cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10782890
title: Duke Lung Cancer Screening Dataset 2024

description: Note - This is part 1 of the dataset.Part 1 can be found at : https://zenodo.org/records/13799069 Part 2 can be found at : https://zenodo.org/records/12784601Part 3 can be found at : https://zenodo.org/records/14659131

Background: Lung cancer risk classification is an increasingly important area of research as low-dose thoracic CT screening programs have become standard of care for patients at high risk for lung cancer. There is limited availability of large, annotated public databases for the training and testing of algorithms for lung nodule classification.

Methods: Screening chest CT scans done between January 1, 2015 and June 30, 2021 at Duke University Health System were considered for this study. Efficient nodule annotation was performed semi-automatically by using a publicly available deep learning nodule detection algorithm trained on the LUNA16 dataset to identify initial candidates, which were then accepted based on nodule location in the radiology text report or manually annotated by a medical student and a fellowship-trained cardiothoracic radiologist.

Results: The dataset contains 1613 CT volumes with 2487 annotated nodules, selected from a total dataset of 2061 patients, with the remaining data reserved for future testing. Radiologist spot-checking confirmed the semi-automated annotation had an accuracy rate of >90%.

Conclusions: The Duke Lung Cancer Screening Dataset 2024 is the first large dataset for CT screening for lung cancer reflecting the use of current CT technology. This represents a useful resource of lung cancer risk classification research, and the efficient annotation methods described for its creation may be used to generate similar databases for research in the future.Dataset part Details:Part 1: DLCS subset 1 to 7 and, metadata and Annotations.Part 2: DLCS subset 8,9 and CT image info metadata.Part 3: DLCS subset 10.

Updates and Versions:



Part 1, Version 1.0 (Published on [03/05/2024]): Released initial dataset, including partial data subsets 1 to 7 and 3D bounding box annotations of the lung nodules.

Part 1, Version 1.1 (Published on [09/19/2024]): Added metadata file (DLCSD24_metadata_v1.1.xlsx) and updated the dataset description and title. 10.5281/zenodo.13799069

Part 2, Version 1.0 (Published on [02/04/2025]): Released DLCS subset 8,9, CT image info metadata (DLCSD24_CT_ImageInfo_v1.csv and metadata documentation).

Part 3, Version 1.0 (Published on [02/04/2025]): Released DLCS subset 10.


Code Repository:To support reproducible open-access research and benchmarking, we have shared several pre-trained models and baseline results in a GitHub and GitLab repository.

GitLab: https://gitlab.oit.duke.edu/cvit-public/ai_lung_health_benchmarkingGitHub: https://github.com/fitushar/AI-in-Lung-Health-Benchmarking-Detection-and-Diagnostic-Models-Across-Multiple-CT-Scan-Datasets

Funding:This work was supported by the Duke Department of Radiology Charles E. Putman Vision Award, NIH/NIBIB P41-EB028744, and NIH/NCI R01-CA261457.
DOI: 10.5281/zenodo.14813948
title: Dataset Media coverage of bots for politics in Mexico

description: This dataset refers to the national media coverage on the use of Bots for politics in Mexico
DOI: 10.5281/zenodo.14813949
title: Dataset Media coverage of bots for politics in Mexico

description: This dataset refers to the national media coverage on the use of Bots for politics in Mexico
DOI: 10.5281/zenodo.14814178
title: Scientific Analysis of Face-Like Feature on Mars: Comparative Study of Potential Artificial Structures

description: This research presents an in-depth scientific analysis of a face-like anomaly detected in NASA's MOC Image E1000462, a high-resolution Mars Orbiter Camera (MOC) photograph. Through a combination of AI-based symmetry detection, 3D depth mapping, erosion modeling, and comparative analysis, this study examines whether the formation is a naturally occurring geological structure or an artificial remnant of possible past civilizations.

 

Key findings include:

 

A Structural Similarity Index (SSIM) score of 0.628, suggesting a notable bilateral symmetry.

 

3D depth mapping confirms a convex elevation pattern, reinforcing its distinction from standard impact craters.

 

Erosion modeling suggests a more resistant composition, indicating potential subsurface extensions.

 

Comparative analysis with the well-known "Face on Mars" in Cydonia reveals similar morphological characteristics.

 

 

The report concludes that this feature warrants further investigation and recommends that NASA and ESA conduct targeted HiRISE imaging and MARSIS radar scans to determine the presence of potential subsurface structures.
DOI: 10.5281/zenodo.14814179
title: Scientific Analysis of Face-Like Feature on Mars: Comparative Study of Potential Artificial Structures

description: This research presents an in-depth scientific analysis of a face-like anomaly detected in NASA's MOC Image E1000462, a high-resolution Mars Orbiter Camera (MOC) photograph. Through a combination of AI-based symmetry detection, 3D depth mapping, erosion modeling, and comparative analysis, this study examines whether the formation is a naturally occurring geological structure or an artificial remnant of possible past civilizations.

 

Key findings include:

 

A Structural Similarity Index (SSIM) score of 0.628, suggesting a notable bilateral symmetry.

 

3D depth mapping confirms a convex elevation pattern, reinforcing its distinction from standard impact craters.

 

Erosion modeling suggests a more resistant composition, indicating potential subsurface extensions.

 

Comparative analysis with the well-known "Face on Mars" in Cydonia reveals similar morphological characteristics.

 

 

The report concludes that this feature warrants further investigation and recommends that NASA and ESA conduct targeted HiRISE imaging and MARSIS radar scans to determine the presence of potential subsurface structures.
DOI: 10.5281/zenodo.10607024
title: MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification

description: These files provide supplementary data underlying the article doi.org/10.1093/bioinformatics/btae601 (see Figure 1 of the article):



37345_filtered_training_and_test_genomes_sequence_files.tar.gz_1 to 37345_filtered_training_and_test_genomes_sequence_files.tar.gz_6: Merge them into a single file using the cat command. The folder produced by decompressing this file contains the filtered RefSeq sequence files of all 37345 training and test genomes, which were used to build the uniform reference database and generate the test reads (The filenames are in the file 37345_filtered_training_and_test_genomes_list.txt at https://dx.doi.org/10.5281/zenodo.10568965).
DOI: 10.5281/zenodo.10607025
title: MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification

description: These files provide supplementary data underlying the article doi.org/10.1093/bioinformatics/btae601 (see Figure 1 of the article):



37345_filtered_training_and_test_genomes_sequence_files.tar.gz_1 to 37345_filtered_training_and_test_genomes_sequence_files.tar.gz_6: Merge them into a single file using the cat command. The folder produced by decompressing this file contains the filtered RefSeq sequence files of all 37345 training and test genomes, which were used to build the uniform reference database and generate the test reads (The filenames are in the file 37345_filtered_training_and_test_genomes_list.txt at https://dx.doi.org/10.5281/zenodo.10568965).
DOI: 10.15468/dl.3yqppm
title: Occurrence Download

description: A dataset containing 122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Urospatha grandis Schott"
 ]
}

 The dataset includes 122 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016589-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14814253
title: Quantitative and large-scale investigation of human TCR-HLA Cross-Reactivity

description: This dataset consists of two files: class1_df.csv and class2_df.csv. Collectively, they document 9 million TCR-HLA pairs exhibiting significant co-occurrence patterns identified across a mixed cohort of 1,603 samples. The class1_df.csv file contains TCRs associated with HLA class I alleles, while class2_df.csv records TCRs associated with HLA class II alleles.
DOI: 10.5281/zenodo.14814254
title: Quantitative and large-scale investigation of human TCR-HLA Cross-Reactivity

description: This dataset consists of two files: class1_df.csv and class2_df.csv. Collectively, they document 9 million TCR-HLA pairs exhibiting significant co-occurrence patterns identified across a mixed cohort of 1,603 samples. The class1_df.csv file contains TCRs associated with HLA class I alleles, while class2_df.csv records TCRs associated with HLA class II alleles.
DOI: 10.5281/zenodo.14814190
title: Dependency Dilemmas: Replication Package

description: The Maven ecosystem forms the backbone of Java dependency management, hosting artifacts that vary significantly in their adoption, security, and ecosystem roles. Artifact reuse is fundamental in software development, with ecosystems like Maven facilitating this process. However, prior studies predominantly analyzed popular artifacts with numerous dependencies, leaving those without incoming dependencies (i.e., independent artifacts) unexplored. In this study, we analyzed 658,078 artifacts, of which 635,003 had at least one release. Among these, 93,101 artifacts (15.4%) were identified as independent (in-degree = 0), while the rest were classified as dependent. We looked at the impact of individual artifacts using PageRank and out- degree centrality and discovered that independent artifacts were very important to the ecosystem. Further analysis across 18 different metrics revealed several advantages and comparability of independent artifacts with dependent artifacts: comparable popularity (25.58 vs. 7.30), fewer vulnerabilities (60 CVEs vs. 179 CVEs), and zero propagated vulnerabilities. Based on these results, it appears that independent artifacts make a difference in the ecosystem and give developers a safe, self-contained alternative to traditional dependencies. These findings suggest that independent artifacts might be a beneficial choice for dependencies but have some maintainability issues. Therefore,developers should carefully incorporate independent artifacts into their projects, and artifact maintainers should prioritize this group of artifacts to mitigate the risk of transitive vulnerability propagation and improve software sustainability. The replication package of our study is available online [1].
DOI: 10.5281/zenodo.14814191
title: Dependency Dilemmas: Replication Package

description: The Maven ecosystem forms the backbone of Java dependency management, hosting artifacts that vary significantly in their adoption, security, and ecosystem roles. Artifact reuse is fundamental in software development, with ecosystems like Maven facilitating this process. However, prior studies predominantly analyzed popular artifacts with numerous dependencies, leaving those without incoming dependencies (i.e., independent artifacts) unexplored. In this study, we analyzed 658,078 artifacts, of which 635,003 had at least one release. Among these, 93,101 artifacts (15.4%) were identified as independent (in-degree = 0), while the rest were classified as dependent. We looked at the impact of individual artifacts using PageRank and out- degree centrality and discovered that independent artifacts were very important to the ecosystem. Further analysis across 18 different metrics revealed several advantages and comparability of independent artifacts with dependent artifacts: comparable popularity (25.58 vs. 7.30), fewer vulnerabilities (60 CVEs vs. 179 CVEs), and zero propagated vulnerabilities. Based on these results, it appears that independent artifacts make a difference in the ecosystem and give developers a safe, self-contained alternative to traditional dependencies. These findings suggest that independent artifacts might be a beneficial choice for dependencies but have some maintainability issues. Therefore,developers should carefully incorporate independent artifacts into their projects, and artifact maintainers should prioritize this group of artifacts to mitigate the risk of transitive vulnerability propagation and improve software sustainability. The replication package of our study is available online [1].
DOI: 10.15468/dl.e9ua86
title: Occurrence Download

description: A dataset containing 290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Sterculia apetala (Jacq.) H.Karst.)",
 "BasisOfRecord is one of (Human Observation, Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Continent is North America"
 ]
}

 The dataset includes 290 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016591-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c858bx
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis dinteri Stapf",
 "Continent is Africa"
 ]
}

 The dataset includes 160 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001578-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ta6znk
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((119.2927 25.66974, 119.4466 25.66974, 119.4466 25.74548, 119.2927 25.74548, 119.2927 25.66974))",
 "Year is greater than or equal to 2013",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001579-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2s24tk
title: Occurrence Download

description: A dataset containing 21598841 species occurrences available in GBIF matching the query:
{
 "Country" : [
 "is Chinese Taipei"
 ]
}

 The dataset includes 21598841 records from 1338 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001553-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.chj7c5
title: Occurrence Download

description: A dataset containing 344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis exasperata Peter",
 "Continent is Africa"
 ]
}

 The dataset includes 344 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001580-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hd5rk
title: Occurrence Download

description: A dataset containing 1333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((112.4946 -8.098015, 112.7605 -8.098015, 112.7605 -7.789546, 112.4946 -7.789546, 112.4946 -8.098015))",
 "Year is greater than or equal to 2013",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 1333 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001581-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hgvxep
title: Occurrence Download

description: A dataset containing 491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dryopteris aemula (Aiton) Kuntze",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 491 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001583-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mx6ejy
title: Occurrence Download

description: A dataset containing 2090 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Geometry POLYGON((-74.90429 8.5584,-76.77666 6.50425,-76.43127 2.90495,-74.19534 1.70518,-69.71303 5.11437,-72.74177 6.91574,-73.19622 8.69721,-74.90429 8.5584))",
 "TaxonKey is Procyon cancrivorus G"
 ]
}

 The dataset includes 2090 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001582-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2knpq4
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis fimbrillata Cope",
 "Continent is Africa"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001586-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.un45cc
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is NHMO Mammal collection",
 "TaxonKey is Petropseudes dahli (Collett, 1895)"
 ]
}

 The dataset includes 18 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001588-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2wmkp
title: Occurrence Download

description: A dataset containing 1587 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((121.2204 28.43394, 121.5594 28.43394, 121.5594 28.70587, 121.2204 28.70587, 121.2204 28.43394))",
 "Year is greater than or equal to 2013",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 1587 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001587-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qmh4jn
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eragrostis flavicans Rendle",
 "Continent is Africa"
 ]
}

 The dataset includes 70 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001590-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m8yw2a
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((121.2896 28.34902, 121.4097 28.34902, 121.4097 28.47642, 121.2896 28.47642, 121.2896 28.34902))",
 "Year is greater than or equal to 2013",
 "HasGeospatialIssue is false",
 "TaxonKey is Aves",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001592-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5wgva2
title: Occurrence Download

description: A dataset containing 9787 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Orthilia secunda (L.) House",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 9787 records from 310 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001591-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0181424.10fu
title: SH0181424.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0181425.10fu
title: SH0181425.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.