cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15458649
title: High-density Phenotype Data of Intermediate Phenotypes Associated with Stalk Lodging Resistance in Maize — Datasets

description: This project includes field metadata, genotype data of inbred lines, and individual plant phenotype data of intermediate phenotypes associated with stalk lodging resistance in maize. Phenotype data was recorded for 11 intermediate phenotypes on 31260 maize stalks corresponding to 566 inbred lines grown in four environmnets. The phenotype dataset presented in this project includes plant- and internode-level phenotypes associated with stalk lodging resistance. The metadata files include weather parameters recorded at the experimental locations and the fieldmaps of the inbred lines along with their field coordinates—indicated by row & column identifiers. Teh genotype data presented here was retrieved from a previous publication (see reference) and processed to only include genotypes evaluated in the current study.
DOI: 10.15468/dl.rn5qra
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Country is one of (United States of America, Mexico)",
 "OccurrenceStatus is Present",
 "TaxonKey is Carcharhinus brevipinna",
 "Year 2005-2025"
 ]
}

 The dataset includes 122 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069478-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14438501
title: Speech_Representation_Project_Data_Annotated

description: This typological dataset was collected within the project "Language emerging from human sociality: the case of speech representation", funded by the University of Helsinki (2018-2022, PI Stef Spronck), and serves as the basis data for the Doctoral Thesis "Conventionalized Inferred Meanings of Reported Speech Constructions: A Crosslinguistic Analysis" Daniela Casartelli (in preparation)The dataset was annotated using the R extension package RQDA for qualitative analysis, and is fully accessible within the R environment and its RQDA extension package. Please find a full description of the dataset below.
description: Here I would like to give a bit more insight in short how the sample was sampled, the coding scheme applied throughout the data set, and the full list of 100 languages therein with the corresponding bibliography.
DOI: 10.5281/zenodo.13929149
title: Supplementary material to support non-fouling assumption (Separation of 5% (w/v) Prolastin)

description: The data set is a part of the PhD thesis of Nattawan Chorhirankul, Wageningen University, The Netherlands.
DOI: 10.5281/zenodo.15173450
title: Apparent Optical Properties DOORS cruise 1, 01-20 May, 2023

description: Apparent Optical Properties of seawater were determined from multispectral free-fall system (MicroPro, Satalantic Inc)  during R/V Mare Nigrum cruise #1 at  10 stations located in  Romanian Black Sea waters . The MicroPro simultaneously measure the upwelling radiance Lu (z, λ), the downward irradiance Ed (z, λ) and the upward irradiance Eu (z, λ) as a function of depth z and wavelength λ, in addition to the above–water downward irradiance Ed (0+λ). All applied sensors (i.e., radiometers of the OCR-507) have equivalent spectral channels with 10 nm bandwidth centered at the nominal wavelengths 412, 443, 490, 510, 555, 665, and 683 nm. Data products from the free-fall optical profilers include spectral values of: remote sensing reflectance, normalized water–leaving radiance, diffuse attenuation coefficient.
DOI: 10.5281/zenodo.15520640
title: Functional stability despite structural changes in freshwater biofilm communities exposed to an antibiotic and an herbicide – the role of nutrient conditions

description: This dataset features data of the associated study, which is currently submitted for publication. The respective DOI will be supplied upon acceptance.
DOI: 10.5281/zenodo.17064588
title: Code and data supporting the paper "Breeding dispersal of Baltic dunlins is not an adaptive response to unexpected nest flooding"

description: Code and data supporting the paper "Breeding dispersal of Baltic dunlins is not an adaptive response to unexpected nest flooding"

 

Provided Data

 

We share the processed tables used in the analyses:

 

- dispersal_between_final.csv – Final dataset used in the models for between year dispersal.  

- male_nest_survival.csv – Final dataset used for analysis of nest surival.  

 

These datasets have been aggregated, and are sufficient to reproduce the results reported in the manuscript.

Due to the endangered status of the species, we are unable to share exact nest locations which are available in raw data files. These tables are accompanied by two metadata files describing each variable. 

 

Provided Code

All models can be run using the FINAL_MODELS_CLEAN.R script. Models were run using R version 4.4.1
DOI: 10.5281/zenodo.13982934
title: Metabolomics data set for the project EHP-BFNU-OVNKM-4-139-2024
DOI: 10.6084/m9.figshare.27212499
title: SCT_norm.rds

description: This is the main Seurat object RDS file used for all analyses in this paper. It is the integrated object that has data from all 39 prairie voles in the experiment. The cells that were filtered out are not in this file.
DOI: 10.6084/m9.figshare.27212499.v1
title: SCT_norm.rds

description: This is the main Seurat object RDS file used for all analyses in this paper. It is the integrated object that has data from all 39 prairie voles in the experiment. The cells that were filtered out are not in this file.
DOI: 10.6084/m9.figshare.29029715
title: Data for Evaluating Bayesian morphological clocks for estimating a dated phylogeny in a relict and fossil- rich family of wasps (Hymenoptera, Chrysidoidea)

description: NEXUS files used for MCMC and SS analyses and resulting tree files.
DOI: 10.6084/m9.figshare.29029715.v1
title: Data for Evaluating Bayesian morphological clocks for estimating a dated phylogeny in a relict and fossil- rich family of wasps (Hymenoptera, Chrysidoidea)

description: NEXUS files used for MCMC and SS analyses and resulting tree files.
DOI: 10.6084/m9.figshare.29047115
title: <b>Habitat filtering and niche specialization of termite mound herbaceous flora in tropical dry woodlands</b>

description: <b>Dataset Description</b>This repository contains the datasets and R scripts associated with the article <i>"Habitat filtering and niche specialization of termite mound herbaceous flora in tropical dry woodlands."</i>The study investigates floristic composition, functional specialization, and environmental variables related to herbaceous plant communities on termite mounds in the Miombo — a type of tropical dry woodland in Africa. Data were collected in Haut-Katanga (DR Congo) and analyzed using various statistical and functional approaches.R scripts are provided to reproduce the analyses, including species association (IndVal), functional niche evaluation, and environmental variable analysis.<b>Main Content</b>Floristic data: Species abundance per vegetation plot.Functional trait data: Functional traits of 68 species and 15 indicator species.Environmental data: Soil variables measured per plot.R scripts: For IndVal, ANOVA, LDA, and functional niche analysis.<b>Compatibility</b>Scripts are compatible with R ≥ 4.2.0.Required packages are listed within each script.<b>Use</b>These files can be used to:Reproduce the results presented in the article.Explore relationships between habitat, functional traits, and CSR strategy.Study the ecological effects of termite mounds on plant community structure in dry forests.For detailed instructions, please refer to the included README file.<br>
DOI: 10.6084/m9.figshare.29047115.v1
title: <b>Habitat filtering and niche specialization of termite mound herbaceous flora in tropical dry woodlands</b>

description: <b>Dataset Description</b>This repository contains the datasets and R scripts associated with the article <i>"Habitat filtering and niche specialization of termite mound herbaceous flora in tropical dry woodlands."</i>The study investigates floristic composition, functional specialization, and environmental variables related to herbaceous plant communities on termite mounds in the Miombo — a type of tropical dry woodland in Africa. Data were collected in Haut-Katanga (DR Congo) and analyzed using various statistical and functional approaches.R scripts are provided to reproduce the analyses, including species association (IndVal), functional niche evaluation, and environmental variable analysis.<b>Main Content</b>Floristic data: Species abundance per vegetation plot.Functional trait data: Functional traits of 68 species and 15 indicator species.Environmental data: Soil variables measured per plot.R scripts: For IndVal, ANOVA, LDA, and functional niche analysis.<b>Compatibility</b>Scripts are compatible with R ≥ 4.2.0.Required packages are listed within each script.<b>Use</b>These files can be used to:Reproduce the results presented in the article.Explore relationships between habitat, functional traits, and CSR strategy.Study the ecological effects of termite mounds on plant community structure in dry forests.For detailed instructions, please refer to the included README file.<br>
DOI: 10.6084/m9.figshare.29302064
title: <b>Spatio-temporal chromosomal arrangements by late-replicating heterochromatin</b>

description: 3D genome organization of human fungal pathogen <i>Cryptococcus neoformans.</i><br>
DOI: 10.6084/m9.figshare.29302064.v1
title: <b>Spatio-temporal chromosomal arrangements by late-replicating heterochromatin</b>

description: 3D genome organization of human fungal pathogen <i>Cryptococcus neoformans.</i><br>
DOI: 10.6084/m9.figshare.29640641
title: Raw linkage map calls from SNP discovery and STACKS pipeline.

description: Raw linkage map calls from SNP discovery and STACKS pipeline.
DOI: 10.6084/m9.figshare.29640641.v1
title: Raw linkage map calls from SNP discovery and STACKS pipeline.

description: Raw linkage map calls from SNP discovery and STACKS pipeline.
DOI: 10.6084/m9.figshare.29875256
title: Pelagia noctiluca Observations in Greece (2025).csv

description: This dataset contains observations of <i>Pelagia noctiluca</i> (commonly known as the mauve stinger) recorded in Greek waters during 2025 as part of the Pelagia Logbook 2025 project by Merman Conservation Expeditions Ltd. Data entries include date, location, and other relevant field notes. The project aims to document the distribution, seasonal patterns, and environmental context of jellyfish sightings in the region. The dataset is currently under embargo to ensure the accuracy, integrity, and proper interpretation of the findings before public release.
DOI: 10.6084/m9.figshare.29875256.v1
title: Pelagia noctiluca Observations in Greece (2025).csv

description: This dataset contains observations of <i>Pelagia noctiluca</i> (commonly known as the mauve stinger) recorded in Greek waters during 2025 as part of the Pelagia Logbook 2025 project by Merman Conservation Expeditions Ltd. Data entries include date, location, and other relevant field notes. The project aims to document the distribution, seasonal patterns, and environmental context of jellyfish sightings in the region. The dataset is currently under embargo to ensure the accuracy, integrity, and proper interpretation of the findings before public release.
DOI: 10.6084/m9.figshare.30372991.v1
title: Crop Wild Relatives in Europe. COUSIN project analysis

description: The COUSIN project aims at developing a unified approach for conserving and using Crop Wild Relatives in Europe. The dataset presented provide detaile elements of this analysis.
DOI: 10.6084/m9.figshare.30417202.v1
title: Supporting data for "<b><i>Tangerine</i></b><b>: a </b><b><i>Starship</i></b><b>-like element in the genomes of </b><b><i>Xanthoria </i></b><b>lichen-forming fungi</b><b><i>"</i></b>

description: The repository contains additional files for the study "<b><i>Tangerine</i></b><b>: a </b><b><i>Starship</i></b><b>-like element in the genomes of </b><b><i>Xanthoria </i></b><b>lichen-forming fungi</b>":<b>alphafold.zip: </b>AlphaFold models generated for the Tangerine captains and a selection of tyrosine recombinases from across fungi.<b>Genome_alignments.zip:</b> whole-genome alignments for the four Xanthoria genomes including in the study generated with MUMmer.<b>Genome_annotations.zip:</b> functional annotations for the four Xanthoria genomes including in the study generated using Funannotate (genes) and EarlGrey (repeats).<b>Orthofinder.zip: </b>Orthogroup analysis on 107 ascomycete genomes, including four Xanthoria genomes, made with Orthofinder. The archive includes species and gene trees, as well as the table with orthogroup assignments<b>Starfish_input.zip:</b> input used for running the Starfish pipeline. Includes nucleotide fastas of genome assemblies, annotation files in gff format, and protein fastas for predicted proteome.<b>Starfish_output.zip:</b> output generated by the Starfish pipline. Includes outputs of geneFinder, elementFinder, and regionFinder modules.<b>YR_sequence_phylogeny.zip:</b> protein sequences of selected tyrosine recombinases and the Tangerine captains, sequence alignments, and phylogeny generated using IQ-TREE
DOI: 10.6084/m9.figshare.30417202
title: Supporting data for "<b><i>Tangerine</i></b><b>: a </b><b><i>Starship</i></b><b>-like element in the genomes of </b><b><i>Xanthoria </i></b><b>lichen-forming fungi</b><b><i>"</i></b>

description: The repository contains additional files for the study "<b><i>Tangerine</i></b><b>: a </b><b><i>Starship</i></b><b>-like element in the genomes of </b><b><i>Xanthoria </i></b><b>lichen-forming fungi</b>":<b>alphafold.zip: </b>AlphaFold models generated for the Tangerine captains and a selection of tyrosine recombinases from across fungi.<b>Genome_alignments.zip:</b> whole-genome alignments for the four Xanthoria genomes including in the study generated with MUMmer.<b>Genome_annotations.zip:</b> functional annotations for the four Xanthoria genomes including in the study generated using Funannotate (genes) and EarlGrey (repeats).<b>Orthofinder.zip: </b>Orthogroup analysis on 107 ascomycete genomes, including four Xanthoria genomes, made with Orthofinder. The archive includes species and gene trees, as well as the table with orthogroup assignments<b>Starfish_input.zip:</b> input used for running the Starfish pipeline. Includes nucleotide fastas of genome assemblies, annotation files in gff format, and protein fastas for predicted proteome.<b>Starfish_output.zip:</b> output generated by the Starfish pipline. Includes outputs of geneFinder, elementFinder, and regionFinder modules.<b>YR_sequence_phylogeny.zip:</b> protein sequences of selected tyrosine recombinases and the Tangerine captains, sequence alignments, and phylogeny generated using IQ-TREE
DOI: 10.5281/zenodo.17064405
title: TEST_OF_EMBARGO
DOI: 10.5281/zenodo.14978829
title: Chlorophyll a, Total Suspended Matter and Secchi Depth - DOORS 1 cruise, May 2023

description: The  datasest contains Chlorophyll a, Total Suspended Matter and Secchi depth data collected during  R/V Mare Nigrum cruise #1 , from 42 stations,  located in the Romanian Black Sea area, 1-20 May, 2023 in the framework H2020 DOORS Project.  Subsurface water samples (at approximately 1 m depth) were collected at each station using the Niskin bottles in a rosette of the CTD system of the vessel at each station. At stations where the CTD system was not deployed due to the bad weather conditions, a sample bottle was used to collect the water samples. For some stations, additional  water samples were collected at the depth where Chl-a maximum appears and the bottom. These discrete water were conditioned for successive laboratory analysis of:



        Chlorophyll a  concentrations determined spectrophotometrically according to Jeffrey and Humphrey, 1975

         Total Suspended Matter  through dry-weighting  according to J. Strickland and T. Parsons, 1972
DOI: 10.5281/zenodo.10977161
title: Copper DIPG
DOI: 10.5281/zenodo.16422030
title: Spectral truncation of out-of-time-ordered correlators in dissipative system

description: Raw data for manuscript Spectral truncation of out-of-time-ordered correlators in dissipative system
DOI: 10.5281/zenodo.17409440
title: Mapping antimicrobial use in brazilian dairy cows during lactation and the dry period
DOI: 10.5281/zenodo.18100930
title: Mapping antimicrobial use in brazilian dairy cows during lactation and the dry period
DOI: 10.5281/zenodo.18097968
title: Philippine Landslide Dataset for Cross-Domain Transferability Experiments

description: The dataset consists of patch-based optical and terrain inputs derived from Sentinel-2 and ALOS-1 PALSAR satellites, and associated ground-truth landslide masks. The data were curated to evaluate cross-domain transferability of deep learning–based landslide detection models trained on the Landslide4Sense benchmark.
DOI: 10.5281/zenodo.18097969
title: Philippine Landslide Dataset for Cross-Domain Transferability Experiments

description: The dataset consists of patch-based optical and terrain inputs derived from Sentinel-2 and ALOS-1 PALSAR satellites, and associated ground-truth landslide masks. The data were curated to evaluate cross-domain transferability of deep learning–based landslide detection models trained on the Landslide4Sense benchmark.
DOI: 10.5281/zenodo.15603770
title: SPATIAL TRANSCRIPTOMICS IDENTIFY HOMOLOGOUS MECHANISMS IN THE PATHOPHYSIOLOGY OF HUMAN AND E4FAD MOUSE CEREBRAL MICROBLEEDS

description: Spatial Transcriptomics data, produced using Nanostrings GeoMx from Human and Mouse tissues, focused on microbleeds and control, healthy regions paired with each microbleed region. 

The data were processed using R and GeoMxTools. Code and reports can be shared upon request.

 

For this paper, the miRNA data were submitted to the NCBI GEO database (GSE288162). 
description: Cerebral microbleeds (CMBs) are age-related vascular lesions, predisposing patients to a lifetime risk of stroke and cognitive decline. Little is known about their cellular or molecular mechanisms. The histopathologic and transcriptomic features of human CMB autopsy tissue and an E4FAD mouse model were investigated, while plasma was further used to identify biomarker candidates. Morphological studies showed increased counts of astrocytes and macrophages in human CMBs, while greater count of astrocytes and microglia in murine CMBs were observed. Spatial transcriptomics identified 781 human and 448 mouse differentially expressed genes (DEGs) with 110 shared pathways related to vascular permeability, endothelial dysfunction, and inflammation. Plasma analyses identified seven protein biomarker candidates, while miRNome sequencing found 2 homologous miRNAs in human CMB patients and E4FAD mice, with biologic plausibility. These findings provide new insights into CMB physiopathogenesis, highlight potential diagnostic biomarkers and suggest pathways for therapeutics.
description: Human data: 

 

- Human_dcc_files.zip: Includes all the dcc files per ROI for human. 

- Hs_R_NGS_WTA_V1.0.pkc: PKC file with Human features information

- Human_annotation_Seq.xlsx: Segment metadata.

- Human_counts_and_normalizations.xlsx: Counts, Q3 and log2 Q3 normalizations.

- Human_DEGS_DeSeq_matched_All.xlsx: DE analysis CMB / control, healthy.

 

Mouse data: 

Two sequencing rounds were performed over the same regions of interest (ROIs), Seq1 and Seq2. 

 

- Mouse_dcc_files.zip: Includes all the dcc files per ROI for mouse. 

- Mm_R_NGS_WTA_V1.0.pkc: PKC file with Human features information

- Mouse_annotation_Seq1.xlsx: Segment metadata, Seq1 run.

- Mouse_annotation_Seq2.xlsx: Segment metadata, Seq2 run.

- Mouse_counts_and_normalizations.xlsx: Counts, Q3 and log2 Q3 normalizations.

- Mouse_DEGS_DeSeq_matched_All.xlsx: DE analysis CMB / control, healthy.
DOI: 10.5281/zenodo.16414695
title: Research Resource Repository (RRR) for the Systematic Literature Review on the Secure Design of RESTful APIs

description: This repository contains all necessary materials to reproduce the results and methods described in the article: “Vulnerabilities and Secure Design Strategies in RESTful Web APIs: A Systematic Literature Review” (Tamariz-Moreno et al., 2025)

This repository supports:

Reproducibility and verification of the resultsFuture replications or extensions of the SLRMeta-analyses and secondary studies in game mechanics design and empirical software engineering

All materials are structured according to the appendix references (A-series) cited in the published article.

Contents:Protocol_SLR.pdfStudies_Included.csvStudies_Excluded.csvData_Extraction_Matrix.csvAnalysis_Script_R.RAnalysis_Script_Python.pyResults_Frequencies.csvSummary_Table.htmlROSES_Diagram.pngGraph.pngLicenseAll documents are shared under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Please cite the associated publication if you reuse or adapt any of the materials.

ContactA. Michelle Tamariz-Moreno (Universidad Veracruzana) michellemoreno1313@gmail.comEduardo Carrera-Colorado (Universidad Veracruzana) eduarcaco@hotmail.comJorge Octavio Ocharán-Hernández (Universidad Veracruzana) jocharan@uv.mxJuan Carlos Pérez Arriaga (Universidad Veracruzana) juaperez@uv.mxXavier Limón (Universidad Veracruzana) hlimon@uv.mx 

Date of Release: 2025--
DOI: 10.5281/zenodo.16787629
title: Source data PFN2 coordinate post-transcriptional regulation manuscript Sangokoya

description: Source data PFN2 coordinate post-transcriptional regulation manuscript
DOI: 10.5281/zenodo.13860023
title: Oligocene-Miocene (24-21 Ma) biogenic carbonate (coccolith and benthic foraminifera) biometry in the South China Sea

description: The spreadsheets include main datasets for the carbonate micro and nannofossil analysis from IODP Site U1505 in the northern South China Sea, covering approximately 24-21 Ma:



Coccolith assemblage data;

Organic carbon content and isotope analysis;

Calculated alkalinity flux;

Benthic formainifera shell weight;

Coccolith morphometry;

Coccolith Sr/Ca ratio;

Age model used in the publication.


The compressed files integrate the figures coccolith cuts from 100 samples (around 8,000 images in total) and 38 samples examined for benthic foraminiferal preservation (Cibicidoides mundulus). The dataset is complemented by:



Photographs of C. mundulus tests with marked length measurements;

Raw data of coccolith morphometry;

Cuts of all the measured coccolith.
DOI: 10.5281/zenodo.14725788
title: 1.2. Human Bone marrow-derived Mesenchymal Stem/Stromal cells' markers characterisation

description: Human Bone marrow-derived Mesenchymal Stem/Stromal cells' markers characterisation by cell cytometry. Files in ".fcs" format.
DOI: 10.5281/zenodo.13880934
title: ClimEmpower: Regional Climate Service Needs

description: In preparation of the D2.1 deliverable within the ClimEmpower project, the project team has performed a survey among the five CoP regions (Costa del sol – Spain, Sicily - Italy, Osijek-Baranja County – Croatia, Troodos Mountain Range – Cyprus, PSTE – Greece) following the climate service typology proposed by Stegmaier & Visscher (2020) and asking them in a structured way what services they need.