cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25919/vq7h-ns35
title: Deep Learning Image Segmentation of Sandy Beaches in Southeastern Australia

description: The collection includes beach coastlines from Southeastern Australia, specifically Victoria and New South Wales, used to train an image segmentation model using the U-Net deep learning architecture for mapping sandy beaches. The dataset contains polygons that represent the outline or extent of the raster images and polygons drawn by citizen-scientists. Additionally, we provide the trained model itself, which can be utilized for further evaluation or refined through fine-tuning. The resulting predictions are also available in Shapefiles format, which can be loaded to NationalMap.

This collection supplements the publication: Regional-Scale Image Segmentation of Sandy Beaches: Comparison of Training and Prediction Across Two Extensive Coastlines in Southeastern Australia (Yong et al. 2025)
DOI: 10.15468/dl.t45kbq
title: Occurrence Download

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

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010549-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rabava
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:AED7717"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010552-250711103210423/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.25687188
title: <b>Besides aridity, plant communities are a non-negligible factor in determining soil bacterial and fungal diversity</b>

description: data
DOI: 10.6084/m9.figshare.25687188.v3
title: <b>Besides aridity, plant communities are a non-negligible factor in determining soil bacterial and fungal diversity</b>

description: data
DOI: 10.6084/m9.figshare.25687188.v2
title: <b>Besides aridity, plant communities are a non-negligible factor in determining soil bacterial and fungal diversity</b>

description: data
DOI: 10.15468/dl.29cjcu
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Türkiye",
 "HasCoordinate is true"
 ]
}

 The dataset includes 71 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010554-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9tfzus
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010555-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/wdfc-3453
title: "Dolphyn - Long-duration storage formulations"

description: "This version of Dolphyn was used for the paper \"Improved formulation for long-duration storage in capacity expansion models using representative periods\". Different long-duration storage formulations are implemented (Explicit-Hourly, Implicit-Hourly, Implicit-Min-Max - see paper for definitions) and tested on three example systems. Run files are available in the \"Example_Systems\" subfolders."
DOI: 10.15468/dl.jquz57
title: Occurrence Download

description: A dataset containing 941 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Observation, Human Observation, Occurrence evidence)",
 "Country is one of (Ecuador, Peru, Colombia, Venezuela (Bolivarian Republic of), Bolivia (Plurinational State of))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gallinago jamesoni",
 "Year 2015-2024"
 ]
}

 The dataset includes 941 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010556-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15877872
title: Task 5.3 - Interview transcripts and notes - Iraq, Nigeria, EU - Case studies international bureaucracy and redocumentation

description: This data set includes transcripts and notes from 12 semi-structured interviews conducted between June 2024 and March 2025. The interviews were conducted with government officials from Nigeria and Iraq along with implementing civil society partners for reintegration programs in these countries. Most interviews were conducted face-to-face in Badgad for Iraq and Abuja for Nigeria. The interviews focused on issues related to the perceived legitimacy and effectiveness of intergovenmental readmission protocols. Material is available in English, in .docx format and weighs approximately 0.5MB.
DOI: 10.5281/zenodo.15877873
title: Task 5.3 - Interview transcripts and notes - Iraq, Nigeria, EU - Case studies international bureaucracy and redocumentation

description: This data set includes transcripts and notes from 12 semi-structured interviews conducted between June 2024 and March 2025. The interviews were conducted with government officials from Nigeria and Iraq along with implementing civil society partners for reintegration programs in these countries. Most interviews were conducted face-to-face in Badgad for Iraq and Abuja for Nigeria. The interviews focused on issues related to the perceived legitimacy and effectiveness of intergovenmental readmission protocols. Material is available in English, in .docx format and weighs approximately 0.5MB.
DOI: 10.6084/m9.figshare.29558162
title: Supplementary material: A protocol for three observational cohort studies evaluating adverse outcomes, excess costs and repeat procedures after surgery for breast cancer in the USA

description: <b>These are peer-reviewed supplementary materials for the article</b><b> </b><b>'</b><b>A protocol for three observational cohort studies evaluating adverse outcomes, excess costs and repeat procedures after surgery for breast cancer in the USA</b><b>'</b><b> </b><b>published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Table S1: </b>Breast resection procedures and cancer diagnosis codes.<b>Table S2:</b> Free text string search terms.<b>Table S3: </b>Variables to be analyzed.<b>Aim:</b> Surgical therapy for early-stage breast cancer, including lumpectomy and mastectomy, are common treatments for early-stage breast cancer. Despite having favorable survival outcomes, these procedures can lead to repeat surgeries, adverse outcomes, excess costs and potentially aggressive resections. This is a protocol for a study aims to evaluate three main areas: the risk factors, costs and complications of re-operations following lumpectomy (‘Lumpectomy Cohort’), the identification of patients potentially overtreated with mastectomy (‘Mastectomy Cohort’) and the cost and healthcare resource utilization associated with nipple necrosis following nipple-sparing mastectomy (NSM) (‘Nipple Necrosis Cohort’). <b>Materials & methods:</b> A retrospective cohort analysis will be conducted using Optum’s de-identified Market Clarity Data (2007–2023), which integrates medical and pharmacy claims with electronic health records. Patients will be included based on specific procedure and diagnosis codes, with additional data extracted from unstructured clinical notes using natural language processing. The study will analyze patient demographics, baseline health, surgical details, and outcomes, including costs, complications, reoperations and mortality. Data will be analyzed descriptively, with Kaplan–Meier analyses for time-to-event outcomes and Wilcoxon Signed Rank tests for cost comparisons. <b>Results:</b> Preliminary cohorts are expected to include 26,472 lumpectomy patients, 16,836 mastectomy patients and 6828 NSM patients with 541 cases of nipple necrosis. <b>Conclusion:</b> This study will provide comprehensive insights into the patient journey – highlighting the costs and patient outcomes following lumpectomy, mastectomy and NSM – potentially guiding better clinical decision-making and resource allocation.
DOI: 10.6084/m9.figshare.29558162.v1
title: Supplementary material: A protocol for three observational cohort studies evaluating adverse outcomes, excess costs and repeat procedures after surgery for breast cancer in the USA

description: <b>These are peer-reviewed supplementary materials for the article</b><b> </b><b>'</b><b>A protocol for three observational cohort studies evaluating adverse outcomes, excess costs and repeat procedures after surgery for breast cancer in the USA</b><b>'</b><b> </b><b>published in the</b><b> </b><b><i>Journal of Comparative Effectiveness Research</i></b><b>.</b><b>Table S1: </b>Breast resection procedures and cancer diagnosis codes.<b>Table S2:</b> Free text string search terms.<b>Table S3: </b>Variables to be analyzed.<b>Aim:</b> Surgical therapy for early-stage breast cancer, including lumpectomy and mastectomy, are common treatments for early-stage breast cancer. Despite having favorable survival outcomes, these procedures can lead to repeat surgeries, adverse outcomes, excess costs and potentially aggressive resections. This is a protocol for a study aims to evaluate three main areas: the risk factors, costs and complications of re-operations following lumpectomy (‘Lumpectomy Cohort’), the identification of patients potentially overtreated with mastectomy (‘Mastectomy Cohort’) and the cost and healthcare resource utilization associated with nipple necrosis following nipple-sparing mastectomy (NSM) (‘Nipple Necrosis Cohort’). <b>Materials & methods:</b> A retrospective cohort analysis will be conducted using Optum’s de-identified Market Clarity Data (2007–2023), which integrates medical and pharmacy claims with electronic health records. Patients will be included based on specific procedure and diagnosis codes, with additional data extracted from unstructured clinical notes using natural language processing. The study will analyze patient demographics, baseline health, surgical details, and outcomes, including costs, complications, reoperations and mortality. Data will be analyzed descriptively, with Kaplan–Meier analyses for time-to-event outcomes and Wilcoxon Signed Rank tests for cost comparisons. <b>Results:</b> Preliminary cohorts are expected to include 26,472 lumpectomy patients, 16,836 mastectomy patients and 6828 NSM patients with 541 cases of nipple necrosis. <b>Conclusion:</b> This study will provide comprehensive insights into the patient journey – highlighting the costs and patient outcomes following lumpectomy, mastectomy and NSM – potentially guiding better clinical decision-making and resource allocation.
DOI: 10.15468/dl.zte47k
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ctenopharyngodon idella",
 "Country is Hungary",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010560-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akghra
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010558-250711103210423/datasets/export for details.
DOI: 10.15468/dl.vx7urf
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oncorhynchus mykiss",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 168 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010559-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pk4w3g
title: Occurrence Download

description: A dataset containing 808344 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bellis perennis"
 ]
}

 The dataset includes 808344 records from 3536 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010411-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syp88d
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dipterocarpus parviflorus Zipp.",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014657-250515123054153/datasets/export for details.
DOI: 10.15468/dl.v8xzar
title: Occurrence Download

description: A dataset containing 586307 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Insect Species Occurrence Data from Multiple Projects Worldwide with Focus on Bees and Wasps in North America"
 ]
}

 The dataset includes 586307 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014651-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e4e2ev
title: Occurrence Download

description: A dataset containing 191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Dominican Republic",
 "TaxonKey is Caulerpa J.V.F.Lamouroux, 1809"
 ]
}

 The dataset includes 191 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014652-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7zecdk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dipterocarpus parvifolius F.Heim",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014663-250515123054153/datasets/export for details.
DOI: 10.6084/m9.figshare.29120024
title: Validity of the CORE Wearable Sensor During Constant-load Cycling Exercise in the Heat.xlsx

description: This dataset includes raw data from a research study assessing the validity of the CORE wearable sensor during exercise in a hot environment. This study was conducted in aerobically-active, otherwise healthy humans.
DOI: 10.6084/m9.figshare.29120024.v1
title: Validity of the CORE Wearable Sensor During Constant-load Cycling Exercise in the Heat.xlsx

description: This dataset includes raw data from a research study assessing the validity of the CORE wearable sensor during exercise in a hot environment. This study was conducted in aerobically-active, otherwise healthy humans.
DOI: 10.18112/openneuro.ds006018.v1.2.2
title: Cognitive Electrophysiology in Socioeconomic Context in Adulthood: An EEG dataset
DOI: 10.15468/dl.f5pd98
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dipterocarpus penangianus Foxw.",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014668-250515123054153/datasets/export for details.
DOI: 10.15468/dl.5ma8f2
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Canadian Museum of Nature Amphibian and Reptile Collection",
 "TaxonKey is Sternotherus odoratus (Latreille, 1802)"
 ]
}

 The dataset includes 62 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014656-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mp56y
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus lentiginosus var. stramineus (Rydb.) Barneby"
 ]
}

 The dataset includes 121 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014654-250515123054153/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.29132000
title: Real data

description: Here are the datasets used in the empirical analysis in the article.
DOI: 10.15468/dl.9fwkuj
title: Occurrence Download

description: A dataset containing 5915 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is Vermont Butterfly Atlas 1.0 (2002-2007)"
 ]
}

 The dataset includes 5915 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014660-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rbvube
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dipterocarpus pentagonus A.DC.",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014671-250515123054153/datasets/export for details.
DOI: 10.15468/dl.w5g2kj
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Geometry POLYGON((0.95854 41.95228,2.72476 41.95228,2.72476 42.65938,0.95854 42.65938,0.95854 41.95228))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Malpolon monspessulanus (Hermann, 1804)",
 "Year 2020-2025"
 ]
}

 The dataset includes 100 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014658-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p8a4xb
title: Occurrence Download

description: A dataset containing 11455 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chrysochus auratus (Fabricius, 1775)"
 ]
}

 The dataset includes 11455 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014655-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15484538
title: What Do Genomic Transformers Attend To? Interpreting Attention Heads Across DNABERT, Nucleotide Transformer, and scGPT

description: Transformer models have shown strong performance on biological sequence prediction tasks, but the interpretability of their internal mechanisms remains underexplored. As the use-case of these models is in the context of biomedical research, mechanistic understanding of the predictions is key to their widespread adoption. We introduce a method to interpret attention heads in genomic transformers by correlating per-token attention scores with curated biological annotations and summarize each head’s focus using GPT-4. Applying this to DNABERT, Nucleotide Transformer, and scGPT, we find that attention heads learn biologically meaningful associations during unsupervised pre-training and that these associations shift with fine-tuning. We show that interpretability varies with tokenization scheme, and that context-dependence plays a key role in head behaviour. Through ablation, we demonstrate that heads strongly associated with biological features are more important for task performance than uninformative heads in the same layers. In DNABERT trained for TATA promoter prediction, we observe heads with positive and negative associations reflecting positive and negative learning dynamics. Our results offer a framework to trace how biological features are learned from random initialization to pretraining to finetuning, enabling insight into how these models represent nucleotides, genes, and cells.
DOI: 10.5281/zenodo.15484539
title: What Do Genomic Transformers Attend To? Interpreting Attention Heads Across DNABERT, Nucleotide Transformer, and scGPT

description: Transformer models have shown strong performance on biological sequence prediction tasks, but the interpretability of their internal mechanisms remains underexplored. As the use-case of these models is in the context of biomedical research, mechanistic understanding of the predictions is key to their widespread adoption. We introduce a method to interpret attention heads in genomic transformers by correlating per-token attention scores with curated biological annotations and summarize each head’s focus using GPT-4. Applying this to DNABERT, Nucleotide Transformer, and scGPT, we find that attention heads learn biologically meaningful associations during unsupervised pre-training and that these associations shift with fine-tuning. We show that interpretability varies with tokenization scheme, and that context-dependence plays a key role in head behaviour. Through ablation, we demonstrate that heads strongly associated with biological features are more important for task performance than uninformative heads in the same layers. In DNABERT trained for TATA promoter prediction, we observe heads with positive and negative associations reflecting positive and negative learning dynamics. Our results offer a framework to trace how biological features are learned from random initialization to pretraining to finetuning, enabling insight into how these models represent nucleotides, genes, and cells.
DOI: 10.15468/dl.v9tukn
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Canada",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Epioblasma triquetra (Rafinesque, 1820)"
 ]
}

 The dataset includes 36 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014665-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.