cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13768607
title: A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease

description: ***These data supersede the previous release. Please disregard data uploaded prior to October 30th as the metadata was incorrect - note the correct data in Supplementary Table 1***

A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. 

GEO ID for bam files and CellRanger pipeline output (filtered and unfiltered): GSE282122

TAURUS_raw_counts_annotated_final.h5ad: This file is the pooled data across all cell types

UMAP_combined_objects.txt.gz: This file has the corresponding UMAP for pooled data

PC_combined_objects.txt.gz: This file has the corresponding PC for pooled data

paired_sample_list.csv: This file has the paired samples used in analysis for baseline/longitudinal analysis. For baseline analyses, please use baseline samples > 6.5 inflammation score to recapitulate the analyses in the paper.

Other data to be uploaded to Zenodo include H&E slides. Please access interactive MDV browser here.
DOI: 10.5281/zenodo.14007626
title: A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease

description: ***These data supersede the previous release. Please disregard data uploaded prior to October 30th as the metadata was incorrect - note the correct data in Supplementary Table 1***

A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease. 

GEO ID for bam files and CellRanger pipeline output (filtered and unfiltered): GSE282122

TAURUS_raw_counts_annotated_final.h5ad: This file is the pooled data across all cell types

UMAP_combined_objects.txt.gz: This file has the corresponding UMAP for pooled data

PC_combined_objects.txt.gz: This file has the corresponding PC for pooled data

paired_sample_list.csv: This file has the paired samples used in analysis for baseline/longitudinal analysis. For baseline analyses, please use baseline samples > 6.5 inflammation score to recapitulate the analyses in the paper.

Other data to be uploaded to Zenodo include H&E slides. Please access interactive MDV browser here.
DOI: 10.5519/qd.sdw53a9f
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (913 records)
DOI: 10.15468/dl.neujjd
title: Occurrence Download

description: A dataset containing 8109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Triatoma gerstaeckeri (Stål, 1859), Triatoma sanguisuga (LeConte, 1856), Triatoma protracta (Uhler, 1894))"
 ]
}

 The dataset includes 8109 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022394-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7x2ywa
title: Occurrence Download

description: A dataset listing the 3 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.80577 4.58336,-73.21096 4.58048,-73.208 4.23853,-72.80228 4.23854,-72.80437 4.46411,-72.80577 4.58336))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset's 3 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022388-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7d3m3r
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cambarus smilax Loughman, Simon & Welsh, 2011"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022396-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.degypp
title: Occurrence Download

description: A dataset containing 1174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Asclepias californica Greene"
 ]
}

 The dataset includes 1174 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022397-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ddykja
title: Occurrence Download

description: A dataset containing 17847 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trachemys scripta (Thunberg In Schoepff, 1792)",
 "Country is France",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 17847 records from 706 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022398-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6uea5c
title: Occurrence Download

description: A dataset containing 610 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sturnella defilippii (Bonaparte, 1850)"
 ]
}

 The dataset includes 610 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022399-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14187819
title: 16545_2019_07_16_aggregates_CTP_switch_2_0glu_0_0glu_URA7young_URA8young_URA8old_secondRun_01 (part 1)

description: High throughput time lapse experiment. Details can be found on the 'txt' files inside.
DOI: 10.5281/zenodo.14187820
title: 16545_2019_07_16_aggregates_CTP_switch_2_0glu_0_0glu_URA7young_URA8young_URA8old_secondRun_01 (part 1)

description: High throughput time lapse experiment. Details can be found on the 'txt' files inside.
DOI: 10.7294/26505913
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 101-150

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26505913.v1
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 101-150

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.15468/dl.764hkv
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.80577 4.58336,-73.21096 4.58048,-73.208 4.23853,-72.80228 4.23854,-72.80437 4.46411,-72.80577 4.58336))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bromeliaceae"
 ]
}

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022382-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kensgp
title: Occurrence Download

description: A dataset containing 8109 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Triatoma gerstaeckeri (Stål, 1859), Triatoma sanguisuga (LeConte, 1856), Triatoma protracta (Uhler, 1894))"
 ]
}

 The dataset includes 8109 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022401-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7294/26506018
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 151-200

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26506018.v1
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 151-200

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26506063
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 201-250

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26506063.v1
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 201-250

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.6084/m9.figshare.25393156.v1
title: Data and Code_Kordon et al. 2024. Factors shaping socio-emotional trajectories in sanctuary-living bonobos: A longitudinal approach

description: This study draws on longitudinal observations in sanctuary-living bonobos to examine how rearing background, sex, and age predict social tendencies like affiliation, consolation, and aggression risk.
DOI: 10.15468/dl.pmj8xd
title: Occurrence Download

description: A dataset containing 573 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Centre for Plant Medicine Research (CPMR) medicinal plants dataset"
 ]
}

 The dataset includes 573 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022402-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7294/26506153
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 251-300

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26506153.v1
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 251-300

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.15468/dl.8r5pd4
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ullucus tuberosus subsp. aborigineus (Brücher) Sperling"
 ]
}

 The dataset includes 57 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022403-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7294/26506213
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 301-350

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.7294/26506213.v1
title: Dangerous Harbor Project - Westmoreland County - Reel 1 - 1665-1677 - TIFFs 301-350

description: This dataset includes 50 TIFF files showing deeds, patents, and wills from Westmoreland County in Virginia. Deeds are documents that transfer land or property from one person to another. Patents identify specific inventions as belonging to an individual and restrict the manufacturing of these inventions to the person they belonged to. Wills were created to settle asset distribution in the event of a person’s death. These documents were collected in association with the Dangerous Harbor Project which used courthouse documents to identify escaped unfree laborers in the 17th century Chesapeake and the punishments associated with their escape. 
<br>
To learn more about this project, please go to the Dangerous Harbor Website.
DOI: 10.5519/qd.mj2dnqto
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (364 records)
DOI: 10.5281/zenodo.14187970
title: MATNLAR TAHLILI ASOSIDA O`QUVCHILARDA LISONIY KOMPETENSIYANI SHAKLLANTIRISH
DOI: 10.5281/zenodo.14187971
title: MATNLAR TAHLILI ASOSIDA O`QUVCHILARDA LISONIY KOMPETENSIYANI SHAKLLANTIRISH
DOI: 10.6084/m9.figshare.27857652
title: Omicron.xlsx

description: <b>A report on the relationship between vaccination status, viral loads and patient outcomes among hospitalized patients during the COVID-19 Omicron variant’s surge in Tehran, Iran</b>age in years / ageGroup: 1-&gt;18-49, 2-&gt;50-64, 3-&gt;65-79, 4&gt;79 / gender: 1-&gt;male, 2-&gt;female / vaccinationStatus: 0-&gt;no, 1-&gt;yes / vaccineType: 1-&gt;sinopharm, 2-&gt;astrazeneca, 3-&gt;barekat, 4-&gt;sputnik, 5-&gt;other / ct: cycle threshold of COVID-19 PCR / ctGroup: 1&lt;21, 2-&gt;21-30, 3&gt;30 / death & ICU & outlier: 0-&gt;no, 1-&gt;yes
DOI: 10.6084/m9.figshare.27857652.v1
title: Omicron.xlsx

description: <b>A report on the relationship between vaccination status, viral loads and patient outcomes among hospitalized patients during the COVID-19 Omicron variant’s surge in Tehran, Iran</b>age in years / ageGroup: 1-&gt;18-49, 2-&gt;50-64, 3-&gt;65-79, 4&gt;79 / gender: 1-&gt;male, 2-&gt;female / vaccinationStatus: 0-&gt;no, 1-&gt;yes / vaccineType: 1-&gt;sinopharm, 2-&gt;astrazeneca, 3-&gt;barekat, 4-&gt;sputnik, 5-&gt;other / ct: cycle threshold of COVID-19 PCR / ctGroup: 1&lt;21, 2-&gt;21-30, 3&gt;30 / death & ICU & outlier: 0-&gt;no, 1-&gt;yes
DOI: 10.15468/dl.pgt6en
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cambarus smilax Loughman, Simon & Welsh, 2011"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022404-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kpaww3
title: Occurrence Download

description: A dataset containing 224 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-118.10623 67.21344,-100.49391 61.81926,-93.60496 59.93455,-86.39106 56.945,-81.97173 55.38524,-81.58179 53.30556,-80.47696 52.07074,-78.72223 52.59066,-79.89205 54.60536,-78.00734 56.62005,-79.50211 59.47962,-78.78722 62.2092,-76.38258 62.8591,-73.52302 62.72912,-69.42864 61.42932,-67.02401 59.08968,-62.14975 62.72912,-59.68013 67.08346,-67.54393 72.34766,-81.64678 75.20722,-100.36393 71.24282,-113.55692 70.59292,-118.10623 67.21344))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Honckenya peploides (L.) Ehrh., Honckenya peploides subsp. diffusa (Hornem.) Hultén ex V.V.Petrovsky, Honckenya peploides subsp. robusta (Fernald) Hultén, Honckenya peploides subsp. peploides, Honckenya peploides subsp. diffusa (Hornem.) Hultén, Honckenya peploides subsp. diffusa (Hornem.) Á.Löve, Honckenya peploides var. diffusa (Hornem.) Ostenf.)"
 ]
}

 The dataset includes 224 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022405-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.d8rkk16j
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (49846 records)
DOI: 10.5281/zenodo.14187973
title: GAP VA UNING ONA TILI TA'LIMIDA O`ZIGA XOSLIGI.
DOI: 10.5281/zenodo.14187974
title: GAP VA UNING ONA TILI TA'LIMIDA O`ZIGA XOSLIGI.
DOI: 10.15468/dl.wv5nz6
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Checklist of threatened Ghanaian medicinal plants"
 ]
}

 The dataset includes 97 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022406-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14108391
title: Polyfunctionality and breadth of HIV-1 antibodies are associated with delayed disease progression

description: HIV-1 infection leads to chronic disease requiring life-long treatment and therefore alternative therapeutics, a cure and/or a protective vaccine are needed. Antibody-mediated effector functions could have a role in the fight against HIV-1. However, the properties underlying the potential beneficial effects of antibodies during HIV-1 infection are poorly understood. 

To identify a specific profile of antibody features associated with delayed disease progression, we studied antibody polyfunctionality during untreated HIV-1 infection in the well-documented Amsterdam Cohort Studies. Serum samples were analyzed from untreated individuals with HIV-1 at approximately 6 months (n = 166) and 3 years (n = 382) post-seroconversion (post-SC). A Luminex antibody Fc array was used to profile 15 different Fc features for serum antibodies against 20 different HIV-1 envelope glycoprotein antigens and the resulting data was also compared with data on neutralization breadth. 

We found that high HIV-1 specific IgG1 levels and low IgG2 and IgG4 levels at 3 years post-SC were associated with delayed disease progression. Moreover, delayed disease progression was associated with a broad and polyfunctional antibody response. Specifically, the capacity to interact with all Fc γ receptors (FcγRs) and C1q, and in particular with FcγRIIa, correlated positively with delayed disease progression. There were strong correlations between antibody Fc features and neutralization breadth and several antibody features that were associated with delayed disease progression were also associated with the development of broad and potent antibody neutralization. 

In summary, we identified a strong association between broad, polyfunctional antibodies and delayed disease progression. These findings contribute new information for the fight against HIV-1, especially for new antibody-based therapy and cure strategies.