cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.k3xxgc
title: Occurrence Download

description: A dataset containing 2465 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (South America, North America)",
 "GbifRegion is one of (Latin America and the Caribbean, North America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bulimulus bonariensis"
 ]
}

 The dataset includes 2465 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006203-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4rwkzx
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus scoparius",
 "Country is Estonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006205-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6gve5
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006208-250920141307145/datasets/export for details.
DOI: 10.15468/dl.hph8vt
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus scoparius",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 21 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006209-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9knauq
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Morocco, Western Sahara)",
 "OccurrenceStatus is Present",
 "TaxonKey is Sturnus vulgaris",
 {
 "or" : [
 "Year 2015-2016",
 "Year 2024-2025"
 ]
 }
 ]
}

 The dataset includes 178 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006210-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dknc86
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Eumops perotis",
 "Year is greater than or equal to 2000",
 "Country is one of (United States of America, Canada)",
 "HasGeospatialIssue is false",
 "CoordinateUncertaintyInMeters is less than or equal to 5000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Specimen)"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006211-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hecw43
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus scoparius",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006212-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.8310363
title: Data from: Dryland rock detention structures increase herbaceous vegetation cover and stabilize shrub cover over 10 years but do not directly affect soil fertility

description: Data to accompany the publication "Dryland rock detention structures increase herbaceous vegetation cover and stabilize shrub cover over 10 years but do not directly affect soil fertility" by Ossanna et al. (2024), Science of the Total Environment, 917, 170194. https://doi.org/10.1016/j.scitotenv.2024.170194. Access the project's GitHub repository for full analysis at https://github.com/lossanna/AVCA_ElkLD.

 

Directory:



bac-arc_clean_asv.txt



Cleaned ASV (amplicon sequence variant) table from 16S rRNA amplion sequencing. Each column (1-20766) is a unique ASV, each row (1-62) is a soil sample, and values are the number of ASV reads found in each sample. Cleaned table produced from DADA2 pipeline and contaminant removal.



fungi_clean_asv.txt



Cleaned ASV table from ITS amplicon sequencing. Each column (1-6823) is a unique ASV, each row is a soil sample (1-62), and values are the number of ASV reads found in each sample. Cleaned table produced from DADA2 pipeline and contaminant removal.



Herb-and-shrub-cover_2012-2021.csv



Percent cover of grasses, forbs, and shrubs (summed together) from 2012 to 2021.



Herb-cover_2012-2021.csv



Percent cover of grasses and forbs (summed together) from 2012 to 2021.



Invasive-cover_2012-2021.csv



Percent cover of invasive plants from 2012 to 2021.



Perennial-plant-diversity_2012-2021.csv



Richness (number of species) and Shannon diversity from 2012 to 2021 (perennial plants only).



sequencing-metadata.csv



Sample numbers and their corresponding treatment (Treated or Control).



Shrub-cover_2012-2021.csv



Percent cover of shrubs from 2012 to 2021.



Species-cover_201212-2021.csv



Plant cover by species; includes common and scientific names, invasive/native status, and functional group (annual/perennial grass or forb, shrub, tree).



Veg-soil-elev_2021.csv



Vegetation cover, soil chemical and microbial data, and change in channel bed elevation from 2021; used for structural equation modeling.
DOI: 10.15468/dl.rf8nc4
title: Occurrence Download

description: A dataset containing 1003 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Morocco, Western Sahara)",
 "OccurrenceStatus is Present",
 "TaxonKey is Passer hispaniolensis",
 {
 "or" : [
 "Year 2015-2016",
 "Year 2024-2025"
 ]
 }
 ]
}

 The dataset includes 1003 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006213-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.5557354
title: MIS 5e relative sea-level index points along the Pacific coast of North America

description: This spreadsheet contains data and metadata on relative sea-level index points and associated ages for the Pacific coast of North America. This is Version 1.1, updated after the peer-review of the associated paper.
DOI: 10.5281/zenodo.5903285
title: MIS 5e relative sea-level index points along the Pacific coast of North America

description: This spreadsheet contains data and metadata on relative sea-level index points and associated ages for the Pacific coast of North America. This is Version 1.1, updated after the peer-review of the associated paper.
DOI: 10.15468/dl.rtmh52
title: Occurrence Download

description: A dataset containing 7989 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Morocco, Western Sahara)",
 "OccurrenceStatus is Present",
 "TaxonKey is Passer domesticus",
 {
 "or" : [
 "Year 2015-2016",
 "Year 2024-2025"
 ]
 }
 ]
}

 The dataset includes 7989 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006214-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p948vj4x
title: Split-beam Echo Sounder and Navigation Data Collected Using a Simrad EK80 Wide Band Tranceiver and ES38-10 Transducer During the Mid-Atlantic Resource Imaging Experiment (MATRIX), USGS Field Activity 2018-002-FA.

description: In summer 2018, the U.S. Geological Survey partnered with the U.S Department of Energy and the Bureau of Ocean Energy Management to conduct the Mid-Atlantic Resources Imaging Experiment (MATRIX) as part of the U.S. Geological Survey Gas Hydrates Project. The field program objectives were to acquire high-resolution 2-dimensional multichannel seismic-reflection and split-beam echosounder data along the U.S Atlantic margin between North Carolina and New Jersey to determine the distribution of methane gas hydrates in below-sea floor sediments and investigate potential connections between gas hydrate dynamics and sea floor methane seepage. MATRIX field work was carried out between August 8 and August 28, 2018 on the research vessel Hugh R. Sharp and resulted in acquisition of more than 2,000 track-line kilometers of multichannel seismic-reflection and colocated split-beam echosounder data, along with wide-angle seismic reflection and refraction data from 63 expendable sonobuoy deployments.
DOI: 10.15468/dl.3khx78
title: Occurrence Download

description: A dataset containing 2418 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Morocco, Western Sahara)",
 "OccurrenceStatus is Present",
 "TaxonKey is Pica mauritanica",
 {
 "or" : [
 "Year 2015-2016",
 "Year 2024-2025"
 ]
 }
 ]
}

 The dataset includes 2418 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006215-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v93jym
title: Occurrence Download

description: A dataset containing 536 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 536 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006216-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9x5wxq
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006217-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x8ar6t
title: Occurrence Download

description: A dataset containing 1307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1307 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006218-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.5341661
title: Last interglacial sea-level index points in the Western Mediterranean

description: Sea-level index points, dated samples and correlated metadata for the Western Mediterranean. This dataset was assembled in the framework of the World Atlas of Last Interglacial Shorelines. Field descriptors are available at: https://walis-help.readthedocs.io/en/latest/


See readme files for updates with respect to version 2.0
DOI: 10.5281/zenodo.4497364
title: Last interglacial sea-level index points in the Western Mediterranean

description: Sea-level index points, dated samples and correlated metadata for the Western Mediterranean. This dataset was assembled in the framework of the World Atlas of Last Interglacial Shorelines. Field descriptors are available at: https://walis-help.readthedocs.io/en/latest/


See readme files for updates with respect to version 2.0
DOI: 10.5281/zenodo.17175828
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: 10.60723/11244
title: Novel de novo JAG1 frameshift mutation in Alagille syndrome with early liver transplant requirement

description: We present the case of a male infant born at 35 weeks gestation as twin 2 (birth weight 1.91kg) who developed persistent conjugated hyperbilirubinemia and prolonged neonatal jaundice. The patient underwent Kasai portoenterostomy for suspected biliary atresia, but liver biopsy revealed intrahepatic cholestasis with ductopenia rather than large duct obstruction. Additional clinical features included butterfly vertebra at T5, hepatomegaly, icteric sclera, and pruritic skin. Family history was notable for twin 1 who died from complex congenital heart disease (univentricular heart with aortic valve stenosis and likely pulmonary atresia). Parents were non-consanguineous and of Han Chinese decent with no family history of liver or metabolic disease. Research exome sequencing revealed a novel de novo frameshift pathogenic variant NM_000214 (JAG1):c.2874_2875delTG;p.(Ala959GlufsTer7), never previously reported in ExAC (at the time) or literature. This variant was consistent with Alagille syndrome diagnosis. Due to progressive cholestasis and absence of suitable living donors, the patient was listed for liver transplantation and subsequently underwent deceased donor liver transplant in China at approximately 12 months of age. The post-transplant course was complicated by infections requiring multiple interventions including PTBD drainage and antimicrobial therapy. This case demonstrates the severe end of the Alagille syndrome spectrum, with early requirement for liver transplantation despite Kasai portoenterostomy. The novel JAG1 frameshift variant expands the known pathogenic variant spectrum for this condition.
DOI: 10.5281/zenodo.17178966
title: TPPR
DOI: 10.5281/zenodo.17178967
title: TPPR
DOI: 10.15468/dl.raxfvd
title: Occurrence Download

description: A dataset containing 5498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "TaxonKey is Milicia excelsa"
 ]
}

 The dataset includes 5498 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006219-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14903542
title: Easy genomic regions for short-read variant calling

description: Panmask easy regions:



pm151a.easy: excluding 151-mers occurring ≥1.01n times in the pangenome, where n is the number of genomes.

pm151b.easy: further excluding low-complexity regions (LCRs) longer than 18bp identified by longdust

pm401a.easy: 401-mers. Not well evaluated.

pm401b.easy: excluding LCRs longer than 30bp

*.longdust.bed.gz: LCRs generated by longdust v1.0 (sligtly different from the latest v1.2)


They exclude all assembly gaps and non-chromosomal contigs. See panmask for details.
DOI: 10.5281/zenodo.16755940
title: Easy genomic regions for short-read variant calling

description: Panmask easy regions:



pm151a.easy: excluding 151-mers occurring ≥1.01n times in the pangenome, where n is the number of genomes.

pm151b.easy: further excluding low-complexity regions (LCRs) longer than 18bp identified by longdust

pm401a.easy: 401-mers. Not well evaluated.

pm401b.easy: excluding LCRs longer than 30bp

*.longdust.bed.gz: LCRs generated by longdust v1.0 (sligtly different from the latest v1.2)


They exclude all assembly gaps and non-chromosomal contigs. See panmask for details.
DOI: 10.34740/kaggle/dsv/13139465
title: Vietnam SARS-CoV-2 | COVID-19 Data
DOI: 10.15468/dl.t3q4ah
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006221-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pybn7z
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is Greece",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006220-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5066/p9ca3d8p
title: Aerial Photogrammetry Data and Products of the North Carolina coast: 2018-10-06 to 2018-10-08, post-Hurricane Florence

description: This data release presents structure-from-motion products derived from imagery taken along the North Carolina coast in response to storm events and the recovery process. USGS researchers use the aerial photogrammetry data and products to assess future coastal vulnerability, nesting habitats for wildlife, and provide data for hurricane impact models. This research is part of the Remote Sensing Coastal Change Project.  Products include digital elevation models and orthorectified imagery (RGB averaged products) created from aerial imagery surveys with precise Global Navigation Satellite Systen (GNSS) navigation data flown in a piloted fixed wing aircraft (available here https://coastal.er.usgs.gov/data-release/doi-P91KB9SF/). The products span the coast over both highly developed towns and natural areas, including federal lands such as Cape Lookout National Seashore and Cape Hatteras National Seashore.  These products represent the coast after Hurricane Florence on October 6-8, 2018, and cover from the Cape Fear area in North Carolina to the Virginia border vicinity (Figure 1). Different products are provided in the Child Items section below and contain all segments of the coastline over multiple days of collection.   To cite an individual product use the following format: Ritchie, A.C., Over, J.R., Kranenburg, C.J., Brown, J.A., Buscombe, D., Sherwood, C.R., Warrick, J.A., and Wernette, P.A, 2021, Digital Elevation Models, in Aerial Photogrammetry Data and Products of the North Carolina coast?2018-10-06 to 2018-10-08, post-Hurricane Florence: U.S Geological Survey data release, https://doi.org/10.5066/P9CA3D8P. [Data directly accessible at https://www.sciencebase.gov/catalog/item/6037cca0d34eb12031175133.]        Figure 1. Map showing the geographic features used to bound the individual products to keep their size manageable.         This work has been supported by the U.S. Geological Survey Coastal/Marine Hazards and Resources Program and by Congressional appropriations through the Additional Supplemental Appropriations for Disaster Relief Act of 2019 (H.R. 2157).
DOI: 10.15468/dl.yjfamr
title: Occurrence Download

description: A dataset containing 862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 862 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006223-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpprj6
title: Occurrence Download

description: A dataset containing 43381 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrence of Acraea Butterflies in Africa, 1892- 2022"
 ]
}

 The dataset includes 43381 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006222-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13139485
title: Antutu Benchmark
DOI: 10.15468/dl.cmfvkh
title: Occurrence Download

description: A dataset containing 437996 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megaptera novaeangliae"
 ]
}

 The dataset includes 437996 records from 629 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006184-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.34yftx
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus sitchensis",
 "Country is Norway",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006224-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.