cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1427471
title: Fitzpatrick_Jeremy_Skin_Sensitization_Data

description: Allergic contact dermatitis (ACD) is estimated to constitute about 10-15% of all occupational diseases. Predictive testing to characterise substances for their skin sensitisation potential has historically been based on animal models such as the Local Lymph Node Assay (LLNA) and the Guinea Pig Maximisation Test (GPMT). In recent years, EU regulations, have provided a strong incentive to develop non-animal alternatives.  Significant progress has been made in developing and evaluating non-animal test methods. There have been efforts to develop and evaluate the utility of in silico models for skin sensitisation including local and global (Q)SARs as well as expert systems. In this study, we selected three different types of expert systems: VEGA (statistical), Derek Nexus (knowledge based), TIMES-SS (hybrid) and evaluated their performance using 2 large datasets of substances that had been assessed for their skin sensitisation potential in animal models. We considered a model to be successful at predicting skin sensitisation potential if it had at least the same balanced accuracy as the LLNA and the GPMT had in predicting the outcomes of one another, which ranged from 79% to 86% depending on the dataset.  We found that none of the expert systems evaluated was able to achieve such a high balanced accuracy in their global predictions, with balanced accuracies ranging from 56% to 65%.  However, for substances within the domain of TIMES-SS, balanced accuracies were found to be 79% and 82%, for the two datasets, in line with the animal data. The expert systems evaluated could be extended in light of the additional data collected as part of this study. The incorrect predictions offer new insights for how the existing alerts within these expert systems could be refined. These datasets also offer exciting opportunities for the development of new models.
DOI: 10.23719/1407570
title: Adult FHM liver gene expression - treated with EE2

description: Male adult FHM liver treated with EE2 - gene expresssion - Agilent-036574 FHM_8x60K_V2 array design
DOI: 10.23719/1407571
title: amphibian_dehydration_uptake_data

description: Bioconcentration data for Glinski DA, Henderson WM, Van Meter RJ, Purucker ST 2017. Effect of hydration status on pesticide uptake in anurans following exposure to contaminated soils.
DOI: 10.23719/1407622
title: National Aquatic Resources Survey datasets

description: The 4 resource surveys (coastal, rivers and streams, lakes and reservoirs, and wetlands) each have datasets covering the biological, chemical, physical habitat, hydrologic and watershed data.
DOI: 10.23719/1390130
title: Cookstove data

description: No dataset available
DOI: 10.23719/1502593
title: Changes in gene expression in Arabidopsis in response to nano CeO2 and nano TiO2

description: - Changes in tissue transcriptomes and productivity of Arabidopsis thaliana were investigated during exposure of plants to two widely used engineered metal oxide nanoparticles, titanium dioxide (nano-titanium) and cerium dioxide (nano-cerium). Microarray analyses confirmed that exposure to either nanoparticle altered the transcriptomes of rosette leaves and roots, with comparatively larger numbers of differentially expressed genes (DEGs) found under nano-titania exposure. Nano-titania induced more DEGs in rosette leaves, whereas roots had more DEGs under nano-ceria exposure.  MapMan analyses indicated that while nano-titania up-regulated overall metabolism metabolism in both tissues, metabolic processes under nano-ceria remained mostly unchanged. Gene enrichment analysis indicated that both nanoparticles mainly enriched ontology groups such as responses to stress (abiotic and biotic), and defense responses (pathogens), and responses to endogenous stimuli (hormones). Nano-titania specifically induced genes associated with photosynthesis, whereas nano-ceria induced expression of genes related to activating transcription factors, most notably those belonging to the ethylene responsive element binding protein family.  Interestingly, there were also increased numbers of rosette leaves and plant biomass under nano-ceria exposure, but not under nano-titania. Other transcriptomic responses did not clearly relate to responses observed at the organism level. This may be due to functional and genomic redundancy in Arabidopsis, which may mask expression of morphological changes, despite discernable responses at the transcriptome level. Additionally, transcriptomic changes often relate with transgenerational phenotypic development, hence it may be productive to direct further experimental work to integrate high-throughput genomic results with longer-term changes in subsequent generations.
DOI: 10.5281/zenodo.8239942
title: Quilt-1M: One Million Image-Text Pairs for Histopathology

description: Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of similar data in the medical field, specifically in histopathology, has slowed similar progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 802,148 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models), handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets, from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new pathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.
description: This version of the dataset has images resized to 512px by 512px, for the original variable-sized images between 1920px -320px please use the Google form to request restricted and timed access to the dataset, see https://quilt1m.github.io/.
DOI: 10.23719/1390262
title: HTTK R Package v1.7 - Evaluation and Calibration of High-Throughput Predictions of Chemical Distribution to Tissues

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: 10.5281/zenodo.8239941
title: Quilt-1M: One Million Image-Text Pairs for Histopathology

description: Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of similar data in the medical field, specifically in histopathology, has slowed similar progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 802,148 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models), handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets, from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new pathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.
description: This version of the dataset has images resized to 512px by 512px, for the original variable-sized images between 1920px -320px please use the Google form to request restricted and timed access to the dataset, see https://quilt1m.github.io/.
DOI: 10.23719/1407700
title: Simmons_DeGroot_Metabolism_mRNA_transfection_ApplInVitroTox_Data

description: The US EPA’s ToxCast program is designed to assess chemical perturbations of molecular and cellular endpoints using a variety of high-throughput screening (HTS) assays. However, existing HTS assays have limited or no xenobiotic metabolism which could lead to false positive (chemical is detoxified in vivo) as well as false negative results (chemical is bioactivated in vivo) and thus potential mischaracterization of chemical hazard. We have addressed this challenge by introducing the ten most prevalent human liver cytochrome P450 (CYP) enzymes into a human cell line (HEK293T) with low endogenous metabolic capacity. The CYP enzymes were introduced via transfection of modified mRNAs as singlets or as a mixture in relative proportions expressed in the liver. Initial experiments using luminogenic CYP450 substrates demonstrate that cell models express metabolic enzymes from the transfected mRNAs and activities are significantly increased when co-transfected with a CYP accessory protein, P450 oxidoreductase (POR). Transfected HEK293T cells demonstrate the ability to produce predicted metabolites following treatment with well-studied CYP substrates, with metabolite formation occurring through 18 hours post-treatment. As a demonstration of how this method can be used to retrofit existing HTS assays, a proof-of-concept screen for cytotoxicity in HEK293T cells was conducted using 56 test compounds. The results demonstrate that the xenobiotic metabolism conferred by transfection of CYP-encoding mRNAs shifts the dose-response relationship for certain test chemicals such as aflatoxin B1 (bioactivation) and fenazaquin (detoxification). Overall, transfection of CYP-encoding mRNAs is an effective and portable solution for retrofitting metabolic competence to existing cell-based HTS assays.
DOI: 10.23719/1434298
title: Model codes and run scripts developed for the addition of Four-Dimensional Data Assimilation (FDDA) to the Model for Prediction Across Scales - Atmosphere (MPAS-A)

description: Web link to a Zenodo repository containing Model codes, run scripts, the computational mesh definition file, and user instructions for the addition of Four-Dimensional Data Assimilation (FDDA) to the Model for Prediction Across Scales - Atmosphere (MPAS-A)
DOI: 10.23719/1369042
title: Placeholder

description: Placeholder
DOI: 10.23719/1431211
title: Evaluation of Formaldehyde Column Observations by Pandora Spectrometers

description: Data collected for this research provides information on mixing heights, surface and column formaldehyde during the KORUS-AQ field campaign and over two research sites in South Korea.
DOI: 10.23719/1502526
title: Additional benefits of federal air quality rules: model estimates of controllable biogenic secondary organic aerosol

description: Dataset is a link to the publically available CMAQ v5.1 model code. The following update was also implemented: 
https://github.com/USEPA/CMAQ/blob/5.2/CCTM/docs/Release_Notes/AH3OPJ_IEPOX_update.md
DOI: 10.23719/1407540
title: Mechanistic modeling of insecticide risks to breeding birds in North American agroecosystems

description: This dataset provides all parameter values necessary to replicate the TIM/MCnest model analysis reported in the manuscript "Mechanistic modeling of insecticide risks to breeding birds in North American agroecosystems"
DOI: 10.23719/1392351
title: Greenhouse gas emissions from lakes and reservoirs. MS in review.

description: Reported carbon dioxide, methane, and nitrous emission rates from lakes and reservoirs across the globe.
DOI: 10.17909/0njr-8110
title: Transmission spectra observations of GJ 1132b (NIRSpec G395H)

description: Transmission spectra observations of the super-Earth GJ 1132b with NIRSpec G395H. Taken as part of JWST Cycle 1 GO Program # 1981.
DOI: 10.23719/1503691
title: MMartin_DFiler_tcpl: the ToxCast pipeline for high-throughput screening data

description: The tcpl package provides a set of tools for processing and modeling high-throughput and high-content chemical screening data.
DOI: 10.23719/1503692
title: Judson_Kleinstreuer_Development and Validation of a Computational Model for Androgen Receptor Activity.

description: Data on 1855 chemicals were generated during ToxCast Phases I and II and Tox21 screening using 11 AR-related in vitro assays to build a computational network model for AR pathway activity.
DOI: 10.23719/1398252
title: Data for Fig. 1 and lake-size by chla distribution

description: Contains the raw data used to generate Fig. 1 and the associated models.  The data also contains the joint lake-size by chla distribution used for the upscaling.
DOI: 10.23719/1503726
title: Total Deposition of Nitrogen and Sulfur from Measurement-Model Fusion for 2010

description: Deposition values for the continguous United States are developed from a measurement-model fusion approach that used data from the Community Multiscale Air Quality Model and the Clean Air Status and Trends Network.
DOI: 10.23719/1424215
title: Dataset for targeted and non-targeted analysis of firefighter breath samples

description: This dataset includes a list of chemicals used to create the ChromGenius retention time prediction model used for validation of non-targeted compounds. The list of identified non-targeted compounds in the samples is also provided.
DOI: 10.23719/1503049
title: Urban Greenery and Body Mass Index

description: The datasets include individual-level BMI in Phoenix, AZ and Portland, OR obtained from the state DMVs, greenery along walkable roads within 500, 1000, 1500, and 2000 network buffers, and covariates.
DOI: 10.23719/1502563
title: Bunker Hill Superfund Site (BHSS) soil and dust ingestion

description: Longitudinal environmental Pb concentration data, children's blood Pb levels, bioavailability information and estimated soil and dust ingestion rates by age for children exposed to Pb at the BHSS
DOI: 10.23719/1502470
title: Screening an alternative flame retardant using biological and transcriptomic endpoints in fish embryos 

description: GEO accession information for omics RNA-seq data
DOI: 10.23719/1503075
title: Associations between access to healthcare, environmental quality, and end-stage renal disease survival time: proportional-hazards models of over 1,000,000 people over 14 years

description: The USRDS is the largest and most comprehensive national ESRD surveillance system in the US (Collins et al., 2015). The USRDS contains data on all ESRD cases in the US through the Medical Evidence Report CMS-2728 which is mandated for all new patients diagnosed with ESRD (Foley and Collins, 2013). Detailed information about the USRDS can be found on their website (http://www.usrds.org). 

The EQI was constructed for 2000-2005 for all US counties and is composed of five domains (air, water, built, land, and sociodemographic), each composed of variables to represent the environmental quality of that domain. Domain-specific EQIs were developed using principal components analysis (PCA) to reduce these variables within each domain while the overall EQI was constructed from a second PCA from these individual domains (L. C. Messer et al., 2014). To account for differences in environment across rural and urban counties, the overall and domain-specific EQIs were stratified by rural urban continuum codes (RUCCs) (U.S. Department of Agriculture, 2015).
DOI: 10.23719/1503871
title: Associations between environmental quality and infant mortality in the United States, 2000-2005

description: Infant mortality was defined as death before completion of first year of life [1]. We obtained linked birth and infant death data from the U.S. Centers for Disease Control and Prevention for the years 2000–2005, corresponding to the time frame covered by the EQI.

The EQI was constructed for 2000-2005 for all US counties and is composed of five domains (air, water, built, land, and sociodemographic), each composed of variables to represent the environmental quality of that domain. Domain-specific EQIs were developed using principal components analysis (PCA) to reduce these variables within each domain while the overall EQI was constructed from a second PCA from these individual domains (L. C. Messer et al., 2014). To account for differences in environment across rural and urban counties, the overall and domain-specific EQIs were stratified by rural urban continuum codes (RUCCs) (U.S. Department of Agriculture, 2015).
DOI: 10.23719/1503872
title: Associations between environmental quality and adult asthma prevalence in medical claims data

description: The MarketScan health claims database is a compilation of nearly 110 million patient records with information from more than 100 private insurance carriers and large self-insuring companies. Public forms
of insurance (i.e., Medicare and Medicaid) are not included, nor are small (< 100 employees) or medium (< 1000 employees) self-insuring companies. For this cross-sectional study, approved claims for the years
2003–2013, which includes 17.5–45.2 million persons annually, are linked across years and geocoded at the county level. The dataset includes both inpatient and outpatient claims, medical procedures and
prescription medications. In addition to diagnostic and pharmacy claims, records include patient's age (in years), county of residence, and sex. This dataset defines the population in which we are estimating
associations, specifically, U.S. adults aged 18–65 with private health insurance, primarily from large employers (those with>1000 employees). We excluded the relatively few (n=6735) individuals over
65 years of age because Medicare is the primary insurance of U.S. adults over 65.

The EQI was constructed for 2000-2005 for all US counties and is composed of five domains (air, water, built, land, and sociodemographic), each composed of variables to represent the environmental quality of that domain. Domain-specific EQIs were developed using principal components analysis (PCA) to reduce these variables within each domain while the overall EQI was constructed from a second PCA from these individual domains (L. C. Messer et al., 2014). To account for differences in environment across rural and urban counties, the overall and domain-specific EQIs were stratified by rural urban continuum codes (RUCCs) (U.S. Department of Agriculture, 2015).
DOI: 10.23719/1503870
title: statistical models of fecal coliform levels

description: fecal coliform data from the Oregon Dept. of Agriculture from 01/2006-12/2015 collected in Tillamook Bay, OR.
DOI: 10.23719/1503042
title: Sustainable Chemistry Expert Framework Source Code

description: Link to Github repository containing the source code that can be used to build the Sustainable Chemistry Expert Framework tool.
DOI: 10.23719/1503743
title: Metadata for FIA P3 data on lichen

description: This data describe the abundance of individual lichen species across the U.S. as recorded in the Forest Health and Monitoring dataset of the Forest Inventory and Analysis program (i.e. Phase 3 plots)
DOI: 10.23719/1503179
title: Generalised Read-Across (GenRA) refinements

description: These new analysis builds on the baseline GenRA approach and presents a proof of concept of how other contexts of similarity namely physchem can be implemented into a search strategy for identification of analogues and how this impacts performance of read-across. Chemicals Involved: Same ToxRef dataset as used in the original GenRA manuscript.
DOI: 10.23719/1503652
title: Supplimental data

description: An Excel file including: raw data, data dictionary, and all final data sets.

A PDF containing detailed equations for calculating the daily dose using the creatinine correction and UFR, figures comparing the HI between the creatinine correction and UFR, figures and tables comparing temporal trends in the MCR between the HI and potency-weighted approach, tables describing frequency of participants by cycle, temporal limit of detection by metabolite, tolerable daily intakes by phthalate, Group designation of the MCR, complete regression equations used in the regression analysis, comparison of Group counts by creatinine correction and UFR, and relative potency factors by phthalate.
DOI: 10.23719/1503184
title: "MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

description: The dataset(s) supporting the conclusions of this article are available via the CompTox Chemistry Dashboard Downloads Page (https://comptox.epa.gov/dashboard/downloads) and MS-Ready GitHub repository (https://github.com/kmansouri/MS-ready). The MetFrag functionality is available through the web interface (https://msbi.ipb-halle.de/MetFragBeta/) and the command line version (http://c-ruttkies.github.io/MetFrag/projects/metfragcl/). All additional data supporting the conclusions of this article are included within the article and its additional files.
DOI: 10.23719/1503902
title: Pyrethroid dietary exposures and intake doses for single food items consumed by adults

description: N/A
DOI: 10.23719/1504002
title: Dataset

description: Publicly available weblinks used to develop research project.
DOI: 10.23719/1503132
title: alpha-pinene-derived organic coatings on acidic sulfate aerosol reduce secondary organic aerosol formation from isoprene in the eastern United States

description: EPA did not generate data as part of this work.
DOI: 10.23719/1500441
title: Kidney injury biomarkers and urinary creatinine

description: The original dataset contains identification information for the sample subjects and all of their descriptors including age, gender, race, and medical screening information.   The analyzed data cannot be made publicly available.
DOI: 10.23719/1500442
title: Inflammatory Cytokines and White Blood Cell Counts Response to Environmental 

description: This dataset contains a summary of compounds found in human blood samples.
DOI: 10.23719/1504036
title: River Metrics Data Ver 1

description: Transcripts from focus groups
DOI: 10.23719/1503532
title: Migration corridor simulation

description: The model scenario and associated outputs of the case study used to illustrate the migration corridor simulation model demonstrating fish fitness outcomes.
DOI: 10.23719/1504117
title: Louisiana breeding bird survey data 

description: The data are maintained by the USGS (https://www.pwrc.usgs.gov/bbs/RawData/) and provide information on the trends and status of North American bird populations reported as population abundance indices.  This research effort analyzed Louisiana breeding bird survey data (total species and total population) for 1990 and 2014.