cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28514069
title: Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria Supplemental Data

description: Type 11 secretion systems (T11SS) are broadly distributed among proteobacteria, with more than 3000 T11SS family outer membrane proteins (OMPs) comprising 10 major sequence similarity network (SSN) clusters. Of these, only 7, all from animal-associated cluster 1, have been experimentally verified as secretins of cargo, including adhesins, hemophores, and metal binding proteins. To identify novel cargo of a more diverse set of T11SS, we identified gene families co-occurring in gene neighborhoods with either cluster 1 or marine microbe-associated cluster 3 T11SS OMP genes. We developed bioinformatic controls to ensure perceived co-occurrences are specific to T11SS, and not general to OMPs. We found that both cluster 1 and cluster 3 T11SS OMPs frequently co-occur with single carbon metabolism and nucleotide synthesis pathways, but that only cluster 1 T11SS OMPs had significant co-occurrence with metal and heme pathways, as well as with mobile genetic islands, potentially indicating diversified function of this cluster. Cluster 1 T11SS co-occurrences included 2556 predicted cargo proteins, unified by the presence of a C-terminal β-barrel domain, which fall into 141 predicted UniRef50 clusters and approximately 10 different architectures: 4 similar to known cargo and 6 uncharacterized types. We experimentally demonstrate T11SS-dependent secretion of an uncharacterized cargo type with homology to Plasmin sensitive protein (Pls). Unexpectedly, genes encoding marine cluster 3 T11SS OMPs only rarely co-occurred with the C-terminal β-barrel domain and instead frequently co-occurred with DUF1194-containing genes. Overall, our results show that with sufficiently large-scale and controlled genomic data, T11SS-dependent cargo proteins can be accurately predicted.
DOI: 10.6084/m9.figshare.28514069.v1
title: Supplementary Data Files for Grossman, Mucci et al. 2025 <b>Bioinformatic discovery of type 11 secretion system (T11SS) cargo </b><b>across the Proteobacteria</b>

description: Type 11 secretion systems (T11SS) are broadly distributed among proteobacteria, with more than 3000 T11SS family outer membrane proteins (OMPs) comprising 10 major sequence similarity network (SSN) clusters. Of these, only 7, all from animal-associated cluster 1, have been experimentally verified as secretins of cargo, including adhesins, hemophores, and metal binding proteins. To identify novel cargo of a more diverse set of T11SS, we identified gene families co-occurring in gene neighborhoods with either cluster 1 or marine microbe-associated cluster 3 T11SS OMP genes. We developed bioinformatic controls to ensure perceived co-occurrences are specific to T11SS, and not general to OMPs. We found that both cluster 1 and cluster 3 T11SS OMPs frequently co-occur with single carbon metabolism and nucleotide synthesis pathways, but that only cluster 1 T11SS OMPs had significant co-occurrence with metal and heme pathways, as well as with mobile genetic islands, potentially indicating diversified function of this cluster. Cluster 1 T11SS co-occurrences included 2556 predicted cargo proteins, unified by the presence of a C-terminal β-barrel domain, which fall into 141 predicted UniRef50 clusters and approximately 10 different architectures: 4 similar to known cargo and 6 uncharacterized types. We experimentally demonstrate T11SS-dependent secretion of an uncharacterized cargo type with homology to Plasmin sensitive protein (Pls). Unexpectedly, genes encoding marine cluster 3 T11SS OMPs only rarely co-occurred with the C-terminal β-barrel domain and instead frequently co-occurred with DUF1194-containing genes. Overall, our results show that with sufficiently large-scale and controlled genomic data, T11SS-dependent cargo proteins can be accurately predicted.
DOI: 10.15468/dl.vym3mz
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Passiflora schlimiana Regel"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006249-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkqzv9
title: Occurrence Download

description: A dataset containing 4505 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is North America",
 "Country is United States of America",
 "Geometry POLYGON((-104.7 44,-104.1 44,-104.1 44.6,-104.7 44.6,-104.7 44))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4505 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006258-250227182400228/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.28541504
title: Supplementary Material for: Edema and Outcome in Patients with Nephrotic-Range Albuminuria and Hypoalbuminemia: A Danish Multicenter cohort study

description: Introduction: Nephrotic syndrome is characterized by proteinuria, hypoalbuminemia, and edema, though not all patients present with edema. This study investigates edema prevalence and its association with venous thromboembolism, kidney failure, and mortality in patients with nephrotic-range albuminuria and hypoalbuminemia.
Methods: We conducted a Danish multicenter cohort study, including patients with plasma albumin &lt;30 g/L and nephrotic-range albuminuria in the Central Denmark Region (2012-2022). Patients were identified using the laboratory information system and followed until death, lost to follow-up, or end of study. Data on demographics, comorbidities, biochemical markers, medical treatment, renal pathology, edema, venous thromboembolism, bleeding, kidney failure, and death were collected. 
Results: Among 1,219 patients, 758 (62%) had edema at diagnosis. Patients with edema had a higher urine albumin creatinine ratio (4245 mg/g [3046-6079] vs. 3546 mg/g [2691-5125]) or a higher 24-hour urine albumin excretion rate (4559 mg/day [3146-6591] vs. 3546 mg/day [2828-5578]) and lower plasma albumin (26 g/l [22-28] vs. 28 g/l [26-29]) than those without edema. Venous thromboembolism occurred in 54 (4%) patients, with an incidence rate of 15 (95% CI, 11-21) per 1000 person-years in patients with edema vs. 10 (95% CI, 10-17) in patients without. Edema was also associated with faster kidney failure progression (edema: 188 days (IQR, 28-581); non-edema: 364 days (IQR, 116-920)) and higher one-year all-cause mortality (edema: 19%; non-edema: 16%).
Conclusion: Edema affects approximately 60% of patients with nephrotic-range albuminuria and hypoalbuminemia, associated with increased risk of venous thromboembolism, faster kidney failure progression, and higher one-year all-cause mortality, highlighting its prognostic information in nephrotic syndrome.
DOI: 10.6084/m9.figshare.28541504.v1
title: Supplementary Material for: Edema and Outcome in Patients with Nephrotic-Range Albuminuria and Hypoalbuminemia: A Danish Multicenter cohort study

description: Introduction: Nephrotic syndrome is characterized by proteinuria, hypoalbuminemia, and edema, though not all patients present with edema. This study investigates edema prevalence and its association with venous thromboembolism, kidney failure, and mortality in patients with nephrotic-range albuminuria and hypoalbuminemia.
Methods: We conducted a Danish multicenter cohort study, including patients with plasma albumin &lt;30 g/L and nephrotic-range albuminuria in the Central Denmark Region (2012-2022). Patients were identified using the laboratory information system and followed until death, lost to follow-up, or end of study. Data on demographics, comorbidities, biochemical markers, medical treatment, renal pathology, edema, venous thromboembolism, bleeding, kidney failure, and death were collected. 
Results: Among 1,219 patients, 758 (62%) had edema at diagnosis. Patients with edema had a higher urine albumin creatinine ratio (4245 mg/g [3046-6079] vs. 3546 mg/g [2691-5125]) or a higher 24-hour urine albumin excretion rate (4559 mg/day [3146-6591] vs. 3546 mg/day [2828-5578]) and lower plasma albumin (26 g/l [22-28] vs. 28 g/l [26-29]) than those without edema. Venous thromboembolism occurred in 54 (4%) patients, with an incidence rate of 15 (95% CI, 11-21) per 1000 person-years in patients with edema vs. 10 (95% CI, 10-17) in patients without. Edema was also associated with faster kidney failure progression (edema: 188 days (IQR, 28-581); non-edema: 364 days (IQR, 116-920)) and higher one-year all-cause mortality (edema: 19%; non-edema: 16%).
Conclusion: Edema affects approximately 60% of patients with nephrotic-range albuminuria and hypoalbuminemia, associated with increased risk of venous thromboembolism, faster kidney failure progression, and higher one-year all-cause mortality, highlighting its prognostic information in nephrotic syndrome.
DOI: 10.15468/dl.9cywk3
title: Occurrence Download

description: A dataset containing 149415 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-35 32,40 32,40 73,-35 73,-35 32))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aquila chrysaetos (Linnaeus, 1758)",
 "Year 2015-2025"
 ]
}

 The dataset includes 149415 records from 352 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006245-250227182400228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sxdcch
title: Occurrence Download

description: A dataset containing 36066 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Danaus chrysippus (Linnaeus, 1758)"
 ]
}

 The dataset includes 36066 records from 263 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004295-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v4jhv5
title: Occurrence Download

description: A dataset containing 690 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Capra sibirica (Pallas, 1776)"
 ]
}

 The dataset includes 690 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004298-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10039197
title: World Weather Repository ( Daily Updating )
DOI: 10.15468/dl.wgceyr
title: Occurrence Download

description: A dataset containing 620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Sasa megalophylla Makino & Uchida)"
 ]
}

 The dataset includes 620 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004299-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6yq69g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Semiaquilegia guangxiensis Yan Liu & Y.S.Huang)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004301-241126133413365/datasets/export for details.
DOI: 10.15468/dl.eq669k
title: Occurrence Download

description: A dataset containing 6372 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Acacia Mill."
 ]
}

 The dataset includes 6372 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004302-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rw9jsr
title: Occurrence Download

description: A dataset containing 4474 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Appias paulina (Cramer, 1777)"
 ]
}

 The dataset includes 4474 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004303-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13881900
title: UNEP GEMS/Water Global Freshwater Quality Archive

description: Large-sample datasets are essential in hydrological science to support modelling studies and global assessments. The present dataset compiles all freshwater quality data that is available under open data policy (CC BY 4.0 or equivalent) at the GEMStat database for global water quality (www.gemstat.org). It includes over 20,000,000 measurements on 608 water quality parameters, covering 13,660 stations in 37 countries over the time period from 1906 to 2023.

GEMStat is operated by the GEMS/Water programme of the United Nations Environment Programme (UNEP) and hosted at the International Centre for Water Resources and Global Change (ICWRGC) and the German Federal Institute of Hydrology (BfG). The data in GEMStat is provided by National Hydrological Services of UN member states.

The data available here at Zenodo consists of a zip archive with individual csv files for different parameter groups. Three csv files provide metadata information on stations (GEMStat_station_metadata.csv), parameters (GEMStat_parameter_metadata.csv) and analytical methods (GEMStat_method_metadata.csv). A text file (README_output_format.txt) gives information on the different entriy classes in the data files.
DOI: 10.15468/dl.m9tvmb
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Sasa miakeana Sad.Suzuki)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004306-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.crdupf
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polygonum dumosum Boiss."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004305-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aqsqtv
title: Occurrence Download

description: A dataset containing 8154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyperus rotundus L.",
 {
 "or" : [
 "Year 1961-1977",
 "Year 2011-2024"
 ]
 }
 ]
}

 The dataset includes 8154 records from 472 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004300-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzy8n9
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Semiaquilegia quelpaertensis D.C.Son & K.H.Lee)"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004308-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ec88ka
title: Occurrence Download

description: A dataset containing 2444 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flore des Pyrénées"
 ]
}

 The dataset includes 2444 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004309-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.354nfs
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Sasa minensis Sad.Suzuki)"
 ]
}

 The dataset includes 39 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004310-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d6upgh
title: Occurrence Download

description: A dataset containing 5955 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acytolepis puspa (Horsfield, 1828)"
 ]
}

 The dataset includes 5955 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004311-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nerh5j
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Urophysa henryi (Oliv.) Ulbr.)"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004312-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pbenwh
title: Occurrence Download

description: A dataset containing 9107 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centrolenidae",
 "HasCoordinate is true",
 "BasisOfRecord is Specimen"
 ]
}

 The dataset includes 9107 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004313-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ur2u5r
title: Occurrence Download

description: A dataset containing 1176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Sasa nipponica (Makino) Makino & Shibata)"
 ]
}

 The dataset includes 1176 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004315-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sscaw5
title: Occurrence Download

description: A dataset containing 483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Polygonum humifusum Mert. ex K.Koch"
 ]
}

 The dataset includes 483 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004314-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.znabu5
title: Occurrence Download

description: A dataset containing 1030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Poa pratensis L."
 ]
}

 The dataset includes 1030 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004316-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n67y9x
title: Occurrence Download

description: A dataset containing 4119 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nacaduba kurava (Moore)"
 ]
}

 The dataset includes 4119 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004317-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pk454a
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Urophysa rockii Ulbr.)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004319-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ubb4bh
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Sasa occidentalis Sad.Suzuki)"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004320-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/ua58-9rj6
title: Measurement of Inorganics in precipitation at Keldsnor

description: Measurement of Inorganics in precipitation at Keldsnor
DOI: 10.15468/dl.zdcp4z
title: Occurrence Download

description: A dataset listing the 13 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sizing Ocean Giants"
 ]
}

 The dataset's 13 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004297-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.