cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ug4h8a
title: Occurrence Download

description: A dataset containing 484 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriochloa villosa",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 484 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006573-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60533/ember-2025-g8j9
title: NWB Example Dataset
DOI: 10.25345/c5bk17303
title: MassIVE MSV000099255 - A Common PD-Risk GBA1 Variant Disrupts LIMP2 Interaction, Impairs Glucocerebrosidase Function, and Drives Lysosomal and Mitochondrial Dysfunction
title: Variants in GBA1 cause Gaucher disease and are the most common genetic risk factor for Parkinsons disease. While some GBA1 variants are associated with both GD and PD, several coding mutations, including E326K, specifically confer risk for PD. The impact of these PD-specific variants on GCase activity and lysosomal and mitochondrial function relevant to PD remains poorly understood. We show the E326K variant reduces lysosomal GCase activity by impairing its delivery to lysosomes via altered interactions with its receptor, LIMP2. Structural analyses reveal that loss of a key salt bridge between E326 and R329 underlies disrupted GCase LIMP2 interaction in cells, as reintroduction of a negative charge at R329 rescues LIMP2 binding. Functionally, the E326K variant produces greater deficits in PD-relevant pathways than GD-linked severe GCase LoF with effects reproduced in CNS cells and human E326K carriers, providing key insights into the nature of GCase dysfunction associated with GBA1-PD.
DOI: 10.15468/dl.neha3q
title: Occurrence Download

description: A dataset containing 2574 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "OccurrenceStatus is Present",
 "TaxonKey is Cygnus columbianus bewickii",
 "Year 2000-2025"
 ]
}

 The dataset includes 2574 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006574-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnm5zk
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eustachys neglecta",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006576-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17603/ds2-vy7w-m141
title: Next Generation Probabilistic Liquefaction Model Building at the Regional Scale

description: This repository contains data and code to reproduce the modeling and figures from "Next Generation Probabilistic Liquefaction Model Building at the Regional Scale" by Schmidt, Dashti, and Torres-Machi (submitted to and in press at Earthquake Spectra).
DOI: 10.15468/dl.62ufwe
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eustachys retusa",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006579-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e5mmwv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eustachys retusa",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006578-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17179604
title: Global inequality in environmental conditions underpinning human rights

description: This repository contains the R code and data to reproduce the findings and figures in "Global inequality in environmental conditions underpinning human rights". 

The analysis quantifies the exposure of populations to a suite of global environmental stressors, identifying the dominant Threats to Human Rights (THRs) at the global and subnational levels. A systematic literature review, aided by LLMs, was also conducted to contextualize the findings.

 

Repository Contents

This repository is structured as an RStudio Project (.Rproj).

Scripts (Root Directory):





01_process_raw_data.r: Ingests and standardizes raw source data.




02_match_rasters.r: Aligns all raster layers to a common global grid.




03_analysis_main.r: Performs core THR calculations and data integration.




04_generate_plots.R: Generates the final bivariate maps.




utils.r: Contains helper functions for bivariate plotting.




05_literature_review.py: A Python script to perform the LLM-aided systematic literature review, from abstract screening to downloading included papers.



Data (/data):





data/raw/: Original, unmodified source datasets (shapefiles, NetCDFs, Web of Science exports, etc.).




data/processed/: Script-generated outputs, including the /matched_rasters/ folder and the final main_analysis_df_standard.RData file.




Data Availability Note: The original, raw source datasets are not redistributed in this repository. Please refer to the accompanying manuscript for a complete list of all data sources and citations. The supplementary materials also include detailed instructions for reproducing the initial data export from the Web of Science database.



Results (/results):





results/figures/: Final figures and maps as PNG files.



 

Replication

Environment:





R: The analysis was performed with R (v4.x) and RStudio. All R package dependencies (e.g., terra, data.table, ggplot2) are managed within the scripts via the pacman package.




Python: The literature review script requires Python 3.x. All Python package dependencies (e.g., pandas, google-generativeai) should be installed via pip.



Workflow:





Open the .Rproj file in RStudio.




Execute the numbered R scripts (01 through 04) in the root directory sequentially.




To reproduce the literature review, execute the 05_literature_review.py script in a Python environment.




Final outputs will be generated in the /results directory.




Sensitivity Analyses: Different sensitivity analyses can be run by modifying the boolean flags (e.g., th_loose, th_restr) at the top of the 03_analysis_main.r script. Changing these flags will use different sets of input data layers for the main calculations.
DOI: 10.5281/zenodo.17175827
title: Global inequality in environmental conditions underpinning human rights

description: This repository contains the R code and data to reproduce the findings and figures in "Global inequality in environmental conditions underpinning human rights". 

The analysis quantifies the exposure of populations to a suite of global environmental stressors, identifying the dominant Threats to Human Rights (THRs) at the global and subnational levels. A systematic literature review, aided by LLMs, was also conducted to contextualize the findings.

 

Repository Contents

This repository is structured as an RStudio Project (.Rproj).

Scripts (Root Directory):





01_process_raw_data.r: Ingests and standardizes raw source data.




02_match_rasters.r: Aligns all raster layers to a common global grid.




03_analysis_main.r: Performs core THR calculations and data integration.




04_generate_plots.R: Generates the final bivariate maps.




utils.r: Contains helper functions for bivariate plotting.




05_literature_review.py: A Python script to perform the LLM-aided systematic literature review, from abstract screening to downloading included papers.



Data (/data):





data/raw/: Original, unmodified source datasets (shapefiles, NetCDFs, Web of Science exports, etc.).




data/processed/: Script-generated outputs, including the /matched_rasters/ folder and the final main_analysis_df_standard.RData file.




Data Availability Note: The original, raw source datasets are not redistributed in this repository. Please refer to the accompanying manuscript for a complete list of all data sources and citations. The supplementary materials also include detailed instructions for reproducing the initial data export from the Web of Science database.



Results (/results):





results/figures/: Final figures and maps as PNG files.



 

Replication

Environment:





R: The analysis was performed with R (v4.x) and RStudio. All R package dependencies (e.g., terra, data.table, ggplot2) are managed within the scripts via the pacman package.




Python: The literature review script requires Python 3.x. All Python package dependencies (e.g., pandas, google-generativeai) should be installed via pip.



Workflow:





Open the .Rproj file in RStudio.




Execute the numbered R scripts (01 through 04) in the root directory sequentially.




To reproduce the literature review, execute the 05_literature_review.py script in a Python environment.




Final outputs will be generated in the /results directory.




Sensitivity Analyses: Different sensitivity analyses can be run by modifying the boolean flags (e.g., th_loose, th_restr) at the top of the 03_analysis_main.r script. Changing these flags will use different sets of input data layers for the main calculations.
DOI: 10.15468/dl.sz2f6m
title: Occurrence Download

description: A dataset containing 78950 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Anthemis arvensis)"
 ]
}

 The dataset includes 78950 records from 924 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006560-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15003252
title: Selecting Effective Anti-Seizure Medications for Early Treatment of SCN8A-Related Epilepsy using a Machine Learning Approach Incorporating Clinician and Caregiver Assessments
DOI: 10.5281/zenodo.15003253
title: Selecting Effective Anti-Seizure Medications for Early Treatment of SCN8A-Related Epilepsy using a Machine Learning Approach Incorporating Clinician and Caregiver Assessments
DOI: 10.15468/dl.6x3hqz
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fargesia spathacea",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006581-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/25213
title: Chandra X-ray Observatory ObsId 25213

description: The quest for the energy source powering Superluminous Supernovae (SLSNe)
DOI: 10.34740/kaggle/dsv/13140582
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.25574/25461
title: Chandra X-ray Observatory ObsId 25461

description: A Chandra Snapshot Survey of the First Gamma-ray detected BAL Quasars
DOI: 10.15468/dl.pag3x6
title: Occurrence Download

description: A dataset containing 48973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "OccurrenceStatus is Present",
 "TaxonKey is Cygnus cygnus",
 "Year 2000-2025"
 ]
}

 The dataset includes 48973 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006580-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28283072
title: Supplemental Tables S1-S2

description: Supplemental Table S1 describes cardiovascular variables before and after the intervention, and Supplemental Table S2 describes cardiovascular variables during FMD test.
DOI: 10.6084/m9.figshare.28283072.v3
title: Supplemental Tables S1-S2

description: Supplemental Table S1 describes cardiovascular variables before and after the intervention, and Supplemental Table S2 describes cardiovascular variables during FMD test.
DOI: 10.6084/m9.figshare.28283072.v2
title: Supplemental Tables S1-S2

description: Supplemental Table S1 describes cardiovascular variables before and after the intervention, and Supplemental Table S2 describes cardiovascular variables during FMD test.
DOI: 10.15468/dl.vcsjwp
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bombus ussurensis Radoszkowski, 1877",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 74 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004947-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14762606
title: Spatialized Data Envelopment Analysis Dataset

description: DATASET of the article: Ramajo, J., Márquez, M.A. and Hewings, G.. (2024): "Addressing spatial dependence when estimating technical efficiency: A spatialized data envelopment analysis of regional productive performance in the European Union", Growth and Change, 55(1), e12711, DOI: 10.1111/grow.12711
DOI: 10.5281/zenodo.14762607
title: Spatialized Data Envelopment Analysis Dataset

description: DATASET of the article: Ramajo, J., Márquez, M.A. and Hewings, G.. (2024): "Addressing spatial dependence when estimating technical efficiency: A spatialized data envelopment analysis of regional productive performance in the European Union", Growth and Change, 55(1), e12711, DOI: 10.1111/grow.12711
DOI: 10.5281/zenodo.14684907
title: Convergence in symbiont-induced plant-mediated responses to herbivory: a case study with bracoviruses and ichnoviruses

description: This dataset describes olfactory responses of insect parasitoids towards herbivore-induced plant volatiles (HIPVs).

Plants were induced with the following caterpillar treatments:

Second-instar Pierisbrassicae were anaesthetized on ice and injected with PBS solutions with components retrieved from Cotesia glomerata (Cg),  or Hyposter ebeninus (He) using the Eppendorf FemtoJet-4x injector equipped with glass capillaries (3.5”, Drummond Scientific. No.3-000-203-G/X). In all experiments, venom, calyx fluid or a mixture of venom and calyx fluid dissolved in 100 nL were injected to prepare the following treatments: 1) C.glomerata calyx fluid containing bracovirus particles (CgBV); 2) C.glomerata venom (V); 3) C.glomerata calyx fluid + venom (CgBV+V); 4) H.ebeninus calyx fluid containing ichnovirus particles (HeIV). Additional treatments were used as controls to test whether the microinjection treatment per se affected the interaction of the caterpillars with the food plant: 5) un-parasitized caterpillars injected with 100 nL of PBS (PBS) (negative controls) and 6) parasitized caterpillars injected with 100 nL of PBS (Cg-PBS, He-PBS) (positive controls).

Wind tunnel and olfactometer assays

To investigate whether different injection treatments of caterpillars affect the plant-mediated foraging behavior of parasitoid females, we carried out olfactory assays using a wind tunnel for C.glomerata and a static two-chamber olfactometer for H.ebeninus.

Cotesia glomerata responses to Herbivore-induced plant volatiles (HIPVs) triggered by micro-injected caterpillars in wind tunnel dual-choice set-up. Parasitoid preference for one of the two offered plants was assessed in terms of first choice, which was considered to be made when the wasp landed on a plant. Each treatment combination was replicated with 10 plant pairs and 10 wasps per plant pair.

Hyposoter ebeninus responses to Herbivore-induced plant volatiles (HIPVs) triggered by micro-injected caterpillars in static olfactometer dual-choice set-up Parasitoid preference for one of the two offered plants was assessed in terms of residence time, over a total time of 300 seconds.. In each bioassay testing a specific leaf pair combination, the response of three female wasps was monitored. To avoid pseudoreplication, the mean response of these 3 wasps was considered a replicate and this procedure was repeated 8 times for each pairwise combination.
DOI: 10.5281/zenodo.14684906
title: Convergence in symbiont-induced plant-mediated responses to herbivory: a case study with bracoviruses and ichnoviruses

description: This dataset describes olfactory responses of insect parasitoids towards herbivore-induced plant volatiles (HIPVs).

Plants were induced with the following caterpillar treatments:

Second-instar Pierisbrassicae were anaesthetized on ice and injected with PBS solutions with components retrieved from Cotesia glomerata (Cg),  or Hyposter ebeninus (He) using the Eppendorf FemtoJet-4x injector equipped with glass capillaries (3.5”, Drummond Scientific. No.3-000-203-G/X). In all experiments, venom, calyx fluid or a mixture of venom and calyx fluid dissolved in 100 nL were injected to prepare the following treatments: 1) C.glomerata calyx fluid containing bracovirus particles (CgBV); 2) C.glomerata venom (V); 3) C.glomerata calyx fluid + venom (CgBV+V); 4) H.ebeninus calyx fluid containing ichnovirus particles (HeIV). Additional treatments were used as controls to test whether the microinjection treatment per se affected the interaction of the caterpillars with the food plant: 5) un-parasitized caterpillars injected with 100 nL of PBS (PBS) (negative controls) and 6) parasitized caterpillars injected with 100 nL of PBS (Cg-PBS, He-PBS) (positive controls).

Wind tunnel and olfactometer assays

To investigate whether different injection treatments of caterpillars affect the plant-mediated foraging behavior of parasitoid females, we carried out olfactory assays using a wind tunnel for C.glomerata and a static two-chamber olfactometer for H.ebeninus.

Cotesia glomerata responses to Herbivore-induced plant volatiles (HIPVs) triggered by micro-injected caterpillars in wind tunnel dual-choice set-up. Parasitoid preference for one of the two offered plants was assessed in terms of first choice, which was considered to be made when the wasp landed on a plant. Each treatment combination was replicated with 10 plant pairs and 10 wasps per plant pair.

Hyposoter ebeninus responses to Herbivore-induced plant volatiles (HIPVs) triggered by micro-injected caterpillars in static olfactometer dual-choice set-up Parasitoid preference for one of the two offered plants was assessed in terms of residence time, over a total time of 300 seconds.. In each bioassay testing a specific leaf pair combination, the response of three female wasps was monitored. To avoid pseudoreplication, the mean response of these 3 wasps was considered a replicate and this procedure was repeated 8 times for each pairwise combination.
DOI: 10.15468/dl.zh697z
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((71.50307 -4.25619,159.13901 -4.25619,159.13901 63.59101,71.50307 63.59101,71.50307 -4.25619))",
 "TaxonKey is one of (Xyleborus glabratus Eichhoff, 1877, Xyleborus kumamotoensis Murayama, 1934)"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004948-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.an6fd8
title: Occurrence Download

description: A dataset listing the 37 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Indonesia",
 "GadmGid is one of (IDN.12_1, IDN.13_1, IDN.14_1, IDN.34_1, IDN.35_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is EN",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 2015-2025"
 ]
}

 The dataset's 37 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004946-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h247hz
title: Occurrence Download

description: A dataset containing 2708 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bombus ardens Smith, 1879",
 "Country is Japan",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 2708 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004949-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xrvgyc
title: Occurrence Download

description: A dataset containing 385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Asthenes palpebralis (Cabanis, 1873)"
 ]
}

 The dataset includes 385 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004950-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uh5dn9
title: Occurrence Download

description: A dataset containing 3818 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Material citation",
 "Continent is Asia",
 "Country is Nepal",
 "DatasetKey is Sharing vertebrate occurrence data from camera traps in Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3818 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004952-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6anrfg
title: Occurrence Download

description: A dataset containing 22268 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paralepista flaccida (Sowerby) Vizzini"
 ]
}

 The dataset includes 22268 records from 313 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004951-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.