cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9jyw8n
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thismia inconspicua Sochor & Dancák"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124096-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.drf3rq
title: Occurrence Download

description: A dataset containing 90840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Culicidae"
 ]
}

 The dataset includes 90840 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124073-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unj6jr
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tephrosia reptans Baker"
 ]
}

 The dataset includes 147 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124097-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qrdmw7
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum subekmanii Rail."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124098-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dnapc4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum fedtschenkoi Hand.-Mazz."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124099-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5nqhsv
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Timonius subavenis (Valeton) S.P.Darwin"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124100-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmd473
title: Occurrence Download

description: A dataset containing 374 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teucrium salviastrum Schreb."
 ]
}

 The dataset includes 374 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124102-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.em8waq
title: Occurrence Download

description: A dataset containing 260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((41.61221 -6.27994,172.59504 -6.27994,172.59504 46.04596,41.61221 46.04596,41.61221 -6.27994))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Manis javanica Desmarest, 1822"
 ]
}

 The dataset includes 260 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124101-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3cmqj2
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thismia javanica J.J.Sm."
 ]
}

 The dataset includes 11 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124103-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9axfxv
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum fennobalticum Sonck & Y.Mäkinen"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124104-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgx7hh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum subelatum G.E.Haglund ex Soest"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124105-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrvt8h
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Timonius subcoriaceus Valeton"
 ]
}

 The dataset includes 18 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124107-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qghjx3
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tephrosia retamoides (Baker) Soler."
 ]
}

 The dataset includes 62 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124106-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.btz5dz
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Teucrium sandrasicum O.Schwarz"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124108-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6dfan9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thismia kelabitiana Dancák, Hrones & Sochor"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124109-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ucgbdp
title: Occurrence Download

description: A dataset containing 111 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taraxacum subericinum Hagend., Soest & Zevenb."
 ]
}

 The dataset includes 111 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0124110-240321170329656/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.26943987.v1
title: Additional file 1 of Genomic variation in Plasmodium relictum (lineage SGS1) and its implications for avian malaria infection outcomes: insights from experimental infections and genome-wide analysis

description: Supplementary Material 1.
DOI: 10.6084/m9.figshare.26943957.v1
title: Additional file 4 of CCT3/ACTN4/TFRC axis protects hepatocellular carcinoma cells from ferroptosis by inhibiting iron endocytosis

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26943987
title: Additional file 1 of Genomic variation in Plasmodium relictum (lineage SGS1) and its implications for avian malaria infection outcomes: insights from experimental infections and genome-wide analysis

description: Supplementary Material 1.
DOI: 10.5281/zenodo.13683340
title: A Dataset with Synthetic Landing Trajectories for Zurich Airport

description: The archive contains synthetic datasets in npy format generated using a TimeGAN-based model designed to capture a range of aircraft landing trajectories at Zurich airport across different operational scenarios and environmental conditions. Each dataset consists of multiple groups representing distinct patterns or behaviors in the trajectory data. The trajectories are segmented in clusters, and to some of them a smoothing filter was applied.

The datasets incorporate a range of variables critical for modeling aircraft landing behaviors. Continuous variables such as longitude, latitude, and altitude exhibit multimodal distributions, capturing different operational phases and conditions within each cluster. The data is stored in an array format with dimensions (number of samples, sequence length, feature dimensions). Here, the number of samples corresponds to the total number of recorded flight trajectories included in the dataset, while the sequence length represents the duration or the number of time steps over which each trajectory is recorded. The feature dimensions denote the various variables (state vector) measured at each time step, consisting of longitude, latitude and altitude. Categorical variables, such as runway identifiers and cluster labels, follow distributions that reflect operational frequencies, with certain clusters or runways being more common under specific conditions. 

The archive contains the following files:

- 5clust0.npy, 5clust1.npy, 5clust2.npy, 5clust3.np & 5clust4.npy (5 clusters of landing trajectories separated)- ma_5clust0.npy, ma_5clust1.npy, ma_5clust2.npy, ma_5clust3.np & ma_5clust4.npy (5 clusters of landing trajectories separated, moving average filter applied)- ma_3clust0.npy, ma_3clust1.npy & ma_3clust2.npy (3 clusters  of landing trajectories separated, moving average filter applied)- run28_syn.npy & run24_syn.npy (groups of landing trajectories per runway)- ma_run28_syn.npy & ma_run24_syn.npy (groups of landing trajectories per runway, moving average filter applied)- go_around_synthetic.npy (go-around landing trajectories on runway 14)
DOI: 10.5281/zenodo.13683341
title: A Dataset with Synthetic Landing Trajectories for Zurich Airport

description: The archive contains synthetic datasets in npy format generated using a TimeGAN-based model designed to capture a range of aircraft landing trajectories at Zurich airport across different operational scenarios and environmental conditions. Each dataset consists of multiple groups representing distinct patterns or behaviors in the trajectory data. The trajectories are segmented in clusters, and to some of them a smoothing filter was applied.

The datasets incorporate a range of variables critical for modeling aircraft landing behaviors. Continuous variables such as longitude, latitude, and altitude exhibit multimodal distributions, capturing different operational phases and conditions within each cluster. The data is stored in an array format with dimensions (number of samples, sequence length, feature dimensions). Here, the number of samples corresponds to the total number of recorded flight trajectories included in the dataset, while the sequence length represents the duration or the number of time steps over which each trajectory is recorded. The feature dimensions denote the various variables (state vector) measured at each time step, consisting of longitude, latitude and altitude. Categorical variables, such as runway identifiers and cluster labels, follow distributions that reflect operational frequencies, with certain clusters or runways being more common under specific conditions. 

The archive contains the following files:

- 5clust0.npy, 5clust1.npy, 5clust2.npy, 5clust3.np & 5clust4.npy (5 clusters of landing trajectories separated)- ma_5clust0.npy, ma_5clust1.npy, ma_5clust2.npy, ma_5clust3.np & ma_5clust4.npy (5 clusters of landing trajectories separated, moving average filter applied)- ma_3clust0.npy, ma_3clust1.npy & ma_3clust2.npy (3 clusters  of landing trajectories separated, moving average filter applied)- run28_syn.npy & run24_syn.npy (groups of landing trajectories per runway)- ma_run28_syn.npy & ma_run24_syn.npy (groups of landing trajectories per runway, moving average filter applied)- go_around_synthetic.npy (go-around landing trajectories on runway 14)
DOI: 10.6084/m9.figshare.26943957
title: Additional file 4 of CCT3/ACTN4/TFRC axis protects hepatocellular carcinoma cells from ferroptosis by inhibiting iron endocytosis

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26944293
title: Additional file 2 of Single-cell RNA sequencing identifies inherent abnormalities of adipose-derived stem cells from nonlesional sites of patients with localized scleroderma

description: Additional file 2: Table S2. Molecular signature for each cell type or cluster.
DOI: 10.6084/m9.figshare.26943894.v1
title: Additional file 2 of Development of a biomarker prediction model for post-trauma multiple organ failure/dysfunction syndrome based on the blood transcriptome

description: Additional file 2
DOI: 10.6084/m9.figshare.26944305.v1
title: Additional file 6 of Single-cell RNA sequencing identifies inherent abnormalities of adipose-derived stem cells from nonlesional sites of patients with localized scleroderma

description: Additional file 6: Table S6. Differentially expressed genes between CD55high and CD55low ASCs.
DOI: 10.6084/m9.figshare.26944074.v1
title: Additional file 2 of Identification of a specific APOE transcript and functional elements associated with Alzheimer’s disease

description: Supplementary Tables: Table S1. Summary statistics for each RNA-Seq dataset. Supplementary Table S2. Analysis models. Supplementary Table S3. APOE genotypes are derived from two APOE SNPs. Supplementary Table S4. APOE expression trajectory during brain development in BrainSpan data. Supplementary Table S5. Summary statistics of GWAS, eQTL, mQTL across DLPFC, PCC, and AC brain regions at the APOE locus. Supplementary Table S6. Association of candidate SNPs with APOE gene level expression. Supplementary Table S7. Association of candidate SNPs with abundance of specific APOE gene transcripts. Supplementary Table S8. Association of APOE2,3,4 determining SNPs (rs429358 and rs7412) with features including APOE gene expression, APOE transcripts expression, and DNA methylation. Supplementary Table S9. Differential analysis of APOE gene between Alzheimer’s disease and controls across ROSMAP DLPFC, AC, and PCC brain regions; between schizophrenia/bipolar disorders/major depression disorders (MDD) and controls in LIBD Caucasian and African Americans. Supplementary Table S10. Differential analysis of junction between APOE exon 1 and exon 2 between Alzheimer's disease and controls across ROSMAP DLPFC, AC, and PCC brain regions; between schizophrenia/bipolar disorders/major depression disorders (MDD) and controls in LIBD Caucasian and African Americans. Supplementary Table S11. APOE expression trajectory during brain development in LIBD data. Supplementary Table S12. Signal peptide prediction of APOE transcripts. Supplementary Table S13. APOE positive selection LRT and positive selection sites. Supplementary Table S14. Differential expression ofAPOE gene in six major brain cell types across diverse diagnoses. Supplementary Table S15. Transcriptional factors binding to our candidate SNPs. Supplementary Table S16. Summary-based Mendelian randomization (SMR) of rs157580 and rs439401 with APOE jxn1.2.2 transcript. Supplementary Table S17. GWAS summary statistics of candidate SNPs.
DOI: 10.6084/m9.figshare.26944308.v1
title: Additional file 7 of Single-cell RNA sequencing identifies inherent abnormalities of adipose-derived stem cells from nonlesional sites of patients with localized scleroderma

description: Additional file 7: Table S7. Intercellular communications in the SVF from patients with LoS and healthy donors inferred by Cellchat.
DOI: 10.5281/zenodo.13643306
title: Viral catalogue from faecal microbiomes of great tits and blue tits

description: Overview:

The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited data on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). High and Medium quality Metagenome Assembled Genomes (MAGs) were assembled from these metagenomes and are made available as a catalogue in this archive.

Methods:

Metagenomic reads were trimmed, and quality controlled using FastP configured to a minimum phred score of 20 and minimum length of 50 bp. The potential viral and plasmidic sequences were retrieved from the assembled contigs using GeNomad v1.8.0 (Camargo et al. 2023) and the quality of these viral sequences was then assessed using CheckV v 1.0.3 (Nayfach et al. 2021) using the checkV database v 1.5. Putative viral sequences longer than 1000bp carrying at least one hallmark viral gene or no detectable cellular genes were considered in this analysis. The viral sequences were clustered into species-level vOTU clusters using mmseqs2 v2.13 using an identity threshold of 95% over 75% of the longest sequence. For viral species identified as Caudoviral, the potential host was inferred using iPhop v1.3.3 (Roux et al 2023).

Files:



The vOTU_characteristics.csv table contains the sequence characteristics from CheckV and the viral taxonomy determined by GeNomad

The vOTU_PredictedHost.csv table contains the viral sequence inferred host from iPhop

The vOTU_representatives.fasta file contains the fasta sequence of the vOTU representatives
DOI: 10.5281/zenodo.13643307
title: Viral catalogue from faecal microbiomes of great tits and blue tits

description: Overview:

The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited data on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). High and Medium quality Metagenome Assembled Genomes (MAGs) were assembled from these metagenomes and are made available as a catalogue in this archive.

Methods:

Metagenomic reads were trimmed, and quality controlled using FastP configured to a minimum phred score of 20 and minimum length of 50 bp. The potential viral and plasmidic sequences were retrieved from the assembled contigs using GeNomad v1.8.0 (Camargo et al. 2023) and the quality of these viral sequences was then assessed using CheckV v 1.0.3 (Nayfach et al. 2021) using the checkV database v 1.5. Putative viral sequences longer than 1000bp carrying at least one hallmark viral gene or no detectable cellular genes were considered in this analysis. The viral sequences were clustered into species-level vOTU clusters using mmseqs2 v2.13 using an identity threshold of 95% over 75% of the longest sequence. For viral species identified as Caudoviral, the potential host was inferred using iPhop v1.3.3 (Roux et al 2023).

Files:



The vOTU_characteristics.csv table contains the sequence characteristics from CheckV and the viral taxonomy determined by GeNomad

The vOTU_PredictedHost.csv table contains the viral sequence inferred host from iPhop

The vOTU_representatives.fasta file contains the fasta sequence of the vOTU representatives
DOI: 10.6084/m9.figshare.26944155.v1
title: Additional file 6 of Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.26944299
title: Additional file 4 of Single-cell RNA sequencing identifies inherent abnormalities of adipose-derived stem cells from nonlesional sites of patients with localized scleroderma

description: Additional file 4: Table S4. Dysregulated pathways in ASCs from nonlesional sites of patients with LoS detected by gene set enrichment analysis.
DOI: 10.5281/zenodo.13692222
title: Actinidia chinensis cv. 'Hayward' Flower Dataset 2024 (augmented version)

description: This dataset is an augmented version of an existing dataset (10.5281/zenodo.13692223), which comprises images annotated according to Actinidia flower gender. The images were acquired in Quinta do Carrazedo (41.32170534304873, -8.661668130688255) with an iPhone Xr with a single camera and a resolution of 640x640 pixels. The dataset includes images of female and male flowers of Actinidia chinensis cv. 'Hayward'.

The augmented images and their annotations are stored in an archive with the following structure:

main_directory/



annotations/



pascalvoc/



PascalVOC annotation files

...



yolo/



YOLO annotation files

...





images/



Image files

...




Each annotation file links to its image by the file name, so if an image is named "TL_Actinidia_Flower_2024_*_type_of_augmentation.jpg", its annotation files are named "TL_Actinidia_Flower_2024_*_type_of_augmentation.xml" (for PascalVOC format) and "TL_Actinidia_Flower_2024_*type_of_augmentation.txt" (for YOLO format) where in the place of the asterisks are numbers.

Also, the subsets that were used to train, validate and test some deep learning models are available in three .TXT files (train.txt, val.txt and test.txt), where each file line corresponds to an image and annotation name.
DOI: 10.6084/m9.figshare.26944152
title: Additional file 5 of Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum

description: Supplementary Material 5
DOI: 10.5281/zenodo.10790404
title: Actinidia chinensis cv. 'Hayward' Flower Dataset 2024 (augmented version)

description: This dataset is an augmented version of an existing dataset (10.5281/zenodo.13692223), which comprises images annotated according to Actinidia flower gender. The images were acquired in Quinta do Carrazedo (41.32170534304873, -8.661668130688255) with an iPhone Xr with a single camera and a resolution of 640x640 pixels. The dataset includes images of female and male flowers of Actinidia chinensis cv. 'Hayward'.

The augmented images and their annotations are stored in an archive with the following structure:

main_directory/



annotations/



pascalvoc/



PascalVOC annotation files

...



yolo/



YOLO annotation files

...





images/



Image files

...




Each annotation file links to its image by the file name, so if an image is named "TL_Actinidia_Flower_2024_*_type_of_augmentation.jpg", its annotation files are named "TL_Actinidia_Flower_2024_*_type_of_augmentation.xml" (for PascalVOC format) and "TL_Actinidia_Flower_2024_*type_of_augmentation.txt" (for YOLO format) where in the place of the asterisks are numbers.

Also, the subsets that were used to train, validate and test some deep learning models are available in three .TXT files (train.txt, val.txt and test.txt), where each file line corresponds to an image and annotation name.