cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1522614
title: High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

description: We screened 44 chemicals in MCF7 cells in concentration response and generated HTTr data using the TempO-Seq hWTv1 assay. First, we provide an outline of the quality of the HTTr data based on a set of QC metrics we developed for this platform. Second, we evaluate the reproducibility and mechanistic accuracy of the HTTr platform using inter-plate analysis of reference samples and comparison of reference chemical treatment effects with CMAP signatures, respectively. Third, we summarize the concentration-dependent HTTr responses for all 44 chemicals to stratify them in terms of their overall effect on the transcriptome. Fourth, we present a new gene signature based concentration-response analysis that provides potency estimates for perturbation of cellular biology (ie, BPACs).
DOI: 10.23719/1520880
title: Figure data for article "Acidity and the multiphase chemistry of atmospheric aqueous particles and clouds"

description: Noting here that data used to make figures in "Acidity and the multiphase chemistry of atmospheric aqueous
particles and clouds" article can be found within the paper and associated supplement.
DOI: 10.23719/1520957
title: CONUS and Alaska MERIS inland lake water quality

description: CONUS and Alaska MERIS inland lake water quality
DOI: 10.23719/1521144
title: Physical habitat, landscape data, and water chemistry in the Karun River Basin

description: Physical habitat, landscape data, and water chemistry in the Karun River Basin
DOI: 10.5281/zenodo.8248361
title: Empirical Models of TEC and Tide-like Signatures In the Ionosphere

description: This empirical model is developed from the global ionospheric maps (GIMs) from the Center for Orbit Determination of Europe (CODE) covering 2000-2021. With the tidal signatures parameterized, the climatic behaviors in the ionosphere could be consequently modeled. This dataset contains the model codes of the tidal signatures and TEC.
DOI: 10.23719/1520867
title: The Changing Face of Floodplains in the Mississippi River Basin Detected by a 60-year Land Use Change Dataset

description: The MRB floodplain land use change dataset is made available through an open-access geospatial data sharing platform HydroShare. Our archive also includes all corresponding input data, intermediate calculations, and supporting information. Table 2 below provides an overview of the file contents. The entire archive can be downloaded as a single zip file from this weblink: https://www.hydroshare.org/resource/41a3a9a9d8e54cc68f131b9a9c6c8c54/
DOI: 10.23719/1520925
title: Estimating Hepatotoxic Doses Using High-content Imaging in Primary Hepatocytes

description: This repository contains the necessary data, python source code and jupyter notebooks to reproduce the results from our manuscript, "Estimating Hepatotoxic Doses Using High-content Imaging in Primary Hepatocytes." Using in vitro data to estimate point of departure (POD) values is an important component of new approach method (NAM)-based chemical risk assessments. In this case study we evaluated a NAM for hepatotoxicity based on rat primary hepatocytes, high-content imaging (HCI) and in vitro to in vivo extrapolation (IVIVE).
DOI: 10.23719/1523474
title: Improved Wetland Soil Organic Carbon Stocks of the Conterminous U.S. Through Data Harmonization

description: Public data used for data harmonization
DOI: 10.23719/1523100
title: Integrating publicly available information to screen candidates for chemical prioritization under the Reauthorized Toxic Substances Control Act: A proof of concept case study using genotoxicity and carcinogenicity

description: Integrating publicly available information to screen candidates for chemical prioritization under the Reauthorized Toxic Substances Control Act: A proof of concept case study using genotoxicity and carcinogenicity
DOI: 10.23719/1519025
title: Fire regimes of the conterminous United States

description: Fire regime information on 256 vegetation communities in the conterminous United States. This information is taken from the US Forest Service's LANDFIRE Rapid Assessment Vegetation Models, which were developed by local experts using available literature, local data, and/or expert opinion. This table summarizes fire regime characteristics for each plant community listed.
DOI: 10.23719/1521105
title: Datasets for manuscript "A data engineering framework for chemical flow analysis of industrial pollution abatement operations"

description: The EPA GitHub repository PAU4ChemAs as described in the README.md file, contains Python scripts written to build the PAU dataset modules (technologies, capital and operating costs, and chemical prices) for tracking chemical flows transfers, releases estimation, and identification of potential occupation exposure scenarios in pollution abatement units (PAUs). These PAUs are employed for on-site chemical end-of-life management. The folder datasets contains the outputs for each framework step. The Chemicals_in_categories.csv contains the chemicals for the TRI chemical categories. 
The EPA GitHub repository PAU_case_study as described in its readme.md entry, contains the Python scripts to run the manuscript case study for designing the PAUs, the data-driven models, and the decision-making module for chemicals of concern and tracking flow transfers at the end-of-life stage. The data was obtained by means of data engineering using different publicly-available databases. The properties of chemicals were obtained using the GitHub repository Properties_Scraper, while the PAU dataset using the repository PAU4Chem.
Finally, the EPA GitHub repository Properties_Scraper contains a Python script to massively gather information about exposure limits and physical properties from different publicly-available sources: EPA, NOAA, OSHA, and the institute for Occupational Safety and Health of the German Social Accident Insurance (IFA).       
Also, all GitHub repositories describe the Python libraries required for running their code, how to use them, the obtained outputs files after running the Python script modules, and the corresponding EPA Disclaimer.
DOI: 10.23719/1518739
title: Datasets for manuscript "COW2NUTRIENT: An environmental GIS-based decision support tool for the assessment of nutrient recovery systems in livestock facilities."

description: https://github.com/gruizmer/COW2NUTRIENT/tree/master/ToolPaper_DataFiles
* These folders supply supporting datasets for the manuscript "COW2NUTRIENT: An environmental GIS-based decision support tool for the assessment of nutrient recovery systems in livestock facilities." 
* The datasets are recorder as comma-separated values (.csv) and Microsoft Excel® (.xlsx) files. Column data entries have names and units. Some data are about animal facility population and location, amount of nutrient-rich waste generated (kg/yr), amount of nutrient recovered (kg P/yr), installing, capital, and maintenance costs (USD), technologies and their ranking and frequency of being selected for each combination of normalization-aggregation methods, average chlorophyll-a concentration in water in the watershed (ug/L), and average phosphorus concentration in water in the watershed (ug/L). 
* The folder “Manuscript” has subfolders with datasets for creating manuscript Figures 4, 8, 9, and 10 as well as datasets for Tables 9 and 10. 
* The folder “Supplementary Material” holds subfolders with datasets for creating Supplementary Material Figures 1-5, 8, 9, 11, and 12.
DOI: 10.5281/zenodo.8238994
title: Dataset of scientific article: "Effect of miR-34a on expression of clock and clock-controlled genes in human cancer DLD1 and Lovo cells with different backgrounds in respect to p53 functionality and 17β-estradiol-mediated regulation"

description: The dataset includes "raw" data used for the calculation of gene expression, wound healing test, fluorescence intensity, and MTS test.
DOI: 10.5281/zenodo.8238993
title: Dataset of scientific article: "Effect of miR-34a on expression of clock and clock-controlled genes in human cancer DLD1 and Lovo cells with different backgrounds in respect to p53 functionality and 17β-estradiol-mediated regulation"

description: The dataset includes "raw" data used for the calculation of gene expression, wound healing test, fluorescence intensity, and MTS test.
DOI: 10.5281/zenodo.8248332
title: Status Quo and Problems of Requirements Engineering for Machine Learning: Results from an International Survey

description: This folder contains the current data used in the paper named 'Status Quo and Problems of Requirements Engineering for Machine Learning: Results from an International Survey'. We make available a ZIP file containing the survey used, the data collected from it and the Jupyter Notebooks used to build our analysis.
DOI: 10.23719/1523391
title: High-throughput transcriptomics platform for screening hepatotoxicants-NCBI/GEO GSE152128

description: We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.
FASTQ files and read counts data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) (GSE152128).
DOI: 10.23719/1522410
title: NADP Total Deposition Data

description: The data are grids of total atmospheric deposition created through a measurement-model fusion process that uses data from the Community Multiscale Air Quality (CMAQ) modeling system and monitoring data from the National Atmospheric Deposition Deposition Program National Trends Network and the EPA Clean Air Status and Trends Network. Additional information about the development of the data can be found on the NADP TDep website (http://nadp.slh.wisc.edu/committees/tdep/tdepmaps/).
DOI: 10.23719/1522604
title: 16S and ITS amplicon sequencing of reconstructed wetland soil metagenomes

description: Experiments tested if changes in soil microbiomes within reconstructed freshwater wetlands were associated with exposure to elevated Cu concentrations originating from immersed Micronized Copper Azole (MCA) treated wood stakes. Soil samples were collected for amplicon sequencing to quantify responses in microbial communities at 15 timepoints, spanning 2 simulated seasonal dry downs, for up to 678 days.
DOI: 10.6084/m9.figshare.22725845
title: Dataset for "Empirical Analysis of Software Vulnerabilities Causing Timing Side Channels"

description: Dataset and data collection code for "Empirical Analysis of Software Vulnerabilities Causing Timing Side Channels"
DOI: 10.6084/m9.figshare.22725845.v1
title: Dataset for "Empirical Analysis of Software Vulnerabilities Causing Timing Side Channels"

description: Dataset and data collection code for "Empirical Analysis of Software Vulnerabilities Causing Timing Side Channels"
DOI: 10.23719/1524279
title: Determining the Predictive Limit of QSAR Models

description: 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.
DOI: 10.23719/1520939
title: Variables for Alzheimer's analysis (without PII data)

description: Organized by zipcode:
Rates of Alzheimer's disease
Percent of landcover types
Modelled PM2.5
Socioeconomic variables
DOI: 10.23719/1524271
title: EPA_PROBsites_wQ.csv

description: Dataset includes compiled flow/no flow observations from past US EPA probabilistic stream
DOI: 10.23719/1523022
title: Data to support Minucci et al. 2021 Ecological Applications

description: 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.
DOI: 10.23719/1524267
title: Figures for EPA White Paper EPA-454/R-21-008: Overview of Progress and Findings from the Cross-EPA Coordination Effort for Understanding and Evaluating NOx Emissions Discrepancies

description: This white paper describes the EPA exploration of a reported discrepancy between estimates of NOX and reactive nitrogen (NOY) concentrations from the Community Multiscale Air Quality (CMAQ) model and ambient measurements.  The paper summarizes analysis that has been published in Toro et al. (2021) and Appel et al. (2017).  The data used in those publications is publicly available from Zenodo and data.gov (links below). 

Figures 1-2:  Appel, et. al, 2017, STICS ORD-018177
Appel, K.W., Napelenok, S.L, Foley, K.M., Pye, H.O.T., Hogrefe, C., Luecken, D.J., Bash, J.O., Roselle, S.J., Pleim, J.E., Foroutan, H., Hutzell, W.T., Pouliot, G.A., Sarwar, G., Fahey, K.M., Gantt, B., Gilliam, R.C., Heath, N.K., Kang, D., Mathur, R., Schwede, D.B., Spero, T.L., Wong, D.C., Young, J.O. (2017) Description and evaluation of the Community Multiscale Air Quality (CMAQ) modeling system version 5.1. Geoscientific Model Development, 10, 1703-1732. https://doi.org/10.5194/gmd-10-1703-2017
DATA:  https://catalog.data.gov/dataset/site-compare-scripts-and-output

Figures 4-10: Toro et. al, 2021, STICS  ORD-039261
Toro, C., Foley, K., Simon, H., Henderson, B., Baker, K.R., Eyth, A., Timin, B., Appel, K.W., Luecken, D., Beardsley, M., Sonntag, D., Possiel, N., Roberts, S. (2021) Evaluation of 15 years of modeled NOX across the contiguous United States. Elementa: Science of the Anthropocene, 9(1). DOI: https://doi.org/10.1525/elementa.2020.20.00158.
DATA:  https://zenodo.org/record/4633517#.YZ0mkNDMJPY

Figure 11 - US EPA 2021 MOVES Technical Report
U.S. EPA (2021c). Overview of EPA’s MOtor Vehicle Emission Simulator (MOVES3).  EPA-420-R-21-004. Office of Transportation and Air Quality, Ann Arbor, MI,  March 2021, https://www.epa.gov/moves/moves-technical-reports.
DOI: 10.23719/1524371
title: 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

description: 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"
DOI: 10.5281/zenodo.8248395
title: 3D Global MHD Simulation in northward IMF

description: MHD data was used in the paper "Identifying and Visualizing Terrestrial Magnetospheric Topology using Geodesic Level Set Method." File 271xyz.mat: xyz grid data 271btotal.mat: physical data nulldata271.mat: magnetic null points coordinates cubic grid size: 241x161x161<br>
DOI: 10.5281/zenodo.8248394
title: 3D Global MHD Simulation in northward IMF

description: MHD data was used in the paper "Identifying and Visualizing Terrestrial Magnetospheric Topology using Geodesic Level Set Method." File 271xyz.mat: xyz grid data 271btotal.mat: physical data nulldata271.mat: magnetic null points coordinates cubic grid size: 241x161x161<br>
DOI: 10.23719/1522631
title: Shell Day Data

description: “Shell Day” was a single-day regional water monitoring event coordinating simultaneous coastal carbonate chemistry observations by 59 community science programs and 7 research institutions in the northeastern United States, in which 410 total alkalinity (TA) samples from 86 stations were collected. Samples were collected at low, mid, and high tide by community science volunteers and brought to partnering research laboratories for sample processing. Minimum requirements for participation in Shell Day were the capacity to measure water temperature and salinity – some organizations used thermometers and refractometers, and others used multiparameter datasondes or handheld units. An analysis and interpretation of the temperature, salinity, and total alkalinity data can be found at Rheuban et al 2020 Environ. Res. Lett. in press https://doi.org/10.1088/1748-9326/abcb39. Included in this dataset are measurements of water temperature, salinity, total alkalinity, pH, dissolved oxygen concentration, dissolved oxygen saturation, total depth, secchi disk depth, chlorophyll, turbidity, as well as air temperature and barometric pressure, and qualitative assessments of wind, weather, and cloud cover.
DOI: 10.23719/1503378
title: Bisphenol A and triclosan levels in individual food items

description: Bisphenol A and triclosan levels in individual food items consumed by 50 adults over six-weeks
DOI: 10.23719/1519259
title: Potential for electric vehicle adoption to mitigate extreme air quality events in China study dataset (please contact Dr. Jordan Schnell (jordan.schnell@noaa.gov) to obtain a copy of the data)

description: simulation results
DOI: 10.23719/1524265
title: Mimicking atmospheric photochemical modeling with a deep neural network

description: Air quality modeling for China
DOI: 10.23719/1504594
title: Air Pollution and Health in the Jackson Heart Study: a Cohort of African Americans in Jackson, Mississippi

description: Data include individual-level health data, including results from cardiovascular tests and medical history. This is linked to air quality data at participants' residence.
DOI: 10.23719/1521109
title: Biological Measurements for Dosed Model Organism

description: Serum PFAS concentrations, pup weights, liver histopathology measurements, lipid panels, fasting insulin measurements
DOI: 10.23719/1520760
title: USGS Feral Swine Dataset

description: The dataset contains quantitative polymerase chain reaction data for microbial source tracking markers screened on water samples collected from streams and rivers within and bounding Congaree National Park from samples collected throughout the year from December 2017 through June 2019. The number of samples collected per event ranged from 4-16 over the span of 11 sample events
DOI: 10.23719/1518473
title: Copyright images from Digital Globe WorldView satellite

description: Copyright images from Digital Globe WorldView satellite
DOI: 10.23719/1520871
title: Cyanobacterial frequency at drinking water intakes

description: This study presents the first large-scale assessment of cyanobacterial frequency and abundance at surface drinking water intakes across the United States. Public water systems serve drinking water to nearly 90% of the United States population. Cyanobacteria and their toxins may degrade the quality of finished drinking water and can lead to negative health consequences. Satellite imagery can serve as a cost-effective and consistent monitoring technique for surface cyanobacterial blooms in source waters and can provide drinking water treatment operators information for managing their systems. This study uses satellite imagery from the European Space Agency’s Ocean and Land Colour Instrument (OLCI) spanning June 2016 through April 2020. At 300-m spatial resolution, OLCI imagery can be used to monitor cyanobacteria in 685 drinking water sources across 285 lakes in 44 states. First, a subset of satellite data was compared to a subset of 99 responses submitted as part of the U.S. Environmental Protection Agency’s fourth Unregulated Contaminant Monitoring Rule (UCMR 4). These UCMR 4 quantitative responses included visual observations of algal bloom presence and absence near drinking water intakes from March 2018 through November 2019. Overall agreement between satellite imagery and UCMR 4 qualitative responses was high at over 94% with a Kappa coefficient of 0.70. Next, temporal frequency of cyanobacterial blooms at all resolvable drinking water sources was assessed. In 2019, bloom frequency averaged 2% and peaked at 100%, where 100% indicated a bloom was always present at the source waters when satellite imagery was available. Monthly cyanobacterial abundances were used to assess short-term trends across all resolvable drinking water sources. Generally, 2016-2020 was an insufficient time period for observing changes at these source waters; On average, a decade of data would be required for observed trends to outweigh variability in the data. However, five source waters did demonstrate a sustained short-term trend, with one increasing in cyanobacterial abundance from June 2016 to April 2020 and four decreasing.
DOI: 10.23719/1520623
title: Identifying chemicals and mixtures of potential biological concern detected in passive samplers from Great Lakes tributaries using high-throughput data and biological pathways

description: Water-borne contaminants were monitored in 69 tributaries of the Laurentian Great Lakes in 2010 and 2014 using semipermeable membrane devices (SPMDs), and polar organic chemical integrative samplers (POCIS).  Analyses included 185 chemicals (143 detected) including PAHs, legacy and current-use pesticides, fire retardants, pharmaceuticals, fragrances, and others.  Hazard quotients were calculated by dividing detected concentrations by biological effect concentrations reported in the ECOTOX Knowledgebase (Toxicity quotients, TQs) or ToxCast database (Exposure Activity Ratios, EARs).
DOI: 10.23719/1502612
title: Ex-R Study Urine Data

description: Emory University (analyzed the urine samples for pyrethroid metabolites)
DOI: 10.23719/1518522
title: A spatially explicit, empirical estimate of biological nitrogen fixation in forests of the United States

description: The supplementary information provides details on the methods used to find the basal area-BNF rate regression, the specific literature that was used to derive both these regressions and the %Ndfa for different genera. The text describes further methods used to compare previous global estimates of BNF to the conterminous US scale and to examine the relevance of P. contorta as an additional source of N.
DOI: 10.23719/1520471
title: Generalised Read-Across Prediction using genra-py 

description: Read-across (RAX) is a widely used data gap filling approach and the authors have developed a data-driven tool, called GenRA, to support expert-driven RAX. This work describes a stand-alone Python 3 package, called genra-py, which enables end-users to conduct hazard identification and point of departure (POD) estimation using GenRA.