cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.s47wpy
title: Occurrence Download

description: A dataset containing 1271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus sinuata Walter)",
 "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 1271 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012634-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sg5s4h
title: Occurrence Download

description: A dataset containing 8295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus stellata Wangenh.)",
 "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 8295 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012635-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zmmb6t
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus tardifolia C.H.Mull.)",
 "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 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012636-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.365rwr
title: Occurrence Download

description: A dataset listing the 2 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Continent is North America",
 "Country is United States of America",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Tropicos Specimens Non-MO, The New York Botanical Garden Herbarium (NY), Morton Arboretum - Vascular Plants, NMNH Extant Specimen Records (USNM, US), University of Mississippi, Thomas M. Pullen Herbarium, Mississippi Museum of Natural Science Herbarium, Robert K. Godfrey Herbarium at Florida State University, Tropicos MO Specimen Data)",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Continent derived from coordinates, Occurrence status inferred from individual count, Different owner institution)",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, 90fd6680-349f-11d8-aa2d-b8a03c50a862, bc092ff0-02e4-11dc-991f-b8a03c50a862, ae447c50-b8a8-11d8-92a4-b8a03c50a862, 6def5a1e-45a9-471c-86c3-06ce0ff76179, 3be011d4-fcc3-4352-a5a2-ddd0dc506135, 5c28b8bf-bb63-472f-8989-1f9c54bcb5eb, 37f13176-4dd6-46bf-9493-09d3513529da)",
 "TaxonKey is Quercus falcata Michx.",
 "Year 1960-2025"
 ]
}

 The dataset's 2 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012607-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsvhxj
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus texana Buckley)",
 "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 47 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012638-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sx2spa
title: Occurrence Download

description: A dataset containing 223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus tomentella Engelm.)",
 "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 223 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012639-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kmjmzx
title: Occurrence Download

description: A dataset containing 315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is South America",
 "Country is Colombia",
 "TaxonKey is Poecilia reticulata Peters, 1859"
 ]
}

 The dataset includes 315 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012640-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcuexz
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus toumeyi Sarg.)",
 "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 89 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012642-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ksbhhv
title: Occurrence Download

description: A dataset containing 2996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus turbinella Greene)",
 "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 2996 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012643-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14803877
title: Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNA/TCR-seq]

description: Seurat Objects froms scRNA/TCR-seq Data Associated with the manuscript: Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade

This dataset is a supplement to our Github Repostory which contains raw data and R markdown files neccesary to generate all figures from our manuscript. 

Three (3) Seurat Objects are available on this page 



scRNA/TCR-seq atlas: Analysis of scRNA/TCR-seq of GP33+ cells (+/- CD62L enrichment): Fig. 1,2 and Extended Data Fig. 1,3,4

Polyclonal Rechallenge: scRNA/TCR-seq from clonal tracing of CD8+ T cells from 100+ dpi of acuure and chronic infection during rechallenge:  Fig. 4 and Extended Data Fig. 6,7

scRNA/TCR-seq aPDL1: Analysis of scRNA/TCR-seq of GP33+ cells after aPDL1 Treatment: Fig. 5 and Extended Data Fig. 8


Raw single cell data are on NCBI GEO at accession numbers GSE285411 (scRNA/TCR-seq atlas), GSE285414 (scRNA/TCR-seq post-rechallenge), and GSE285412 (scRNA/TCR-seq αPD-L1).

Manuscript Abstract:

Immune checkpoint blockade can facilitate tumor clearance by T cells, resulting in long term patient survival. However, the capacity of exhausted CD8+ T cells (Tex), present during chronic antigen exposure, to form memory after antigen clearance remains unclear. Here, we performed longitudinal single cell RNA/T cell receptor sequencing and ATAC-sequencing on antigen-specific T cells after the peripheral clearance of chronic lymphocytic choriomeningitis virus infection. These data revealed the formation of a robust population of memory CD8+ T cells that transcriptionally, epigenetically, and functionally resemble central memory T cells (Tcm) that form after clearance of acute infection. To lineage trace the origin and memory recall response of Tex-derived memory clones, we utilized T cell receptor sequencing over the course of primary infection and rechallenge. We show that chronic Tcm are a clonally distinct lineage of Tex derived from progenitor exhausted cells, persist long-term in the absence of antigen, and undergo rapid clonal expansion during rechallenge. Finally, we demonstrate that αPD-L1 immune checkpoint blockade selectively expands clones which form Tcm after clearance. Together, these data support the concept that chronically stimulated T cells form bona fide functional memory T cells through an analogous differentiation pathway to acutely stimulated T cells, which may have significant implications for enhancing immune memory to cancer through checkpoint blockade and vaccination.
DOI: 10.5281/zenodo.14803876
title: Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade [scRNA/TCR-seq]

description: Seurat Objects froms scRNA/TCR-seq Data Associated with the manuscript: Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade

This dataset is a supplement to our Github Repostory which contains raw data and R markdown files neccesary to generate all figures from our manuscript. 

Three (3) Seurat Objects are available on this page 



scRNA/TCR-seq atlas: Analysis of scRNA/TCR-seq of GP33+ cells (+/- CD62L enrichment): Fig. 1,2 and Extended Data Fig. 1,3,4

Polyclonal Rechallenge: scRNA/TCR-seq from clonal tracing of CD8+ T cells from 100+ dpi of acuure and chronic infection during rechallenge:  Fig. 4 and Extended Data Fig. 6,7

scRNA/TCR-seq aPDL1: Analysis of scRNA/TCR-seq of GP33+ cells after aPDL1 Treatment: Fig. 5 and Extended Data Fig. 8


Raw single cell data are on NCBI GEO at accession numbers GSE285411 (scRNA/TCR-seq atlas), GSE285414 (scRNA/TCR-seq post-rechallenge), and GSE285412 (scRNA/TCR-seq αPD-L1).

Manuscript Abstract:

Immune checkpoint blockade can facilitate tumor clearance by T cells, resulting in long term patient survival. However, the capacity of exhausted CD8+ T cells (Tex), present during chronic antigen exposure, to form memory after antigen clearance remains unclear. Here, we performed longitudinal single cell RNA/T cell receptor sequencing and ATAC-sequencing on antigen-specific T cells after the peripheral clearance of chronic lymphocytic choriomeningitis virus infection. These data revealed the formation of a robust population of memory CD8+ T cells that transcriptionally, epigenetically, and functionally resemble central memory T cells (Tcm) that form after clearance of acute infection. To lineage trace the origin and memory recall response of Tex-derived memory clones, we utilized T cell receptor sequencing over the course of primary infection and rechallenge. We show that chronic Tcm are a clonally distinct lineage of Tex derived from progenitor exhausted cells, persist long-term in the absence of antigen, and undergo rapid clonal expansion during rechallenge. Finally, we demonstrate that αPD-L1 immune checkpoint blockade selectively expands clones which form Tcm after clearance. Together, these data support the concept that chronically stimulated T cells form bona fide functional memory T cells through an analogous differentiation pathway to acutely stimulated T cells, which may have significant implications for enhancing immune memory to cancer through checkpoint blockade and vaccination.
DOI: 10.15468/dl.yex7yp
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus vaseyana Buckley)",
 "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 244 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012644-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.afs3sz
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus viminea Trel.)",
 "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 59 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012645-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zz5qqe
title: Occurrence Download

description: A dataset containing 6118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus virginiana Mill.)",
 "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 6118 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012646-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gq3fdm
title: Occurrence Download

description: A dataset containing 2968 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus wislizeni A.DC.)",
 "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 2968 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012647-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.44vzbp
title: Occurrence Download

description: A dataset containing 2473 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya elliptica Douglas ex Lindl.)",
 "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 2473 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012648-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xh379q
title: Occurrence Download

description: A dataset containing 869 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya flavescens S.Watson)",
 "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 869 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012650-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cq276x
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya fremontii Torr.)",
 "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 282 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012651-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gr7292
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya veatchii Kellogg)",
 "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 297 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012653-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kzjjvk
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya ovata Benth.)",
 "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 43 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012652-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y65emr
title: Occurrence Download

description: A dataset containing 928 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Garrya wrightii Torr.)",
 "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 928 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012654-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b2p8et
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Geranium arboreum A.Gray)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012655-250127130748423/datasets/export for details.
DOI: 10.15468/dl.4zgdnq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyrtandra pickeringii A.Gray)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012657-250127130748423/datasets/export for details.
DOI: 10.15468/dl.m886bt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyrtandra giffardii Rock)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012656-250127130748423/datasets/export for details.
DOI: 10.15468/dl.qr9fbz
title: Occurrence Download

description: A dataset containing 17483296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Year 2010-2010"
 ]
}

 The dataset includes 17483296 records from 1067 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012621-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/rbd68k
title: Thesea pyrrha sp. nov., a new shallow-water octocoral (Cnidaria, Anthozoa) from southwestern Atlantic, and implications on the systematics of the genus

description: This dataset contains the digitized treatments in Plazi based on the original journal article Carpinelli, Ágatha Nascimento, Cordeiro, Ralf Tarciso Silva, Castro, Clovis Barreira, Kitahara, Marcelo Visentini (2022): Thesea pyrrha sp. nov., a new shallow-water octocoral (Cnidaria, Anthozoa) from southwestern Atlantic, and implications on the systematics of the genus. Zootaxa 5116 (1): 89-106, DOI: 10.11646/zootaxa.5116.1.4AbstractThe family Plexauridae Gray, 1859 is characterized by grouping octocorals that have thick branches and coenenchyme. However, due to their relatively simple body plan, the establishment of homologous and, therefore, systematically informative morphological characters is a challenge for the systematics of Octocorallia. During the last decade, molecular studies suggested that Plexauridae is polyphyletic, with representatives grouping with Acanthogorgiidae Gray, 1859 and also Gorgoniidae Lamouroux, 1812. Represented by 22 extant species, mostly of which occur in the Atlantic Ocean, the plexaurid genus Thesea Duchassaing & Michelotti, 1860 has also been purported to be polyphyletic, with a Pacific lineage related to the former “ Paramuriceidae ” and an Atlantic lineage more closely related to Gorgoniidae. Thus, aiming to further improve our understanding of the evolutionary position of the Southwestern Atlantic Thesea, sequencing of the extended Octocorallia barcode reinforces the need for a re-evaluation of the position of the genus within plexaurids. Molecular and macro and micromorphological analyzes indicate the occurrence of an undescribed species distributed from Rio de Janeiro to Santa Catarina, here named Thesea pyrrha sp. nov. Results presented herein also suggest that T. pyrrha is close related to Adelogorgia and Psammogorgia, both genera exclusive to the Pacific Ocean.
DOI: 10.15468/rdgbtd
title: Paracanestrinia denmarkica nov. gen., nov. sp. (Astigmata: Canestriniidae) from Denmark

description: This dataset contains the digitized treatments in Plazi based on the original journal article Haitlinger, Ryszard (2017): Paracanestrinia denmarkica nov. gen., nov. sp. (Astigmata: Canestriniidae) from Denmark. Linzer biologische Beiträge 49 (1): 657-662, DOI: 10.5281/zenodo.13151163