AndreaBozzo/ceres-open-data-index huggingface dataset:
Mimicking atmospheric photochemical modeling with a deep neural network

Air quality modeling for China. This dataset is not publicly accessible because: Data was generated and owned by Tsinghua University. It can be accessed through the following means: Data can be accessed from lead author at Tsinghua University: xingjia@tsinghua.edu.cn. Format: Air quality modeling data for China. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: atmospheric-photochemistry, chemical-transport-model, deep-learning, emissions, meteorology, ozone
Organization: U.S. Environmental Protection Agency
Van Genderen at al. 2020 Supplemental Information Data

Van Genderen at al. 2020 Supplemental Information Data is an Excel database for demonstrating Zn case study for associated journal article Best Practices for Derivation and Application of Thresholds for Metals Using Bioavailability‐Based Approaches, https://doi.org/10.1002/etc.4559. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: bioavailabilitybased-approaches, thresholds-for-metals, zinc
Organization: U.S. Environmental Protection Agency
Data for "Characterizing Nitrogen Oxides and Fine Particulate Matter Near Major Highways in the United States Using the National Near-Road Monitoring Network"

This dataset represents the raw hourly, daily, and design value data used in this article.  All of the data was downloaded from EPA's Air Quality System (AQS) with the exception of the list of near-road sites which was downloaded from https://www.epa.gov/amtic/no2-monitoring-near-road-monitoring.  The datasets are named based on their AQS parameter code (see https://www.epa.gov/aqs/aqs-code-list), averaging time, and years included. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: fine-particulate-matter-pm2-5, near-road, nitrogen-dioxide-no2
Organization: U.S. Environmental Protection Agency
USEEIO v2.0.1-411

This dataset provides the waste sector disaggregation data, model component matrices, model result matrices, model price adjustment matrices, demand vectors,  and associated metadata for the USEEIO v2.0.1-411 model. This model was generated using useeior v1.0.0 (https://github.com/USEPA/useeior/tree/v1.0.0/) by calling the buildModel() function and passing "USEEIOv2.0.1-411" as the model. This uses the model configuration file, which can be found @ https://github.com/USEPA/useeior/blob/v1.0.0/inst/extdata/modelspecs/USEEIOv2.0.1.yml.  The model is named according to the USEEIO model versioning scheme, https://github.com/USEPA/USEEIO/blob/8a43f7f5f847fe1ca6dadca3c433bceb3f29981b/VersioningScheme.md. The resulting model was exported using the writeModeltoXLSX() function to create this dataset. The waste disaggregation data are required for model building and also embedded in useeior. The generateModelIdentifier() function was used on the same model create the model identifier. The US dollar (USD) year for the model data, where USD is used, is 2012. See any additional notes in Contents on specific components. A complete description can be found in the associated manuscript. 


Tags: carbon-footprint-tool, eeio, eio, environmental-input-output, input-output, life-cycle-assessment, us-consumption, us-production
Organization: U.S. Environmental Protection Agency
Comparing the performance and coverage of selected in silico (liver) metabolism tools relative to reported studies in the literature to inform analogue selection in read-across: A case study

Dataset for journal article "Comparing the performance and coverage of selected in silico (liver) metabolism tools relative to reported studies in the literature to inform analogue selection in read-across: A case study". 

This dataset is associated with the following publication:
Boyce, M., B. Meyer, C. Grulke, L. Lizarraga, and G. Patlewicz. Comparing the performance and coverage of selected in silico (liver) metabolism tools relative to reported studies in the literature to inform analogue selection in read-across: A case study.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 21: 100208, (2022).

Tags: in-silico, metabolism, new-approach-methodologies, read-across
Organization: U.S. Environmental Protection Agency
Incorporating human exposure information in a weight of evidence approach to inform design of repeated dose animal studies

Dataset for "Incorporating human exposure information in a weight of evidence approach to inform design of repeated dose animal studies". 

This dataset is associated with the following publication:
Lowe, K., J. Dawson, K. Phillips, J. Minucci, J. Wambaugh, H. Qian, T. Ramanarayanan, P. Egeghy, B. Ingle, R. Brunner, E. Mendez, M. Embry, and C. Tan. Incorporating human exposure information in a weight of evidence approach to inform design of repeated dose animal studies.   REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 127: 105073, (2021).

Tags: exposure, kinetically-derived-maximum-dose, top-dose-selection, toxicokinetics, weight-of-evidence
Organization: U.S. Environmental Protection Agency
Chern et al 2020 SciHUB Data

Concentration estimates of culturable cells and genetic markers for different fecal indicator bacterial groups in freshwater microcosms inoculated with disinfected and non-disinfected wastewaters and held for 0-6 days at different temperatures reflecting different seasons, i.e. winter, summer, spring/fall

Tags: decay-rate, fecal-indicator-bacteria, genetic-marker, qpcr
Organization: U.S. Environmental Protection Agency
Coral microplastic ingestion and calyx size data used for model development

The dataset include ingestion data of microplastics by four Atlantic coral species. Ingestion data are reported as proportions from 0-1 from microplastics offered to each coral fragment. Additionally, the dataset include calyx measurements from all coral species. 

This dataset is associated with the following publication:
Hankins, C., S. Raimondo, and D. Lasseigne. Microplastic ingestion by coral as a function of the interaction between calyx and microplastic size..   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 810: 152333, (2022).

Tags: coral-microplastic-ingestion-calyx-model
Organization: U.S. Environmental Protection Agency
Data to support Minucci et al. 2021 Ecological Applications

The U.S. Environmental Protection Agency (USEPA) and U.S. Department of Agriculture (USDA) are developing the VarroaPop+Pesticide model which simulates the dynamics of honey bee colonies and how they respond to multiple stressors, including weather, Varroa mites and pesticides. To evaluate this model, we used Approximate Bayesian Computation to fit field data from an empirical study where honey bee colonies were fed the insecticide clothianidin.

Model input data (Minucci 2021a) are available on Figshare: https://doi.org/10.6084/m9.figshare.c.5402901.v1. Scripts (Minucci 2021b) to run this analysis are available on Zenodo: https://doi.org/10.5281/zenodo.4721797. 

This dataset is associated with the following publication:
Minucci, J., R.J. Curry, G. DeGrandi-Hoffman, C. Douglass, K. Garber, and S. Purucker. Inferring pesticide toxicity to honey bees from a field-based feeding study using a colony model and Bayesian inference.   ECOLOGICAL APPLICATIONS. Ecological Society of America, Ithaca, NY, USA, 31(8): e02442, (2021).

Tags: approximate-bayesian-computation, bayesian-inference, colony-feeding-study, colony-models, honey-bees-apis-mellifera, pesticides, risk-assessment
Organization: U.S. Environmental Protection Agency
Sensitivity of Riparian Buffer Designs to Climate Change

In this study, we assessed sensitivity of watershed-specific riparian buffer zone (RBZ) designs to water quality indicator parameters  in the contemporary climate and in future extreme climatic conditions. we summarized the RBZ design strategy and evaluated five water quality indicator (WQI) parameters: Dissolved Oxygen (DO), Total Phosphorous (TP), Total Nitrogen (TN), Sediment (SD), and Biochemical Oxygen Demand (BD) as component of watershed ecosystem services through sensitivity analyses of 135 simulation scenarios. The scenarios included the width variation of six baseline RBZs (Grass, Urban, Two-zone Forest, Three-zone Forest, Wildlife, and Naturalized) in three watersheds within the Albemarle-Pamlico river basin (USA). Analyses revealed optimal RBZ designs. 

This dataset is associated with the following publication:
Ghimire, S., J. Corona, R. Parmar, G. Mahadwar, R. Srinivasan, K. Mendoza, and J. Johnston. Sensitivity of Riparian Buffer Designs to Climate Change—Nutrient and Sediment Loading to Streams: A Case Study in the Albemarle-Pamlico River Basins (USA) Using HAWQS.   Sustainability. MDPI AG, Basel,  SWITZERLAND, 13(22): 12380, (2021).

Tags: climate-change, hawqs, riparian-buffer-zone, water-quality, watershed
Organization: U.S. Environmental Protection Agency
Human-health impacts of controlling secondary air pollution precursors

Dataset includes CMAQv5.3.1 code used for emission reduction simulations and output from CMAQ for each pollutant at the county level.

Tags: air-quality-health-impacts, ammonium, cmaq, fine-particulate-matter-pm2-5, health, nitrate, ozone, soa, sulfate
Organization: U.S. Environmental Protection Agency
Long-term performance of three mesophilic anaerobic digesters to convert animal and agro-industrial wastes into organic fertilizer

Anaerobic digestion (AD) is a process used to convert animal and agro-industrial wastes to organic fertilizers. Since digester effluents are used as for cropland applications, we are interested to find out whether the quality of these organic fertilizers are impacted by the AD process. In addition, few studies have investigated the performance of AD in field conditions. In this study, we monitored the performance of three operational AD systems for two years. These three systems have different retention times (9, 12 and 34 days), that is how long the waste materials stay in the digester. We collected influent and effluent samples every two months and analyzed for pH, nutrients and metals. We found that the two shorter retention systems slightly decreased effluent pH while the long retention system significantly increased the effluent pH, i.e., by 1.8 unit. The 34-day retention system also removed more solids and increased ammonium-nitrogen in the effluent. We found no significant changes in the metals that we analyzed. These findings can assist in developing strategies for cleaner production using AD in an environmentally sustainable manner. 

This dataset is associated with the following publication:
Zhang, X., I. Lopes, J. Ni, Y. Yuan, C. Huang, D.R.  Smith, I. Chaubey, and S. Wu. Long-term performance of three mesophilic anaerobic digesters to convert animal and agro-industrial wastes into organic fertilizer.   JOURNAL OF CLEANER PRODUCTION. Elsevier Science Ltd, New York, NY, USA, 307: 127271, (2021).

Tags: ammonium-nitrogen, anaerobic-digestion, effluent, metals, nitrogen-and-co-pollutants, total-solids
Organization: U.S. Environmental Protection Agency
ExpoKids Input and Output Data 2019

There are 3 types of data: 1) ExpoFIRST outputs for DEHP, Mn, Endosulfan (both per- and post-ban); 2) ExpoKids inputs for DEHP, Mn, Endosulfan (both per- and post-ban); and 3)  ExpoKids output plots for DEHP, Mn, Endosulfan (both per- and post-ban). 

This dataset is associated with the following publication:
Dai, M., S. Euling, L. Phillips, and G. Rice. ExpoKids: An R-Based Tool for Characterizing Aggregate Chemical Exposure During Childhood.   Journal of Exposure Science and Environmental Epidemiology. Nature Publishing Group, London,  UK, 31: 233-247, (2021).

Tags: aggregate, children, exposure, lifestage, tool
Organization: U.S. Environmental Protection Agency
Climate change, riverine flood risk and adaptation for the conterminous United States

Files contain:
1) expected annual damages summed by HUC10, for baseline climate and future climates of 1C-5C warmer than baseline, and 
2) expected annual damages due to adaptation based on benefit cost ratios of 1, 2, and 4, and net benefits of adaptation under each BCR scenario. Tabs are results for discount rates of 1, 3, and 6 (see text). Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: adaptation, climate, flooding, risk
Organization: U.S. Environmental Protection Agency
Data associated with article virus transport from drywells under constant head conditions: a modeling study

The spreadsheet accompanies the journal article Sasidharan et al (2021) Water Research, Virus transport from drywells under constant head conditions: a modeling study.  The worksheets include metadata and data associated with all Tables and Figures.  The spreadsheet includes a link to the PC-PROGRESS website that contains examples HYDRUS (2D/3D) run files for the drywell setup discussed in the paper. 

This dataset is associated with the following publication:
Sasidharan, S., S. Bradford, J. Simunek, and S. Kraemer. Virus Transport from Drywells Under Constant Head Conditions: A Modeling Study.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 197: 117040, (2021).

Tags: drywell, hydrus-2d-3d, managed-aquifer-recharge, vadose-zone, virus, water-quality
Organization: U.S. Environmental Protection Agency
A state-of-the-science review of polychlorinated biphenyl exposures at background levels: relative contributions of exposure routes

Data set resulting from a targeted literature review of PCB concentrations in environmental media, as well as of total PCB dietary intake. Table S1 shows all studies that underwent full-text review (Figure 1). Table S2 shows all included studies and resulting PCB exposure estimates (used to generate Figures 2-4). Table S3 provides the data and analysis used to examine the effect of congener number on diet studies. 

This dataset is associated with the following publication:
Weitekamp, C., L. Phillips, L. Carlson, N. DeLuca, E. Hubal, and G. Lehmann. A state-of-the-science review of polychlorinated biphenyl exposures at background levels: relative contributions of exposure routes.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 776: 1-8, (2021).

Tags: air-pollution-exposure, dietary-exposure, polychlorinated-biphenyls-pcbs
Organization: U.S. Environmental Protection Agency
Collodal-Copper based pesticide and wood preservatives against microbial acitivies

Copper-based pesticides and wood preservative fungicides could end up in the environment during production, use, and end-of-life via different pathways that could cause unintended ecological and adverse health effects. This research provides the effect of colloid-size Cu-based pesticides (), micronized Cu azole (MCA-1 and MCA-2) and alkaline Cu quaternary (ACQ) treated woods, ionic Cu, ionic Cu spiked untreated wood (UTW), and CuCO3 solutions against Gram-positive Bacillus species using five-day biochemical oxygen demand (BOD5) standard test. 

This dataset is associated with the following publications:
Tegenaw, A., G.A. Sorial , and E. Sahle-Demessie. Effect of colloid-size copper-based pesticides and wood preservatives against microbial activities of Gram-positive Bacillus species using five-day biochemical oxygen demand test.   Journal of Environmental Sciences. Elsevier BV, AMSTERDAM,  NETHERLANDS, 105: 71-80, (2021).
Tegenaw, A., G.A. Sorial, E. Sahle-Demessie, and C. Han. Role of water chemistry on stability, aggregation, and dissolution of uncoated and carbon-coated copper nanoparticles.   ENVIRONMENTAL RESEARCH. Elsevier B.V., Amsterdam,  NETHERLANDS, 187: 109700, (2020).

Tags: bacillus-species, bod5, colloid-size-cu-based-pesticides, leaching, wood-preservatives
Organization: U.S. Environmental Protection Agency
Figure 1: Association between cytokines assessed in EBC and the clinical outcomes of CPIS and CXRAY using a generalized estimating equations model

Association between cytokines assessed in EBC and the clinical outcomes of CPIS and CXRAY using a generalized estimating equations model. CPIS = clinical pulmonary infection score; CXRAY = chest radiograph score. 

This dataset is associated with the following publication:
Davis, M., B. Winters, M. Madden, J. Pleil, C. Sessler, A. Wallace, C. Ward-Caviness, and A. Montpetit. Exhaled breath condensate biomarkers in critically ill, mechanically ventilated patients..   Journal of Breath Research. Institute of Physics Publishing, Bristol,  UK, 15(1): 1752-7163, (2021).

Tags: cytokines, exhaled-breath-condensate, intensive-care-unit, mechanically-ventilated, sepsis
Organization: U.S. Environmental Protection Agency
HexSim

Not applicable. This dataset is not publicly accessible because: Source code comments are the only item that meets the stated criteria for data.
The source code is not meaningful to store in ScienceHub and stored in with redundancy both on and off site.
It changes frequently. It can be accessed through the following means: The source code lives within a version control application and is not generally available to the public. Format: There are no datasets to add. 

This dataset is associated with the following publication:
Dunk, J.R., B. Woodbridge, E.M. Glenn, R.J. Davis, K. Fitzgerald, P. Henson, D.W. LaPlante, B.G. Marcot, B.R. Noon, M.G. Raphael, N. Schumaker , and B. White. The Scientific Basis for Modeling Northern Spotted Owl Habitat: A Response to Loehle, Irwin, Manly, and Merrill.   FOREST ECOLOGY AND MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 358: 355-360, (2015).

Tags: hexsim, plants, simulation-model, wildlife
Organization: U.S. Environmental Protection Agency
Variables for Alzheimer's analysis (without PII data)

Organized by zipcode:
Rates of Alzheimer's disease
Percent of landcover types
Modelled PM2.5
Socioeconomic variables. 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: Lucas Neas (CPHEA/PHESD/EB) is the owner of the copy of this dataset that was used. Format: Medicare database. 

This dataset is associated with the following publication:
Wu, J., and L. Jackson. Greenspace inversely associated with the risk of Alzheimer’s disease in the mid-Atlantic United States.   Earth. MDPI AG, Basel,  SWITZERLAND, 2(1): 140-150, (2021).

Tags: alzheimers-disease, fine-particulate-matter-pm2-5, greenspace, water
Organization: U.S. Environmental Protection Agency
Repeat-dose toxicity prediction with Generalized Read-Across (GenRA) using targeted transcriptomic data

Here are all of the data files used for this manuscript. Please note that this is all published data. Imran Shah 1.1060+ Chemicals and Chemical controls 2. Chemical descriptors (chm): 2048 Morgan (mrgn) 2048 Topological Torsion (tptr) 729 ToxPrints (toxp) 3. Transcriptomic descriptors(bio): 95 Gene (ge) 189 Assay (asy) 4. 922 Toxicity outcomes(tox) 5. 86 Predefined Chemical Clusters

Tags: chemical-safety-research, curated-data, models, pharmacokinetics
Organization: U.S. Environmental Protection Agency
Determining the Predictive Limit of QSAR Models

The research done to evaluate how the predictivity of models are effected by error in either the training or the test set is simple to describe conceptually. Benchmark datasets are downloaded from reputable sources. Then the datasets are split into training and test sets. Randomized error is added and then models created on both error laden and native training sets. Those models are used to predict both error laden and native test sets. Differences in standard statistics commonly used to assess predictivity are observed. 

This dataset is associated with the following publication:
Kolmar, S., and C. Grulke. The Effect of Noise on the Predictive Limit of QSAR Models.   Journal of Cheminformatics. Springer, New York, NY, USA, 13: 92, (2021).

Tags: error, gaussian-process, model-evaluation, prediction-error
Organization: U.S. Environmental Protection Agency
H12221: NOS Hydrographic Survey , OCNMS, WA, 2010-06-27

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, bathymetry, bathymetry/seafloor topography, cape alava, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, marine sediments, mbes, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, ocean, oceans, olympic coast national marine sanctuary, passive remote sensing, positioning/navigation, profilers/sounders, seafloor topography, sediment composition, ships, sonar, sound navigation and ranging, u.s. department of commerce, united states of america, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce