AndreaBozzo/ceres-open-data-index huggingface dataset:
Evans_2022_PFAS_in-vitro_manuscript_ScienceHub_2022-6-24

Dataset of medium throughput (96 well plate) in vitro nuclear receptor activation assays for peroxisome proliferator activated receptor alpha (PPARa), PPAR gamma (PPARg), and estrogen receptor (ER) across a panel of per- and polyfluoroalkyl substances (PFAS), fatty acids, and pharmaceuticals. 

This dataset is associated with the following publication:
Evans, N., J. Conley, M. Cardon, P. Hartig, E. Medlock Kakaley, and L. Gray. In vitro activity of a panel of per- and polyfluoroalkyl substances (PFAS), fatty acids, and pharmaceuticals in peroxisome proliferator-activated receptor (PPAR) alpha, PPAR gamma, and estrogen receptor.   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 449(116136): 1, (2022).

Tags: adverse-outcome-pathways-aops, bioactivity, childrens-environmental-health, in-vitro, pfas, screening
Organization: U.S. Environmental Protection Agency
Chicago TW II Manuscript Data

A single excel file describes data from the manuscript entitled In vitro effects-based method and water quality screening model for use in pre- and post-distribution treated waters. The file is separated by figure, or figure panels, using tabbed sheet pages. Metadata, such as column headings with experimental details such as specific units of measure, sampling sites and treatments are included for each data set. A glossary of terms is provided to define the many abbreviations and acronyms used throughout the data file. Finally, narrative information has been added in data margins to describe data analysis. 

This dataset is associated with the following publication:
Medlock Kakaley, E., M. Cardon, N. Evans, L. Iwanowicz, J. Allen, E. Wagner, H. Hur, K. Bokenkamp, S. Richardson, M. Plewa, P. Bradley, K. Romanok, D. Kolpin, J. Conley, E. Gray, P. Hartig, and V. Wilson. In vitro effects-based method and water quality screening model for use in pre- and post-distribution treated waters.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 768(144750): 1, (2021).

Tags: androgen, chicago, estrogen, in-vitro-bioassay, in-vitro-bioassays, tapwater
Organization: U.S. Environmental Protection Agency
Sound Pressure Spectral Density at 1 Hertz and 1 Hour Resolution Recorded at SanctSound Site PHRB_12_Part1

This record represents the sound pressure spectral density (PSD) levels derived from raw passive acoustic data. The hourly PSD levels were calculated as the median of mean-square pressure amplitude (ÂµPa^2) with a frequency resolution of 1 Hz from 20 Hz to 24,000 Hz over no less than 1800 seconds in each hour and converted to decibels (dB re 1 ÂµPa^2/Hz). These data were recorded at SanctSound site PHRB_12 between October 15, 2018 and June 10, 2019, and represent 1 of 3 parts.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, biological classification, biosphere, central pacific ocean, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hawaiian islands, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, ocean, ocean acoustics, oceans, pacific ocean, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Environmental Fate of Cl-PFPECAs: Predicting the Formation of PFAS Transformation Products in New Jersey Soils

This file contains data from estimated chloro perfluoro polyether carboxylate (Cl-PFPECA) transformation products in soil samples collected in New Jersey by New Jersey state government personnel. Samples were originally processed and extracted in Athens, GA EPA/ORD/NERL/EMMD laboratory by Tom Jenkins and John Washington. Samples were analyzed for transformation products on the Waters LC-MS/MS instruments in Athens, GA EPA/ORD/CEMM/EPD laboratory by Marina Evich and John Washington. Instrument output was reviewed and optimized by Marina Evich and John Washington. 

This dataset is associated with the following publication:
Evich, M., M. Davis, E. Weber, C. Stevens, B. Acrey, W. Henderson, S. Goodrow, E. Bergman, and J. Washington. Environmental Fate of Cl-PFPECAs: Predicting the Formation of PFAS Transformation Products in New Jersey Soils.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 56(12): 7779–7788, (2022).

Tags: chemical-transformation-simulator, environmental-transformation, high-resolution-mass-spectrometry, next-generation-chemicals, pfas-alternatives, polyfluorinated-alkyl-substances
Organization: U.S. Environmental Protection Agency
Data for changes in ozone chemical regime over CONUS inferred by the inversion of NOx and VOCn

The dataset was created by University of Houston. For details, please contact Jia Jung at helloiamjia@gmail.com. 

This dataset is associated with the following publication:
Jung, J., Y. Choi, S. Mousavinezhad, D. Kang, J. Park, A. Pouyaei, M. Ghahremanloo, M. Momeni, and H. Kim. Changes in the ozone chemical regime over the contiguous United States inferred by the inversion of NOx and VOC emissions using satellite observation.   Atmospheric Research. Elsevier Science BV, Amsterdam,  NETHERLANDS, 270: 106076, (2022).

Tags: air-quality, background-ozone, chemistry-regime, satellite-no2-columns
Organization: U.S. Environmental Protection Agency
FFPE_DNA_MS_v12_20210211

The primary goal of this study was to investigate the effects of whether organocatalyst (ORGΔ) treatment improves DNA-sequencing data by overcoming formalin-induced artifacts from clinical formalin-fixed paraffin-embedded (FFPE) samples.  We isolated RNA and DNA ± ORGΔ from paired FFPE and frozen human renal and ovarian carcinoma specimens collected as part of the National Cancer Institute Biospecimen Pre-analytical Variables program. Tumor types were microscopically confirmed from adjacent tissue sections. Following extraction, DNA was fragmented and sequence differences were compared between frozen and FFPE sample pairs. Treatment with ORGΔ improved concurrent SNP calls in FFPE DNA compared to non-ORGΔ FFPE samples and enhanced confidence in SNP calls for all FFPE DNA samples, beyond that of matched frozen samples. In general, the concordant SNPs identified in paired frozen and FFPE DNA samples agreed for both genotype and homozygosity vs. heterozygosity of calls regardless of ORGΔ treatment. The increased confidence in ORGΔ FFPE DNA variant calls relative to the matched frozen DNA suggests a novel application of this method. With further optimization, this method may improve quality of DNA-sequencing data in frozen as well as FFPE tissue samples. These findings could have important implications for studies using FFPE samples, especially if adequate matched controls are not available. 

This dataset is associated with the following publication:
Wehmas, L., C. Wood, P. Guan, M. Gosink, and S. Hester. Organocatalyst treatment improves variant calling and mutant detection in archival clinical samples.   Scientific Data. Springer Nature, New York, NY,  12: 6509, (2022).

Tags: archival, dna-seq, exome, human-tumors, single-nucleotide-polymorphism-snp
Organization: U.S. Environmental Protection Agency
Targeted RNA-sequencing of aged FFPE liver tissue data

Gene expression data on >20 year-old, paired frozen and archival FFPE liver samples generated using targeted resequencing (TempO-Seq) and whole-genome RNA-sequencing methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313 and 427 mg/kg-day, (n=6/dose) by drinking water for 6 days. Portions of this dataset are inaccessible because: Including all of these files on ScienceHub would exceed the 1 Gb limit. They can be accessed through the following means: The data is stored on the L: Drive. Information on all of the files and file paths are indicated in the 20210923_Readme.xlsx file uploaded with the data. Format: Excel files, tab delimited files, csv files, and sequencing FASTQ files. 

This dataset is associated with the following publication:
Cannizzo, M., C. Wood, S. Hester, and L. Wehmas. Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action.   Toxicology Reports. Elsevier B.V., Amsterdam,  NETHERLANDS, 9: 883-894, (2022).

Tags: benchmark-dose-analysis, dichloroacetic-acid, formalin-fixed-paraffin-embedded-ffpe, rna-sequencing
Organization: U.S. Environmental Protection Agency
Biochar Pb Bioaccessibility

Data describes the impact of biochar amendments on soil lead bioaccessibility. It contains the raw soil bioaccessibility information. 

This dataset is associated with the following publication:
Plunkett, S., C. Eckley, T. Luxton, and M. Johnson. The effects of biochar and redox conditions on soil Pb bioaccessibility to people and waterfowl.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 294: 133675, (2022).

Tags: bioaccessibility, biochar, heavy-metals, remediation, soil
Organization: U.S. Environmental Protection Agency
Thermal Tracker - California - Thermal Tracker (120), Humboldt - Raw Data

**Overview**

ThermalTracker offshore validation

Tags: 00, a2e, atmosphere-to-electrons, buoy, california, eere, offshore-wind-energy-buoy-lidar-project, raw-data, thermal-tracker, thermal-tracker-120-humboldt, tracker, weto, wind, z05
Organization: Department of Energy
Blue Whale Sound Production Recorded at SanctSound Site FK04_02

This record represents blue whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for blue whales was built for the data sampled at 120 Hz, and created for A, B, and AB phrases. All detections with a Mahalanobis distance of 5.0 or less were manually screened. Daily presence for blue whales was confirmed if there were three song phrases visible, including at least one true detection. Only accepting detections when three or more phrases occurred ensured our confidence in blue whale song presence. These data were recorded at SanctSound site FK04_02 between May 21, 2019 and August 23, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fin Whale Sound Production Recorded at SanctSound Site FK04_02

This record represents fin whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for fin whale 20-Hz pulses was built for the data sampled at 120 Hz. All fin whale detections with a Mahalanobis distance of 3.0 or less were manually verified for true detections. A logistic regression was applied to these results to facilitate reducing the size of the dataset that ultimately needed to be manually verified for confident species detection. This analysis revealed that a minimum number of 29 detections per time window used (hour or day) need to be detected to ensure that a fin whale was truly detected with a confidence of 90%. All days with at least 29 detections were manually verified for daily presence of fin whale 20-Hz pulses. From days with 29 or more detections, fin whales were considered present for that day if a true detection was found within a regular inter-pulse interval pattern of at least three other 20-Hz pulses. These data were recorded at SanctSound site FK04_02 between May 21, 2019 and August 23, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Blue Whale Sound Production Recorded at SanctSound Site SB02_01

This record represents blue whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for blue whales was built for the data sampled at 120 Hz, and created for A, B, and AB phrases. All detections with a Mahalanobis distance of 5.0 or less were manually screened. Daily presence for blue whales was confirmed if there were three song phrases visible, including at least one true detection. Only accepting detections when three or more phrases occurred ensured our confidence in blue whale song presence. These data were recorded at SanctSound site SB02_01 between November 12, 2018 and January 28, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Sound Pressure Levels for 200 to 1000 Hz at 1 Hour Resolution Recorded at SanctSound Site HI01_02

This record represents the sound pressure levels (SPLs) derived from raw passive acoustic data. SPLs were calculated in Pamguide with a 3600 second resolution over the frequency band of 200 to1000 Hz and converted to decibels (dB re 1 ÂµPa). These data were recorded at SanctSound Site HI01_02 between November 05, 2019 and January 14, 2020.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, biological classification, biosphere, central pacific ocean, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hawaiian islands, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, ocean, ocean acoustics, oceans, pacific ocean, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fin Whale Sound Production Recorded at SanctSound Site FK02_01

This record represents fin whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for fin whale 20-Hz pulses was built for the data sampled at 120 Hz. All fin whale detections with a Mahalanobis distance of 3.0 or less were manually verified for true detections. A logistic regression was applied to these results to facilitate reducing the size of the dataset that ultimately needed to be manually verified for confident species detection. This analysis revealed that a minimum number of 29 detections per time window used (hour or day) need to be detected to ensure that a fin whale was truly detected with a confidence of 90%. All days with at least 29 detections were manually verified for daily presence of fin whale 20-Hz pulses. From days with 29 or more detections, fin whales were considered present for that day if a true detection was found within a regular inter-pulse interval pattern of at least three other 20-Hz pulses. These data were recorded at SanctSound site FK02_01 between December 18, 2018 and April 21, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fin Whale Sound Production Recorded at SanctSound Site SB03_05

This record represents fin whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for fin whale 20-Hz pulses was built for the data sampled at 120 Hz. All fin whale detections with a Mahalanobis distance of 3.0 or less were manually verified for true detections. A logistic regression was applied to these results to facilitate reducing the size of the dataset that ultimately needed to be manually verified for confident species detection. This analysis revealed that a minimum number of 29 detections per time window used (hour or day) need to be detected to ensure that a fin whale was truly detected with a confidence of 90%. All days with at least 29 detections were manually verified for daily presence of fin whale 20-Hz pulses. From days with 29 or more detections, fin whales were considered present for that day if a true detection was found within a regular inter-pulse interval pattern of at least three other 20-Hz pulses. These data were recorded at SanctSound site SB03_05 between August 2, 2019 and October 5, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
North Atlantic Right Whale Sound Production Recorded at SanctSound Site FK04_02

This record represents north atlantic right whale sound production detected from raw passive acoustic data. The Low Frequency Detection and Classification System (LFDCS) call library for right whale low-frequency modulated upsweep (upcall) was used for the data. All North Atlantic Right Whale (NARW) upcall detections with a Mahalanobis distance less than or equal to 3.0 were manually screened due to variability in NARW upcalls and overlap with other speciesâ vocalizations, such as upsweeps produced by humpback whales. A given day was marked as having NARWs present if three or more true upcall detections. These data were recorded at SanctSound site FK04_02 between May 21, 2019 and August 23, 2019.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, atlantic ocean, biological classification, biosphere, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, north atlantic ocean, ocean, ocean acoustics, oceans, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Octave Band Sound Pressure Levels at 1 Hertz and 1 Hour Resolution Recorded at SanctSound Site PHRB_12_Part1

This record represents the octave band sound pressure levels (OLs) derived from raw passive acoustic data. OLs were calculated by integration of sound pressure spectral density estimates of the mean-square pressure with a 1 Hz/1 second resolution over 10 octave bands with the center frequencies ranging from 31.5 to 16,000 Hz. The result is then calculated per hour as a median over no less than 1800 1-second values for that hour and converted to decibels (dB re 1 ÂµPa). These data were recorded at SanctSound site PHRB_12 between October 15, 2018 and June 10, 2019, and represent 1 of 3 parts.

Tags: acoustic sounders, ambient noise, animals/invertebrates, animals/vertebrates, aquatic ecosystems, aquatic sciences, biological classification, biosphere, central pacific ocean, cetaceans, doc/noaa/nesdis/ncei, doc/noaa/nmfs, doc/noaa/nos/nms, dod/usnavy, earth science, earth science oceans, fish, fisheries, fixed observation stations, hawaiian islands, hydrophones, mammals, marine environment monitoring, marine habitat, national centers for environmental information, national marine fisheries service, national marine sanctuaries, national ocean service, nesdis, noaa, noaa-navy sanctuary soundscapes monitoring project, ocean, ocean acoustics, oceans, pacific ocean, passive acoustic recorder, recorders/loggers, sanctsound, u.s. department of commerce, u.s. department of defense, u.s. navy, vertical location, water column
Organization: National Oceanic and Atmospheric Administration, Department of Commerce