cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48443/3czr-g515
title: Soil microbe community composition (DP1.10081.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory data and metadata for NEON's soil bacterial, archaeal, and fungal community composition analysis derived from soil microbial sampling. Taxon tables are derived from the 16S and ITS marker gene sequencing data product, NEON.DP1.10108. The DNA sequence data are processed using standard bioinformatics software to generate taxonomic data. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mcc\_soilSeqVariantMetadata\_16S:  730

mcc\_soilSeqVariantMetadata\_ITS:  730

mcc\_taxonTableLabSummary:  7
description: Soil sampling occurs annually at a minimum of one site per domain and once (sites with short growing seasons) to three times per year (sites with longer growing seasons), with collections occurring at every sampled site during the historic peak in vegetation greenness. Three pre-determined, randomly assigned locations are selected for each sampling event within each of 10 plots distributed throughout a site; sampling locations within a plot are not re-sampled. Soil samples are collected to a maximum depth of 30 cm, with organic and mineral soils sampled separately. The same samples are used for measurement of soil physical and chemical properties to maintain temporal and spatial connectivity. Subsamples of homogenized soil (rocks, roots and organic debris removed) from each of the 3 sampling locations are stored in sterile containers, frozen on dry ice in the field and shipped to an analytical facility for DNA sequence analysis using primer sets targeting the small subunit of the ribosomal RNA gene. Sequence data undergo QAQC and are processed bioinformatically using an in-house pipeline to identify unique sequence variants in the data and to taxonomically identify each sequence variant.
DOI: 10.25387/g3.13635110.v1
title: Supplemental Material for Barbitoff et al., 2021

description: This fileset contains supplementary materials for "Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage" by Barbitoff et al.Supplementary Figures S1 - S6 and Supplementary Tables S1-S2 and S6 are available as part of the Supplementary Figures and Tables document (Barbitoff2021_SupplFiguresTables.pdf). Table S3 and Table S4 contain the results of structural variant analysis (raw, Table S3; and curated, Table S4). Table S5 contains the results of CGH analysis. All code relevant to this submission, as well as some of the additional data files, are uploaded to the GitHub repository at https://github.com/mrbarbitoff/pgc_genomes_ont
DOI: 10.25387/g3.13635110
title: Supplemental Material for Barbitoff et al., 2021

description: This fileset contains supplementary materials for "Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage" by Barbitoff et al.Supplementary Figures S1 - S6 and Supplementary Tables S1-S2 and S6 are available as part of the Supplementary Figures and Tables document (Barbitoff2021_SupplFiguresTables.pdf). Table S3 and Table S4 contain the results of structural variant analysis (raw, Table S3; and curated, Table S4). Table S5 contains the results of CGH analysis. All code relevant to this submission, as well as some of the additional data files, are uploaded to the GitHub repository at https://github.com/mrbarbitoff/pgc_genomes_ont
DOI: 10.6084/m9.figshare.13637984
title: Additional Supporting Materials for Zhou et al 2021 Gerontology

description: <b>Background:</b> The genetic locus 3p21.31 has been associated with severe coronavirus disease 2019 (COVID-19), but the underlying pathophysiological mechanism is unknown. <b>Methods:</b> To identify intermediate traits associated with the 3p21.31 locus, we first performed a phenome-wide association study (PheWAS) with 923 phenotypes in 310,999 European individuals from the UK Biobank. For genes potentially regulated by the COVID-19 risk variant, we examined associations between their expression and the polygenic score (PGS) of 1,263 complex traits in a meta-analysis of 31,684 blood samples. For the prioritized blood cell traits, we tested their associations with age and sex in the same UK Biobank sample. <b>Results:</b> Our PheWAS highlighted multiple blood cell traits to be associated with the COVID-19 risk variant, including monocyte count and percentage (<i>p</i> = 1.07x10<sup>-8</sup><i>,</i> 4.09x10<sup>-13</sup>), eosinophil count and percentage (<i>p</i> = 5.73x10<sup>-3</sup>, 2.20x10<sup>-3</sup>), and neutrophil percentage (<i>p</i> = 3.23x10<sup>-3</sup>). The PGS analysis revealed positive associations between the expression of candidate genes and genetically predicted counts of specific blood cells: <i>CCR3</i> with eosinophil and basophil (<i>p</i> = 5.73x10<sup>-21</sup>, 5.08x10<sup>-19</sup>); <i>CCR2</i> with monocytes (<i>p</i> = 2.40x10<sup>-10</sup>); and <i>CCR1</i> with monocytes and neutrophil (<i>p</i> = 1.78x10<sup>-6</sup>, 7.17x10<sup>-5</sup>). Additionally, we found that almost all examined white blood cell traits are significantly different across age and sex groups. <b>Conclusions:</b> Our findings suggest that altered blood cell traits, especially those of monocyte, eosinophil, and neutrophil, may represent the mechanistic links between the genetic locus 3p21.31 and severe COVID-19. They may also underlie the increased risk of severe COVID-19 in older adults and men.
DOI: 10.25810/es52-xr23.33
title: Canadian Newspaper Coverage of Climate Change or Global Warming, 2000-2020 - December 2020

description:         The Media and Climate Change Observatory Data monitors 120 sources (across newspapers, radio and TV) in 54 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.6084/m9.figshare.13637966
title: Tumor Classification Model

description: A pytorch loadable model for tumor classification
DOI: 10.48443/wyn4-9x37
title: Triple aspirated air temperature (DP1.00003.001)
title: RELEASE-2021

description: Triple aspirated air temperature measurements, available as one- and thirty-minute averages of 1 Hz observations. Temperature is one of the most fundamental physical measurements. It is a primary driving factor for countless physical, chemical, and biological processes. The triple aspirated sensor assembly comprises three individual Platinum Resistance Thermometers (PRTs) housed within an aspirated shield.

Latency:
Data collected in any given month are published during the second full week of the following month.
description: The Triple Aspirated Air Temperature assembly is deployed at core and relocatable tower sites. It is located on the top level of the tower infrastructure. Instrumentation: Thermometrics Climate RTD 100 Ω Probe, housed within a Met One 076B fan aspirated radiation shield
DOI: 10.48443/1xxb-1143
title: Riparian composition and structure (DP1.20275.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from the composition and structure components of NEON's riparian habitat assessment protocol. This protocol provides a rapid estimate of the riparian vegetation, human impacts, and bank characteristics at NEON Aquatic lakes, rivers, and streams. For additional details, see protocol [NEON.DOC. 003826] (http://data.neonscience.org/api/v0/documents/NEON.DOC.003826vB): AOS Protocol and Procedure: Riparian Habitat Assessment and science design [NEON.DOC.001152](http://data.neonscience.org/api/v0/documents/NEON.DOC.001152vA): Aquatic Sampling Design.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

rip_assessment:  30
description: Each aquatic site is surveyed once per year within the site-specific peak greenness window. Ten riparian transects are evenly distributed throughout the 1km wadeable stream biological sampling reach. At lake sites, 10 evenly spaced transects are established around the lake perimeter. Large river sites include 5 right bank and 5 left bank transects that are evenly spaced throughout the 1km reach. At each transect the physical habitat is characterized including vegetation structure and composition, dominant plant species, bank characteristics including bank angle, revetment, and bank texture. Instrumentation: NA
DOI: 10.48443/cyxz-9m03
title: Benthic microbe community composition (DP1.20086.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory data and metadata for NEON's benthic bacterial, archaeal, and fungal community composition analysis derived from microbial sampling in wadeable streams. Taxon tables are derived from the 16S and ITS marker gene sequencing data product, NEON.DP1.20280. The DNA sequence data are processed using standard bioinformatics software to generate taxonomic data. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mcc\_benthicSeqVariantMetadata\_16S:  730

mcc\_benthicSeqVariantMetadata\_ITS:  730

mcc\_taxonTableLabSummary:  7
description: Benthic microbe samples are collected at the same time and location as periphyton (microalgae) samples three times per year in wadeable streams during aquatic biology bout windows, roughly in spring, summer and fall. Samples are collected using aseptic methods using the most appropriate sampler for the habitat and substratum type, including rock scrubs, grab samples, and epiphyton. Samples are collected in the two most dominant benthic habitat types (e.g. riffles, runs, pools, step pools). Cobble scrubs are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. Grab samples of sediment (silt, sand) or plant material/epiphyton are collected when appropriate. All samples are frozen on dry ice in the field and are shipped frozen to an analytical facility for DNA sequence analysis using primer sets targeting the small subunit of the ribosomal RNA gene. Sequence data undergo QAQC and are processed bioinformatically using an in-house pipeline to identify unique sequence variants in the data and to taxonomically identify each sequence variant.
DOI: 10.48443/k1yw-z025
title: Temperature at specific depth in surface water (DP1.20264.001)
title: RELEASE-2021

description: Temperature at specific depths on buoys is measured every minute and is reported as 1-minute instantaneous measurements and 30-minute mean values. A temperature chain with between 3 and 10 thermistors (depending on lake depth) is affixed from the buoy at the water surface. The shallowest thermistor is located at 5 cm below the water surface. Deeper thermistors have their depth published with the data and vary for each lake or river.

Latency:
Data collected in any given month are published during the second full week of the following month.
description: The buoys are comprised of sensor sets which measure meteorological parameters over a water surface along with submerged sensors that measure physical and chemical parameters of the water body. Some of these sensors are unique to the buoy subsystem and others are shared with other NEON subsystems, such as the wadeable stream sensor sets or terrestrial towers. Due to power, space, and data storage constraints on the buoy, the configuration of sensors deployed on a buoy may be different than those in other parts of NEON. Instrumentation: Precision Measurement Engineering Inc. - T-Chain RS 232/485
DOI: 10.48443/bxr4-d303
title: Surface water microbe marker gene sequences (DP1.20282.001)
title: RELEASE-2021

description: This data product contains the quality-controlled laboratory metadata and 16S and ITS marker gene sequences derived from NEON's surface water microbial sampling. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Queries for the basic data product package will return metadata tables that include laboratory methods and DNA extraction, PCR amplification, and sequencing metadata for samples from the queried sites and date range. Queries for the expanded package will also include a table containing links to the raw sequence data files, which can be used to download the sequences from the NEON data portal. Some of the sequence data are also publicly available and may be queried on the [Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST)](http://metagenomics.anl.gov/) server. 

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

amc_fieldGenetic:  30

amc_fieldSuperParent:  30

mmg_swDnaExtraction:  240

mmg\_swMarkerGeneSequencing\_16S:  240

mmg\_swMarkerGeneSequencing\_ITS:  240

mmg\_swPcrAmplification\_16S:  240

mmg\_swPcrAmplification\_ITS:  240

mmg_swRawDataFiles: 240
description: Surface water microbe samples are collected at the same time and location as surface water cell count samples and surface water chemistry samples once per month in wadeable streams (12 times per year) and every-other month in lakes and rivers (6 times per year). In wadeable streams, surface water microbe samples are collected near the downstream S2 sensor location. In lakes and rivers, microbial samples are collected near the buoy sensor set at 1 sampling depth in unstratified systems and up to 3 depths in stratified lakes. Surface water grab samples are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. The filters are stored and shipped frozen to an analytical facility for DNA extraction, sample preparation and high-throughput sequence analysis using primer sets targeting the ribosomal RNA gene operon. Laboratory metadata are passed through the NEON automated ingest process for QC testing and are published on the NEON data portal. DNA sequence data undergo QC testing and unique URLs are generated to enable data download.
DOI: 10.48443/c0cy-kx61
title: Plant phenology observations (DP1.10055.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from in-situ observations of plant leaf development and reproductive phenophases, at each of NEON's terrestrial sites. Phenophase status and intensity definitions follow those of the USA National Phenology Network (USA-NPN).  Status and intensity data are reported per phenophase per individual or patch, for each day observed. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

phe_perindividual:  30

phe_perindividualperyear:  30

phe_statusintensity:  30
description: 90-100 individual plants or plant patches are monitored at each site. Individuals of 3 dominant species at each site are targeted for monitoring during initial operations After which the pool of species monitored may expand up to 20 species. Sampling intervals at sites with clear seasonal patterns varies based on plant activitiy, ranging from 2-3x weekly during periods of rapid phenological transition to much less frequently during other times of year. Sites with less defined growing season are monitored year-round at weekly intervals. NEON employs status-based monitoring in which the phenological condition of an individual is reported any time that individual is observed. Depending on the growth form, an individual may have between 1 and 7 phenophases reported per observation event.
DOI: 10.48443/50gf-9h72
title: Chemical properties of groundwater (DP1.20092.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from NEON's groundwater chemistry sampling protocol. Subsamples are analyzed at NEON domain headquarters for alkalinity and acid neutralizing capacity (ANC); other subsamples are sent to external facilities for a broad suite of analytes, including dissolved and total nutrients and carbon, cations and anions, and general chemistry. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage.

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.
 
gwc_domainLabData:  60

gwc_externalLabData:  150

gwc_fieldData:  30

gwc_fieldSuperParent:  30

gwc_externalLabSummaryData:  14
description: Grab samples of groundwater are collected twice per year at NEON aquatic sites from permanently installed groundwater wells. There are up to eight small (2-in diameter) shallow (<100 ft depth) groundwater observation wells at each site, from which a subset of four wells are sampled. The field protocol used by NEON for collecting groundwater chemistry samples follows the general procedure for minimal drawdown sampling detailed by EPA report Low-Flow (Minimal Drawdown) Ground-Water Sampling Procedures (Puls and Barcelona, 1996). Sample handling and preparation portions of this protocol follow the general requirements set forth by the USGS National Water-Quality Assessment (NAWQA) Program (USGS 2006). (http://data.neonscience.org/api/v0/documents/NEON.DOC.002905vD).
DOI: 10.48443/j1g9-2j27
title: Small mammal box trapping (DP1.10072.001)
title: RELEASE-2021

description: This data product contains the quality-controlled, native sampling resolution data from NEON's small mammal sampling protocol. Small mammal abundance and diversity are sampled at regular intervals by NEON field technicians at core and relocatable sites. Here small mammals are defined based on a combination of behavioral, dietary, and size constraints, as the NEON design is limited to species sampled by box traps. This definition includes any mammal that is (1) nonvolant; (2) nocturnally active; (3) forages predominantly aboveground; and (4) is greater than 5 grams but less than approximately 500-600 g. In North America, this includes cricetids, heteromyids, small sciurids, and introduced murids. It does not include shrews, large squirrels, rabbits, or weasels, despite the fact that individuals of these species may be incidentally captured. Products resulting from this sampling include the species identification and unique identifier for each individual captured, as well as a suite of standard size measurements and reproductive condition data. Sample identifiers for any blood, ear, hair, whisker, fecal, and/or voucher samples collected are also provided. For additional details, see the user guide, protocols, and science design listed in the Documentation section in this data product's details webpage. For spatial data (text and shapefiles), download [`NEON_TOS_Plots`](https://data.neonscience.org/api/v0/documents/All_NEON_TOS_Plots_V7).

Latency:
The expected time from data and/or sample collection in the field to data publication is as follows, for each of the data tables (in days) in the downloaded data package. See the Data Product User Guide for more information.

mam_perplotnight:  45

mam_pertrapnight:  45

mam_voucher:  45
description: Small mammal sampling is based on the lunar calendar, with timing of sampling constrained to occur within 10 days before or after the new moon. Typically, core sites are sampled 6 times per year, and relocatable sites 4 times per year. Small mammals are sampled using box traps (models LFA, XLK, H.B. Sherman Traps, Inc., Tallahassee, FL, USA). Box traps are arrayed in three to eight (depending on the size of the site) 10 x 10 grids with 10m spacing between traps at all sites. Small mammal trapping bouts are comprised of one or three nights of trapping, depending on whether a grid is designated for pathogen sample collection (3 nights) or not (1 night).
DOI: 10.48443/qser-8m94
title: Elevation of surface water (DP1.20016.001)
title: RELEASE-2021

description: Surface water elevation is controlled by precipitation at both the landscape and channel scales, overland flow, interflow and groundwater flow. It is correlated to discharge and is critical to understanding how water moves through the environment, carrying nutrients and sediment, modulating aquatic ecosystem structure and function. This data product contains continuous, quality-controlled, surface water depth converted to elevation above mean sea level. Measurements are captured once per minute and reported as 1-minute instantaneous measurements and 30-minute averages.

Latency:
Data collected in any given month are published during the second full week of the following month.
description: Elevation of surface water will be used to provide continuous discharge measurements in wadeable streams, rivers and lakes where flowing inlet and outlet streams are present. Pressure transducers will be placed at both the upstream and downstream sensor stations in wadeable streams, at a single station in rivers and at the inlet and outlet locations of lake sites. Instrumentation: In-Situ, Inc. - Level TROLL 500