cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26030/2q5v-by72
title: Planetary Protection Low Biomass Nanopore Pilot Study

description: Sequencing optimization experiments using different Oxford Nanopore Technology library preparation methods and input DNA values to determine best method for low-biomass sequencing. This pilot study serves as a technical assessment of wet and dry lab methods for processing and analysis of future NASA cleanroom samples. Microbial standards of known composition were used as input DNA. Data from 4 experiments are provided. The NBD (Native Barcode Kit) experiment utilized the Nanopore Rapid PCR Barcoding Kit 24 V14 and tested nanogram-level input amounts (5ng and 11ng). The three Rapid experiments utilized the Nanopore Rapid PCR Barcoding Kit 24 V14 and tested different input amounts and spike-ins. Rapid1 tested low input amounts (100pg and 500pg), Rapid2 tested ultra-low input amounts (1pg and 10pg), and Rapid3 tested ultra-low input amounts (5pg and 10pg) with and without lambda spike-in. Different data processing pipelines were tested with each set of experimental data as described below. Data from each of the 3 Rapid experiments were processed using 4 different tool combinations for read- and assembly-based processing protocols. The following shows the 4 different combinations tested for the read-based processing approach: Tool combination number, tool used to removed contaminants (blank reads), tool used to remove human reads, tool used for taxonomy assignments, output file suffixes used Test1, Minimap2, Kraken2, Kaiju, “_kraken2-kaiju”, Test2, Minimap2, Kraken2, Kraken2, “_kraken2-kraken2”, Test3, Chopper, Chopper, Kaiju, “_chopper-kaiju”, Test4, Chopper, Chopper, Kraken2, “_chopper-kraken2”. The following shows the 4 different combinations tested for the assembly-based processing approach: Tool combination number, tool used to removed contaminants (blank reads), tool used to remove human reads, tool used for assembly polishing, output file suffixes used: Test1, Minimap2, Kraken2, Medaka, “_kraken2-medaka”, Test2, Minimap2, Kraken2, Minimap2+racon, “_kraken2-racon”, Test3, Chopper, Chopper, Medaka, “_chopper- medaka”, Test4, Chopper, Chopper, Minimap2+racon, “_chopper- racon”. Data from the NBD experiment was processed using 16 different approaches to test different tool combinations, different order of contaminant and human read removal steps, and to test differences in assembling blank reads or not before removing them. Each of the 4 different tool combinations for read- and assembly-based processing protocols described for the Rapid experiments were tested with the NBD data using either unassembled or assembled blank reads, making up 8 different approaches. Those 8 approaches were tested with removing blank reads first followed by human read removal or removing human reads first followed by blank read removal, totaling 16 approaches. The 16 different approaches and respective output file prefixes are detailed in the README.txt file associated with the NBD assay table.
DOI: 10.15468/dl.4rckaj
title: Occurrence Download

description: A dataset containing 1813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "Geometry POLYGON((4.07631 46.78107,3.46318 45.75496,4.01177 44.77838,7.20651 44.64077,7.62602 46.64832,4.07631 46.78107))",
 "HasGeospatialIssue is false",
 "TaxonKey is Vespa velutina"
 ]
}

 The dataset includes 1813 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000580-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zecnzv
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Andrena brooksi"
 ]
}

 The dataset includes 32 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000581-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9qjax
title: Occurrence Download

description: A dataset containing 40594738 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tachyphonus rufus, Taeniopygia guttata, Tarsiger cyanurus, Telespiza cantans, Thraupis episcopus, Thraupis palmarum, Tiaris olivaceus, Tityra cayana, Trochalopteron erythrocephalum, Trochalopteron milnei, Turdus dissimilis, Turdus grayi, Turdus kessleri, Turdus merula, Turdus philomelos, Turdus poliocephalus, Turdus rufopalliatus, Uraeginthus angolensis, Uraeginthus bengalus, Uraeginthus cyanocephalus, Urocissa erythroryncha, Vidua chalybeata, Vidua macroura, Vidua paradisaea, Vidua regia, Vireo altiloquus, Yuhina diademata, Zonotrichia albicollis, Zonotrichia capensis, Zonotrichia leucophrys)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40594738 records from 8425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000531-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.23719/1369030
title: Evaluation of a Low-Cost Volatile Organic Compound Passive Sampling Method and Laboratory Intercomparison

description: This project “fenceline Passive Sampler and Sensor Studies” contains information on several related field efforts that examine use of passive sorbent tubes and prototype fenceline sensor technologies near sources of volatile organic compounds, with particular emphasis on the compound benzene.  There are three primary data sets included with multiple journal articles linked to these data sets.  The data sets with metadata and data dictionaries are as follows:

Corpus Christi Passive Sampler Study data set:  Two week duration time-integrated passive sampler concentration data, identity of passive samplers, sampling date and time periods for passive deployments, GPS locations of passive samplers, benzene data from automated gas chromatograph (TCEQ site), metrological data (TCEQ site).

Multiregional Passive Sampler Study data set:  Two week duration time-integrated passive sampler concentration data, identity of passive samplers, sampling date and time periods for passive deployments, GPS locations of passive samplers, metrological data (local airports).

Philadelphia Sensor Studies data sets:  Baseline corrected five-minute time-resolved fenceline sensor (concetrion and wind field) data for (1) alpha version prototype system and (2) beta version prototype system, sampling time periods for utilized sensor deployments, GPS locations of all sensors,  five-minute time-resolved concentration data from co-located optical spectroscopy system (City of Philadelphia Air Measurements Services), metrological data (Philadelphia airport).
DOI: 10.23719/1379171
title: The impact of variation in scaling factors on the estimation of internal dose metrics:  a case study using bromodichloromethane (BDCM)

description: This dataset contains model code and supporting analysis files necessary to evaluate the impact of variability in human hepatic  scaling factors.  Variation in scaling factor values impacts metabolic rate parameter estimates (Vmax) and hence estimates of internal dose used in dose response analysis and biomarkers of exposure that are important for interpretation of epidemiology studies.
DOI: 10.23719/1390071
title: Methane Transect Dataset

description: This project area “OTM 33 Mobile Emission Measurements” covers research on remote emissions quantification with the various forms of mobile monitoring approaches. There will be multiple data sets included in this project. The metadata and data dictionaries are included with each data set. The data sets with metadata and data dictionaries are as follows:

Methane Transect data Set:   The dataset contains mobile methane concentration measurements acquired at 10 samples per second data acquisition rate, collected while driving along transects downwind of a methane source.  The data consists of GPS coordinates, methane concetrion data and transect indicators.  The controlled methane release experiment was conducted on May 15, 2010 in Durham, North Carolina, where three passes were made for the one CR experiment and the point-source release rate was controlled at S = 0.6 g/s. Additionally, the dataset contains four field studies conducted in Colorado on four separate days in July 2010, with the number of passes for each study ranging from two to five.
DOI: 10.23719/1390073
title: Biomarkers of Human Exposure: Plasma data (Augustine et al. 2015)

description: The data contained in this worksheet provides the median flourescence Intensity (MFI) readings for the plasma samples used to measure human antibody responses to the pathogens used in the multiplex.
DOI: 10.23719/1390077
title: Data for "Estimates of reservoir methane emissions based on a spatially balanced probabilistic-survey"

description: Measured diffusive and ebullitive methane emission rates from 115 sites in William H Harsha Lake.  File also contains fields required for GRTS analysis.
DOI: 10.23719/1390080
title: Determining Pathogen and Indicator Levels in Class B Municipal Organic Residuals Used for Land Application

description: Biosolids are nutrient rich organic residuals that are currently used to amend soils for food production.  Treatment requirements to inactivate pathogens for production of Class A biosolids are energy intensive.  One less energy intensive alternative is to treat biosolids to Class B standards, but it could result in higher pathogen loads.  Quantitative microbial risk assessments models have been developed on land application of Class B biosolids, but contain many uncertainties because of limited data on specific pathogen densities and the use of fecal indicator organisms as accurate surrogates of pathogen loads.   To address this gap, a 12-month study of the levels and relationships between Cryptosporidium, Giardia, and human adenovirus (HAdV) with fecal coliform, somatic and F-RNA coliphage levels in Class B biosolids from nine wastewater treatment plants throughout the United States was conducted.  Results revealed that fecal coliform, somatic, and F-RNA coliphage densities were consistent throughout the year.  More importantly, results revealed that HAdV (=2.5x103 genome copies/dry g) and Giardia (=4.14 x103 cysts/dry g) were in all biosolids samples regardless of treatment processes, location, or season.  Cryptosporidium oocysts were also detected (38 % positive; range: 0 -1.9 x 103 oocysts/dry g), albeit sporadically.  Positive correlations among three fecal indicator organisms and HAdV, but not protozoa, were also observed.  Overall, study reveals the high concentrations of enteric pathogens (e.g., Cryptosporidium, Giardia, and HAdV) are present in biosolids throughout the US.  Microbial densities found can further assist management and policy makers establish more accurate risk assessment models associated with land application of Class B biosolids.
DOI: 10.23719/1390085
title: NWCA Enzyme Decomposition Model

description: Dataset contains wetland site information, microbial respiration and ecoenzyme data, enzyme decomposition model, and the program file to run the data analyses.
DOI: 10.23719/1390103
title: PM and levoglucosan data

description: These are GC-MS data for producing the levoglucosan plot, black carbon data from an aethalometer, time series data of wind speed and normalized PM concentrations. As well as certain particle number and CO concentration data deltas.
DOI: 10.23719/1407504
title: Use of Bayesian Modeling to Assess Occurrence of Viral Pathogens in Multiple US Drinking Water Systems

description: Drinking water treatment plants rely on purification of contaminated source waters to provide communities with potable water.  One group of possible contaminants are enteric viruses.  Measurement of viral quantities in environmental water systems are often performed using polymerase chain reaction (PCR) or quantitative PCR (qPCR). However, true values may be underestimated due to challenges involved in a multi-step viral concentration process and due to PCR inhibition.  In this study, water samples were concentrated from 25 drinking water treatment plants (DWTPs) across the US to study the occurrence of enteric viruses in source water and removal after treatment.  The five different types of viruses studied were adenovirus, norovirus GI, norovirus GII, enterovirus, and polyomavirus. Quantitative PCR was performed on all samples to determine presence or absence of these viruses in each sample.  Ten DWTPs showed presence of one or more viruses in source water, with four DWTPs having treated drinking water testing positive.  Furthermore, PCR inhibition was assessed for each sample using an exogenous amplification control, which indicated that all of the DWTP samples, including source and treated water samples, had some level of inhibition, confirming that inhibition plays an important role in PCR-based assessments of environmental samples.   PCR inhibition measurements, viral recovery, and other assessments were incorporated into a Bayesian model to more accurately determine viral load in both source and treated water.  Results of the Bayesian model indicated that viruses are present in source water and treated water.  By using a Bayesian framework that incorporates inhibition, as well as many other parameters that affect viral detection, this study offers an approach for more accurately estimating the occurrence of viral pathogens in environmental waters.
DOI: 10.23719/1407542
title: Human BDCM Mulit-Route PBPK Model

description: This data set contains the code for the BDCM human multi-route model written in the programming language acsl.  The final published manuscript is provided since it contains all the model parameters and data (from published literature).
DOI: 10.23719/1372312
title: Polycyclic aromatic hydrocarbon in fine particulate matter emitted from burning kerosene, liquid petroleum gas, and wood fuels in household cookstoves

description: This dataset includes all data in figures in the manuscript and supporting information for the publication entitled "Particulate polycyclic aromatic hydrocarbon emissions from burning kerosene, liquid petroleum gas, and wood fuels in household cookstoves."
DOI: 10.23719/1373293
title: Bioaerosol concentrations - Figure 3 and Figure 4

description: Bioaerosol concentrations
DOI: 10.23719/1375404
title: Haw River PFCs Data Set

description: PFAS concentrations in river and drinking water in and around the Haw River in North Carolina
DOI: 10.23719/1376218
title: Chemical agnostic hazard prediction: Statistical inference of toxicity pathways - data for Figure 2

description: This dataset comprises one SigmaPlot 13 file containing measured survival data and survival data predicted from the model coefficients selected by the LASSO procedure.
DOI: 10.23719/1377593
title: CFD Model Data

description: Data associated with the development of the CFD model for spore deposition in respiratory systems of rabbits and humans.
DOI: 10.23719/1389264
title: DEVELOPMENT OF A SCREENING APPROACH TO DETECT THYROID DISRUPTING CHEMICALS THAT INHIBIT THE HUMAN SODIUM IODIDE SYMPORTER (NIS)

description: Data pertaining to a NIS-expressing cell line, hNIS-HEK293T-EPA, and its screening capabilities for determining inhibitors of NIS-mediated iodide uptake.
DOI: 10.23719/1390075
title: A small, lightweight multipollutant sensor system for ground-mobile and aerial emission sampling from open area sources

description: Emission data from UAV flights
DOI: 10.23719/1390081
title: Indianapolis Research Duplex Total Database

description: Complete database for research conducted at the EPA's research house in Indianapolis, IN.  Data contained includes weather parameters, sampling dates/times/method, and resultant VOC contaminants
DOI: 10.23719/1390082
title: Near-Port Air Quality Assessment Utilizing a Mobile Monitoring Approach

description: Near-Port Air Quality Assessment Utilizing a Mobile Monitoring Approach
DOI: 10.23719/1390083
title: Urban soil ecosystem services

description: This dataset is representative of the subset of measured urban soil hydrologic, taxonomic, and fertility data that was used to support the results and conclusions of this paper.
DOI: 10.23719/1390086
title: Doc Title:  Adult Hippocampal Neurogenesis is Impaired by Transient Developmental Thyroid Hormone Disruption

description: Severe thyroid hormone (TH) deprivation during development impairs neurogenesis throughout the brain. The hippocampus also maintains a capacity for neurogenesis throughout life which is reduced in adult-onset hypothyroidism. This study examined hippocampal volume in the neonate and adult hippocampal neurogenesis after developmental and adult-onset TH insufficiency. Pregnant rat dams were administered 0, 3, or 10 ppm of propylthiouracil (PTU) via drinking water from gestational day (GD) 6 until weaning. PTU at the high dose reduced body, brain, hippocampal weights on postnatal day (PN) 14, 21 and 78. Sub-regional analysis revealed decrements in hippocampal volumes at 10 but not 3 ppm PTU on PN23. In Experiment 2, one pair of adult male offspring of 0 and 3ppm-teated dams was placed on 3 ppm PTU from PN60, while a 2nd pair remained on control water. Adult neurogenesis was assessed by bromodeoxyuridine (BrdU, 50mg/kg, ip, 2X daily, X5 days) starting on PN90. Brains from animals perfused 1 and 28 days later were processed for immunohistochemistry. Although no volume changes were seen in neonates at 3ppm, thinning of the granule cell layer emerged in adulthood. Developmental TH insufficiency reduced BrdU+ve cells at 1-day with no further reduction at 28-days post-BrdU, indicative of a selective effect on cell proliferation. This was supported by fewer cells staining for the proliferative marker, Ki67. Adult only PTU did not impair neurogenesis or exacerbate effects seen with developmental exposure. A reduced capacity for neurogenesis may contribute to cognitive deficits evident in adults following moderate degrees of developmental TH insufficiency.
DOI: 10.23719/1390087
title: Supporting Simulation Output - Earth Interactions article "The Effects of Downscaling Method on the Variability of Simulated Watershed Response to Climate Change in Five U.S. Basins"

description: Monthly summaries of simulated watershed responses to mid-century climate change scenarios in 5 U.S. basins
DOI: 10.23719/1390094
title: Li et al nitrification inhibition review

description: Li et al nitrification inhibition review
DOI: 10.23719/1390097
title: CHARACTERIZING EMISSIONS FROM OPEN BURNING OF MILITARY FOOD WASTE AND PACKAGING FROM FORWARD OPERATING BASES

description: Data for tables and figures.
DOI: 10.23719/1390099
title: ACTIVE VERSUS SEDENTARY LIFESTYLE FROM WEANING TO ADULTHOOD AND SUSCEPTIBILITY TO OZONE IN RATS

description: The prevalence of a sedentary (SED) life style combined with calorically rich diets has spurred the rise in childhood obesity which, in turn, translates to adverse health effects in adulthood. Obesity and lack of active (ACT) lifestyle may increase susceptibility to air pollutants. We housed 22 day-old female Long-Evans rats in a cage without (SED) or with a running wheel (ACT). After 10 weeks the rats ran 310 ± 16.3 km (SEM).  Responses of SED and ACT rats to whole-body O3 (0, 0.25, 0.5, or 1.0 ppm; 5 hr/day for 2 days) was assessed. Glucose tolerance (GTT) was performed following the first day of O3. ACT rats had less body fat and an improved glucose tolerance (GTT).  Ventilatory function (plethysmography) of SED and ACT groups was similarly impaired by O3. Bronchoalveolar lavage fluid (BALF) was collected after the second O3 exposure. SED and ACT rats were hyperglycemic following 1.0 ppm O3.  GTT was impaired by O3 in both groups; however, ACT rats exhibited improved recovery to 0.25 and 1.0 ppm O3. BALF cell neutrophils and total cells were similarly increased in ACT and SED groups exposed to 1.0 ppm O3. O3-induced increase in eosinophils was exacerbated in SED rats. Chronic exercise from post-weaning to adulthood improved some of the metabolic and pulmonary responses to O3 (GTT and eosinophils) but several other parameters were unaffected. The reduction in O3-induced rise in BALF eosinophils in ACT rats suggests a possible link between a SED lifestyle and incidence of asthma-related symptoms from O3.
DOI: 10.23719/1390105
title: MARGA_Chen et al_2016

description: These data describe the chromatography characteristics of the MARGA instrument software as compared to an alternative, independent technique for chromatogram processing, including an assessment of accuracy, precision and method detection limit.
DOI: 10.23719/1390108
title: Tetrabromobisphenol A In vitro Dermal Absopriton Data

description: In vitro dermal absorption data of tetrabromobisphenol A using human cadaver and rat skin.
DOI: 10.23719/1390120
title: Quantitative Adverse Outcome Pathway for Neurodevelopmental Effects of Thyroid Peroxidase-Induced Thyroid Hormone Synthesis Inhibition

description: Adequate levels of thyroid hormones (TH) are needed for proper brain development, deficiencies may lead to adverse neurological outcomes in humans and animal models. Environmental chemicals have been linked to TH disruption, yet the relationship between developmental exposures and decline in serum TH resulting in neurodevelopmental impairment is poorly understood. The present study developed a quantitative adverse outcome pathway (qAOP) where serum thyroxin (T4) reduction following inhibition of thyroperoxidase in the thyroid gland are described and related to deficits in fetal brain TH and the development of a brain malformation, subcortical band heterotopia. Pregnant dams were exposed to 6-propylthiouracil (PTU  0, 0.1, 0.5, 1, 2, or 3 ppm) from gestational day 6-20, increasing PTU concentrations in maternal thyroid gland and serum as well as in fetal serum. Dams exposed to 0.5 ppm PTU and higher exhibited dose-dependent decreases in thyroidal T4. Serum T4 levels in the dam were significantly decreased with exposure to 2 and 3 ppm PTU. In the fetus, T4 decrements were first observed at a lower dose of 0.5 ppm PTU. Based on these data, fetal brain T4 levels were estimated from published literature sources, and quantitatively linked to increases in the size of the heterotopia present in the brains of offspring. These data show the potential of in vivo assessments and computational descriptions of biological responses to predict the development of this structural brain malformation and use of qAOP approach to evaluate brain deficits that may result from exposure to other TH disruptors.
DOI: 10.23719/1390123
title: Inactivation Data.xlsx

description: The data set is a spreadsheet that contains results of inactivation experiments that were conducted to to determine the effectiveness of chlorine in inactivating B. anthracis spore surrogates in wash waters similar to waters that would be generated during building decontamination activities.
DOI: 10.23719/1390155
title: Cockle Temperature Exposure Lab Experiment (2016)

description: We carried out a lab experiment in which we exposed cockles to a range of air temperatures to simulate the physiological rigors of exposure to sunlight and air at the sediment surface during daytime low tides.  Cockles were subjected to twelve different temperature (6, 14, 21, 30, 34, 38 ± 1.0 °C) x time (2, 4 hrs) treatments within temperature-controlled chambers, representing the temperature and exposure durations regularly observed on Yaquina Bay mid-intertidal flats during daytime low tides in the summer.  This dataset contains all data collected during that lab experiment.
DOI: 10.23719/1393582
title: Age-related differences in pulmonary effects of acute and subchronic episodic ozone exposures in Brown Norway rats 

description: This data set provides the biological endpoints collected from individual animals that culminated into a published paper.