cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fmjed3
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Papua New Guinea",
 "Country is Indonesia",
 "Country is Brunei Darussalam",
 "Country is Malaysia",
 "Country is Philippines",
 "Country is Singapore",
 "Country is Timor-Leste"
 ]
 },
 "HasCoordinate is true",
 "TaxonKey is Cystodium J.Sm.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 273 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004441-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10964844
title: AI research space conditions country academic performance

description: Data used for generating AI research space
DOI: 10.15468/dl.sx44xj
title: Occurrence Download

description: A dataset containing 475 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Callimedusa tomopterna (Cope, 1868)"
 ]
}

 The dataset includes 475 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021002-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v54w5x
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chinese Taipei",
 "TaxonKey is Leucogeranus leucogeranus (Pallas, 1773)"
 ]
}

 The dataset includes 345 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008296-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10964843
title: AI research space conditions country academic performance

description: Data used for generating AI research space
DOI: 10.5281/zenodo.10976825
title: AI research space conditions country academic performance

description: Data used for generating AI research space
DOI: 10.15468/dl.sknu7c
title: Occurrence Download

description: A dataset containing 515120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plantae",
 "Country is Argentina"
 ]
}

 The dataset includes 515120 records from 185 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004442-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pc28sd
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.03028 21.30723,-89.01752 21.31013,-89.0162 21.32432,-89.02415 21.32551,-89.02314 21.32973,-89.0155 21.32817,-89.0149 21.33342,-89.01162 21.333,-89.01127 21.3364,-89.00998 21.33645,-89.00969 21.34017,-88.99812 21.33946,-88.9988 21.34592,-88.99244 21.34539,-88.9915 21.36364,-88.99819 21.36246,-89.00974 21.35391,-89.00968 21.35518,-89.01747 21.35393,-89.0131 21.35355,-89.01412 21.3465,-89.02121 21.34699,-89.02508 21.34732,-89.02522 21.35015,-89.02965 21.35054,-89.02962 21.34485,-89.0512 21.34642,-89.05099 21.3434,-89.05549 21.34379,-89.05549 21.34233,-89.07034 21.34314,-89.07044 21.34135,-89.07334 21.34171,-89.07501 21.32524,-89.05832 21.32381,-89.05842 21.3219,-89.05621 21.32112,-89.0505 21.3208,-89.05099 21.31762,-89.03803 21.31665,-89.03684 21.32916,-89.02588 21.32772,-89.03028 21.30723))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 14 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0198450-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t9phwt
title: Occurrence Download

description: A dataset containing 119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 {
 "or" : [
 "TaxonKey is Lithophyllum corallinae (P.Crouan & H.Crouan) Heydr.",
 "TaxonKey is Lithophyllum depressum A.B.Villas-Boas",
 "TaxonKey is Lithophyllum frondosum (Dufour) G.Furnari, Cormaci & Alongi",
 "TaxonKey is Lithophyllum stictiforme (Areschoug) Hauck",
 "TaxonKey is Lithophyllum johansenii Woelk. & S.J.Campb.",
 "TaxonKey is Lithophyllum margaritae (Hariot) Heydr.",
 "TaxonKey is Mesophyllum erubescens (Foslie) M.Lemoine",
 "TaxonKey is Lithothamnion superpositum Foslie",
 "TaxonKey is Lithothamnion brasiliense Foslie"
 ]
 }
 ]
}

 The dataset includes 119 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007686-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0dh2oj
title: Occurrence Download

description: A dataset containing 582 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Digitaria argillacea (Hitchc. & Chase) Fernald"
 ]
}

 The dataset includes 582 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004442-150831095807960/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umel3q
title: Occurrence Download

description: A dataset containing 283 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Callosobruchus chinensis (Linnaeus, 1758)"
 ]
}

 The dataset includes 283 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0027434-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.61nymt
title: Occurrence Download

description: A dataset containing 330 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Antennarius commerson (Latreille, 1804)"
 ]
}

 The dataset includes 330 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004442-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10977091
title: Tourist Perceptions of Campina de Faro

description: Survey on tourists’ familiarity with and associations with the name ‘Campina de Faro’ carried out in Algarve, Portugal, November 29 – October 2nd.

The aim of the survey was to provide a stronger basis for evaluating, utilizing, and generalizing the (preliminary) results gained and innovations tested by the Portuguese pilot to enhance their applicability also to other pilots and stakeholder networks involved.
DOI: 10.5281/zenodo.10977044
title: The Noise Matters In Destinations! Case of The Historical Galata Tower Region Residents' Happiness, Stress Levels , and Neighborhood Perceptions in Istanbul
DOI: 10.5281/zenodo.10977088
title: THE "BUSINESS EXCELLENCE" MECHANISM FOR ASSESSING WOMEN'S ENTREPRENEURIAL ABILITIES AND ITS METHODOLOGICAL FOUNDATIONS.
DOI: 10.5281/zenodo.10976870
title: Trees and Alignments for: Expanding Ventilago to incorporate Smythea: new combinations in Ventilago (Rhamnaceae)

description: Alignments, gene trees, and species trees from the phylogenomic analyses in Miller et al. (in prep.), Expanding Ventilago to incorporate Smythea: new combinations in Ventilago (Rhamnaceae).

Raw sequence data are deposited in Sequence Read Achive (SRA) data available on NCBI server under BioProject number PRJNA1100519. Scripts for all phylogenomic analyses were followed https://github.com/pebgroup/Maesa_sptree.
DOI: 10.5281/zenodo.10976871
title: Trees and Alignments for: Expanding Ventilago to incorporate Smythea: new combinations in Ventilago (Rhamnaceae)

description: Alignments, gene trees, and species trees from the phylogenomic analyses in Miller et al. (in prep.), Expanding Ventilago to incorporate Smythea: new combinations in Ventilago (Rhamnaceae).

Raw sequence data are deposited in Sequence Read Achive (SRA) data available on NCBI server under BioProject number PRJNA1100519. Scripts for all phylogenomic analyses were followed https://github.com/pebgroup/Maesa_sptree.
DOI: 10.5281/zenodo.10977090
title: Tourist Perceptions of Campina de Faro

description: Survey on tourists’ familiarity with and associations with the name ‘Campina de Faro’ carried out in Algarve, Portugal, November 29 – October 2nd.

The aim of the survey was to provide a stronger basis for evaluating, utilizing, and generalizing the (preliminary) results gained and innovations tested by the Portuguese pilot to enhance their applicability also to other pilots and stakeholder networks involved.
DOI: 10.15468/dl.qcpjz3
title: Occurrence Download

description: A dataset containing 25839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The cnidarians collection (IK) of the Muséum national d'Histoire naturelle (MNHN - Paris)"
 ]
}

 The dataset includes 25839 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008303-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10149720
title: Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle

description: Nutrient availability during early stages of development (embryogenesis and the first week of life) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu+ and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu+ line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu+ and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients.
DOI: 10.5281/zenodo.10974783
title: 4DHydro_Results01_Tetis_Po_7p5sec_daily_exp10_19900101_20221231

description: Modeling results with TETIS software, for Po River with a spatial resolution of 7.5 sec, and temporal resolution daily. Experiment 10

Includes results for the following variables:



Catchement mask.

Upstream catchment area in square meters

Discharge flux in m-3 s-1

Volumetric soil moisture content in percentage
DOI: 10.5281/zenodo.10977045
title: The Noise Matters In Destinations! Case of The Historical Galata Tower Region Residents' Happiness, Stress Levels , and Neighborhood Perceptions in Istanbul
DOI: 10.5281/zenodo.10977087
title: THE "BUSINESS EXCELLENCE" MECHANISM FOR ASSESSING WOMEN'S ENTREPRENEURIAL ABILITIES AND ITS METHODOLOGICAL FOUNDATIONS.
DOI: 10.15468/dl.ogpqdx
title: Occurrence Download

description: A dataset containing 668 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vigna Savi",
 "Country is Tanzania, United Republic of",
 "Geometry POLYGON((21.31 -14.31,21.31 3.16,49.00 3.16,49.00 -14.31,21.31 -14.31))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 668 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004442-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10149721
title: Ontogeny of hepatic metabolism in two broiler lines divergently selected for the ultimate pH of the Pectoralis major muscle

description: Nutrient availability during early stages of development (embryogenesis and the first week of life) can have long-term effects on physiological functions and bird metabolism. The embryo develops in a closed structure and depends entirely on the nutrients and energy available in the egg. The aim of this study was to describe the ontogeny of pathways governing hepatic metabolism that mediates many physiological functions in the pHu+ and pHu- chicken lines, which are divergently selected for the ultimate pH of meat, a proxy for muscle glycogen stores, and which differ in the nutrient content and composition of eggs. Our study provides the first detailed description of the evolution of different hepatic metabolic pathways during the early development of embryos and post-hatching chicks. We found a metabolic orientation for the pHu+ line towards proteolysis, glycogen degradation, ATP synthesis and autophagy, likely in response to a higher energy requirement compared with pHu- embryos. The metabolic orientations specific to the pHu+ and pHu- lines are established very early, probably in relation with their different genetic background and available nutrients.
DOI: 10.5281/zenodo.10604493
title: Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation

description: Data for "Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation"

Data directories



bulk-1week


Contains processed bulk TCR sequencing data from cohort 1.



longitudinal


Contains processed bulk TCR sequencing data from cohort 2.Note that this is the same dataset as reported in the following reference (it is included again in this repository for completeness):B. Ogunjimi, J. Van den Bergh, P. Meysman, S. Heynderickx, K. Bergs, H. Jansens, E. Leuridan, A. Vorsters, H. Goossens, K. Laukens, N. Cools, V. Van Tendeloo, N. Hens, P. Van Damme, E. Smits, P. Beutels, Multidisciplinary study of the secondary immune response in grandparents re-exposed to chickenpox. Sci Rep 7, 1077 (2017).



single-cell


Contains processed single cell data from cohort 1.



stim


Contains TCR data from stimulation experiments.

Script directories



src


Contains various scripts used to generate the results and figures in the manuscript.

Result directories



results


Contains the inbetween files for many of the analyses.Contains the Seurat object for the single cell analysis reported in the paper.Also used as output directory for the scripts listed in src.



tcrex_results


Full results from using the aforementioned data sets with the TCRex tool:https://tcrex.biodatamining.be/
DOI: 10.5281/zenodo.10907108
title: Dataset associated to "Annotation matters: the effect of structural gene annotation on orthology"

description: Dataset including the input and output files in "Annotation matters: the effect of structural gene annotation on orthology".



Input proteomes for OMA and their corresponding splice files are in the OMAproteomes zipped folder. The OMA results for each annotation method are in the zipped folders with the method name (e.g. Augustus.zip).

The fasta files (proteomes) are the same for OrthoFinder input in the cases of UniProt and Augustus (as they only have one isoform per gene). In these cases, the OrthoFinder folders (e.g. OFUniProt.zip), include the OrthoFinder output for that proteomes set. For Ensembl and NCBI, given the different approach each orthology method follows, the specific orthofinder proteomes are also included in the OrthoFinder (OF) zipped folder (e.g. OFtopNCBI.zip), in their corresponding primary_transcripts subfolder. 

The folder GSTDBenchmarOutput.zip contains the results from the Generalized Species Tree Discordance Benchmark.

topNCBI/topEnsembl correspond to the original proteomes downloaded from the databases.

priNCBI/primEnsembl correspond to the proteomes sets which include only the genes found on the primary assembly (reference sequences).

For the species code to species name correspondance, please check the Code-Species.csv file.
DOI: 10.5281/zenodo.10974782
title: 4DHydro_Results01_Tetis_Po_7p5sec_daily_exp10_19900101_20221231

description: Modeling results with TETIS software, for Po River with a spatial resolution of 7.5 sec, and temporal resolution daily. Experiment 10

Includes results for the following variables:



Catchement mask.

Upstream catchment area in square meters

Discharge flux in m-3 s-1

Volumetric soil moisture content in percentage
DOI: 10.5281/zenodo.10907107
title: Dataset associated to "Annotation matters: the effect of structural gene annotation on orthology"

description: Dataset including the input and output files in "Annotation matters: the effect of structural gene annotation on orthology".



Input proteomes for OMA and their corresponding splice files are in the OMAproteomes zipped folder. The OMA results for each annotation method are in the zipped folders with the method name (e.g. Augustus.zip).

The fasta files (proteomes) are the same for OrthoFinder input in the cases of UniProt and Augustus (as they only have one isoform per gene). In these cases, the OrthoFinder folders (e.g. OFUniProt.zip), include the OrthoFinder output for that proteomes set. For Ensembl and NCBI, given the different approach each orthology method follows, the specific orthofinder proteomes are also included in the OrthoFinder (OF) zipped folder (e.g. OFtopNCBI.zip), in their corresponding primary_transcripts subfolder. 

The folder GSTDBenchmarOutput.zip contains the results from the Generalized Species Tree Discordance Benchmark.

topNCBI/topEnsembl correspond to the original proteomes downloaded from the databases.

priNCBI/primEnsembl correspond to the proteomes sets which include only the genes found on the primary assembly (reference sequences).

For the species code to species name correspondance, please check the Code-Species.csv file.
DOI: 10.5281/zenodo.10977128
title: 4DHydro_Results02_Tetis_Po_7p5sec_daily_exp10_19900101_20221231

description: Modeling results with TETIS software, for Po River with a spatial resolution of 7.5 sec, and temporal resolution daily. Experiment 10

Includes results for the following variables:



Total evapotranspiration flux in kg m-2 s-1

Snow water equivalent in kg m-2
DOI: 10.5281/zenodo.10977270
title: Instagram 2023-2024 Serie B Collective Emotions (First Round)

description: The dataset contains collective emotional reactions extracted from user comments on Instagram posts from the 20 official Italian soccer teams competing in the 2023-24 Serie B (https://en.wikipedia.org/wiki/2023-24_Serie_B), the second tier of the Italian football league system.Data spans from the day preceding the beginning of the championship, 15/08/2023, to the day following the conclusion of the first round, 27/12/2023.

Emotional responses are categorized into four categories: anger, fear, joy, and sadness, inferred using "feel-it", a python library for emotion classification trained on Italian texts, to reconstruct the emotional content of users' comments. 

Each emotion has corresponding files:

{values,barcodes}_{anger,fear,joy,sadness}.txt,

whereas "values_anger.txt", for instance, contains the relative frequency of comments classified as conveying "anger" on a post, and "barcodes_anger.txt"contains information indicating whether anger is a collective emotional reaction to a post (0 denotes absence/not relevant, 1 denotes maximal presence).

In each file, the first column represents the name of the team's account, while the other columns represent the values/barcodes of the target emotion across the teams' posting activities from 15/08/2023 to 27/12/2023.

The dataset also includes:

date_posts.txt: Timestamps for each post published by each team.number_comments.txt: The number of classified comments, capped at 100 maximum comments.

The dataset offers insights into the emotional dynamics and fandom engagement surrounding Serie B teams during the specified timeframe.It was utilized to quantify burstiness and memory in collective emotional reactions.

The process of emotion classification in user comments and the association of each post with an aggregate value/barcode constitutes an anonymization procedure ensuring that the original user comments cannot be traced.
DOI: 10.5281/zenodo.10977271
title: Instagram 2023-2024 Serie B Collective Emotions (First Round)

description: The dataset contains collective emotional reactions extracted from user comments on Instagram posts from the 20 official Italian soccer teams competing in the 2023-24 Serie B (https://en.wikipedia.org/wiki/2023-24_Serie_B), the second tier of the Italian football league system.Data spans from the day preceding the beginning of the championship, 15/08/2023, to the day following the conclusion of the first round, 27/12/2023.

Emotional responses are categorized into four categories: anger, fear, joy, and sadness, inferred using "feel-it", a python library for emotion classification trained on Italian texts, to reconstruct the emotional content of users' comments. 

Each emotion has corresponding files:

{values,barcodes}_{anger,fear,joy,sadness}.txt,

whereas "values_anger.txt", for instance, contains the relative frequency of comments classified as conveying "anger" on a post, and "barcodes_anger.txt"contains information indicating whether anger is a collective emotional reaction to a post (0 denotes absence/not relevant, 1 denotes maximal presence).

In each file, the first column represents the name of the team's account, while the other columns represent the values/barcodes of the target emotion across the teams' posting activities from 15/08/2023 to 27/12/2023.

The dataset also includes:

date_posts.txt: Timestamps for each post published by each team.number_comments.txt: The number of classified comments, capped at 100 maximum comments.

The dataset offers insights into the emotional dynamics and fandom engagement surrounding Serie B teams during the specified timeframe.It was utilized to quantify burstiness and memory in collective emotional reactions.

The process of emotion classification in user comments and the association of each post with an aggregate value/barcode constitutes an anonymization procedure ensuring that the original user comments cannot be traced.