cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.696xbn
title: Occurrence Download

description: A dataset containing 48536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen, Occurrence evidence, Material sample, Living Specimen)",
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "GadmGid is one of (ESP, FRA, PRT, GBR, IRL, ISL, NOR, SWE, FIN, BEL, NLD, DEU, CHE, ITA, AUT, CZE, SVN, HRV, BIH, MNE, ALB, GRC, MKD, BGR, SRB, ROU, HUN, SVK, POL, LTU, LVA, EST, UKR, BLR)",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Peltigera Willd., 1787",
 "Year 1980-2022"
 ]
}

 The dataset includes 48536 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0166746-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9t5nw3
title: Occurrence Download

description: A dataset containing 25333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coeligena coeligena (R.Lesson, 1833))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 25333 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0291238-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gd5r4a
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.979 47.668,11.17 47.668,11.17 47.728,10.979 47.728,10.979 47.668))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Falco subbuteo Linnaeus, 1758, Porzana porzana (Linnaeus, 1766), Crex crex (Linnaeus, 1758), Gallinago gallinago (Linnaeus, 1758), Anthus pratensis (Linnaeus, 1758), Luscinia svecica (Linnaeus, 1758), Saxicola rubetra (Linnaeus, 1758), Saxicola rubicola (Linnaeus, 1766), Lanius collurio Linnaeus, 1758, Carpodacus erythrinus (Pallas, 1770), Grus grus (Linnaeus, 1758), Lanius excubitor Linnaeus, 1758, Mergus merganser Linnaeus, 1758, Botaurus stellaris (Linnaeus, 1758), Falco peregrinus Tunstall, 1771, Numenius arquata (Linnaeus, 1758))"
 ]
}

 The dataset includes 35 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0166584-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6g4sg
title: Occurrence Download

description: A dataset containing 17133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coeligena wilsoni (Delattre & Bourcier, 1846))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 17133 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0291242-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.757uym
title: Occurrence Download

description: A dataset containing 10226 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bidens bipinnata L."
 ]
}

 The dataset includes 10226 records from 382 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0167189-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5065/d6j1019p
title: Sea Ice Melt Ponds: Individual Line Photos, Version 1.0

description: Photos were taken from ~2.5 meters behind the transect, looking across to the pristine side. The location where 5 meter spaced albedo measurements were collected is in the bottom center of the frame. The tape measure which is on the transect line can be seen in the bottom of most frames. A mark on the tape indicating the 5 m locations is sometimes visible.
DOI: 10.5065/d6ns0s08
title: North American Tundra NEE modeled from MODIS data, Version 1.0

description: This data set provides growing season Net Ecosystem CO2 exchange (NEE) between tundra ecosystems and the atmosphere for North America. Data are produced over the growing season (Julian Day 177 - 241) for the years 2003 - 2005. The data are modeled following the approach of Loranty et al [2011], using Moderate Resolution Imaging Spectroradiometer (MODIS) observation. These preliminary data have been validated for only one site at Daring Lake, Canada. Data for each year (2003-2005) are in separate GeoTIF files.
DOI: 10.5065/d6x928f9
title: Barrow Area Remote Sensing- MET Data, Version 1.0

description: This dataset includes meteorology data from 3 towers: BE North (BEN) BE Central (BEC) BE South (BES) Met data are contained in several files, one file per location per year. Files are named: BEX_MET_YYYY.csv where "X" is N, C, or S; and "YYYY" is the data year. Column names are included as first line in each file. For each tower, column names are explained in detail, including measurement units, in a file named: BEX_MET_Fields.csv where "X" is N, C, or S.
DOI: 10.5065/d65t3hm5
title: West Siberian Lowland Peatland GIS Data Collection, Version 1.0

description: This dataset contains the West Siberian Lowland (WSL) peatland GIS data collection. The collection covers the entire West Siberian lowland and was compiled from a wide array of data under the auspices of the NSF-funded Sensitivity of the West Siberian Lowland to Past and Present Climate project (Smith et al., 2000; Smith et al., 2004). Detailed physical characteristics of 9,691 individual peatlands (patches) were obtained from previously unpublished Russian field and ancillary map data, previously published depth measurements, and field depth and core measurements taken throughout the region during field campaigns in 1999, 2000, and 2001. The data collection features eight layers containing the detailed peatland inventory, political, and hydrographic information. Point data consist of field and laboratory measurements of peat depth, ash content, and bulk density. This research was funded by the National Science Foundation (NSF) Office of Polar Programs (OPP), grant number OPP-9818496.
DOI: 10.5065/d69g5jzm
title: Barrow Area Remote Sensing - Tramlines, Version 1.0

description: This data set contains data from tramlines constructed at the Barrow Biocomplexity Experiment 2006. Data were derived using the Barrow Arctic Science Consortium Differential GPS System (BASC DGPS) and exported as GIS shape files. These shape files are contained in a single ZIP file.
DOI: 10.5065/d6k072d2
title: Polar Bears: Location and movements, Version 1.0

description: A subset of captured polar bears were fitted with GPS satellite collars or glue-on tags. Location data was recorded hourly. Concurrently, data on activity, ambient temperature, and salinity were recorded. Information on bear IDs, dates of capture, and location is not available because of the threatened species status of the subjects.
DOI: 10.5065/d6pr7t43
title: North Pole Environmental Observatory (NPEO) Seawater Chemistry, 2000-2005, Version 1.0

description: This data set includes diverse measurements of seawater chemistry along with supplementary Conductivity, Temperature, Depth (CTD); pressure; salinity; potential temperature; and density data from the Arctic Ocean near the North Pole. Measurements were taken from sea ice platforms each April or May from 2000-2005. Investigators used a CTD-O2 system to measure seawater conductivity, temperature, depth, and dissolved oxygen content, and collected Niskin bottle samples for measurements of salinity, oxygen isotope composition, and concentrations of phosphate, silicic acid, nitrate, nitrite, ammonium, and barium. The available in situ dissolved oxygen measurements were collected beginning in 2002. The North Pole Environmental Observatory (NPEO) is a year-round, automated scientific observatory, deploying various instruments each April in order to learn how the world's northernmost sea helps regulate global climate. It consists of a set of unmanned scientific platforms that record oceanographic, cryospheric, and atmospheric data throughout the year.
DOI: 10.5065/d6z899k4
title: ArcticRIMS: NCEP Reanalysis Wind Speed, Aggregated by Administrative Regions, Version 1.0

description: This dataset contains NCEP Reanalysis Wind Speed Data, Aggregated by Administrative Regions. Gridded daily time step data from Ohio State University based on National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis data, interpolated from the NCEP/NCAR grids (~209km) to the 25km Northern Hemisphere Equal-Area Scalable Earth Grid (EASE-Grid) using a bi-lagrange interpolation formula. As part of the data processing of Arctic Rapid Integrated Monitoring System (ArcticRIMS) based at the Water Systems Analysis Group (WSAG), University of New Hampshire all data sets have been aggregated to multiple temporal and spatial resolutions. The data is presented in 24 sub-datasets of different spatial and temporal aggregations.
DOI: 10.5065/d6319t10
title: Barrow Area Remote Sensing - Brw Be Treatment Areas, Version 1.0

description: Modeled treatment areas within the Barrow Biocomplexity study area. Data were derived using the Digital Elevation Model derived for the study area from airborne Light Detection and Ranging (LiDAR) data in the Arc Hydro extension to ArgGIS 9.2. Treatment areas were defined from the catchment area of the thaw lake basin and the location of the dikes that were installed to separate the basin in to the different treatment areas. The northern treatment area became the flooded treatment, the central area the drained treatment area and the southern treatment the control area.
DOI: 10.34740/kaggle/dsv/10552930
title: Top Spotify Songs in 73 Countries (Daily Updated)
DOI: 10.6073/pasta/5ee51b53807596009e8d99d1195af113
title: Lower American River restoration spawning surveys at project and control reaches (2022 - 2024)

description: Sacramento Water Forum has implemented spawning and rearing habitat enhancement projects on the Lower American River at the Lower Sailor Bar, Nimbus Basin, Upper River Bend and Lower River Bend reaches. Enhancements include installation of gravel to restore over 28 acres of spawning habitat and in-channel/floodplain grading to create over 44 acres of rearing habitat. Construction of Lower Sailor Bar and Nimbus Basin were completed in summer 2022, Upper River Bend was completed in summer 2023, and Lower River Bend was completed in summer 2024. The goal of the projects is to increase existing spawning and rearing habitat for salmonids under typical flows. This work supports effectiveness monitoring for this project, including spawning and rearing (snorkel) surveys before and after restoration. This work also informs performance metrics and adaptive management strategies.
DOI: 10.15468/dl.eqv6x8
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.04234 40.29152,4.51413 40.29152,4.51413 42.07947,0.04234 42.07947,0.04234 40.29152))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trachymela sloanei (Blackburn, 1896)"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001963-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n6d8wz
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-110.3637 0.56473,-63.89477 0.56473,-63.89477 37.76332,-110.3637 37.76332,-110.3637 0.56473))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asymmetron lucayanum Andrews, 1893"
 ]
}

 The dataset includes 12 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001964-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jecssn
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-99.84216 47.17246,-42.96813 47.17246,-42.96813 72.7773,-99.84216 72.7773,-99.84216 47.17246))",
 "HasGeospatialIssue is false",
 "Month is July",
 "TaxonKey is Ursus maritimus Phipps, 1774",
 "Year 2024-2024"
 ]
}

 The dataset includes 24 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001965-250121130708018/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/h522-xx30
title: Data for AT 2023adsv

description: Analyzed in Coulter+2025
DOI: 10.6084/m9.figshare.28259876
title: Cardona Jimenez et al.-Experimental results.xlsx

description: An approach to subcritical fluid and natural deep eutectic solvent-ultrasound assisted extractions as green alternatives for Pecan nutshell phenolic compounds recovery
DOI: 10.6084/m9.figshare.28259876.v1
title: Cardona Jimenez et al.-Experimental results.xlsx

description: An approach to subcritical fluid and natural deep eutectic solvent-ultrasound assisted extractions as green alternatives for Pecan nutshell phenolic compounds recovery
DOI: 10.5281/zenodo.14722133
title: Case study data for 'Upsampling DINOv2 features for unsupervised vision tasks and weakly supervised materials segmentation'

description: Raw micrographs, training labels and resulting segmentations for 'Upsampling DINOv2 features for unsupervised vision tasks and weakly supervised materials segmentation'
DOI: 10.5281/zenodo.14722134
title: Case study data for 'Upsampling DINOv2 features for unsupervised vision tasks and weakly supervised materials segmentation'

description: Raw micrographs, training labels and resulting segmentations for 'Upsampling DINOv2 features for unsupervised vision tasks and weakly supervised materials segmentation'
DOI: 10.25345/c51834f1p
title: MassIVE MSV000096914 - Characterization phosphoproteome of RAW264.7 cells infected with quorum sensing ON and OFF Group A Strep
title: Phosphoproteome of RA264.7 macrophages 30m post infection with quorum sensing ON or OFF or both Streptococcus pyogenes (Group A Strep), or uninfected
DOI: 10.5281/zenodo.13910049
title: Orthrus: Towards Evolutionary and Functional RNA Foundation Models

description: Orthrus is a mature RNA model for RNA property prediction. It uses a Mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.

 

Two versions of Orthrus are available:



4-track base version: Encodes the mRNA sequence with a simplified one-hot approach.

6-track large version: Adds biological context by including splice site indicators and coding sequence markers, which is crucial for accurate mRNA property prediction such as RNA half-life, ribosome load, and exon junction detection.


This repository contains the annotations used to train Orthrus, as well as processed datasets used to evaluate Orthrus's ability to perform RNA property prediction. The datasets are taken from the following sources:



Protein Subcellular Localization: Thul, P. J. et al. A subcellular map of the human proteome. Science 356 (2017).

Mean Ribosome Load: Sugimoto, Y. & Ratcliffe, P. J. Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer. Nature Structural Molecular Biology 29, 871–880 (2022).

RNA Halflife: Agarwal, V. & Kelley, D. R. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 23, 245 (2022).

GO Molecular Function: Consortium, T. G. O. et al. The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).


Dataset files encode sequence using a one-hot encoding using the vocabulary: [A, C, G, T].
DOI: 10.5281/zenodo.13910050
title: Orthrus: Towards Evolutionary and Functional RNA Foundation Models

description: Orthrus is a mature RNA model for RNA property prediction. It uses a Mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.

 

Two versions of Orthrus are available:



4-track base version: Encodes the mRNA sequence with a simplified one-hot approach.

6-track large version: Adds biological context by including splice site indicators and coding sequence markers, which is crucial for accurate mRNA property prediction such as RNA half-life, ribosome load, and exon junction detection.
DOI: 10.5281/zenodo.14618726
title: Orthrus: Towards Evolutionary and Functional RNA Foundation Models

description: Orthrus is a mature RNA model for RNA property prediction. It uses a Mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.

 

Two versions of Orthrus are available:



4-track base version: Encodes the mRNA sequence with a simplified one-hot approach.

6-track large version: Adds biological context by including splice site indicators and coding sequence markers, which is crucial for accurate mRNA property prediction such as RNA half-life, ribosome load, and exon junction detection.
DOI: 10.5281/zenodo.14708163
title: Orthrus: Towards Evolutionary and Functional RNA Foundation Models

description: Orthrus is a mature RNA model for RNA property prediction. It uses a Mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.

 

Two versions of Orthrus are available:



4-track base version: Encodes the mRNA sequence with a simplified one-hot approach.

6-track large version: Adds biological context by including splice site indicators and coding sequence markers, which is crucial for accurate mRNA property prediction such as RNA half-life, ribosome load, and exon junction detection.


This repository contains the annotations used to train Orthrus, as well as processed datasets used to evaluate Orthrus's ability to perform RNA property prediction. The datasets are taken from the following sources:



Protein Subcellular Localization: Thul, P. J. et al. A subcellular map of the human proteome. Science 356 (2017).

Mean Ribosome Load: Sugimoto, Y. & Ratcliffe, P. J. Isoform-resolved mRNA profiling of ribosome load defines interplay of HIF and mTOR dysregulation in kidney cancer. Nature Structural Molecular Biology 29, 871–880 (2022).

RNA Halflife: Agarwal, V. & Kelley, D. R. The genetic and biochemical determinants of mRNA degradation rates in mammals. Genome Biol 23, 245 (2022).

GO Molecular Function: Consortium, T. G. O. et al. The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).


Dataset files encode sequence using a one-hot encoding using the vocabulary: [A, C, G, T].
DOI: 10.5281/zenodo.14721972
title: Dataset of Membrane lipid adaptation to phosphate concentration and HHP of an anaerobic piezotolerant
DOI: 10.6084/m9.figshare.28259873
title: Effect of PCE-SP on OPC-CSA Mortar

description: This data contains the experimental results investigating the effect of PCE-SP dosage on the early-age behavior of OPC-CSA-based mortar. Experimental techniques, including isothermal calorimetry, ultrasonic pulse velocity, compressive strength testing, Vicat needle, and dynamic flow table were employed to characterize the hydration process, setting time, and compressive strength development up to 28 days. Water-to-cement ratio of 0.3, cement-to-fine aggregate ratio of 1.0, and curing temperature of 25C were adopted for this research while all samples were prepared using Hobart benchtop mixer in accordance with ASTM standard.
DOI: 10.5281/zenodo.14699968
title: Scripts and data for "Impacts of rainfall spatiotemporal variability on pressurized flow conditions in urban drainage systems"

description: Supporting files for manuscript Impacts of rainfall spatiotemporal variability on pressurized flow conditions in urban drainage systems (preprint published at https://doi.org/10.22541/essoar.173757610.02817416/v1).
DOI: 10.5281/zenodo.14641261
title: Sample of Aquila data

description: This a sample of 1000 measurements using the QuEra Aquila device and a jupyternotebook to read the json file
DOI: 10.5281/zenodo.14641262
title: Sample of Aquila data

description: This a sample of 1000 measurements using the QuEra Aquila device and a jupyternotebook to read the json file
DOI: 10.6084/m9.figshare.21183871.v4
title: Evaluating the Lithospheric Structure and Regional/Residual Bouguer Anomalies in Peninsular India through Potential Field Modeling and Thermal Analysis

description: The dataset offers detailed crustal and lithospheric mapping, with a specific emphasis on the peninsular region of India. This mapping utilizes geoid, topography, and thermal analysis techniques under local isostasy and thermal steady-state conditions. The Geoid dataset is available for download in various orders and degrees from the http://icgem.gfz-potsdam.de/calcgrid website. Additionally, the Anomaly file showcases the calculated regional gravity effect and residual anomalies across the entire area, derived from the crustal and lithospheric structures.
DOI: 10.25345/c5wh2ds6p
title: MassIVE MSV000096915 - Machine learning reveals genes impacting oxidative stress resistance across yeasts
title: Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterized the variation in resistance to ROS across the ancient yeast subphylum Saccharomycotina and used machine learning (ML) to identify gene families whose sizes were predictive of ROS resistance. The most predictive features were enriched in gene families related to cell wall organization and included two reductase gene families. We estimated the quantitative contributions of features to each species' classification to guide experimental validation and showed that overexpression of the old yellow enzyme (OYE) reductase increased ROS resistance in Kluyveromyces lactis, while Saccharomyces cerevisiae mutants lacking multiple mannosyltransferase-encoding genes were hypersensitive to ROS. Altogether, this work provides a framework for how ML can uncover genetic mechanisms underlying trait variation across diverse species and inform trait manipulation for clinical and biotechnological applications.
DOI: 10.6084/m9.figshare.21183871.v5
title: Evaluating the Lithospheric Structure and Regional/Residual Bouguer Anomalies in Peninsular India through Potential Field Modeling and Thermal Analysis

description: The dataset provides comprehensive crustal and lithospheric mapping, with a specific focus on the peninsular region of India. This mapping is achieved through the integration of geoid, topography, and thermal analysis techniques under the framework of local isostasy and thermal steady-state conditions. The geoid dataset, which supports this mapping, is accessible for download in various orders and degrees from the ICGEM website (http://icgem.gfz-potsdam.de/calcgrid). Furthermore, the anomaly file presents the computed regional gravity effects and residual anomalies across the entire study area, derived from detailed crustal and lithospheric structures. Notably, all data utilized in the modeling process, including the geoid, and topography, are also available for download, enabling reproducibility and further analysis.