cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15408120
title: ML-Driven Localization of Infection Sources in the Human Cardiovascular System

description: Short Description of the Paper

In vivo localization of infection sources is essential for effective diagnosis and targeted disease treatment. In this work, we leverage machine learning models to associate the temporal dynamics of biomarkers as detected at static gateway positions with different infection source locations. In particular, we introduce a simulation that models infection sources, the release of biomarkers, and their decay as they flow through the bloodstream. From this, we extract time-series biomarker data with varying decay rates to capture temporal patterns from different infection sources at specific gateway positions. We then train a stacked ensemble model using LightGBM and BernoulliNB to analyze biomarker time-series data for classification.

Data and Code

We publish our simulation data and the Python code to process it as described in the paper here on Zenodo and in a GitHub repository under the CC BY and MIT licenses, respectively.

Supplementary_Data.pdf provides an overview of biomarker distributions from different infection sources and classification results for the 70/30 split, complementing the 80/20 results in the main manuscript.

Contact

If you have any questions or suggestions for improvements, feel free to contact me.



Saswati Pal



 Email: pal@ccs-labs.org
DOI: 10.15468/dl.22fnh6
title: Occurrence Download

description: A dataset containing 24646 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((25.28115 47.92169,56.79775 47.92169,56.79775 60.51402,25.28115 60.51402,25.28115 47.92169))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acer negundo L."
 ]
}

 The dataset includes 24646 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030403-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9grfgf
title: Occurrence Download

description: A dataset containing 795 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Demosthenesia A.C.Sm."
 ]
}

 The dataset includes 795 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030407-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffu4ug
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fritillaria tortifolia X.Z.Duan & X.J.Zheng",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030408-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cukeda
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fritillaria verticillata Willd.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation)"
 ]
}

 The dataset includes 47 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030409-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14278/rodare.3003
title: VACVPlaque: mobile photography of Vaccinia virus plaque assay with segmentation masks

description: <strong>How to Cite Us</strong>

De, T., Thangamani, S., Urbański, A., & Yakimovich, A. (2025). A digital photography dataset for Vaccinia Virus plaque quantification using Deep Learning. <em>Scientific Data</em>, <em>12</em>(1), 719.


<pre>@article{de2025digital,
 title={A digital photography dataset for Vaccinia Virus plaque quantification using Deep Learning},
 author={De, Trina and Thangamani, Subasini and Urba{\'n}ski, Adrian and Yakimovich, Artur},
 journal={Scientific Data},
 volume={12},
 number={1},
 pages={719},
 year={2025},
 publisher={Nature Publishing Group UK London}
}</pre>


 

<strong>Data Description</strong>

The VACVPlaque dataset comprises spatially correlated objects, specifically virological plaques, which are circular phenotypes indicative of vaccinia virus (VACV) spread, and the wells of the assay plate. The virus plaque assay is a common method performed by infecting a monolayer of host cells (indicator cells) that are grown in the wells of assay plates or dishes. The host cells are infected with varying concentrations of a highly diluted virus inoculum. After an incubation period, typically around 48 hours, the cells are fixed with formaldehyde and stained with a dye to reveal the plaques or areas of cell death. By counting these plaques, researchers can calculate the number of infectious particles present in the original inoculum as described in [1].

This dataset consists of mobile photographs of 6-well tissue culture plates where the VACV plaque assay was conducted. The photographs were taken using two different mobile phones, resulting in 211, 8-bit RGB images with a resolution of 2448 x 3264 pixels. Each plate was photographed from two different perspectives using two different devices, meaning there are two images of the same plate but from different angles and devices.

To aid in the training of machine learning models, the dataset is divided into training, validation, and test subsets in a 70:20:10 ratio. To prevent data leaks, only one perspective of each image is included in the validation and test subsets. The training subset, which includes images from both perspectives, consists of 148 images.

<strong>File Description:</strong>

VACVPlaque_train.zip -&gt; train holdout

VACVPlaque_validation.zip -&gt; validation holdout

VACVPlaque_test.zip -&gt; test holdout

Each zip file contains:

images -&gt; {filename}.tif

plaque_masks -&gt; {filename}.tif

well_masks -&gt; {filename}.tif

<strong>References:</strong>

1. Dulbecco, Renato. "Production of plaques in monolayer tissue cultures by single particles of an animal virus." Proceedings of the National Academy of Sciences 38, no. 8 (1952): 747-752.
DOI: 10.6084/m9.figshare.28958849
title: Reference assemblies used in the empirical evaluation in the Amira paper.

description: Reference assemblies for 32 <i>Escherichia coli </i>used to generate the results of the empirical analysis in the Amira paper.
DOI: 10.15468/dl.6cgwwr
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ethiopia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Verbesina encelioides (Cav.) Benth. & Hook.fil. ex A.Gray"
 ]
}

 The dataset includes 27 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030410-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.26gu36
title: Occurrence Download

description: A dataset containing 1246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dendrobangia Rusby"
 ]
}

 The dataset includes 1246 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030411-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y54gzq
title: Occurrence Download

description: A dataset containing 32137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is one of (Antennaria umbrinella Rydb., Antennaria microphylla Rydb., Antennaria rosea Greene, Antennaria anaphaloides Rydb., Antennaria parvifolia Nutt., Antennaria racemosa Hook., Antennaria corymbosa E.E.Nelson, Antennaria media Greene, Antennaria monocephala DC., Antennaria dimorpha (Nutt.) Torr. & A.Gray, Antennaria howellii Greene, Antennaria neglecta Greene)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 32137 records from 252 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030413-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13211197
title: Datasets of "FraSSD: a framework to help teachers in the challenge of developing hard and soft skills in Software Engineering students"

description: Hard and soft skills are essential for software professionals to perform their daily activities successfully, considering the specificities of the area, which requires a combination of different skills during the software development cycle. Thus, professionals must develop such skills from undergraduate onwards. In this context, although there are related works in the literature, no results were found that were aimed at supporting teachers in developing students' soft skills in the classroom through active education methodologies, focusing on student motivation. Therefore, to provide a model to help teachers in the challenge of contemplating hard and soft skills in a more meaningful teaching-learning process for students enrolled in Software Engineering subjects, this paper presents a framework based on the active methodologies PBL - Project Based Learning and role-play. Emphasis was placed on the six main soft skills required of software engineers: communication, teamwork, organization, leadership, learning, and creativity. To complement the motivational elements, the framework, called FraSSD – Framework for Soft Skills Development, uses some gamification elements, namely competition, scoring, and scoreboard. Finally, the activities established for students are based on Bloom's Taxonomy, which provides progressive knowledge development. As a proof of concept, FraSSD was applied in two Software Engineering classes, and a self-evaluation was conducted on the part of the students before and after the development of the project proposed by the framework, in which students evaluated their level of development in each of the six soft skills worked on during the course. The results were compared through statistical testing, showing an increase in the level of development of soft skills worked on, emphasizing organization, creativity, and teamwork in Class 1 and teamwork, creativity, and leadership in Class 2. Furthermore, a phenomenological analysis of an open question in the self-evaluation enabled FraSSD's positive points to be observed, as well as suggestions for improvements. From the teachers' point of view who applied the framework, although they suggested some modifications, they considered the FraSSD model easy to implement, which helped motivate students as opposed to traditional teaching methods.
DOI: 10.5281/zenodo.13211196
title: Datasets of "FraSSD: a framework to help teachers in the challenge of developing hard and soft skills in Software Engineering students"

description: Hard and soft skills are essential for software professionals to perform their daily activities successfully, considering the specificities of the area, which requires a combination of different skills during the software development cycle. Thus, professionals must develop such skills from undergraduate onwards. In this context, although there are related works in the literature, no results were found that were aimed at supporting teachers in developing students' soft skills in the classroom through active education methodologies, focusing on student motivation. Therefore, to provide a model to help teachers in the challenge of contemplating hard and soft skills in a more meaningful teaching-learning process for students enrolled in Software Engineering subjects, this paper presents a framework based on the active methodologies PBL - Project Based Learning and role-play. Emphasis was placed on the six main soft skills required of software engineers: communication, teamwork, organization, leadership, learning, and creativity. To complement the motivational elements, the framework, called FraSSD – Framework for Soft Skills Development, uses some gamification elements, namely competition, scoring, and scoreboard. Finally, the activities established for students are based on Bloom's Taxonomy, which provides progressive knowledge development. As a proof of concept, FraSSD was applied in two Software Engineering classes, and a self-evaluation was conducted on the part of the students before and after the development of the project proposed by the framework, in which students evaluated their level of development in each of the six soft skills worked on during the course. The results were compared through statistical testing, showing an increase in the level of development of soft skills worked on, emphasizing organization, creativity, and teamwork in Class 1 and teamwork, creativity, and leadership in Class 2. Furthermore, a phenomenological analysis of an open question in the self-evaluation enabled FraSSD's positive points to be observed, as well as suggestions for improvements. From the teachers' point of view who applied the framework, although they suggested some modifications, they considered the FraSSD model easy to implement, which helped motivate students as opposed to traditional teaching methods.
DOI: 10.15468/dl.zk4u3h
title: Occurrence Download

description: A dataset containing 9431718 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 9431718 records from 2877 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030388-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nxbtfd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.11.103_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007812-260108223611665/datasets/export for details.
DOI: 10.5281/zenodo.18238495
title: Telmatoblechnum serrulatum (Rich.) Perrie, D.J.Ohlsen & Brownsey. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238496
title: Telmatoblechnum serrulatum (Rich.) Perrie, D.J.Ohlsen & Brownsey. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238500
title: Thelypteridaceae Ching ex Pic.Serm. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238501
title: Thelypteridaceae Ching ex Pic.Serm. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.15468/dl.mz57n2
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.11.104_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 15 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007813-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14723456
title: Metabolite MR
DOI: 10.5281/zenodo.14723455
title: Metabolite MR
DOI: 10.5281/zenodo.18238505
title: Trichomanes L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238504
title: Trichomanes L. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.6084/m9.figshare.31053529
title: Supplementary Materials for:Genotype–Phenotype Correlation of Biallelic DUOX2 Mutations in Transient and Permanent Congenital Hypothyroidism.

description: Supplementary Data for: "Genotypic and Phenotypic Comparison in Patients with Biallelic DUOX2 Mutations: Differentiating Transient and Permanent Congenital Hypothyroidism"
DOI: 10.6084/m9.figshare.31053529.v3
title: Supplementary Materials for:Genotype–Phenotype Correlation of Biallelic DUOX2 Mutations in Transient and Permanent Congenital Hypothyroidism.

description: Supplementary Data for: "Genotypic and Phenotypic Comparison in Patients with Biallelic DUOX2 Mutations: Differentiating Transient and Permanent Congenital Hypothyroidism"
DOI: 10.6084/m9.figshare.31053529.v2
title: Supplementary Materials for: Genotypic and Phenotypic Comparison in Patients with Biallelic DUOX2 Mutations: Differentiating Transient and Permanent Congenital Hypothyroidism

description: Supplementary Data for: "Genotypic and Phenotypic Comparison in Patients with Biallelic DUOX2 Mutations: Differentiating Transient and Permanent Congenital Hypothyroidism"
DOI: 10.15468/dl.zyj4re
title: Occurrence Download

description: A dataset containing 1268 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Antarctic Krill occurrence data from US AMLR \"US Antarctic Marine Living Resources\" Program"
 ]
}

 The dataset includes 1268 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007814-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18238509
title: Trichomanes anadromum Rosenst. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238508
title: Trichomanes anadromum Rosenst. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.48436/bke4a-sq149
title: The data for "Single-band fluorides akin to infinite-layer cuprate superconductors"

description: This repository contains the data behind the figures of the paper "Single-band fluorides akin to infinite-layer cuprate superconductors" by  Wenfeng Wu et al.

Research context: Single-band fluorides studied by density functional and dynamical mean field theory as well as dynamical vertex approximation.

Purpose of the data: to make the results and figures of the aforementioned article reproducible by other groups

Relation to the article: the repository contains the data used to generate the figures of the aforementioned article
DOI: 10.48436/x5zsx-4rz78
title: The data for "Single-band fluorides akin to infinite-layer cuprate superconductors"

description: This repository contains the data behind the figures of the paper "Single-band fluorides akin to infinite-layer cuprate superconductors" by  Wenfeng Wu et al.

Research context: Single-band fluorides studied by density functional and dynamical mean field theory as well as dynamical vertex approximation.

Purpose of the data: to make the results and figures of the aforementioned article reproducible by other groups

Relation to the article: the repository contains the data used to generate the figures of the aforementioned article
DOI: 10.15468/dl.rqju5y
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"USA.11.105_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007816-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18238514
title: Trichomanes cristatum Kaulf. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37
DOI: 10.5281/zenodo.18238515
title: Trichomanes cristatum Kaulf. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:37