Development and applications.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(6): 1723-1733, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
in vitro and microsome experiment data

exposure_experiment.csv: 
time: length of time that amphibian was exposed to that pesticide in hours.  
parent: is the active ingredient that the amphibian was exposed to.  
analyte: either the main parent compound or the metabolite that was quantified.  
matrix: the sample that was analyzed either the amphibian or soil.  
conc: is the concentration for that specific analyte in that matrix for that specific species in microg/g
replicate: is the individual amphibian or soil exposed to that pesticide.

microsome_experiment3.csv:  
time: is the length of time that the microsomes were exposed before being quenched in minutes.  
parent: is the active ingredient that the amphibian was exposed to.  
analyte: either the main parent compound or the metabolite that was quantified.  
matrix: the sample that was analyzed microsomes.  
conc: is the concentration for that specific analyte in that matrix for that specific species.  in micromolar (uM)
replicate: is the individual microsome exposed to that pesticide. 
microMexp: is the concentration in micromolar (uM) that the microsomes were exposed to for that pesticide. 

This dataset is associated with the following publication:
Glinski, D., M. Henderson, R. Van Meter, and T. Purucker. Using in vitro derived enzymatic reaction rates of metabolism to inform pesticide body burdens in amphibians.   TOXICOLOGY LETTERS. Elsevier Science Ltd, New York, NY, USA, 288: 9-16, (2018).

Tags: amphibians, metabolism, microsomes, pesticides
Organization: U.S. Environmental Protection Agency
Supporting Simulation Output - Earth Interactions article "The Effects of Downscaling Method on the Variability of Simulated Watershed Response to Climate Change in Five U.S. Basins"

Monthly summaries of simulated watershed responses to mid-century climate change scenarios in 5 U.S. basins. 

This dataset is associated with the following publication:
Nover, D., J. Witt , J. Butcher, T. Johnson , and C. Weaver. The Effects of Downscaling Method on the Variability of Simulated Watershed Response to Climate Change in Five U.S. Basins.   Earth Interactions. American Meteorological Society, Boston, MA, USA, 20, 1-27, (2016).

Tags: change, climate, climate-change-streamflow-water-quality-downscaling, downscaling, method
Organization: U.S. Environmental Protection Agency
Climate differentiates forest structure across a residential macrosystem

The extent of urban ecological homogenization depends on how humans build, inhabit, and manage cities.  Morphological and socio-economic facets of neighborhoods can drive the homogenization of forest cover, thus affecting urban ecological and hydrological processes, and ecosystem services.  Recent evidence, however, suggests that the same biophysical drivers differentiating composition and structure of natural forests can further counteract the homogenization of urban forests.  We hypothesize that climate can differentiate forest structure across residential macrosystems, regional-to-continental discontinuous systems of urban land.  To test this hypothesis, forest structure (tree and shrub cover and volume) was measured using LiDAR data and multispectral imagery across a residential macrosystem composed of 9 cities, 1503 neighborhoods, and 1.4 million residential parcels.  Cities were selected along a potential evapotranspiration (PET) gradient in the conterminous United States, ranging from the colder continental climate of Fargo, North Dakota (PET = 66.21 mm) to the hotter subtropical climate of Tallahassee, Florida (PET = 160.49 mm).  The relative effects of climate, urban morphology, and socio-economic variables on residential forest structure were assessed by using generalized linear models.  Climate differentiated forest structure of the residential macrosystem as hypothesized.  Average forest cover doubled along the PET gradient (0.39 - 0.78 m2 m-2), whereas average forest volume had a threefold increase (2.50 – 8.12 m3 m-2).  Forest volume across neighborhoods increased exponentially with forest cover.  Urban morphology had a greater effect in homogenizing forest structure on residential parcels compared to socio-economics.  Climate and urban morphology variables best predicted residential forest structure, whereas socio-economic variables had the lowest predictive power.  Results indicate that climate can differentiate forest structure across residential macrosystems and may counteract the homogenizing effects of urban morphology and socio-economic drivers at city-wide scales.  This resonates with recent empirical work suggesting the existence of complex multi-scalar mechanisms that regulate ecological homogenization and ecosystem convergence among cities.  The study initiates high-resolution assessments of forest structure across entire urban macrosystems and breaks new ground for research on the ecological and hydrological significance of urban vegetation at subcontinental scale. 

This dataset is associated with the following publication:
Ossola, A., and M. Hopton. Climate differentiates forest structure across a residential macrosystem.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 639: 1164-1174, (2018).

Tags: ecosystem-services, green-infrastructure, socio-ecological-systems, urban-ecology, urban-ecosystem-convergence-theory, urban-trees
Organization: U.S. Environmental Protection Agency
Las Vegas Data

Las Vegas Near Road Data. 

This dataset is associated with the following publication:
Kimbrough , S., C. Owen, M. Snyder, and J. Richmond-Bryant. NO to NO2 conversion rate analysis and implications for dispersion model chemistry
methods using Las Vegas, Nevada near-road field measurements.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 165: 23-24, (2017).

Tags: air-pollution, air-quality, near-source, no2, no2-nox-ratio, nox
Organization: U.S. Environmental Protection Agency
Comparative study on the performance of Anaerobic and Aerobic Biotrickling Filter for the Removal of Chloroform

Method for the removal and degradation of harmful disinfection byproducts from drinking water. 

This dataset is associated with the following publication:
Mezgebe, B., K. Palanisamy,, G. Sorial, E. Sahle-Demessie, A. Aly Hassan, and J. Lu. Comparative Study on the Performance of Anaerobic and Aerobic Biotrickling Filter for Removal of Chloroform.   ENVIRONMENTAL ENGINEERING SCIENCE. Mary Ann Liebert, Inc., Larchmont, NY, USA, 35(5): 462-471, (2017).

Tags: aerobic, anaerobic, biotrickling-filter, microbial-diversity, trihalomethanes
Organization: U.S. Environmental Protection Agency