cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23949519
title: <b>Evidence that multiple anthropogenic stressors cumulatively affect foraging and vigilance behaviour in an urban-living bird</b>

description: Data set for manuscript entitled '<b>Evidence that multiple anthropogenic stressors cumulatively affect foraging and vigilance behaviour in an urban-living bird</b>'
DOI: 10.5281/zenodo.7597517
title: Supplemental materials for studying GPU programming with Stack Overflow posts

description: It includes the data used in our study of GPU programming and the complete results obtained from the study.
DOI: 10.5281/zenodo.7597518
title: Supplemental materials for studying GPU programming with Stack Overflow posts

description: It includes the data used in our study of GPU programming and the complete results obtained from the study.
DOI: 10.6084/m9.figshare.23949522
title: The zooxanthellae density and stable nitrogen isotope data

description: The zooxanthellae density and stable nitrogen isotope data used in the paper.
DOI: 10.6084/m9.figshare.23949522.v1
title: The zooxanthellae density and stable nitrogen isotope data

description: The zooxanthellae density and stable nitrogen isotope data used in the paper.
DOI: 10.5281/zenodo.8248161
title: Supplemental materials for studying GPU programming with Stack Overflow posts

description: It includes the data used in our study of GPU programming and the complete results obtained from the study.
DOI: 10.5281/zenodo.8248160
title: Supplemental materials for studying GPU programming with Stack Overflow posts

description: It includes the data used in our study of GPU programming and the complete results obtained from the study.
DOI: 10.23719/1390068
title: HexSim

description: Not applicable
DOI: 10.23719/1367522
title: The Application of a Highly Purified Rat Leydig Cell Assay as a Complement to the H295R Steroidogenesis Assay for the Evaluation of Toxicant Induced Alterations in Testosterone Production

description: The greater dynamic range of testosterone production in a highly purified rat Leydig cell assay permitted the detection of chemical induced inhibition that was not detected by the high throughput screening format of the H295R steroidogenesis assay.
DOI: 10.23719/1367565
title: NWCA 2011 Soil Chemistry - Data

description: NWCA 2011 Soil Chemistry Data
DOI: 10.23719/1369565
title: First Generation Annotations for the Fathead Minnow (Pimephales promelas) Genome

description: The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks.
DOI: 10.23719/1373748
title: Soil organic matter and amphibian exposure dataset.

description: Dermal uptake from soil is known to occur in amphibians, but predicting pesticide availability and bioconcentration across soil types is not well understood. The present study was designed to compare uptake of 5 current-use pesticides (imidacloprid, atrazine, triadimefon, fipronil, and pendimethalin) in American toads (Bufo americanus) from exposure on soils with significant organic matter content differences (14.1% = high organic matter and 3.1% = low organic matter). We placed toads on high- or low-organic matter soil after applying individual current-use pesticides on the soil surface for an 8-h exposure duration. Whole body tissue homogenates and soils were extracted and analyzed using liquid chromatography–mass spectrometry to determine pesticide tissue and soil concentration, as well as bioconcentration factor in toads. Tissue concentrations were greater on the low-organic matter soil than the high-organic matter soil across all pesticides (average ± standard error; 1.23 ± 0.35 ppm and 0.78 ± 0.23 ppm, respectively), and bioconcentration was significantly higher for toads on the low-organic matter soil (analysis of covariance p = 0.002). Soil organic matter is known to play a significant role in the mobility of pesticides and bioavailability to living organisms. Agricultural soils typically have relatively lower organic matter content and serve as a functional habitat for amphibians. The potential for pesticide accumulation in amphibians moving throughout agricultural landscapes may be greater and should be considered in conservation and policy efforts
DOI: 10.23719/1373743
title: amphibian_biomarker_data

description: Amphibian metabolite data used in Snyder, M.N., Henderson, W.M., Glinski, D.G., Purucker, S. T., 2017. Biomarker analysis of american toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles following exposure to atrazine. Aquatic Toxicology, 182(184-193). doi: 10.1016/j.aquatox.2016.11.018.
DOI: 10.23719/1374152
title: WRF Model Output

description: This dataset contains WRF model output.  There are three months of data: July 2012, July 2013, and January 2013.  For each month, several simulations were made: A control and two lightning assimilation runs using different suppression techniques.  For July 2012, and additional simulation was made with a third suppression technique.  Please refer to the manuscript for a full description of each simulation.
DOI: 10.23719/1371573
title: A case study on the use of exposure-activity ratios (EARs) to prioritize sites, chemicals, and bioactivities of concern in Great Lakes waters

description: As a case study, chemical occurrence data from a 2012 study in the Great Lakes Basin along with the ToxCast™ effects database were used to calculate exposure-activity ratios (EARs) as a prioritization tool. Technical considerations of data processing and use of the ToxCast™ database are presented and discussed. EAR prioritization identified multiple sites, biological pathways, and chemicals that warrant further investigation. Biological pathways were then linked to adverse outcome pathways to identify potential adverse outcomes and biomarkers for use in subsequent monitoring efforts.
DOI: 10.23719/1375430
title: Association between adverse cardiovascular outcomes and PM2.5 data obtained from monitors, CMAQ models, and satellite models.

description: Background: Adverse cardiovascular events have been linked with PM2.5 exposure obtained primarily from air
quality monitors, which rarely co-locate with participant residences. Modeled PM2.5 predictions at finer resolution
may more accurately predict residential exposure; however few studies have compared results across
different exposure assessment methods.
Methods: We utilized a cohort of 5679 patients who had undergone a cardiac catheterization between
2002–2009 and resided in NC. Exposure to PM2.5 for the year prior to catheterization was estimated using data
from air quality monitors (AQS), Community Multiscale Air Quality (CMAQ) fused models at the census tract and
12 km spatial resolutions, and satellite-based models at 10 km and 1 km resolutions. Case status was either a
coronary artery disease (CAD) index>23 or a recent myocardial infarction (MI). Logistic regression was used to
model odds of having CAD or an MI with each 1-unit (μg/m3) increase in PM2.5, adjusting for sex, race, smoking
status, socioeconomic status, and urban/rural status.
Results: We found that the elevated odds for CAD>23 and MI were nearly equivalent for all exposure assessment
methods. One difference was that data from AQS and the census tract CMAQ showed a rural/urban difference
in relative risk, which was not apparent with the satellite or 12 km-CMAQ models.
Conclusions: Long-term air pollution exposure was associated with coronary artery disease for both modeled and
monitored data.
DOI: 10.23719/1372883
title: Literature review tables for Karna et al. 2017

description: N/A. Users will need to access the manuscript to see non-EPA data presented in tables and figures.
DOI: 10.23719/1372884
title: Understanding arsenic dynamics in agronomic systems to predict and prevent uptake by crop plants

description: N/A. This is a review article and no data were generated in the process of the review.
DOI: 10.23719/1375439
title: NLCD - MODIS land cover- albedo dataset for the continental United States

description: The NLCD-MODIS land cover-albedo database integrates high-quality MODIS albedo observations with areas of homogeneous land cover from NLCD. The spatial resolution (pixel size) of the database is 480m-x-480m aligned to the standardized UGSG Albers Equal-Area projection. The spatial extent of the database is the continental United States.
DOI: 10.23719/1377811
title: Gomphid DNA sequence data

description: DNA sequence data for several genetic loci.
DOI: 10.23719/1378322
title: Conolly, R.B., Ankley, G.T., Cheng, WY., Mayo, M.L., Miller, D.H., Perkins, E.J., Villeneuve, D.L., and Watanable, K.H. (2017). Quantitative adverse outcome pathways and their application ot predictive toxicology. Environ. Sci. Technol. 51, 4661–4672

description: A publised mansucript describing a quantitative adverse outcome pathway (qAOP) and its relevance to risk assessment.
DOI: 10.23719/1378449
title: Datasets will not be made accessible to the public due to the fact that they include household level data with PII.

description: Datasets will not be made accessible to the public due to the fact that they include household level data with PII.
DOI: 10.23719/1380229
title: UCMR3 data

description: Zipped UCMR3 data
DOI: 10.23719/1379481
title: Global Mercury Observation System (GMOS) surface observation data from around the world.

description: GMOS Network Data
DOI: 10.23719/1389321
title: Sustainable pathway to furanics from biomass via heterogeneous organo-catalysis

description: Electronic supplementary information provides all the data
DOI: 10.23719/1389545
title: A sustainable approach to empower the bio-based future: upgrading of biomass via process intensification

description: An economically viable and environmentally benign continuous flow intensified process has been developed that demonstrates its ability to upgrade biomass into potential biofuels, solvents, and pharmaceutical feedstocks using a bimetallic AgPd@g-C3N4 catalyst.
DOI: 10.23719/1389860
title: European Centre for Medium-Range Weather Forecasts

description: Global sea surface temperature (SST) anomalies can affect terrestrial precipitation via ocean-atmosphere interaction known as climate teleconnection. Non-stationary and non-linear characteristics of the ocean-atmosphere system make the identification of the teleconnection signals difficult to be detected at a local scale as it could cause large uncertainties when using linear correlation analysis only. This paper explores the relationship between global SST and terrestrial precipitation with respect to long-term non-stationary teleconnection signals during 1981-2010 over three regions in North America and one in Central America. Empirical mode decomposition as well as wavelet analysis is utilized to extract the intrinsic trend and the dominant oscillation of the SST and precipitation time series in sequence.  After finding possible associations between the dominant oscillation of seasonal precipitation and global SST through lagged correlation analysis, the statistically significant SST regions are extracted based on the correlation coefficient. With these characterized associations, individual contribution of these SST forcing regions linked to the related precipitation responses are further quantified through nonlinear modeling with the aid of extreme learning machine. Results indicate that the non-leading SST regions also contribute a salient portion to the terrestrial precipitation variability compared to some known leading SST regions. In some cases, these estimated contributions reveals some clues of the coupling interactions between oceanic and atmospheric processes.
DOI: 10.23719/1390705
title: Dilbit Data

description: The data is in the form of degradation of hydrocarbons over time at two temperatures and the relative abundance of bacterial taxa identified in the microcosms
DOI: 10.23719/1390706
title: Accumulibacter data

description: Number of gene copies associated with phosphate accumulation using qPCR and relative abundance of bacterial groups
DOI: 10.23719/1390250
title: Identifying Known Unknowns Using the USEPA CompTox Chemistry Dashboard AnalytBioanlytChem Data

description: In this research, the performance of the Dashboard for identifying “known unknowns” was evaluated against that of the online ChemSpider database, one of the primary resources used by mass spectrometrists, using multiple previously studied datasets reported in the peer-reviewed literature totaling 162 chemicals. These chemicals were examined using both applications via molecular formula and monoisotopic mass searches followed by rank-ordering of candidate compounds by associated references or data sources.  A greater percentage of chemicals ranked in the top position when using the Dashboard, indicating an advantage of this application over ChemSpider for identifying known unknowns using data source ranking. Additional approaches are being developed for inclusion into a non-targeted analysis workflow as part of the CompTox Chemistry Dashboard.
DOI: 10.23719/1379478
title: Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169T version MRBR00000000.1

description: The dataset contains the first draft genome sequence of the type strain of Mycobacterium chimaera, Fl-0169.
DOI: 10.23719/1390232
title: Mixing at double-Tee junctions with unequal pipe sizes in water distribution systems

description: Pipe flow mixing with various solute concentrations and flow rates at pipe junctions is investigated. The degree of mixing affects the spread of contaminants in a water distribution system. Many studies have been conducted on the mixing at the cross junctions. Yet few have focused on double-Tee junctions of unequal pipe sizes. To investigate the solute mixing at double-Tee junctions with unequal pipe sizes, a series of experiments were conducted in a turbulent regime (Re=12500–50000) with different Reynolds number ratios and connecting pipe lengths. It is found that dimensionless outlet concentrations depended on mixing mechanism at the impinging interface of pipe junctions. Junction with a larger pipe size ratio is associated with more complete mixing. The inlet Reynolds number ratio affects mixing more strongly than the outlet Reynolds number ratio. Furthermore, the dimensionless connecting pipe length in a double-Tee played an important and complicated role in the flow mixing. Based on these results, two-dimensional isopleth maps were developed for the calculation of normalized north outlet concentration.
DOI: 10.23719/1393586
title: Climiate Resilience Screening Index and Domain Scores

description: CRSI and related-domain scores for all 50 states and 3135 counties in the U.S.
DOI: 10.23719/1392996
title: Retrospective_Mining_of_Tox_Data_Anemia_Case_Study_RegToxPharm Data

description: Data from a study to critically examine some of the issues of using data from ToxRefDB, a database largely composed of guideline studies for pesticidal active ingredients, using a case study focusing on chemically-induced anemia.
DOI: 10.23719/1395041
title: Computational Model of Secondary Palate Fusion and Disruption ChemResTox Data

description: Morphogenetic events are driven by cell-generated physical forces and complex cellular dynamics. To improve our capacity to predict developmental effects from cellular alterations, we built a multi-cellular agent-based model in CompuCell3D that recapitulates the cellular networks and collective cell behavior underlying growth and fusion of the mammalian secondary palate. The model incorporated multiple signaling pathways (TGF?, BMP, FGF, EGF, SHH) in a biological framework to recapitulate morphogenetic events from palatal outgrowth through midline fusion. It effectively simulated higher-level phenotypes (e.g., midline contact, medial edge seam (MES) breakdown, mesenchymal confluence, fusion defects) in response to genetic or environmental perturbations. Perturbation analysis of various control features revealed model functionality with respect to cell signaling systems and feedback loops for growth and fusion, diverse individual cell behaviors and collective cellular behavior leading to physical contact and midline fusion, and quantitative analysis of the TGF/EGF switch that controls MES breakdown – a key event in morphogenetic fusion. The virtual palate model was then executed with theoretical chemical perturbation scenarios to simulate switch behavior leading to a disruption of fusion following chronic (e.g., dioxin) and acute (e.g., retinoic acid, hydrocortisone) toxicant exposures. This computer model adds to similar systems models toward a ‘virtual embryo’ for simulation and quantitative prediction of adverse developmental outcomes following genetic perturbation and/or environmental
DOI: 10.23719/1390267
title: HTTK R Package v1.4 - JSS Article on HTTK: R Package for High-Throughput Toxicokinetics

description: httk: High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
DOI: 10.23719/1390268
title: HTTK R Package v1.5 - Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability

description: httk: High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK").
DOI: 10.23719/1394621
title: Judson_Mansouri_Automated_Chemical_Curation_QSAREnvRes_Data

description: Here we describe the development of an automated  KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publically available PHYSPROP physico-chemical properties and environmental fate datasets. The workflow first assembles structure-identity pairs using up to four provided chemical identifiers, including chemical name, CASRNs, SMILES, and MolBlock. Problems detected  included errors and mismatches in chemical structure formats, identifiers, and various structure validation issues, including hypervalency and stereochemistry descriptions. Subsequently, a machine learning procedure was applied to evaluate the impact of this curation process. The performance of QSAR models built on only the highest quality subset of the original dataset was compared to the larger curated and corrected data set. The latter showed statistically improved predictive performance. The final workflow was used to curate the full list of PHYSPROP datasets, and is being made publically available for further usage and integration by the scientific community.
DOI: 10.23719/1395040
title: IATA-Bayesian Network Model for Skin Sensitization Data

description: Since the publication of the Adverse Outcome Pathway (AOP) for skin sensitization, there have been many efforts to develop systematic approaches to integrate the information generated from different key events for decision making. The types of information characterizing key events in an AOP can be generated from in silico, in chemico, in vitro or in vivo approaches. Integration of this information and interpretation for decision making are known as integrated approaches to testing and assessment or IATA. One such IATA that has been developed was published by Jaworska et al (2013) which describes a Bayesian network model known as ITS-2. The current work evaluated the performance of ITS-2 using a stratified cross validation approach.  We also characterized the impact of refinements to the network by replacing the most significant component, the output from a commercial expert system TIMES-SS with structural alert information readily generated from the freely available OECD QSAR Toolbox. Lack of any structural alert flags or TIMES-SS predictions, yielded a sensitization potential prediction of 79% +3%/-4%. If the TIMES-SS prediction was replaced by an indicator for the presence of a structural alert, the network predictivity increased to 84% +2%/-4%, which was only slightly less than found for the original network (89% &plusmn;2%). The local applicability domain of the original ITS-2 network was also evaluated using reaction mechanistic domains to better understand what types of chemicals ITS-2 was able to make the best predictions for &ndash; i.e. a local validity domain analysis.  We ultimately found that the original network was successful at predicting which chemicals would be sensitizers, but not at predicting their relative potency.
DOI: 10.23719/1395052
title: Identifying Prevalent Chemical Mixtures in the US Population EHP Data

description: Frequent itemset mining (FIM), a technique used for finding patterns in consumer purchasing behavior, can be applied to data from large-scale biomonitoring studies to identify combinations of chemicals that frequently co-occur in people. As a proof of concept, we applied FIM to biomonitoring data from the National Health and Nutrition Examination Survey. In this way, we identified 90 chemical combinations consisting of relatively few chemicals that occur in at least 30% of the US population, as well as 3 super-combinations consisting of relatively many chemicals that occur in a small but non-negligible proportion of the US population. Thus, we have demonstrated a technique for narrowing a large number of possible chemical combinations down to a much smaller collection of prevalent chemical combinations.