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

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Garrulax taewanus",
 "Country is one of (Brunei Darussalam, Indonesia, Philippines, Timor-Leste, Singapore)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031818-250920141307145/datasets/export for details.
DOI: 10.5281/zenodo.15261376
title: Supplementary file S1 for manuscript entitled "Cultivation and genomic characterization of a novel Ca. Syntrophosphaera thermopropionivorans of the candidate phylum Cloacimonadota"
DOI: 10.5281/zenodo.13684221
title: Thesis Tables

description: Tables referenced in Thesis publication
DOI: 10.5281/zenodo.15575787
title: Raw data for measurement of bulk porosity during freezing in brine using THz-TDS

description: This dataset contains the raw and processed data corresponding to the key figures presented in the manuscript entitled "Dynamic measurement of bulk porosity during freezing in NaCl solutions using broadband terahertz time-domain spectroscopy".  The data include measurements obtained using terahertz time-domain spectroscopy (THz-TDS) during the freezing process of NaCl solutions with varying salinities.  Each data file corresponds to a specific figure in the paper and provides the underlying numerical values used to generate the plots.  These data are provided to ensure transparency and reproducibility of the results.
DOI: 10.5281/zenodo.8391636
title: Experimental Database of deterministic wave prediction built from synchronous measurements from an X-band pulse radar and met-ocean sensors deployed on the Floatgen floating wind turbine and its vicinity on SEM-REV test site.

description: This dataset is a deliverable of the FLOATECH project, funded under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101007142.
The aim of this dataset is a result of the field experiments carried out at the Floatgen FOWT located at the SEM-REV test site.
DOI: 10.5281/zenodo.14054264
title: SERENA EJP Soil Green house gas aplication Moravia region, Czechia

description: The present dataset corresponds to a map of Net Ecosystem Productivity (NEP) for Moravia region in Czechia classified as wheat by the Eurocrop 2028 spatial product (d’Andrimont et al. 2021). The map is the result of applying the NEP cookbook developed in SERENA/EJP-Soil to the area of interest (AOI) input data. NEP is expressed for a single 8-day period in early summer as it is the date with the highest value. The NEP value is a 2010-2014 average for the particular 8-day period. The data description document of the cookbook (hereafter “GHG cookbook”) itself corresponds to other document of the SERENA project.
DOI: 10.5281/zenodo.11877096
title: Data and code for: Heat tolerance and its plasticity in freshwater and marine fishes are linked to their thermal regimes (v0.1).

description: Data and code for: Heat tolerance and its plasticity in freshwater and marine fishes are linked to their thermal regimes (v0.1).
DOI: 10.5281/zenodo.15261234
title: Supplementary file S1 for thesis manuscript entitled "Uncovering syntrophic potential from metagenomic community analysis of suspended and granular AD sludges"

description: Supplementary file S1 for manuscript entitled "Uncovering syntrophic potential from metagenomic community analysis of suspended and granular AD sludges".
DOI: 10.5281/zenodo.15713160
title: Supplementary Data: Identification of hematopoietic cell state markers in acute leukemia using explainable machine learning

description: Supplementary Data for "Identification of hematopoietic cell state markers in acute leukemia using explainable machine learning" 

File Description



IsoMarker Output.zip: Output of IsoMarker applied to integrated AML pseudo-bulk RNA-seq atlas.

aml_raw_expression.csv.zip: Raw expression counts of AML pseudo-bulk RNA-seq atlas, stratified by donor and cell state.

aml_raw_expression.csv.zip: VST-normalized expression counts of AML pseudo-bulk RNA-seq atlas, stratified by donor and cell state.

aml_atlas_metadata.csv.zip: Metadata of AML pseudo-bulk RNA-seq atlas.

AML_Atlas.h5ad: Full AML pseudo-bulk RNA-seq atlas in H5AD format.

AML_Atlas_LeukemiavsHealthy.h5ad: AML pseudo-bulk RNA-seq atlas with Leukemia and Healthy annotations in H5AD format.
DOI: 10.5281/zenodo.15818858
title: Deciphering antigen-specific T cell navigation tactics and cancer immune evasion in co-cultures_Code and datasets during revision

description: The main primary codes and datasets for the paper "Deciphering antigen-specific T cell navigation tactics and cancer immune evasion in co-cultures" are available via https://doi.org/10.5281/zenodo.15342510 and https://doi.org/10.5281/zenodo.15342510. During revision, additional codes and additional experimental datasets are provided here.
DOI: 10.5281/zenodo.15463499
title: Analysis of fluorescent images of respiratory epithelial cells from healthy donors

description: We applied automated image analysis to systematically examine the influence of samples’ storage conditions on the specificity of IF staining with eight polyclonal antibodies routinely used for diagnostics of primary ciliary dyskinesia, PCD. We used antibodies targeting epitopes of proteins representing various axoneme structural complexes. Seven various combinations of temperatures and storage times were tested to mimic the procedures of handling epithelial brushing on glass slides: at the clinic, during transport, or after reception at the diagnostic laboratory.

Our study revealed that proper slide storage conditions are essential for the reliable PCD diagnosis via IF staining. 

Storage temperatures tested and their symbols used in the data files: 








 Condition symbol



Group



Conditions (temperature and duration time)





1



-80_28d

(best conditions)



-80°C 28 days





3



-20_28d



-20°C28 days





4



-20_8w



-20°C 

 8 weeks





5



-20/RT/-80



-20°C

11 days



RT

3 days



-80°C

14 days





6



4/RT/-80



4 °C

11 days



RT

3 days



-80°C

14 days





7



RT/RT/-80



RT

11 days



RT

3 days



-80°C

14 days





2



RT_28d 

(worst conditions)



RT 28 days
DOI: 10.5281/zenodo.15079079
title: From policy to practice: the impact of monitoring declines on Pacific salmon conservation in Canada

description: Repository to support an analysis of spawner escapement monitoring for Pacific salmon since 1950 and its relevance to conservation decision making under Canada's Wild Salmon Policy
DOI: 10.5281/zenodo.15479519
title: Synthesized Inventory of Relevant Infrastructure and Utilized Areas, Including Contaminated Sites (SIRIUS)

description: The SIRIUS inventory integrates data from



OpenStreetMap for infrastructure and land use information (OpenStreetMap Contributors and Geofabrik GmbH, 2018),

the modeled Northern Hemisphere permafrost map by Obu et al. (2018),

the contaminated sites database and reports by the State of Alaska Department of Environmental Conservation (2023) (DEC),

the inventory of contaminated sites in Canada by the Treasury Board of Canada Secretariat (FCSI) (2024),

a compilation of contaminated sites in Greenland and Norway from the NGO Robin des Bois (2009a, 2009b) (RdB), 

projections of the timing of first talik formation, a model output from the CryoGridLite permafrost model (Langer et al., 2024)


for the Arctic regions of Alaska (AK), Canada (CA), Greenland (GL), and Norway (NO). 

This dataset is provided as a GeoPackage, enabling seamless integration with spatial databases (e.g., PostgreSQL/PostGIS), Geographic Information Systems (e.g., QGIS), and geospatial processing libraries (e.g., Python's GeoPandas). All layers can be queried either independently or in combination with one another.

The GeoPackage contains 17 separate layers. 

The contaminated sites layers contain detailed information on contaminants haromized into chemical classifications based on the Agency for Toxic Substances and Disease Registry (ATSDR). Additionally, each contaminated sites layer includes projections of talik formation as complementary attributes. These projections are provided for SSP1-2.6 and SSP5-8.5 scenarios, specifying the 5th, 50th (median), and 95th percentiles of the year when talik formation is expected to occur for the first time.  

The layers of the infrastructure and human-impacted areas are further divided into points of interest (POI), polygonal infrastructure, and linear road and rail networks (RRNetwork) for each Arctic region (AK, CA, GL, and NO). The permafrost extent is provided as a single pan-Arctic layer.

Contaminated Sites:



AK_ContaminatedSites_DEC

CA_ContaminatedSites_FCSI

GL_ContaminatedSites_RdB

NO_ContaminatedSites_RdB


Infrastructure and Human-Impacted Areas:



NO_POI_InfrastructureHIElements_OSM

NO_InfrastructureHIElements_OSM

NO_InfrastructureHIElements_RRNetwork_OSM

GL_POI_InfrastructureHIElements_OSM

GL_InfrastructureHIElements_OSM

GL_InfrastructureHIElements_RRNetwork_OSM

AK_POI_InfrastructureHIElements_OSM

AK_InfrastructureHIElements_OSM

AK_InfrastructureHIElements_RRNetwork_OSM

CA_POI_InfrastructureHIElements_OSM

CA_InfrastructureHIElements_OSM

CA_InfrastructureHIElements_RRNetwork_OSM


Permafrost Extent:



PermafrostZones_UiO


Download Data



pan-arctic_SIRIUS_v1.0.gpkg
DOI: 10.5281/zenodo.15482247
title: Dataset and input files for the 2025 Mw7.7 Myanmar earthquake
DOI: 10.5281/zenodo.13323248
title: Aligned DNA sequence matrix for phylogenetic analyses in the article "A new glassfrog of the genus Nymphargus (Anura: Centrolenidae) from Cordillera del Cóndor, Ecuador"

description: Aligned DNA sequence matrix for phylogenetic analyses of the article "A new glassfrog of the genus Nymphargus (Anura: Centrolenidae) from Cordillera del Cóndor, Ecuador"

The matrix is in NEXUS format and has 6613 bp and 102 terminals.

Partitions are as follows:



charset 12S = 1-944;

charset 16S = 945-2093;

charset BNDFcodonPos1 =  2096-2792\3;

charset BNDFcodonPos2 =  2094-2793\3;

charset BNDFcodonPos3 =  2095-2791\3;

charset ND1codonPos1 =  2795-3749\3;

charset ND1codonPos2 =  2796-3750\3;

charset ND1codonPos3 =  2794-3751\3;

charset CXCR4codonPos1 =  3753-4107\3;

charset CXCR4codonPos2 =  3754-4105\3;

charset CXCR4codonPos3 =  3752-4106\3;

charset cmyccodonPos1 =  4108-4507\3;

charset cmyccodonPos2 =  4109-4508\3;

charset cmyccodonPos3 =  4110-4509\3;

charset POMCcodonPos1 =  4511-5120\3;

charset POMCcodonPos2 =  4512-5121\3;

charset POMCcodonPos3 =  4510-5122\3;

charset RAG1codonPos1 =  5123-5576\3;

charset RAG1codonPos2 =  5124-5577\3;

charset RAG1codonPos3 =  5125-5578\3;

charset SLC8A1codonPos1 =  5580-6120\3;

charset SLC8A1codonPos2 =  5581-6118\3;

charset SLC8A1codonPos3 =  5579-6119\3;

charset SLC8A3codonPos1 =  6122-6587\3;

charset SLC8A3codonPos2 =  6123-6585\3;

charset SLC8A3codonPos3 =  6121-6586\3;
DOI: 10.5281/zenodo.13951143
title: SERENA EJP Soil: Green House Gas Regulation Application Emilia-Romagna, Italy (Summer)

description: The internal EJP SOIL project SERENA contributed to the evaluation of soil multifunctionality aiming at providing assessment tools for land planning and soil policies at different scales. By co-working with relevant stakeholders, the project provided co-developed indicators and associated cookbooks to assess and map them, to report both on soil degradation, soil-based ecosystem services and their bundles, under actual conditions and for climate and land-use changes, at the regional, national, and European scales.
description: The present dataset corresponds to a map of Net Ecosystem Productivity (NEP) for areas of the Emilia-Romagna region in Italy classified as wheat by the Eurocrop 2028 spatial product (d’Andrimont et al. 2021). The map is the result of applying the NEP cookbook developed in SERENA/EJP-Soil to the area of interest (AOI) input data. NEP is expressed for a single 8-days period in early summer (May 1st) as it is the date with the highest values. The NEP value is a 2010-2014 average for the particular 8-days period. The data set corresponds of (1) a geopackage file with embedded matadata and (2) an optional QGIS style file ("IT_GHG_cookbook_style.qml") to render the NEP legend.
description: The data are derived from the calculation of indicators based on a standard methodology established as part of the EJP Soil SERENA programme. Please keep in mind that:

It is the result of a modelling exercise and does not necessarily reflect reality.

Despite the efforts made to provide reliable data, the results may contain inconsistencies, depending in particular on the raw data available and level of accuracy of the techniques chosen and their prior knowledge . 

It is necessary to consider how the results have been obtained in order to decide on their relevance in relation to the intended purpose of reuse.

These results are interesting from a scientific point of view, but their use for environmental management and policy issues should be done keeping the previous aspects in mind and complementing when necessary the provided results with the best available data. 

Finally, it is the responsibility of the users of this information to decide whether it is appropriate to use these data and whether the data meet their needs. The authors of this resource can in no way be held responsible for the results obtained from the use of this data.
DOI: 10.5281/zenodo.14002136
title: SERENA EJP Soil: Bundles' cookbook exemplary datasets

description: The internal EJP SOIL project SERENA contributed to the evaluation of soil multifunctionality aiming at providing assessment tools for land planning and soil policies at different scales. By co-working with relevant stakeholders, the project provided co-developed indicators and associated cookbooks to assess and map them, to report both on soil degradation, soil-based ecosystem services and their bundles, under actual conditions and for climate and land-use changes, at the regional, national, and European scales.
description: The present dataset corresponds to 4 maps of soil-based ecosystem services and soil threats for the area of the EU. The maps are the result of applying the bundles cookbook developed in SERENA/EJP-Soil to the area of interest (AOI) input data. The resulting bundles are clusters of SESs/STs where the intra-cluster variability is lower than the inter-cluster variability in the mean values of the selected SESs/STs to identify the bundles.
description: The data are derived from the calculation of indicators based on a standard methodology established as part of the EJP Soil SERENA programme. Please keep in mind that:

It is the result of a modelling exercise and does not necessarily reflect reality.

Despite the efforts made to provide reliable data, the results may contain inconsistencies, depending in particular on the raw data available and level of accuracy of the techniques chosen and their prior knowledge .

It is necessary to consider how the results have been obtained in order to decide on their relevance in relation to the intended purpose of reuse.

These results are interesting from a scientific point of view, but their use for environmental management and policy issues should be done keeping the previous aspects in mind and complementing when necessary the provided results with the best available data.

Finally, it is the responsibility of the users of this information to decide whether it is appropriate to use these data and whether the data meet their needs. The authors of this resource can in no way be held responsible for the results obtained from the use of this data.
DOI: 10.5281/zenodo.15044411
title: Spatial Analysis of the Tumor Microenvironment in Diffuse Large B-Cell Lymphoma Reveals Clinically Relevant Cell Interactions and Recurrent Cellular Neighborhoods

description: Raw single-cell data extracted from segmented multiplex immunofluorescense staining images (99 DLBCL patients, 12 protein markers, and spatial data).
DOI: 10.5281/zenodo.17035888
title: Chromatin Structural Gene Expression Stratifies Cardiac Cell Populations in Health and Disease [Dataset]

description: Chromatin structure plays a central role in regulating gene expression and maintaining cellular identity, yet the structural factors driving these processes in cardiac disease remain poorly defined. To investigate whether these factors can distinguish healthy from diseased cardiac cell populations, we generated a comprehensive list of chromatin structural genes based on an extensive literature review. Applying this list to a published single-nuclei RNA sequencing (snRNA-seq) dataset from human hearts with and without dilated cardiomyopathy (DCM), we found that chromatin structural gene expression effectively stratified cardiomyocyte and fibroblast populations by disease status. Diseased cardiomyocytes exhibited reduced expression of contractile genes and increased expression of cardiomyopathy markers, while fibroblasts showed enhanced activation signatures. Among these factors, HMGN3 emerged as a candidate of interest, showing consistent downregulation in cardiomyocytes from human patients, as well as in mouse (pressure overload) and pig (myocardial infarction) models of heart failure. Functional studies in AC16 cells revealed that HMGN3 depletion promoted apoptosis, induced significant changes in gene expression, and reorganized chromatin structure by altering the distribution of the H3K27ac histone mark. These findings identify HMGN3 as a potential regulator of chromatin architecture in diseased cardiomyocytes, highlight the utility of chromatin structural changes in distinguishing pathological cardiac states, and reinforce the role of chromatin organization in shaping the cardiac phenotype.

 
description: All raw data included in the manuscript is availble in this folder.
DOI: 10.5281/zenodo.14680105
title: Rig Operations data from the Terrebonne Basin, Walker Ridge Block 313, Site H, Expedition UT-GOM2-2

description: This dataset contains the daily reports, borehole reports, operational reports, and integrated rig and wireline data for Expedition UT-GOM2-2. Methods are documented in Expedition UT-GOM2-2 Methods: Drilling Operations, Depth References, and Downhole Tools (Flemings et al., 2025a, https://doi.org/10.5281/zenodo.13971228).

The attached readme file, previewed below, describes all the data files in this dataset and their contents. The readme file also contains links to where the data is presented in the expedition proceedings.

Additional data you might expect to find in this dataset can instead be found at the following locations:

A summary of expedition operations outlining major activities can be found in Expedition UT-GOM2-2 Site H, Appendix A (Flemings et al., 2025b, https://doi.org/10.5281/zenodo.13971276). A copy of the daily science reports can be found in Expedition UT-GOM2-2 Site H, Appendix B (Flemings et al., 2025b, https://doi.org/10.5281/zenodo.13971276). Daily reports contain interpretations of events that may or may not reflect the final summary interpretation.

Logs of coring data, acquired cores, cut sections-pieces, and locations of samples and measurements can be found in the curation dataset http://doi.org/10.5281/zenodo.14926309. For coring logs, download the files GoM2-2 H003 AS DRILLED.pdf and GoM2-2 H002 AS DRILLED v1.pdf.  For core, section, and sampling logs, download the file UT-GOM2-2 CORE LOG depths – sortable.xlsx. See tabs “Core log”, “Section-piece log”, and “Sample-measurement log”.

Pressure coring reports can be found in the pressure coring dataset (http://doi.org/10.5281/zenodo.14104224) and hand-written conventional core curation reports can be found in the conventional coring dataset (https://doi.org/10.5281/zenodo.14518080).

Daily discharge data were also entered and summed up into a discharge monitoring workbook and reported in EPA NPDES Quarterly Discharge Monitoring Reports (DMR) that summarize activities for The University of Texas at Austin. This discharge data can be downloaded at FRS Facility Detail Report | Envirofacts | US EPA.

M-I SWACO mercury and cadmium results were also summarized and reported in EPA NPDES Quarterly Discharge Monitoring Reports for the The University of Texas at Austin. The summary can be downloaded at FRS Facility Detail Report | Envirofacts | US EPA.

Plug and abandonment records are on file with the Bureau of Safety and Environmental Enforcement, API: 608124014800 and API: 608124014900. Plug and abandonment is also discussed in Site H, Plug and Abandonment (Flemings et al., 2025b, https://doi.org/10.5281/zenodo.13971276).
DOI: 10.5281/zenodo.14143461
title: Calcareous Nannofossil Biostratigraphy from the Terrebonne Basin, Gulf of Mexico, Walker Ridge Block 313, Site H, Expedition UT-GOM2-2

description: These data include calcareous nannofossil abundance data collected on paleontology samples (sample code PAL). Specimens were examined and documented via photomicroscopy in a transmitted light microscope. A modified version of Styzen's (1997) quantitative counting method of calcareous nannofossils was applied to each sample examined ensuring precise interpretation of the age and assemblage. Biostratigraphic events, such as First and Last Appearance Datums (FAD and LAD), were determined, and known ages for these datums were plotted by depth. See Expedition UT-GOM2-2 Methods: Biostratigraphy (Flemings et al., 2025a, https://doi.org/10.5281/zenodo.13971228).

The attached readme file, previewed below, describes all the data files in this dataset and their contents. The readme file also contains links to where the data is presented in the expedition proceedings.

Additional data you might expect to find in this dataset can instead be found at the following locations:

The sample depths can be found in the curation dataset (http://doi.org/10.5281/zenodo.14926309). Download the file UT-GOM2-2 CORE LOG depths – sortable.xlsx, see tab “Sample-measurement log” sample code PAL. Not all samples were examined during the expedition.
DOI: 10.5281/zenodo.14518081
title: Conventional Coring in the Terrebonne Basin, Walker Ridge Block 313, Site H, Expedition UT-GOM2-2

description: This dataset contains conventional coring deployment data from Geotek Advanced Piston Coring Tool (G-APC, code H) and the Geotek Extended Core Barrel (G-XCB, code X) coring deployments including G-APC Firing Pressure, G-APC offset, G-APC shear pin information, G-APC Speed control valve settings, core interval, and recovery. Core processing data on handwritten core curation sheets with core section depths, sample designations, void gas depths and raw hand vane and pocket penetrometer measurements. See Expedition UT-GOM2-2 Methods: Conventional Coring Tools, and Conventional Coring Results (Flemings et al., 2025a, https://doi.org/10.5281/zenodo.13971228).

The attached readme file, previewed below, describes all the data files in this dataset and their contents. The readme file also contains links to where the data is presented in the expedition proceedings.

Additional data you might expect to find in this dataset can instead be found at the following locations:

Pressure coring deployment data can be found in the pressure coring dataset (http://doi.org/10.5281/zenodo.14104224).

Logs of coring data and acquired cores can be found in the curation dataset (http://doi.org/10.5281/zenodo.14926309). For coring logs, download the files GoM2-2 H003 AS DRILLED.pdf and GoM2-2 H002 AS DRILLED v1.pdf.  For the core log, download file UT-GOM2-2 CORE LOG depths – sortable.xlsx. See tab “Core type”, “H” for G-APC and “X” for G-XCB conventional cores.

Cut sections, gas sample depths, and measurement depths are also archived in the curation dataset (http://doi.org/10.5281/zenodo.14926309).

Void gas composition can be found in the gas geochemistry dataset (https://doi.org/10.5281/zenodo.15626975). Hand vane and pocket penetrometer measurements can also be found in the undrained strength dataset (http://doi.org/10.5281/zenodo.14107263).