cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8387553
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.
DOI: 10.5281/zenodo.8393490
title: Data and Code for "An updated end-to-end ecosystem model of the Northern California Current"

description: This upload contains all data and code for "An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heat waves", submitted to PLOS ONE. Manuscript abstract is pasted below: The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (<em>Oncorhynchus tshawytscha</em>) and southern resident killer whales (<em>Orcinus orca</em>). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 100-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.
DOI: 10.5281/zenodo.8270764
title: Single Cell RNA sequencing data of ADT treated Prostate cancer patients

description: The data was generated from a study that was conducted according to guidelines approved by the Review Board at the University of Texas Southwestern Medical Center. We procured patient biopsy samples from two distinct studies. The first is titled "Tissue Collection and Results Gathering for Radiotherapy Patients & Healthy Individuals" (STU 072010-098), and the second is a Phase I Clinical Study on Stereotactic Ablative Radiotherapy (SABR) for Pelvic and Prostate Areas in High-Risk Prostate Cancer Patients (STU062014-027). The single-cell RNA sequencing (scRNA-seq) took place in Dr. Douglas Strand's laboratory, adhering to the method outlined in Henry et al<sup>1</sup>. We used a 1-hour treatment with 5mg/ml of collagenase type I, 10mM of ROCK inhibitor, and 1mg of DNase. Barcode labeling for 3' GEX was done using a 10X machine, and the sequencing process utilized an Illumina NextSeq 500 device. 1. Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J., ... & Strand, D. W. (2018). A cellular anatomy of the normal adult human prostate and prostatic urethra. <em>Cell reports</em>, <em>25</em>(12), 3530-3542.
description: The study is funded by the following NIH grants: RC2 DK129994 R01 DK115477 R01 DK135535
DOI: 10.5066/p9xsm9ry
title: Photogrammetry-derived digital elevation models and source images for an inactive perched lava lake formed at Pu?u???? (K?lauea) in 2014

description: Lava flow hazards are usually thought to end when the erupting vent becomes inactive, but this is not always the case. At K?lauea in August 2014, a spiny ?a?? flow erupted from the levee of a crusted perched lava lake that had been inactive for a month, and the surface of the lava lake subsided as the flow advanced downslope over the following few days. Topography constructed from oblique aerial photographs using structure-from-motion (SfM) software shows that the volume of the flow (~68,000 m3) closely matches the volume of subsidence of the crusted lava lake (~64,000 m3). The similarity of these volumes, along with the textural characteristics of the lava, shows that the lava that fed the flow had been stored beneath the surface of the perched lava lake, and that the flow was not generated by reactivation of the vent. This extends the duration of the local lava flow hazard presented by perched lava lakes and similar flow field structures that store lava, such as rootless shields.
DOI: 10.6084/m9.figshare.24205938
title: RNA reads

description: The fastq files of the three metatranscriptomic samples analyzed in Whaley-Martin and Chen et al., 2023, “O<sub>2</sub> partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters” (https://doi.org/10.1038/s41467-023-37426-8).
DOI: 10.6084/m9.figshare.24205938.v1
title: RNA reads

description: The fastq files of the three metatranscriptomic samples analyzed in Whaley-Martin and Chen et al., 2023, “O<sub>2</sub> partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters” (https://doi.org/10.1038/s41467-023-37426-8).
DOI: 10.5281/zenodo.8393536
title: A New Mechanism for Stishovite Formation During Rapid Compression of Quartz and Implications for Asteroid Impacts

description: Data for A New Mechanism for Stishovite Formation During Rapid Compression of Quartz and Implications for Asteroid Impacts
DOI: 10.5066/p9vwvav6
title: Drainage Areas for Stream Segments in Western San Diego County

description: Drainage areas (or watersheds) were calculated for each stream segment in the National Hydrography Dataset High Resolution Plus Beta (NHD HR Plus Beta) using non-end junction points and the provided hydrologically enforced Digital Elevation Model (DEM). The DEM was used to create a flow direction raster. The pour points used were determined from junction points at each stream intersection excluding stream ends (i.e. channel heads are not included). Watershed calculations were automated using the ArcGIS "watershed" tool and then edited manually for accuracy. In western San Diego County (non-desert) there were 39,980 drainage areas calculated. The percent impervious in each watershed was calculated using the National Land Cover Dataset 2019 Impervious surface.
DOI: 10.5066/p9c94l2l
title: Water chemistry and biological data of Rainbow Trout following aquatic exposure to weathered wildland fire retardants after application to substrate

description: We investigated whether the length of time fire chemical weathers on a terrestrial substrate before mixing into aquatic environments alters the chemical?s toxicity when encountered by juvenile rainbow trout. We also looked at whether the type of substrate where the chemical is applied affects its toxicity to juvenile rainbow trout after mixing into water. Two fire chemicals (Phos Chek LC95A-R and Phos Chek MVP-Fx) were applied to four substrate media (low organic content soil, high organic content soil, duff, and gravel) and allowed to age on the substrate for 7, 14, 28 or 56 days. At the end of the assigned weathering period, 96-hour assays were conducted by adding water to the dosed substrate and stocking each experimental unit with juvenile rainbow trout. The fish were added to the experimental units after allowing the substrate to settle for 60 minutes. Water chemistry parameters were measured at the initiation of each assay, including water temperature, dissolved oxygen, specific conductance, pH, alkalinity, hardness, and total ammonia. Observations on mortality of rainbow trout were made daily and dead fish were removed upon discovery. The experiment concluded 96 hours after fish entered the experiment.
DOI: 10.5281/zenodo.8132285
title: Potential distribution dynamics of Araucaria (Araucariaceae) in South America

description: The distribution dynamics of the genus <em>Araucaria</em> in South America over time was analyzed by obtaining species distribution models for <em>Araucaria angustifolia</em> and <em>A. araucana</em> from the Last Interglacial to present.
DOI: 10.5281/zenodo.7114653
title: The Standardized Vegetation Optical Depth Index SVODI

description: <strong>Related paper with detailed description: </strong>https://doi.org/10.5194/bg-19-5107-2022 <strong>Short summary:</strong> The Standardized Vegetation Optical Depth index (SVODI) can be used to monitor the vegetation condition, such as whether the vegetation is unusually dry or wet. SVODI has global coverage and spans the past three decades and is derived from multiple space-borne passive microwave sensors of that period. SVODI is based on a new probabilistic merging method that allows the merging of normally distributed data, even if the data is not gap-free. <strong>Files: </strong> "SVODI_v01.zip" Contains the bulk SVODI data, globally, from 1987-07-10 to 2019-12-31. Files are daily global netcdf images, with a 0.25 degree spatial resolution. Is unzipped roughly the same size. "svodi_v01_0_2006-06-26.nc" An arbitrary file from SVODI_V01.zip. For your convenience in case you want to see an example first without downloading the whole thing. "ESA-CCI-SOILMOISTURE-LAND_AND_RAINFOREST_MASK-fv04.2.nc" Grid of SVODI, Source: https://github.com/TUW-GEO/smecv-grid <strong>Data fields:</strong> "svodi" The standardized vegetation optical depth index unitless range: -inf, inf "flag" Bit-flag indicating which &lt;sensor&gt;-&lt;band&gt; combination contributed to each observation 1: AMSRE-C 2: AMSR2-C 3: WindSat-C 4: AMSRE-X 5: AMSR2-X 6: WindSat-X 7: TMI-X 8: AMSRE-Ku 9: AMSR2-Ku 10: WindSat-Ku 11: TMI-Ku 12: SSMI-Ku
DOI: 10.5281/zenodo.7114654
title: The Standardized Vegetation Optical Depth Index SVODI

description: <strong>Related paper with detailed description: </strong>https://doi.org/10.5194/bg-19-5107-2022 <strong>Short summary:</strong> The Standardized Vegetation Optical Depth index (SVODI) can be used to monitor the vegetation condition, such as whether the vegetation is unusually dry or wet. SVODI has global coverage and spans the past three decades and is derived from multiple space-borne passive microwave sensors of that period. SVODI is based on a new probabilistic merging method that allows the merging of normally distributed data, even if the data is not gap-free. <strong>Files: </strong> "SVODI_v01.zip" Contains the bulk SVODI data, globally, from 1987-07-10 to 2019-12-31. Files are daily global netcdf images, with a 0.25 degree spatial resolution. Is unzipped roughly the same size. "svodi_v01_0_2006-06-26.nc" An arbitrary file from SVODI_V01.zip. For your convenience in case you want to see an example first without downloading the whole thing. "ESA-CCI-SOILMOISTURE-LAND_AND_RAINFOREST_MASK-fv04.2.nc" Grid of SVODI, Source: https://github.com/TUW-GEO/smecv-grid <strong>Data fields:</strong> "svodi" The standardized vegetation optical depth index unitless range: -inf, inf "flag" Bit-flag indicating which &lt;sensor&gt;-&lt;band&gt; combination contributed to each observation 1: AMSRE-C 2: AMSR2-C 3: WindSat-C 4: AMSRE-X 5: AMSR2-X 6: WindSat-X 7: TMI-X 8: AMSRE-Ku 9: AMSR2-Ku 10: WindSat-Ku 11: TMI-Ku 12: SSMI-Ku
DOI: 10.5281/zenodo.7461175
title: Calliope-ENBIOS process Dictionary

description: This is a dictionary to connect Carriers and technologies from the Calliope Software with the processors of the ENBIOS tool
DOI: 10.5281/zenodo.7461174
title: Calliope-ENBIOS process Dictionary

description: This is a dictionary to connect Carriers and technologies from the Calliope Software with the processors of the ENBIOS tool
DOI: 10.5281/zenodo.8069703
title: Geodiversity Index and sub-indices Map of French Guiana

description: This file contains: 1) The vector (.shp) of the Geodiversity Index Map of French Guiana. The attribute table includes the following fields: - "id": as the code identifier for each grid-cell; - "CODE": as the number of each grid-cell; - "LITHO", "MIN", "HYDRO", "GEOM": as the abundance of respectively lithological, mineralogical, hydrological, geomorphological entities per each cell according to the methodology described in the main paper (see below). - "CLS_L", "CLS_M", "CLS_Gm", "CLSH3": as geodiversity sub-indices values (i.e. respectively, lithodiversity, mineral diversity, geomorphodiversity, hydrodiversity) on a scale between 1 (low diversity) and 4 (very high diversity). - "TOT_GI3": the sum of the sub-indices values -"GI_CLS3": the final Geodiversity Index 2) The rasterized (.tiff) version of the map The spatial data are associated with the following paper: Scammacca, O., Bétard, F., Aertgeerts, G. <em>et al.</em> Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. <em>Geoheritage</em> <strong>14</strong>, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6
description: Scammacca, O., Bétard, F., Aertgeerts, G. et al. Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. Geoheritage 14, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6
description: {"references": ["Scammacca, O., B\u00e9tard, F., Aertgeerts, G. et al. Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. Geoheritage 14, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6"]}
DOI: 10.5281/zenodo.8069704
title: Geodiversity Index and sub-indices Map of French Guiana

description: This file contains: 1) The vector (.shp) of the Geodiversity Index Map of French Guiana. The attribute table includes the following fields: - "id": as the code identifier for each grid-cell; - "CODE": as the number of each grid-cell; - "LITHO", "MIN", "HYDRO", "GEOM": as the abundance of respectively lithological, mineralogical, hydrological, geomorphological entities per each cell according to the methodology described in the main paper (see below). - "CLS_L", "CLS_M", "CLS_Gm", "CLSH3": as geodiversity sub-indices values (i.e. respectively, lithodiversity, mineral diversity, geomorphodiversity, hydrodiversity) on a scale between 1 (low diversity) and 4 (very high diversity). - "TOT_GI3": the sum of the sub-indices values -"GI_CLS3": the final Geodiversity Index 2) The rasterized (.tiff) version of the map The spatial data are associated with the following paper: Scammacca, O., Bétard, F., Aertgeerts, G. <em>et al.</em> Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. <em>Geoheritage</em> <strong>14</strong>, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6
description: Scammacca, O., Bétard, F., Aertgeerts, G. et al. Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. Geoheritage 14, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6
description: {"references": ["Scammacca, O., B\u00e9tard, F., Aertgeerts, G. et al. Geodiversity Assessment of French Guiana: Challenges and Implications for Sustainable Land Planning. Geoheritage 14, 83 (2022). https://doi.org/10.1007/s12371-022-00716-6"]}
DOI: 10.5281/zenodo.8215151
title: Input Data for TEMIR v1.0

description: This dataset contains the necessary input data for the Terrestrial Ecosystem Model in R (TEMIR) version 1.0 (https://github.com/amospktai/TEMIR).
DOI: 10.5281/zenodo.8215152
title: Input Data for TEMIR v1.0

description: This dataset contains the necessary input data for the Terrestrial Ecosystem Model in R (TEMIR) version 1.0 (https://github.com/amospktai/TEMIR).
DOI: 10.5281/zenodo.6001540
title: CORINE land cover - Catalan land cover taxonomy dictionary for metropolitan Barcelona

description: This dataset includes Catalan Land Cover categories that are relevant for metropolitan Barcelona and their translation to CORINE land cover categories. This work has been developed for the ERC project URBAG Original Catalan land cover map: https://www.creaf.uab.es/mcsc/ CORINE land cover: https://land.copernicus.eu/pan-european/corine-land-cover
DOI: 10.5281/zenodo.6001541
title: CORINE land cover - Catalan land cover taxonomy dictionary for metropolitan Barcelona

description: This dataset includes Catalan Land Cover categories that are relevant for metropolitan Barcelona and their translation to CORINE land cover categories. This work has been developed for the ERC project URBAG Original Catalan land cover map: https://www.creaf.uab.es/mcsc/ CORINE land cover: https://land.copernicus.eu/pan-european/corine-land-cover
DOI: 10.5281/zenodo.8042049
title: 'Danum Revised' forest field plot data for twenty 0.28 hectare field plots, measured in 2017

description: Permanent forest plot data from Sabah, Malaysia. Danum Valley Conservation Area. Here we provide a brief description of the permanent plot data collected following the same protocols utilized within the Kuamut forest reserve. Twenty circular field plots with a 30 m radius that were established across the protected area as part of a collaboration between SEARRP and the Carnegie Airborne Observatory (CAO) in 2017. These plots were surveyed following the same protocols as those described by the Kuamut conservation project. The field protocol is provided. Field plot locations where selected using airborne LiDAR to specifically target both high Aboveground Carbon Density (ACD) areas, and also areas with different ACD predictions based on a draft set of carbon mapping models. See Jucker et al. (2018) and Asner et al. (2017) for further details. Note subsequent measurements (in 2020) include more plots. Subsequent measurements allowed further data checking and corrections, so some minor updates to the 2017 dataset have been made since the previous publications. Please see additional Zenodo data entries for the 2020 measure. Use of these data require citation of this dataset and citation of the two original journal articles that delivered and explain the work, and that you inform us of the use of the data. We would also appreciate the opportunity to be involved in work making use of this data. The required citations are as follows: Asner, Gregory P., Philip G. Brodrick, Christopher Philipson, Nicolas R. Vaughn, Roberta E. Martin, David E. Knapp, Joseph Heckler, et al. 2017. “Mapped Aboveground Carbon Stocks to Advance Forest Conservation and Recovery in Malaysian Borneo.” <em>Biological Conservation</em> 217 (June 2017): 289–310. https://doi.org/10.1016/j.biocon.2017.10.020 Jucker, Tommaso, Gregory P. Asner, Michele Dalponte, Philip G. Brodrick, Christopher D. Philipson, Nicholas R. Vaughn, Yit Arn Teh, et al. 2018. “Estimating Aboveground Carbon Density and Its Uncertainty in Borneo’s Structurally Complex Tropical Forests Using Airborne Laser Scanning.” <em>Biogeosciences</em> 15 (12): 3811–30. https://doi.org/10.5194/bg-15-3811-2018 This work would not be possible without the incredibly hard work and dedication of the entire SEARRP field team, including Philip Ak Ulok; Hii Siew Yee; Remmy Bin Murus; Alexander Karolus; Andy Brian Karolus; Frederica Karolus; Zidey Fulgentius; Welday Bin Girang; Mohamad Taufiq Bin Sumin, Mohd Fadil Bin Abd Karim, Joulu Rasion, and Japin Bin Rasion. We are very grateful to the help of all the field staff not specifically mentioned here.­
description: subsequent measurements include more plots. Please see additional data entries
description: {"references": ["https://doi.org/10.1016/j.biocon.2017.10.020", "https://doi.org/10.5194/bg-15-3811-2018"]}
DOI: 10.26093/cds/vizier.18139015
title: Dwarf galaxies in Fornax cluster from NGFS

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'Unveiling a rich system of faint dwarf galaxies in the Next Generation Fornax Survey.' (bibcode: 2015ApJ...813L..15M)
DOI: 10.25345/c50863g7f
title: MassIVE MSV000093003 - 09-27-2023 Labeled Glucose Fasting Length Pilot
title: Pilot studying investigating whether a 3 hour fast or no fast before injection with labeled C13 glucose is better for maximum labeling.
DOI: 10.26093/cds/vizier.18550142
title: Next Generation Fornax Survey (NGFS) II.

description: VizieR online Data Catalogue associated with article published in journal Astronomical Journal (AAS) with title 'The Next Generation Fornax Survey (NGFS). II. The central dwarf galaxy population.' (bibcode: 2018ApJ...855..142E)