cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.t6gw3q
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.41961 42.98656,11.45085 42.2527,12.25665 41.62916,12.75069 42.23831,12.48208 42.62203,12.45331 42.89063,12.07918 43.36548,10.58312 43.55584,10.43923 43.34959,10.41961 42.98656))",
 "TaxonKey is Asplenium scolopendrium L."
 ]
}

 The dataset includes 159 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006217-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.egpkva
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Anolis bombiceps Cope, 1875"
 ]
}

 The dataset includes 72 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006212-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gz3xt
title: Occurrence Download

description: A dataset containing 48648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Patagioenas cayennensis (Bonnaterre, 1792)",
 "Year 1000-2024"
 ]
}

 The dataset includes 48648 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006216-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14884152
title: Dataset of Appendix of Collimated γ-flash emission along the target surface irradiated by a laser at non-grazing incidence

description: This repository contains data for the Appendix of the paper M. Matys et al., accepted in New Journal of Physics (2025);  The data were obtained by the particle-in-cell code EPOCH (https://github.com/Warwick-Plasma/epoch , https://epochpic.github.io). The data are in the .sdf output format of the EPOCH code, the reader for them is here https://github.com/Warwick-Plasma/SDF . The dataset of the main body of the paper is in a separate file: 10.5281/zenodo.14887837
DOI: 10.5281/zenodo.14884153
title: Dataset of Appendix of Collimated γ-flash emission along the target surface irradiated by a laser at non-grazing incidence

description: This repository contains data for the Appendix of the paper M. Matys et al., accepted in New Journal of Physics (2025);  The data were obtained by the particle-in-cell code EPOCH (https://github.com/Warwick-Plasma/epoch , https://epochpic.github.io). The data are in the .sdf output format of the EPOCH code, the reader for them is here https://github.com/Warwick-Plasma/SDF . The dataset of the main body of the paper is in a separate file: 10.5281/zenodo.14887837
DOI: 10.5281/zenodo.14917703
title: Pattern Formation in Catalytic H2 Oxidation on Rh: Zooming in by Correlative Microscopy - Dataset

description: Dataset to for the article "Pattern Formation in Catalytic H2 Oxidation on Rh: Zooming in by Correlative Microscopy" published in ACS Catalysis in 2022 (https://doi.org/10.1021/acscatal.2c03692)
DOI: 10.5281/zenodo.14917704
title: Pattern Formation in Catalytic H2 Oxidation on Rh: Zooming in by Correlative Microscopy - Dataset

description: Dataset to for the article "Pattern Formation in Catalytic H2 Oxidation on Rh: Zooming in by Correlative Microscopy" published in ACS Catalysis in 2022 (https://doi.org/10.1021/acscatal.2c03692)
DOI: 10.5281/zenodo.14975124
title: CRISPRome: A Comprehensive CRISPR-Cas Resource Database

description: CRISPRome is a large publicly available CRISPR-Cas system database to date, systematically characterizing CRISPR-Cas elements across a diverse set of bacterial and archaeal genomes. This resource serves as a foundation for studying the global distribution and characteristics of CRISPR systems in microbes.



Data Collection


To construct CRISPRome, we compiled data from multiple sources:





RefGen Database:



1,414,360 bacterial genomes

13,258 archaeal genomes

Extracted from GenBank and RefSeq





Metagenomic Datasets:



26,565 genomes/metagenome-assembled genomes (MAGs)

Collected from three human body sites and three natural environments






CRISPR-Cas System Identification


We identified CRISPR-Cas systems using CRISPRCasFinder v2.0.355, extracting both spacers and CRISPR arrays:





Spacers:



21,282,263 total spacers

14,968,498 (70%) associated with Cas proteins





CRISPR Arrays:



3,937,928 total arrays

1,429,909 (36%) linked to Cas proteins




Spacer-Target Identification Process



Spacer Deduplication & Alignment



Spacers were deduplicated and aligned using Blastn-short to a database of 7,042,467 genomes from RefSeq, GenBank, ICEberg, IMG/VR, and PLSDB.

makeblastdb was used to convert genome sequences into searchable databases.



Blastn Alignment & Optimization



Blastn was run with optimized parameters (word_size 11, qcov_hsp_perc 95, perc_identity 95, max_hsps 3) to balance speed and accuracy.

High-performance computing clusters managed by Slurm were used for large-scale processing.



Filtering & Prioritization



Hits were sorted by bitscore, keeping the top 10% for accuracy.

Prioritization order: viruses > plasmids = ICE > other sources, reflecting CRISPR-Cas immunity targets.



Removing CRISPR Array Artifacts



Alignments overlapping known CRISPR array regions were removed to avoid false positives.

Additional CRISPR arrays were identified from NCBI genome annotations to refine filtering.



Detecting Potential CRISPR Arrays



Arrays were defined by detecting regularly interspaced protospacers.

A threshold of ≥4 protospacers was used to minimize false positives, leading to the exclusion of 16,777 targets.



LCA-Based One-to-One Spacer-Target Assignment



TaxonKit lca was used to determine the Lowest Common Ancestor (LCA) of multiple target matches.

This ensured each spacer was assigned to a single, biologically relevant target.
DOI: 10.5281/zenodo.14975125
title: CRISPRome: A Comprehensive CRISPR-Cas Resource Database

description: CRISPRome is a large publicly available CRISPR-Cas system database to date, systematically characterizing CRISPR-Cas elements across a diverse set of bacterial and archaeal genomes. This resource serves as a foundation for studying the global distribution and characteristics of CRISPR systems in microbes.



Data Collection


To construct CRISPRome, we compiled data from multiple sources:





RefGen Database:



1,414,360 bacterial genomes

13,258 archaeal genomes

Extracted from GenBank and RefSeq





Metagenomic Datasets:



26,565 genomes/metagenome-assembled genomes (MAGs)

Collected from three human body sites and three natural environments






CRISPR-Cas System Identification


We identified CRISPR-Cas systems using CRISPRCasFinder v2.0.355, extracting both spacers and CRISPR arrays:





Spacers:



21,282,263 total spacers

14,968,498 (70%) associated with Cas proteins





CRISPR Arrays:



3,937,928 total arrays

1,429,909 (36%) linked to Cas proteins




Spacer-Target Identification Process



Spacer Deduplication & Alignment



Spacers were deduplicated and aligned using Blastn-short to a database of 7,042,467 genomes from RefSeq, GenBank, ICEberg, IMG/VR, and PLSDB.

makeblastdb was used to convert genome sequences into searchable databases.



Blastn Alignment & Optimization



Blastn was run with optimized parameters (word_size 11, qcov_hsp_perc 95, perc_identity 95, max_hsps 3) to balance speed and accuracy.

High-performance computing clusters managed by Slurm were used for large-scale processing.



Filtering & Prioritization



Hits were sorted by bitscore, keeping the top 10% for accuracy.

Prioritization order: viruses > plasmids = ICE > other sources, reflecting CRISPR-Cas immunity targets.



Removing CRISPR Array Artifacts



Alignments overlapping known CRISPR array regions were removed to avoid false positives.

Additional CRISPR arrays were identified from NCBI genome annotations to refine filtering.



Detecting Potential CRISPR Arrays



Arrays were defined by detecting regularly interspaced protospacers.

A threshold of ≥4 protospacers was used to minimize false positives, leading to the exclusion of 16,777 targets.



LCA-Based One-to-One Spacer-Target Assignment



TaxonKit lca was used to determine the Lowest Common Ancestor (LCA) of multiple target matches.

This ensured each spacer was assigned to a single, biologically relevant target.
DOI: 10.15468/dl.m7rvzp
title: Occurrence Download

description: A dataset containing 25367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is one of (Brazil, Argentina, Paraguay)",
 "TaxonKey is Patagioenas plumbea (Vieillot, 1818)",
 "Year 1000-2024"
 ]
}

 The dataset includes 25367 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006218-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14975301
title: Amplicon sequencing data from: "Reusable and modular combinatorial libraries for iterative metabolic engineering of Saccharomyces cerevisiae"

description: We have developed a methodology for generating reusable and modular integration-based combinatorial libraries and demonstrate their usefulness by engineering red beet pigment production in the yeast Saccharomyces cerevisiae. Here we share the long-read amplicon sequencing data from the combinatorial library DNA integrated in the high-performing library members isolated from each round of engineering.
DOI: 10.5281/zenodo.14975369
title: ampelosycios_leandrii_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.14975370
title: ampelosycios_leandrii_decontaminated_FSCR.fasta.gz
DOI: 10.6084/m9.figshare.28541276
title: Data for Teixido et al. 2025. European Journal of Forest Research

description: Habitat loss and fragmentation globally threat biodiversity and ecosystem services. However, major research biases and knowledge gaps in biogeographical regions, taxonomic groups, landscape metrics and species’ biological responses studied, are recurrent in fragmentation studies. Detecting these biases and associated gaps is crucial to steer future research efforts and to guide applicable conservation policies. We conducted a systematic literature review and extracted data from 107 articles to evaluate biogeographic, taxonomic and ecological biases in fragmentation research on the highly-diverse terrestrial fauna in peninsular Spain. We observed that research was biased towards mountain ranges, southeastern drylands and nearly largest cities. Specifically, the Cantabrian Range comprised the highest density of studies, while open <i>dehesas</i> in western Spain and Atlantic coastal forests in the northwest were overlooked. We also found an overrepresentation of studies (77%) on vertebrates and a high positive relative bias for birds, while several invertebrate taxa were neglected in the literature. Fragmentation was more frequently considered than habitat loss. Habitat degradation and patch size reduction were the most studied metrics, while patch isolation, edge effect and matrix contrast were underrepresented. Assemblage-level species responses (abundance and richness) comprised 86% of studies, while interspecific interactions, genetics and individual conditions were largely underrepresented. Our findings indicate major gaps in the studies focused on the effects of habitat loss and fragmentation on the Spanish fauna. We recommend that fragmentation research in this diverse region from southern Europe needs to consider undersampled taxa, further fragmentation metrics and biological responses to avoid inappropriate inferences for conservation actions.
DOI: 10.15468/dl.weyy8m
title: Occurrence Download

description: A dataset containing 15664 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bromus secalinus L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 15664 records from 509 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006215-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14975328
title: Seasonal and Inter-Annual Dynamics of a Macrocystis Pyrifera Forest in Concepcion Bay, Chile

description: Dataset for "Seasonal and inter-annual variation of a giant kelp forest, Macrocystis pyrifera, in Concepción Bay, Chile"

Author: Daniel Gonzalez-AragonDOI of the article: http://dx.doi.org/10.2139/ssrn.5042009

Description

This dataset contains the results presented in the associated article. The included Excel file (data.xlsx) consists of four sheets:

1) Interannual Landsat



Complete Landsat time series.

ENSO index values used in the analysis, as described in the Methods section of the article.


2) Seasonal Sentinel-2

This sheet contains the full Sentinel-2 time series, including:



The date and season of each image.

The Sentinel-2 satellite source (A or B).

Sea level data for each date.

The Normalized Difference Turbidity Index (NDTI) value for each image.

The Normalized Difference Red-Edge Blue (NDREB) vegetation index:



NDREB values greater than 0 (NDREB > 0).

NDREB values obtained using the dynamic threshold described in the Methods section.

The threshold value used in the latter.




3) In situ nutrient values



Nutrient data collected from Macrocystis pyrifera populations at Punta de Parra, Concepción.

Includes values for nitrate, nitrite, phosphate, and silicate, along with their corresponding standard deviations.


4) In situ biomass estimation



Maximum depth of the sampling location.

Number of individuals.

Weight of the individuals.

Number of fronds.

Number of blades.

Length of the longest frond.


Satellite Data Processing

The satellite data were obtained using Google Earth Engine. The script used for processing is also available in the associated article:https://code.earthengine.google.com/df92ced1763815d2d520dc23ab0b5814
DOI: 10.5281/zenodo.14975329
title: Seasonal and Inter-Annual Dynamics of a Macrocystis Pyrifera Forest in Concepcion Bay, Chile

description: Dataset for "Seasonal and inter-annual variation of a giant kelp forest, Macrocystis pyrifera, in Concepción Bay, Chile"

Author: Daniel Gonzalez-AragonDOI of the article: http://dx.doi.org/10.2139/ssrn.5042009

Description

This dataset contains the results presented in the associated article. The included Excel file (data.xlsx) consists of four sheets:

1) Interannual Landsat



Complete Landsat time series.

ENSO index values used in the analysis, as described in the Methods section of the article.


2) Seasonal Sentinel-2

This sheet contains the full Sentinel-2 time series, including:



The date and season of each image.

The Sentinel-2 satellite source (A or B).

Sea level data for each date.

The Normalized Difference Turbidity Index (NDTI) value for each image.

The Normalized Difference Red-Edge Blue (NDREB) vegetation index:



NDREB values greater than 0 (NDREB > 0).

NDREB values obtained using the dynamic threshold described in the Methods section.

The threshold value used in the latter.




3) In situ nutrient values



Nutrient data collected from Macrocystis pyrifera populations at Punta de Parra, Concepción.

Includes values for nitrate, nitrite, phosphate, and silicate, along with their corresponding standard deviations.


4) In situ biomass estimation



Maximum depth of the sampling location.

Number of individuals.

Weight of the individuals.

Number of fronds.

Number of blades.

Length of the longest frond.


Satellite Data Processing

The satellite data were obtained using Google Earth Engine. The script used for processing is also available in the associated article:https://code.earthengine.google.com/df92ced1763815d2d520dc23ab0b5814
DOI: 10.6084/m9.figshare.28541126
title: Artificial Neural Network Model for Predicting the Viscosity of Crosslinked Polyacrylamide and Polyethylenimine Polymer Gel for Oilfield Water Control

description: This study addresses a gap in applying machine learning for polymer gel viscosity prediction in improved oil recovery (IOR). A baseline ANN model was developed using 418 experimental datasets from crosslinked PAM/PEI gels under varied conditions, achieving excellent predictive accuracy and demonstrating potential for enhanced oilfield water control.<b>Repository Description</b>This repository contains all the underlying data and materials necessary to reproduce the study "Development of an Artificial Neural Network Model for Predicting the Viscosity of Crosslinked Polyacrylamide and Polyethylenimine Polymer Gel for Oilfield Water Control." The work was performed using MATLAB 2022b, and the model was developed with MATLAB’s Neural Network Toolbox.<b>Included Materials:</b><br><b>Raw Experimental Data</b>:All 418 experimental datasets are provided. These datasets include measurements of polymer gel viscosity under varying conditions—shear rate, salinity, ammonium chloride concentration, and silica nanoparticle content.<b>Model Input Data and Parameters:</b>The repository contains the complete variable dataset used as input for the ANN model. This includes detailed descriptions of the input variables, along with the corresponding raw data.<b>Model Architecture and Replication Details:</b>The ANN model is a two-layer feed-forward neural network featuring a single hidden layer with 10 neurons. The model was trained using the Levenberg-Marquardt algorithm. The hidden layer uses the tangent sigmoid (Tansig) activation function, and the output layer employs a linear (Purelin) activation function. Detailed model parameters, including neuron weights and biases, are included to facilitate replication.<b>Software and Commands:</b>MATLAB 2022b was used to develop the model. The “nftool” command from MATLAB’s Neural Network Toolbox was specifically employed to access the Neural Net Fitting app and build the model. All commands, settings, and parameters are documented within the repository.<br>No data involving human participants were collected, and all experimental data adhered to the relevant institutional and legal standards.<br>This comprehensive dataset and detailed methodology ensure that other researchers can fully interpret, replicate, and build upon this work in the field of improved oil recovery
DOI: 10.15468/dl.92amcf
title: Occurrence Download

description: A dataset containing 60320 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Vicia sepium L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 60320 records from 247 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006205-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m46b8t
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "TaxonKey is Gongora fulva Lindl."
 ]
}

 The dataset includes 35 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006219-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6gm7ub
title: Occurrence Download

description: A dataset containing 36987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Living Specimen, Occurrence evidence)",
 "Geometry POLYGON((-112.37352 31.65091,-112.3427 31.76186,-114.92538 32.58166,-114.96236 32.49536,-112.37352 31.65091))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 36987 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006216-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39m3z3
title: Occurrence Download

description: A dataset containing 12934 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bromus squarrosus L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 12934 records from 379 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006217-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vh4xvj
title: Occurrence Download

description: A dataset containing 253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Vittadinia eremaea N.T.Burb.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 253 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006219-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3u678f
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Anolis calimae Ayala, Harris & Williams, 1983"
 ]
}

 The dataset includes 17 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006218-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rnjmen
title: Occurrence Download

description: A dataset containing 1659 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Pleurothallis ruscifolia (Jacq.) R.Br."
 ]
}

 The dataset includes 1659 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006222-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.