cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15128189
title: Data and code for "PD-1 and ICOS are co-expressed in T follicular helper cells but define three stages of maturation of T follicular regulatory cells"

description: Data associated with the manuscript:

"PD-1 and ICOS are co-expressed in T follicular helper cells but define three stages of maturation of T follicular regulatory cells"

This dataset contains fluorescence values extracted from flow cytometry data processed in FlowJo and used for principal component analysis (PCA) of T follicular helper (Tfh) and T follicular regulatory (Tfr) cells from different human tonsils. Cells were gated as follows:



TFH cells: lymphocytes/singlets/live CD4⁺FOXP3⁻CD25⁻CXCR5⁺

TFR cells: lymphocytes/singlets/live CD4⁺FOXP3⁺CXCR5⁺


The dataset includes samples from four different human tonsils, labeled as: t0, t1, t2, and t3.

Available data files

The uploaded ZIP file includes the following subfolders and files:

1. /raw_data: 



t0_TFH.csv, t1_TFH.csv, t2_TFH.csv, t3_TFH.csv: raw protein expression data for TFH cells (fluorescence values).

t0_TFR.csv, t1_TFR.csv, t2_TFR.csv, t3_TFR.csv: raw protein expression data for TFR cells (fluorescence values).


2. /preprocessed_data:



t0_tfh_pcs_subset.rds, t1_tfh_pcs_subset.rds, t2_tfh_pcs_subset.rds, t3_tfh_pcs_subset.rds: preprocessed TFH cell with data principal component scores.

t0_tfr_pcs_subset.rds, t1_tfr_pcs_subset.rds, t2_tfr_pcs_subset.rds, t3_tfr_pcs_subset.rds: preprocessed TFR cell data with principal component scores.

t0_combined_pcs.rds: preprocessed data for the combined PCA analysis of TFH and TFR cells from t0.


3. /documentation:



tonsils_analysis_code.Rmd: R Markdown file with the code used for PCA analysis, visualization of PCA plots, and correlation heatmaps.

tonsil_analysis_code.pdf: PDF version of the analysis code (rendered from the R Markdown file).

tonsil_analysis_code.html: HTML version of the analysis code (rendered from the R Markdown file).


 

Analysis and Code

The R Markdown (RMD) file included in the repository provides:



step-by-step code for PCA analysis

visualization of PCA plots and correlation heatmaps shown in the manuscript
DOI: 10.15468/dl.3dgnu6
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008055-190621201848488/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f9t16q
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006157-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39fwgb
title: Occurrence Download

description: A dataset containing 19929 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Global compendium of Aedes aegypti occurrence"
 ]
}

 The dataset includes 19929 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071443-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ugiu46
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001669-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cezmuc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015686-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nsug5s
title: Occurrence Download

description: A dataset containing 12370 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Chronicle of Nature - Phenology of Plants of State Nature Reserve Stolby"
 ]
}

 The dataset includes 12370 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0434525-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vndkhm
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033189-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uoqce2
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000646-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqvd38
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "Geometry POLYGON((-89.07617 -35.38213,-36.07057 -35.38213,-36.07057 -14.16893,-89.07617 -14.16893,-89.07617 -35.38213))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus baeri Vachal, 1904"
 ]
}

 The dataset includes 49 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071444-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lza5ng
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006167-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8win3f
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000794-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcsh5b
title: Occurrence Download

description: A dataset containing 72990 species occurrences available in GBIF matching the query:
{
 "and" : [
 "License is CC-BY 4.0",
 "OccurrenceStatus is Present",
 "TaxonKey is Rupicapra rupicapra (Linnaeus, 1758)"
 ]
}

 The dataset includes 72990 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0182951-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8cypy4
title: Occurrence Download

description: A dataset containing 821504650 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (United States of America, United States Minor Outlying Islands, American Samoa, Micronesia (Federated States of), Guam, Marshall Islands, Northern Mariana Islands, Puerto Rico, Palau, Virgin Islands (U.S.))",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
}

 The dataset includes 821504650 records from 4999 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071447-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gks6a8
title: Occurrence Download

description: A dataset containing 224723 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Daphne mezereum L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 224723 records from 578 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014005-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cmydkc
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Linum macraei marticorenae"
 ]
}

 The dataset includes 25 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006801-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thzcy4
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scutarcopagia scobinata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 221 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006802-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcrd2e
title: Occurrence Download

description: A dataset containing 371 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "TaxonKey is Eucheuma J.Agardh, 1847"
 ]
}

 The dataset includes 371 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0325378-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unh4mw
title: Occurrence Download

description: A dataset containing 7146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((0.401 43.07681,0.44907 43.10289,0.4422 43.15601,0.31998 43.15801,0.31174 43.08083,0.401 43.07681))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7146 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0219720-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8afzn6
title: Occurrence Download

description: A dataset containing 1470 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Fiji",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrura pealii Hartlaub, 1852"
 ]
}

 The dataset includes 1470 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214052-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tynbcm
title: Occurrence Download

description: A dataset containing 5131 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caragana arborescens Lam."
 ]
}

 The dataset includes 5131 records from 162 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012604-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.groj8b
title: Occurrence Download

description: A dataset containing 17740 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eichhornia crassipes (Mart.) Solms"
 ]
}

 The dataset includes 17740 records from 360 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003172-180824113759888/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ynr4c1
title: Occurrence Download

description: A dataset containing 351 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptodactylus labyrinthicus (Spix, 1824)"
 ]
}

 The dataset includes 351 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012605-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.udnug6
title: Occurrence Download

description: A dataset containing 32347 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Veronica filiformis Sm."
 ]
}

 The dataset includes 32347 records from 299 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214012-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxykn5
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Buxus madagascarica Baill."
 ]
}

 The dataset includes 140 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239993-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vkm75e
title: Occurrence Download

description: A dataset containing 338061 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Phoenicurus ochruros (S.G.Gmelin, 1774)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 338061 records from 506 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012605-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34976/9x2b-nd72
title: Performance Monitoring and Accountability 2020 (PMA2020) Uganda Round 6 Follow-up Household and Female Survey
DOI: 10.15468/dl.ch4nxu
title: Occurrence Download

description: A dataset containing 10328 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Muraena helena Linnaeus, 1758",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 10328 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055202-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mf69rz
title: Occurrence Download

description: A dataset containing 2855 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dianthus armeria L.",
 "Geometry POLYGON((-109 26, -87 26, -87 44, -109 44, -109 26))"
 ]
}

 The dataset includes 2855 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055203-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6aeah
title: Occurrence Download

description: A dataset containing 1426 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mustelus asterias Cloquet, 1819",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 1426 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055204-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nd4pu8
title: Occurrence Download

description: A dataset containing 1597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mustelus mustelus (Linnaeus, 1758)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 1597 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055206-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dgaat3
title: Occurrence Download

description: A dataset containing 638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diodia teres Walter",
 "Geometry POLYGON((-109 26, -87 26, -87 44, -109 44, -109 26))"
 ]
}

 The dataset includes 638 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055207-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxzcrw
title: Occurrence Download

description: A dataset containing 18423 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bombina bombina (Linnaeus, 1761)"
 ]
}

 The dataset includes 18423 records from 147 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055205-241126133413365/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.27047812
title: Arsenic and cadmium in the hydrological cycle and soil in a maquis broadleaved evergreen forest stand in Greece. Sources of some uncertainties

description: The concentrations and fluxes of arsenic (As) and cadmium (Cd) were examined in the hydrological cycle, litterfall and soils in a maquis broadleaved evergreen forest stand in western Greece. The concentrations of the metals in the hydrological cycle ranged from 0.076 to 0.306 μg L<sup>−1</sup> and 0.040–0.050 μg L<sup>−1</sup> for As and Cd, respectively. It was found that the enrichment of As in the atmosphere was both due to suspended geogenic material and long range transfer, whereas for Cd the long range transfer was the predominant way for deposition. Two models were assessed to find the volumes of percolation water to compare the fluxes with the estimated ones derived from soil solution measurements. The daily deterministic forest-hydrological model (WBS3) was found to perform better than the physically based 1D semi-distributed soil-plant-atmosphere model (BROOK90). When calculating the total amounts of the heavy metals in soils, the statistical uncertainty derived from every soil layer has to be taken into account. The residence time of Cd in the forest floor (L + FH) of the soils was found 6.4 years, whereas that of As 36.3 years. This difference shows the mobility of Cd in comparison to As in the soils of the area.
DOI: 10.6084/m9.figshare.27047812.v1
title: Arsenic and cadmium in the hydrological cycle and soil in a maquis broadleaved evergreen forest stand in Greece. Sources of some uncertainties

description: The concentrations and fluxes of arsenic (As) and cadmium (Cd) were examined in the hydrological cycle, litterfall and soils in a maquis broadleaved evergreen forest stand in western Greece. The concentrations of the metals in the hydrological cycle ranged from 0.076 to 0.306 μg L<sup>−1</sup> and 0.040–0.050 μg L<sup>−1</sup> for As and Cd, respectively. It was found that the enrichment of As in the atmosphere was both due to suspended geogenic material and long range transfer, whereas for Cd the long range transfer was the predominant way for deposition. Two models were assessed to find the volumes of percolation water to compare the fluxes with the estimated ones derived from soil solution measurements. The daily deterministic forest-hydrological model (WBS3) was found to perform better than the physically based 1D semi-distributed soil-plant-atmosphere model (BROOK90). When calculating the total amounts of the heavy metals in soils, the statistical uncertainty derived from every soil layer has to be taken into account. The residence time of Cd in the forest floor (L + FH) of the soils was found 6.4 years, whereas that of As 36.3 years. This difference shows the mobility of Cd in comparison to As in the soils of the area.
DOI: 10.34976/a0v4-5r28
title: Performance Monitoring and Accountability 2020 (PMA2020) Kenya Nutrition Round 1 Household and Female Survey
DOI: 10.15468/dl.6k5xzp
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mustelus punctulatus Risso, 1827",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 206 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055209-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jer9yn
title: Occurrence Download

description: A dataset containing 4604 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Diodia virginiana L.",
 "Geometry POLYGON((-109 26, -87 26, -87 44, -109 44, -109 26))"
 ]
}

 The dataset includes 4604 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055210-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.