cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17251324
title: Data for "Drone-Imaging Assisted GWAS Reveal Key QTLs for Emergence and Late Blight Resistance in Tetraploid Potato"

description: The data applied in the study includes phenotypic and genotypic information on two panels of breeding clones from Danespo A/S. Due to proprietary rights of the clones, they are masked by IdX numbers in the data. The genotypic data was generated by SNP array using a custom 20k Affymetrix chip. This chip is also proprietary, and the SNP positions on each chromosome are also masked, but retain chronology along the chromosome. The phenotypic data was computed from image data as a commercial service by Phenoyard AB without preprocessing. The phenotypes submitted here include the 1-9 grading of clone emergence across day 0-20 of the early growth season. 9 denotes early emergence, and 1 denotes late emergence. Late blight resistance is reported as an area-under-disease-progression-curve normalized by total monitoration period, i.e. a single across-season phenotype for each clone. 

File descriptions:SNP_map.RData - .RData file holding the masked marker coordinates on the chromosomes. Chromosome 0 is scaffolds, chromosome 13 is unmapped. The SNPs are based on the v6.1 potato DM reference genome, but positions are masked within chromosome.

gt_emergence_panel.RData - .RData file holding imputed genotypic data of 8,731 SNPs for 2,576 clones in the emergence panel. The row names are clone IdX. The column names are SNP ID. 

gt_late_blight_resistance_panel.RData - .RData file holding imputed genotypic data of 8,731 SNPs for 1,520 clones in the late blight resistance panel. The row names are clone IdX. The column names are SNP ID. 

pt_emergence.RData - .RData file holding "Emergence" phenotypic data for the emergence panel, including 6,262 observations. Also including metadata such as field location, year of phenotyping, and clone market group.

pt_late_blight_resistance.RData - .RData file holding "LC_AUDPC" late blight resistance phenotypic data for the late blight resistance panel, including 6,972 observations. Also including metadata such as field location, year of phenotyping, and clone market group.
DOI: 10.15468/dl.fjv4n8
title: Occurrence Download

description: A dataset containing 13108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caprimulgiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((30 0,60 0,60 30,30 30,30 0))"
 ]
}

 The dataset includes 13108 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058084-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17286646
title: Stakeholder evaulation survey results

description: The data are the summarized, quantitative information of the stakeholder identification and classification across the 5 case studies throughout the 4 years of the project (v1 - at the end of year 1 of the project, v2 - at the end of year 2 of the project, etc.). The data was generated by compilation and gathering of stakeholders by the case study leads based on the guidance provided by AVA in the individual and yearly stakeholder engagement plans for each of the case studies and years. The classification was based on guidance by AVA and was assessed by case study leads. The guidance can be found in D5.1 and in Avellán et al., 2025 (https://doi.org/10.1016/j.envsci.2025.104029). The dataset will be used by NXG for further scientific publications on the quality of the process and outcomes of the stakeholder engagement process. The dataset can be used by others as an examplary result of a standardized stakeholder identification and classification in nexus projects.
DOI: 10.5281/zenodo.17286647
title: Stakeholder evaulation survey results

description: The data are the summarized, quantitative information of the stakeholder identification and classification across the 5 case studies throughout the 4 years of the project (v1 - at the end of year 1 of the project, v2 - at the end of year 2 of the project, etc.). The data was generated by compilation and gathering of stakeholders by the case study leads based on the guidance provided by AVA in the individual and yearly stakeholder engagement plans for each of the case studies and years. The classification was based on guidance by AVA and was assessed by case study leads. The guidance can be found in D5.1 and in Avellán et al., 2025 (https://doi.org/10.1016/j.envsci.2025.104029). The dataset will be used by NXG for further scientific publications on the quality of the process and outcomes of the stakeholder engagement process. The dataset can be used by others as an examplary result of a standardized stakeholder identification and classification in nexus projects.
DOI: 10.5281/zenodo.17224527
title: Shallow Cumulus Cloud Statistics in Realistic LES Datasets during FESSTVaL

description: This repository provides the tracked statistics of shallow cumulus clouds (SCC) derived from large-eddy simulations (LES) with the ICON model during the FESSTVaL campaign on 09, 17, and 27 June 2021. The datasets include both instantaneous (df_Stats) and lifetime-mean (df_mean) properties of clouds, interpolated from the native ICON triangular grid to a uniform 80 m rectangular grid. Soil moisture sensitivity experiments were conducted by scaling the default soil moisture by different percentages (20–200%). These datasets support the study “Shallow Cumulus Cloud Statistics in Realistic LES and Their Sensitivity to Soil Moisture” (submitted to JAMES).
DOI: 10.5281/zenodo.17224528
title: Shallow Cumulus Cloud Statistics in Realistic LES Datasets during FESSTVaL

description: This repository provides the tracked statistics of shallow cumulus clouds (SCC) derived from large-eddy simulations (LES) with the ICON model during the FESSTVaL campaign on 09, 17, and 27 June 2021. The datasets include both instantaneous (df_Stats) and lifetime-mean (df_mean) properties of clouds, interpolated from the native ICON triangular grid to a uniform 80 m rectangular grid. Soil moisture sensitivity experiments were conducted by scaling the default soil moisture by different percentages (20–200%). These datasets support the study “Shallow Cumulus Cloud Statistics in Realistic LES and Their Sensitivity to Soil Moisture” (submitted to JAMES).
DOI: 10.15468/dl.574m5g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tortulosa tortuosa"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058085-250920141307145/datasets/export for details.
DOI: 10.15468/dl.gybwpz
title: Occurrence Download

description: A dataset containing 1031 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Illicium henryi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1031 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058087-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pb8wvm
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Somalia",
 "OccurrenceStatus is Present",
 "TaxonKey is Loxodonta africana"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058088-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vj9vf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinopsis pachanoi",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058089-250920141307145/datasets/export for details.
DOI: 10.15468/dl.fpshek
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echinopsis pachanoi",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058090-250920141307145/datasets/export for details.
DOI: 10.15468/dl.pudpd7
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Polygala vayredae)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058091-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/xiur2c
title: Modulating backbone flexibility in hydroxamate siderophores for improved iron chelation and peptide nucleic acid (PNA) delivery into bacteria

description: Data:RP-HPLC spectra of pure siderophores and siderophore-PNA conjugates.CD spectra of siderophores.Spectrophotometric data for competition assay with EDTA. Data for calibration curve for each siderophore is included.Optical density at 600 nm (OD600) of E.coli mutants recorded in growth recovery assay in the presence of ferric-siderophores.Measurements of fluorescence of red fluorescent protein (RFP) expressed in the E.coli JW0669 Δfur culture with siderophores and siderophore-PNA conjugates.Top-scoring docking poses. Each file consists of a protein with docked ligand, and cofactors or other crystallographic ligands, when necessary.Input files for molecular dynamics simulations of siderophores in the "nonbonded" model. Input structures in the PDB format, topology files, and initial coordinate files are included.Data used to analyze the distances between the iron ion and oxygen atoms from the siderophore hydroxamate groups. Data was obtained in molecular dynamics simulations using the "nonbonded" model of iron(III)-siderophore interactions.
DOI: 10.6084/m9.figshare.30295204
title: Pham clustering of <i>Acinetobacter</i> phage proteins

description: Data accompanying Pang et al. (unpublished) Genomic Landscape of Complete Acinetobacter Phages: Clustering, Core-Shell Genes, and Synteny Insights. "PHAMS_Acinetobacter_Phages.faa" contains the list of clustered <i>Acinetobacter</i> phage protein phamilies using PhaMMseqs with default parameters.
DOI: 10.6084/m9.figshare.30295204.v1
title: Pham clustering of <i>Acinetobacter</i> phage proteins

description: Data accompanying Pang et al. (unpublished) Genomic Landscape of Complete Acinetobacter Phages: Clustering, Core-Shell Genes, and Synteny Insights. "PHAMS_Acinetobacter_Phages.faa" contains the list of clustered <i>Acinetobacter</i> phage protein phamilies using PhaMMseqs with default parameters.
DOI: 10.6084/m9.figshare.30178082
title: Molecular epidemiology of pESI-carrying <i>Salmonella</i> Infantis in Korea: insights from a one health framework

description: The emergence and global dissemination of <i>Salmonella</i> Infantis carrying the pESI megaplasmid is a growing public health concern owing to its association with multidrug resistance (MDR), enhanced virulence, and increased environmental adaptability. This study investigated the molecular epidemiology and transmission dynamics of pESI-carrying <i>S.</i> Infantis in the poultry production chain and human clinical cases in Korea. A total of 295 <i>Salmonella</i> isolates were collected from poultry sources (farms, slaughterhouses, and retail meats) in 2023, of which 219 (74.2%) were identified as <i>S.</i> Infantis. Additionally, 22 human-origin <i>S</i>. Infantis isolates collected between 2016 and 2023 were included in this study. Among these 241 <i>S</i>. Infantis isolates, 218 from poultry and one from a human case (collected in 2023) were MDR and carried pESIs, most of which carried <i>blaCTX-M-65</i> and multiple other resistance genes. Comparative whole-genome sequencing revealed a high degree of genetic similarity between poultry and human pESI-carrying <i>S.</i> Infantis isolates, suggesting probable zoonotic transmission through the chicken supply chain. Structural comparison of complete plasmid sequences further revealed close similarity between Korean and US pESIs, suggesting a potential epidemiological link. This study identified the rapid clonal spread of pESI-carrying <i>S</i>. Infantis in the Korean poultry sector and reported the first identification of pESI-carrying <i>S</i>. Infantis in human clinical isolates in Korea. These findings underscore the urgent need for global surveillance, enhanced biosecurity measures in the poultry industry, and stricter regulations to prevent further dissemination of MDR <i>S</i>. Infantis.
DOI: 10.6084/m9.figshare.30178082.v2
title: Molecular epidemiology of pESI-carrying <i>Salmonella</i> Infantis in Korea: insights from a one health framework

description: The emergence and global dissemination of <i>Salmonella</i> Infantis carrying the pESI megaplasmid is a growing public health concern owing to its association with multidrug resistance (MDR), enhanced virulence, and increased environmental adaptability. This study investigated the molecular epidemiology and transmission dynamics of pESI-carrying <i>S.</i> Infantis in the poultry production chain and human clinical cases in Korea. A total of 295 <i>Salmonella</i> isolates were collected from poultry sources (farms, slaughterhouses, and retail meats) in 2023, of which 219 (74.2%) were identified as <i>S.</i> Infantis. Additionally, 22 human-origin <i>S</i>. Infantis isolates collected between 2016 and 2023 were included in this study. Among these 241 <i>S</i>. Infantis isolates, 218 from poultry and one from a human case (collected in 2023) were MDR and carried pESIs, most of which carried <i>blaCTX-M-65</i> and multiple other resistance genes. Comparative whole-genome sequencing revealed a high degree of genetic similarity between poultry and human pESI-carrying <i>S.</i> Infantis isolates, suggesting probable zoonotic transmission through the chicken supply chain. Structural comparison of complete plasmid sequences further revealed close similarity between Korean and US pESIs, suggesting a potential epidemiological link. This study identified the rapid clonal spread of pESI-carrying <i>S</i>. Infantis in the Korean poultry sector and reported the first identification of pESI-carrying <i>S</i>. Infantis in human clinical isolates in Korea. These findings underscore the urgent need for global surveillance, enhanced biosecurity measures in the poultry industry, and stricter regulations to prevent further dissemination of MDR <i>S</i>. Infantis.
DOI: 10.6084/m9.figshare.30178082.v1
title: Molecular epidemiology of pESI-carrying <i>Salmonella</i> Infantis in Korea: Insights from a One Health framework

description: The emergence and global dissemination of <i>Salmonella</i> Infantis carrying the pESI megaplasmid is a growing public health concern owing to its association with multidrug resistance (MDR), enhanced virulence, and increased environmental adaptability. This study investigated the molecular epidemiology and transmission dynamics of pESI-carrying <i>S.</i> Infantis in the poultry production chain and human clinical cases in Korea. A total of 295 <i>Salmonella</i> isolates were collected from poultry sources (farms, slaughterhouses, and retail meats) in 2023, of which 219 (74.2%) were identified as <i>S.</i> Infantis. Additionally, 22 human-origin <i>S</i>. Infantis isolates collected between 2016 and 2023 were included in this study. Among these 241 <i>S</i>. Infantis isolates, 218 from poultry and one from a human case (collected in 2023) were MDR and carried pESIs, most of which carried <i>bla<sub>CTX-M-65</sub></i> and multiple other resistance genes. Comparative whole-genome sequencing revealed a high degree of genetic similarity between poultry and human pESI-carrying <i>S.</i> Infantis isolates, suggesting probable zoonotic transmission through the chicken supply chain. Structural comparison of complete plasmid sequences further revealed close similarity between Korean and U.S. pESIs, suggesting a potential epidemiological link. This study identified the rapid clonal spread of pESI-carrying <i>S</i>. Infantis in the Korean poultry sector and reported the first identification of pESI-carrying <i>S</i>. Infantis in human clinical isolates in Korea. These findings underscore the urgent need for global surveillance, enhanced biosecurity measures in the poultry industry, and stricter regulations to prevent further dissemination of MDR <i>S</i>. Infantis.
DOI: 10.5281/zenodo.17280070
title: Extended data - Lituya Bay, Alaska

description: This is the supplementary data to "Rapid delta growth and tsunami disturbance in Lituya Bay, Alaska"

Contents: 

bay_sedimentation:

DOD_1959-1926.tif & DOD_1959-2023.tif: DEMs of difference between the bathymetric surveys of Lituya Bay

DOD_1959-1926_0.tif & DOD_1959-2023_0.tif: DEMs of difference between the bathymetric surveys of Lituya Bay based on adjusted rasters that assume a water depth of 0 m for areas that were covered or newly exposed by advance and retreat of Lituya and North Crillon glaciers between two successive surveys.

zones_bay.gpkg: Polygons delineating the regions used to estimate the sedimentation in northern Lituya Bay and at the head of Lituya Bay, respectively. 

zones_deltas.gpkg: Polygons delineating the regions used to estimate the accumulation volumes of Lituya and Crillon deltas. 

boulder_size:

boulder_data.csv: Table containing the boulder locations  and axes measurements

delta_growth_1985-2025:

area_change.gpkg: Areal delta progradation polygons

delta_fronts.gpkg: Line features of the mapped delta fronts

delta_polygons.gpkg: Delta polygons based on the mapped delta fronts and the 1985 glacier extents

area_change.csv: Table summarizing the area change of the deltas in five-year intervals between 1985 and 2025

progradation rates: Input files used to estimate delta progradation including the R-code, the transects along which we measure progradation, the mapped delta fronts, and R-data files of the output

glacier_elevation_change: 

DOD1 & DOD2: Folders containing the co-registered DEMs used to estimate the surface elevation changes of the glaciers in Lituya Bay between 2016 and 2019. The original ArcticDEM strips (pre co-registration) were retrieved from Porter, Claire, et al., 2022, “ArcticDEM – Strips, Version 4.1”, https://doi.org/10.7910/DVN/C98DVS, Harvard Dataverse, V1.

zones_stats.gpkg: Geopackage containing the polygones used to estimate the glacier elevation changes of lower Lituya and North Crillon glaciers.
DOI: 10.5281/zenodo.17280071
title: Extended data - Lituya Bay, Alaska

description: This is the supplementary data to "Rapid delta growth and tsunami disturbance in Lituya Bay, Alaska"

Contents: 

bay_sedimentation:

DOD_1959-1926.tif & DOD_1959-2023.tif: DEMs of difference between the bathymetric surveys of Lituya Bay

DOD_1959-1926_0.tif & DOD_1959-2023_0.tif: DEMs of difference between the bathymetric surveys of Lituya Bay based on adjusted rasters that assume a water depth of 0 m for areas that were covered or newly exposed by advance and retreat of Lituya and North Crillon glaciers between two successive surveys.

zones_bay.gpkg: Polygons delineating the regions used to estimate the sedimentation in northern Lituya Bay and at the head of Lituya Bay, respectively. 

zones_deltas.gpkg: Polygons delineating the regions used to estimate the accumulation volumes of Lituya and Crillon deltas. 

boulder_size:

boulder_data.csv: Table containing the boulder locations  and axes measurements

delta_growth_1985-2025:

area_change.gpkg: Areal delta progradation polygons

delta_fronts.gpkg: Line features of the mapped delta fronts

delta_polygons.gpkg: Delta polygons based on the mapped delta fronts and the 1985 glacier extents

area_change.csv: Table summarizing the area change of the deltas in five-year intervals between 1985 and 2025

progradation rates: Input files used to estimate delta progradation including the R-code, the transects along which we measure progradation, the mapped delta fronts, and R-data files of the output

glacier_elevation_change: 

DOD1 & DOD2: Folders containing the co-registered DEMs used to estimate the surface elevation changes of the glaciers in Lituya Bay between 2016 and 2019. The original ArcticDEM strips (pre co-registration) were retrieved from Porter, Claire, et al., 2022, “ArcticDEM – Strips, Version 4.1”, https://doi.org/10.7910/DVN/C98DVS, Harvard Dataverse, V1.

zones_stats.gpkg: Geopackage containing the polygones used to estimate the glacier elevation changes of lower Lituya and North Crillon glaciers.
DOI: 10.15468/dl.qu7mkm
title: Occurrence Download

description: A dataset containing 3596 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Caprimulgiformes)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((0 0,30 0,30 30,0 30,0 0))"
 ]
}

 The dataset includes 3596 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058092-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.