cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.13026/p7kf-t860
title: CXRGraph: Using Information Extraction to Normalize the Training Data for Automatic Radiology Report Generation

description: CXRGraph is a dataset of structured radiology reports dataset following the
RadGraph format, which has been tailored for the Automatic Radiology Report
Generation (ARRG) task. CXRGraph assorts clinical information from full-text
radiology reports into five entity types and four relation types similar to
RadGraph. CXRGraph introduces three entity attributes, which are optionally
associated with an entity to provide additional information (e.g. abnormality)
and handle hallucinated prior references for the ARRG task. We manually
annotated the reports originally formatted in RadGraph, including 550 MIMIC-
CXR reports for model training and evaluation and 50 CheXpert reports for
evaluating the model generalization ability. By using the ground-truth data,
we developed a joint entity and relation model, achieving a micro-F1 of 96.6%
and 96.1% on named entity recognition, 94.0% and 89.8% on entity attribute
recognition, and 89.5% and 86.6% on relation extraction, on the MIMIC-CXR and
CheXpert test sets, respectively. Using the trained model, we automatically
annotated 227,835 MIMIC-CXR reports. Both the ground-truth and inference data
are available in CXRGraph. Given that the MIMIC-CXR and RadGraph have been de-
identified already, no protected health information (PHI) is included.
DOI: 10.5281/zenodo.14794778
title: CRAM Format DNA Data of an entity known as "eiritana" EIRI_CRAM.7z.003

description: CRAM data for the entity known as "eiritana"

7z.003

use with notification / attribution 

contact for archive pw
DOI: 10.5281/zenodo.14794779
title: CRAM Format DNA Data of an entity known as "eiritana" EIRI_CRAM.7z.003

description: CRAM data for the entity known as "eiritana"

7z.003

use with notification / attribution 

contact for archive pw
DOI: 10.13026/5gte-bv70
title: MIMIC-IV-Ext-BHC: Labeled Clinical Notes Dataset for Hospital Course Summarization

description: This dataset presents a curated collection of preprocessed and labeled
clinical notes derived from the MIMIC-IV-Note database. The primary aim of
this resource is to facilitate the development and training of machine
learning models focused on summarizing brief hospital courses (BHC) from
clinical discharge notes.

The dataset contains 270,033 meticulously cleaned and standardized clinical
notes containing an average token length of 2,267, ensuring usability for
machine learning (ML) applications. Each clinical note is paired with a
corresponding BHC summary, providing a robust foundation for supervised
learning tasks. The preprocessing pipeline employed uses regular expressions
to address common issues in the raw clinical text, such as special characters,
extraneous whitespace, inconsistent formatting, and irrelevant text, to
produce a high-quality, structured dataset with separated clinical note
sections through appropriate headings.

By offering this resource, we aim to support healthcare professionals and
researchers in their efforts to enhance patient care through the automation of
BHC summarization. This dataset is ideal for exploring various NLP techniques,
developing predictive models, and improving the efficiency and accuracy of
clinical documentation practices. We invite the research community to utilize
this dataset to advance the field of medical informatics and contribute to
better health outcomes.
DOI: 10.13026/fh2q-4148
title: MIMIC-IV-Ext-BHC: Labeled Clinical Notes Dataset for Hospital Course Summarization

description: This dataset presents a curated collection of preprocessed and labeled
clinical notes derived from the MIMIC-IV-Note database. The primary aim of
this resource is to facilitate the development and training of machine
learning models focused on summarizing brief hospital courses (BHC) from
clinical discharge notes.

The dataset contains 270,033 meticulously cleaned and standardized clinical
notes containing an average token length of 2,267, ensuring usability for
machine learning (ML) applications. Each clinical note is paired with a
corresponding BHC summary, providing a robust foundation for supervised
learning tasks. The preprocessing pipeline employed uses regular expressions
to address common issues in the raw clinical text, such as special characters,
extraneous whitespace, inconsistent formatting, and irrelevant text, to
produce a high-quality, structured dataset with separated clinical note
sections through appropriate headings.

By offering this resource, we aim to support healthcare professionals and
researchers in their efforts to enhance patient care through the automation of
BHC summarization. This dataset is ideal for exploring various NLP techniques,
developing predictive models, and improving the efficiency and accuracy of
clinical documentation practices. We invite the research community to utilize
this dataset to advance the field of medical informatics and contribute to
better health outcomes.
DOI: 10.13026/vr29-4d92
title: MIMIC-IV-Ext-BHC: Labeled Clinical Notes Dataset for Hospital Course Summarization

description: This dataset presents a curated collection of preprocessed and labeled
clinical notes derived from the MIMIC-IV-Note database. The primary aim of
this resource is to facilitate the development and training of machine
learning models focused on summarizing brief hospital courses (BHC) from
clinical discharge notes.

The dataset contains 270,033 meticulously cleaned and standardized clinical
notes containing an average token length of 2,267, ensuring usability for
machine learning (ML) applications. Each clinical note is paired with a
corresponding BHC summary, providing a robust foundation for supervised
learning tasks. The preprocessing pipeline employed uses regular expressions
to address common issues in the raw clinical text, such as special characters,
extraneous whitespace, inconsistent formatting, and irrelevant text, to
produce a high-quality, structured dataset with separated clinical note
sections through appropriate headings.

By offering this resource, we aim to support healthcare professionals and
researchers in their efforts to enhance patient care through the automation of
BHC summarization. This dataset is ideal for exploring various NLP techniques,
developing predictive models, and improving the efficiency and accuracy of
clinical documentation practices. We invite the research community to utilize
this dataset to advance the field of medical informatics and contribute to
better health outcomes.
DOI: 10.15468/dl.k9bhkv
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhazya stricta Decne.",
 "Year 1980-2025"
 ]
}

 The dataset includes 190 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010820-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15472/2pcntm
title: Biodiversidad asociada al proyecto Línea de Transmisión Bello-Guayabal-Ancón Sur 230 kV

description: Los datos de este recurso son procedentes del Estudio de Impacto Ambiental realizado para la obtención de la licencia ambiental para el proyecto que consistió en el diseño, adquisición de suministros, construcción, pruebas, operación y mantenimiento de las obras definidas en el “Plan de expansión de referencia Generación – Transmisión 2012-2025 para la conexión Bello – Guayabal – Ancón Sur 230 kV”, adoptado mediante la Resolución del Ministerio de Minas y Energía 180423 de marzo 21 de 2012 y modificada por la Resolución MME No. 91159 del 26 de diciembre de 2013.
description: El proyecto de conexión se ejecutó bajo el “Plan de expansión de referencia Generación – Transmisión 2012-2025 para la conexión Bello – Guayabal – Ancón sur a 230 kV”, lo que permitió construir una interconexión en el Sistema de Transmisión Nacional (STN) para que la energía fluyera directamente desde el norte de Antioquia hacia el sur del país, sin congestionar las redes regionales que atienden la demanda del Área Metropolitana del Valle de Aburrá (AMVA).
description: En el marco de la elaboración de Estudio de Impacto Ambiental (EIA), se registró para el año 2015, 11.841 registros biológicos (Plantae 11.212, Animalia 464 y Fungi 165) tomados en los municipios de Bello, Medellín, Sabaneta, Envigado y Copacabana. Estos datos corresponden a información sobre el inventario forestal realizado y sus medidas adicionales respectivas (Circunferencia a la altura del pecho (CAP), área basal (AB), Altura total, Altura del fuste, entre otras), así como la información de algunos registros de fauna.
description: Por otro lado, 150 de los registros biológicos correspondientes a julio del 2022 hacen parte de un monitoreo de fauna (herpetos, aves y mamíferos) realizado en el área de estudio como parte de los monitoreos establecidos en el plan de compensación de pérdida de biodiversidad por construcción y operación de la línea de transmisión Bello-Guayabal-Ancón a 230 Kv. Los otros 526 del mismo periodo corresponden a monitoreo de fauna silvestre presente en la vereda Media Luna del municipio de Medellín, Predio Hogares Claret, en el marco del mismo proyecto de compensación.
description: Adicionalmente, los datos de noviembre a diciembre del 2022 corresponden al segundo monitoreo y seguimiento de fauna y flora en los hábitats conservados en la servidumbre línea Bello-Guayabal-Ancón sur 230Kv para la evaluación de la diversidad y estructura en cada uno de los hábitats conservados dentro de la servidumbre del proyecto BGA y aprobados por la Licencia Ambiental Resolución 0781 de 2016 y su respectiva modificación (Resolución 0433 de 2017). Para el segundo monitoreo de flora se tuvieron en cuenta variables dasométricas como altura y CAP (circunferencia a la altura del pecho), además, estado estructural y estado fitosanitario (presencia de insectos, hongos, enfermedades, entre otras) de los individuos.
DOI: 10.17632/2nkw2kskp2.1
title: bk-chikv

description: Data collected during a chikv kap survey at Kenyan coast
DOI: 10.5281/zenodo.14796352
title: LearnedCloudCT datasets

description: This document contains all links for the datasets needed to train and evaluate ProbCT. The data is freely available online on the Zenodo platform. The datasets include the training and test sets. These consist of 3D cloud scenes, their corresponding multi-view images, and NASA's AirMSPI images.
DOI: 10.5281/zenodo.14796353
title: LearnedCloudCT datasets

description: This document contains all links for the datasets needed to train and evaluate ProbCT. The data is freely available online on the Zenodo platform. The datasets include the training and test sets. These consist of 3D cloud scenes, their corresponding multi-view images, and NASA's AirMSPI images.
DOI: 10.5281/zenodo.14691106
title: Supplementary material: "A Revised Oceanic Plate Cooling Model"

description: Supplementary material for "A Revised Oceanic Plate Cooling Model" by Holdt M. C., White, N. J., & Richards, F. D., submitted for publication in Journal of Geophysical Research: Solid Earth. This repository contains data (age-depth, heat flow) and code (Python, Fortran) to compute the thermal evolution of oceanic lithosphere. Three best-fit models (HWR-1, HWR-2 and HWR-3) have been identified. Please see Holdt et al., (in review) for a detailed discussion of these models.

Repository Structure: 

Data

This directory contains age-depth and heat flow measurements.These measurements are included as both binned and unbinned datasets (see Figure 2).

Code

This directory contains code used to generate plate models, identify the best-fit model and plot results.

    a) run plate_model_generation.* to generate plate models that sweep though ranges for Tp, zp and zr (output directory: plate_model_output).

    b) run 01_plate_model_sweep_SOURCE*.sh to identify best-fit model (output directory: plate_model_output_RMS_misfit, plate_model_output_FINAL).

    c) run 02_plate_model_sweep_PLOT.sh to plot figures (output directory: plate_model_output_PLOTS).

Please note that this code was originally written for a study by Richards et al., 2018. The parameterization of this code was subsequently updated by Richards et al., 2020 and by Holdt et al., 2022. It has been further modified for this study (Holdt et al., in review), with detailed comments included in the code. If using the code, please cite Richards et al., 2018. If using the specific model outputs and/or input parameterizations of HWR-1, HWR-2, or HWR-3, please cite Holdt et al., (in review). 

Models

This directory contains the final models (HWR-1, HWR-2, HWR-3) presented in Holdt et al., (in review).

Citations

Holdt M. C., White, N. J., & Richards, F. D. (in review). A Revised Oceanic Plate Cooling Model. Journal of Geophysical Research: Solid Earth

Holdt, M. C., White, N. J., Stephenson, S. N., & Conway-Jones, B. W. (2022). Densely Sampled Global Dynamic Topographic Observations and Their Significance. Journal of Geophysical Research: Solid Earth, 127 (7), e2022JB024391. doi: 10.1029/2022JB024391

Richards, F. D., Hoggard, M., Crosby, A., Ghelichkhan, S., & White, N. J. (2020). Structure and dynamics of the oceanic lithosphere-asthenosphere system. Physics of the Earth and Planetary Interiors, 309 (July), 106559. doi:10.1016/j.pepi.2020.106559

Richards, F. D., Hoggard, M. J., Cowton, L. R., & White, N. J. (2018). Reassessing the Thermal Structure of Oceanic Lithosphere With Revised Global Inventories of Basement Depths and Heat Flow Measurements. Journal of Geophysical Research: Solid Earth, 123 (10), 9136–9161. doi: 10.1029/2018JB015998

Contact

For questions, comments or feedback, please reach out to Megan Holdt (mch74@cam.ac.uk), Fred Richards (f.richards19@imperial.ac.uk) or Nicky White (njw10@cam.ac.uk).
DOI: 10.5281/zenodo.14691107
title: Supplementary material: "A Revised Oceanic Plate Cooling Model"

description: Supplementary material for "A Revised Oceanic Plate Cooling Model" by Holdt M. C., White, N. J., & Richards, F. D., submitted for publication in Journal of Geophysical Research: Solid Earth. This repository contains data (age-depth, heat flow) and code (Python, Fortran) to compute the thermal evolution of oceanic lithosphere. Three best-fit models (HWR-1, HWR-2 and HWR-3) have been identified. Please see Holdt et al., (in review) for a detailed discussion of these models.

Repository Structure: 

Data

This directory contains age-depth and heat flow measurements.These measurements are included as both binned and unbinned datasets (see Figure 2).

Code

This directory contains code used to generate plate models, identify the best-fit model and plot results.

    a) run plate_model_generation.* to generate plate models that sweep though ranges for Tp, zp and zr (output directory: plate_model_output).

    b) run 01_plate_model_sweep_SOURCE*.sh to identify best-fit model (output directory: plate_model_output_RMS_misfit, plate_model_output_FINAL).

    c) run 02_plate_model_sweep_PLOT.sh to plot figures (output directory: plate_model_output_PLOTS).

Please note that this code was originally written for a study by Richards et al., 2018. The parameterization of this code was subsequently updated by Richards et al., 2020 and by Holdt et al., 2022. It has been further modified for this study (Holdt et al., in review), with detailed comments included in the code. If using the code, please cite Richards et al., 2018. If using the specific model outputs and/or input parameterizations of HWR-1, HWR-2, or HWR-3, please cite Holdt et al., (in review). 

Models

This directory contains the final models (HWR-1, HWR-2, HWR-3) presented in Holdt et al., (in review).

Citations

Holdt M. C., White, N. J., & Richards, F. D. (in review). A Revised Oceanic Plate Cooling Model. Journal of Geophysical Research: Solid Earth

Holdt, M. C., White, N. J., Stephenson, S. N., & Conway-Jones, B. W. (2022). Densely Sampled Global Dynamic Topographic Observations and Their Significance. Journal of Geophysical Research: Solid Earth, 127 (7), e2022JB024391. doi: 10.1029/2022JB024391

Richards, F. D., Hoggard, M., Crosby, A., Ghelichkhan, S., & White, N. J. (2020). Structure and dynamics of the oceanic lithosphere-asthenosphere system. Physics of the Earth and Planetary Interiors, 309 (July), 106559. doi:10.1016/j.pepi.2020.106559

Richards, F. D., Hoggard, M. J., Cowton, L. R., & White, N. J. (2018). Reassessing the Thermal Structure of Oceanic Lithosphere With Revised Global Inventories of Basement Depths and Heat Flow Measurements. Journal of Geophysical Research: Solid Earth, 123 (10), 9136–9161. doi: 10.1029/2018JB015998

Contact

For questions, comments or feedback, please reach out to Megan Holdt (mch74@cam.ac.uk), Fred Richards (f.richards19@imperial.ac.uk) or Nicky White (njw10@cam.ac.uk).
DOI: 10.5281/zenodo.13348559
title: Understanding the Adoption of Modern JavaScript Features: An Empirical Study on Open-Source Systems

description: This repository contains the data and analysis from an empirical study investigating the adoption trends of modern JavaScript features introduced with ECMAScript 6 (ES6) and beyond. By mining the source code history of 158 open-source JavaScript projects, the study identifies efforts to rejuvenate legacy code by replacing outdated constructs with modern ones. The findings highlight the extensive use of modern features, their widespread adoption within one to two years after ES6's release, and ongoing trends in the rejuvenation of JavaScript codebases.





scripts.zip: Contains Python scripts used to analyze data and generate the graphs presented in the study's results.


scripts-threats-analysis.zip:  Contains the Python scripts used to analyze the projects without applying the study's filtering criteria and to generate the table presented in the Threats to Validity section.



jsminer-tool.zip: Includes the tool developed to analyze GitHub repository history and collect metrics on the adoption of modern JavaScript features.




jsminer_database_backup.zip: Provides a PostgreSQL database dump containing all code review comments from the repositories analyzed in the study.
DOI: 10.5281/zenodo.14796287
title: Understanding the Adoption of Modern JavaScript Features: An Empirical Study on Open-Source Systems

description: This repository contains the data and analysis from an empirical study investigating the adoption trends of modern JavaScript features introduced with ECMAScript 6 (ES6) and beyond. By mining the source code history of 158 open-source JavaScript projects, the study identifies efforts to rejuvenate legacy code by replacing outdated constructs with modern ones. The findings highlight the extensive use of modern features, their widespread adoption within one to two years after ES6's release, and ongoing trends in the rejuvenation of JavaScript codebases.





scripts.zip: Contains Python scripts used to analyze data and generate the graphs presented in the study's results.


scripts-threats-analysis.zip:  Contains the Python scripts used to analyze the projects without applying the study's filtering criteria and to generate the table presented in the Threats to Validity section.



jsminer-tool.zip: Includes the tool developed to analyze GitHub repository history and collect metrics on the adoption of modern JavaScript features.




jsminer_database_backup.zip: Provides a PostgreSQL database dump containing all code review comments from the repositories analyzed in the study.
DOI: 10.5281/zenodo.14796318
title: Datasets for "Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity: Modeled with a Statistical Framework for Biphasic Systems"

description: The experimental data in this file is from a manuscript which was titled "Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity: Modeled with a Statistical Framework for Biphasic Systems". The manuscript authors are Sharon N. Greenwood, Alexis N. Dispensa, Matthew Wang, Justin R. Bauer, Timothy D. Vaden, Zhiwei Liu, and Brian P. Weiser. The manuscript was submitted for publication in 2025. Requests for information regarding the data in this file should be directed to Brian P. Weiser from Rowan University (Stratford, NJ  USA) (weiser@rowan.edu).
DOI: 10.5281/zenodo.14796319
title: Datasets for "Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity: Modeled with a Statistical Framework for Biphasic Systems"

description: The experimental data in this file is from a manuscript which was titled "Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity: Modeled with a Statistical Framework for Biphasic Systems". The manuscript authors are Sharon N. Greenwood, Alexis N. Dispensa, Matthew Wang, Justin R. Bauer, Timothy D. Vaden, Zhiwei Liu, and Brian P. Weiser. The manuscript was submitted for publication in 2025. Requests for information regarding the data in this file should be directed to Brian P. Weiser from Rowan University (Stratford, NJ  USA) (weiser@rowan.edu).
DOI: 10.15468/dl.g2ghsq
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "Geometry POLYGON((-82.78 41.9,-73.02 41.9,-73.02 45.82,-82.78 45.82,-82.78 41.9))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Macropis nuda (Provancher, 1882)"
 ]
}

 The dataset includes 99 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010822-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14690844
title: Data to Supplemental Material: Effects of isotope and chemical incoherence on self-diffusion of atoms in liquid alloys of gallium with isotopes of nickel: Experiments based on quasielastic neutron scattering versus molecular dynamics simulations (supplementary information data)

description: The data provided relates to the supplementary information of a publication in Physical Review B (10.1103/PhysRevB.111.064302).

Here supplementary MD trajectories are provided. Two subdirectories, Ga9Ni_60 and Ga49Ni_60, are included each of which contains zip-compressed archives named TrajectoriesXXX.zip, according to the corresponding temperatures XXX. For T=823 K, 1073 K, 1173 K, each such archive contains ten subdirectories with the results of ten runs of simulations performed with the VASP software, https://www.vasp.at/. For T=1273 K in Ga49Ni_60, the archive contains five subdirectories with five runs of simulations. The trajectory files are in XDATCAR format and compressed using gzip.
DOI: 10.5281/zenodo.14690845
title: Data to Supplemental Material: Effects of isotope and chemical incoherence on self-diffusion of atoms in liquid alloys of gallium with isotopes of nickel: Experiments based on quasielastic neutron scattering versus molecular dynamics simulations (supplementary information data)

description: The data provided relates to the supplementary information of a publication in Physical Review B (10.1103/PhysRevB.111.064302).

Here supplementary MD trajectories are provided. Two subdirectories, Ga9Ni_60 and Ga49Ni_60, are included each of which contains zip-compressed archives named TrajectoriesXXX.zip, according to the corresponding temperatures XXX. For T=823 K, 1073 K, 1173 K, each such archive contains ten subdirectories with the results of ten runs of simulations performed with the VASP software, https://www.vasp.at/. For T=1273 K in Ga49Ni_60, the archive contains five subdirectories with five runs of simulations. The trajectory files are in XDATCAR format and compressed using gzip.