cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.8qvp3t
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Percina tanasi Etnier, 1976"
 ]
}

 The dataset includes 59 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0283607-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g674hh
title: Occurrence Download

description: A dataset containing 1392 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epinephelus malabaricus (Bloch & Schneider, 1801)"
 ]
}

 The dataset includes 1392 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017302-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxfu8r
title: Occurrence Download

description: A dataset containing 388563 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-145.23047 80.30742,-40.7461 58.51055,-15.15236 58.36992,4.57031 87.7711,-171.77344 87.7711,-145.23047 80.30742))",
 "HasCoordinate is true",
 "TaxonKey is Tracheophyta",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 388563 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001124-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xapt4g
title: Occurrence Download

description: A dataset containing 25242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myocastor coypus (Molina, 1782)",
 "Year is one of (1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023)",
 "Country is one of (Germany, Belgium, Netherlands)"
 ]
}

 The dataset includes 25242 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008301-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sve4fp
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Grampus griseus (G.Cuvier, 1812)"
 ]
}

 The dataset includes 112 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008302-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c56h4d23c
title: MassIVE MSV000095209 - sample001, 002, raw data_microMASST try 1
title: sample001, 002, raw data_microMASST try 1 _24.07.02
DOI: 10.15468/dl.pv8f5h
title: Occurrence Download

description: A dataset containing 257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hippoglossoides dubius Schmidt, 1904",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 257 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008303-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17031/668280a84bfe2
title: 2000-2001 Strong et al. UK Sargassum muticum records

description: A collection of Non-Native Species sightings from James Strong. The species listed is Sargassum muticum.
description: Part of MSFD NNS baseline data collation project (Jan 2016). Subset of a dataset as we were only pulling out records for a selection of INNS. Contains records for Sargassum muticum.
See Strong, J. A., Dring, M. J., Maggs, C. A. (2006). Colonisation and modification of soft substratum habitats by the invasive macroalga Sargassum muticum. Marine Ecology Progress Series, 321, 87-97. for original source.
DOI: 10.15468/dl.v3jv3w
title: Occurrence Download

description: A dataset containing 17346 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ondatra zibethicus (Linnaeus, 1766)",
 {
 "not" : {
 "DatasetKey" : [
 "is one of (MICA - Muskrat occurrences collected by RATO in East Flanders, Belgium, MICA - Muskrat and coypu camera trap observations in Belgium, the Netherlands and Germany, MICA - Muskrat occurrences collected by VMM in Flanders, Belgium, Mica - Muskrat, Raccoon and Coypu occurrences collected by ITAW in Germany, Muskrat captures in Flanders, Belgium, MICA - Muskrat and coypu occurrences collected by UVW in the Netherlands, Muskrat trapping data in the Netherlands 1987 – 2014, RATO - daily operations commissioned by the province East Flanders, Belgium, VMM - Rat control occurrences in Flanders, Belgium)"
 ]
 }
 },
 "Year is one of (1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023)",
 "Country is one of (Germany, Belgium, Netherlands)"
 ]
}

 The dataset includes 17346 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008304-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4j3994
title: Occurrence Download

description: A dataset containing 98802 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dryas octopetala L."
 ]
}

 The dataset includes 98802 records from 602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008292-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fhcfv
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cynoglossus joyneri Günther, 1878",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 208 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008305-240626123714530/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.26145340
title: ISIC 2016 Dataset with background remove

description: This dataset is part of research to provide high level local explantions
DOI: 10.6084/m9.figshare.26145340.v1
title: ISIC 2016 Dataset with background remove

description: This dataset is part of research to provide high level local explantions
DOI: 10.15468/dl.k8s67v
title: Occurrence Download

description: A dataset containing 725 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vatica odorata (Griff.) Symington"
 ]
}

 The dataset includes 725 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008306-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17633/rd.brunel.26139844
title: Unveiling the inherent properties and impact of ultrafine nanobubbles in polar and alcoholic media through unsupervised machine learning and atomic insight

description: The dataset include all the data used in the following publication.
Hassanloo, Hamidreza, and Xinyan Wang. "Unveiling the inherent properties and impact of ultrafine nanobubbles in polar and alcoholic media through unsupervised machine learning and atomic insight." <em>International Journal of Thermofluids</em> (2024): 100734.
<br>
<br>
DOI: 10.17633/rd.brunel.26139844.v1
title: Unveiling the inherent properties and impact of ultrafine nanobubbles in polar and alcoholic media through unsupervised machine learning and atomic insight

description: The dataset include all the data used in the following publication.
Hassanloo, Hamidreza, and Xinyan Wang. "Unveiling the inherent properties and impact of ultrafine nanobubbles in polar and alcoholic media through unsupervised machine learning and atomic insight." <em>International Journal of Thermofluids</em> (2024): 100734.
<br>
<br>
DOI: 10.15468/dl.4a4a4c
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "TaxonKey is Hyperoodon planifrons Flower, 1882"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008307-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x5kquy
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vatica perakensis King"
 ]
}

 The dataset includes 34 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008309-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gc5mea
title: Occurrence Download

description: A dataset containing 253 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Apostichopus japonicus (Selenka, 1867)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 253 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008308-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wx4z66
title: Occurrence Download

description: A dataset containing 14539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myocastor coypus (Molina, 1782)",
 {
 "not" : {
 "DatasetKey" : [
 "is one of (MICA - Muskrat occurrences collected by RATO in East Flanders, Belgium, MICA - Muskrat and coypu camera trap observations in Belgium, the Netherlands and Germany, MICA - Muskrat occurrences collected by VMM in Flanders, Belgium, Mica - Muskrat, Raccoon and Coypu occurrences collected by ITAW in Germany, Muskrat captures in Flanders, Belgium, MICA - Muskrat and coypu occurrences collected by UVW in the Netherlands, Muskrat trapping data in the Netherlands 1987 – 2014, RATO - daily operations commissioned by the province East Flanders, Belgium, VMM - Rat control occurrences in Flanders, Belgium)"
 ]
 }
 },
 "Year is one of (1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023)",
 "Country is one of (Germany, Belgium, Netherlands)"
 ]
}

 The dataset includes 14539 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008310-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzkj66
title: Occurrence Download

description: A dataset containing 1011 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Vatica rassak (Korth.) Blume"
 ]
}

 The dataset includes 1011 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008311-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12620771
title: The Hitchhiker's Guide to scRNA-seq course

description: This repository comprises the intermediate results, data, and the respective script to create it, to be use on the second day of the course The Hitchhiker's Guide to scRNA-seq (08-12/07/2024, iMM, Lisbon, Portugal), focused on integration. 

File description: 



data: 



pbmcref.rds: a Seurat R object of a reference of PBMCs retrieved from the R package SeuratData (v.0.2.2.9001)

pbmc3k_panc8.rds: a Seurat R object of two data sets - 3k human PBMCs from 10X Genomics and pancreatic islets from indrop1 - retrieved from SeuratData package (v.0.2.2.9001) 

jurkat.rds: a Seurat R object comprising three data sets - Jurkat, HEK293T and Jurkat:HEK293T (50:50) - retrieved from 10X genomics and published by Zheng et al., 2017

ifnb.rds: a Seurat R object of two human PBMCs data sets - resting/control and interferon-stimulated - retrieved from the R package SeuratData (v.0.2.2.9001)

covid.rds: a Seurat R object of a COVID-19 PBMCs data set from Guo et al., 2020 retrieved from cziscience



01_create_datasets.R: R script used to retrieve and parse all the Seurat R objects mentioned above

results.zip: compressed folder with intermediate results used for the hands-on exercises
DOI: 10.5281/zenodo.12620772
title: The Hitchhiker's Guide to scRNA-seq course

description: This repository comprises the intermediate results, data, and the respective script to create it, to be use on the second day of the course The Hitchhiker's Guide to scRNA-seq (08-12/07/2024, iMM, Lisbon, Portugal), focused on integration. 

File description: 



data: 



pbmcref.rds: a Seurat R object of a reference of PBMCs retrieved from the R package SeuratData (v.0.2.2.9001)

pbmc3k_panc8.rds: a Seurat R object of two data sets - 3k human PBMCs from 10X Genomics and pancreatic islets from indrop1 - retrieved from SeuratData package (v.0.2.2.9001) 

jurkat.rds: a Seurat R object comprising three data sets - Jurkat, HEK293T and Jurkat:HEK293T (50:50) - retrieved from 10X genomics and published by Zheng et al., 2017

ifnb.rds: a Seurat R object of two human PBMCs data sets - resting/control and interferon-stimulated - retrieved from the R package SeuratData (v.0.2.2.9001)

covid.rds: a Seurat R object of a COVID-19 PBMCs data set from Guo et al., 2020 retrieved from cziscience



01_create_datasets.R: R script used to retrieve and parse all the Seurat R objects mentioned above

results.zip: compressed folder with intermediate results used for the hands-on exercises
DOI: 10.6084/m9.figshare.26038018.v1
title: Supplementary Reproducible Workflow Datapack for Veseli et al. 2023

description: Datapack for the supplementary reproducible workflow associated with the study by Veseli et al. titled "Microbes with higher metabolic independence are enriched in human gut microbiomes under stress" (https://doi.org/10.7554/eLife.89862.1). Contains data, scripts, and output files used to validate our approach to compute per-population copy numbers of metabolic pathways from metagenomic data. See
DOI: 10.5281/zenodo.12530688
title: Düsseldorf Pelikan Apotheke

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963[Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).
DOI: 10.15468/dl.h858cv
title: Occurrence Download

description: A dataset containing 8825 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Argyroneta aquatica (Clerck, 1757)"
 ]
}

 The dataset includes 8825 records from 191 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008312-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12621726
title: Freshwater ecosystem transitions due to artisanal sand mining in Rwanda, Africa

description: Artisanal small-scale mining (ASM) of sand, gravel and crushed stones plays an economically important role through its value as a ‘development mineral’ for a growing population in sub-saharan Africa. The extracted material is used in developing and expanding urban areas and infrastructure and provides income for the population involved in the sector. However, the extraction of aggregates has shown to have large and often complex ecological and socio-economical consequences with potential significant health effects on the miners and the environment in which the mining takes place. Furthermore, the extent in which these negative effects do arise from ASM in sub-Saharan still remains anecdotal and are largely unknown. Here we show that ASM in a river channel in central Rwanda causes a systemic shift in freshwater biodiversity by changing species assemblages from being riverine towards communities representing standing waters. Based on 101 point samples, we find that ponds created due to mining activities act as habitats for freshwater insects associated with wetland habitats. Furthermore, these mining ponds did also act as breeding sites for mosquitoes and thereby potentially increase the presence of vector borne diseases such as malaria. These findings show how ASM can generate a landscape level shift in freshwater biodiversity and introduces the apparent paradox that while aggregates are critical building blocks in mitigating malaria transmissions and prevalence through improved housing, the mining practices unwillingly can create new breeding ground for malaria mosquitos, thus increasing the risk of malaria spreading to nearby communities.
DOI: 10.5281/zenodo.12621727
title: Freshwater ecosystem transitions due to artisanal sand mining in Rwanda, Africa

description: Artisanal small-scale mining (ASM) of sand, gravel and crushed stones plays an economically important role through its value as a ‘development mineral’ for a growing population in sub-saharan Africa. The extracted material is used in developing and expanding urban areas and infrastructure and provides income for the population involved in the sector. However, the extraction of aggregates has shown to have large and often complex ecological and socio-economical consequences with potential significant health effects on the miners and the environment in which the mining takes place. Furthermore, the extent in which these negative effects do arise from ASM in sub-Saharan still remains anecdotal and are largely unknown. Here we show that ASM in a river channel in central Rwanda causes a systemic shift in freshwater biodiversity by changing species assemblages from being riverine towards communities representing standing waters. Based on 101 point samples, we find that ponds created due to mining activities act as habitats for freshwater insects associated with wetland habitats. Furthermore, these mining ponds did also act as breeding sites for mosquitoes and thereby potentially increase the presence of vector borne diseases such as malaria. These findings show how ASM can generate a landscape level shift in freshwater biodiversity and introduces the apparent paradox that while aggregates are critical building blocks in mitigating malaria transmissions and prevalence through improved housing, the mining practices unwillingly can create new breeding ground for malaria mosquitos, thus increasing the risk of malaria spreading to nearby communities.
DOI: 10.15468/dl.psa948
title: Occurrence Download

description: A dataset containing 254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Doederleinia berycoides (Hilgendorf, 1879)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 254 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008313-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17031/668285e25e953
title: 2008 Mineur et al. UK west coast records for Bonnemaisonia hamifera

description: It has traditionally been considered that areas with high natural species richness are likely to be more resistant to non-indigenous species than those with lower numbers of species. However, this theory has been the subject of a debate ove rthe last decade, since some studies have shown the opposite trend. In the present study, a macroalgal survey was carried out at 24 localities in Northern Ireland and southern England, using a quadrat approach in the lower littoral. The two opposing hypotheses were tested (negative versus positive relationship between native and non-indigenous species richness) in this marine environment. The effect of the presence of ‘impacts’, potential sources of disturbance and species introduction(e.g. marina, harbour or aquaculture), was also tested. A positive relationship was found between the number of non-indigenous species and the native species richness at the three different scales tested (quadrats, sites and localities). At no scale did a richer native assemblage appear to restrict the establishment of introduced species. The analyses revealed greater species richness and different community composition, as well as more non-indigenous species, in southern England relative to Northern Ireland. The presence of the considered impacts had an effect on the community composition and species richness in southern England but not in Northern Ireland. Such impacts had no effect on the non-indigenous species richness in either area.
description: Part of MSFD NNS baseline data collation project (Jan 2016). Subset of a dataset as we were only pulling out records for a selection of INNS. Contains records for Bonnemaisonia hamifera.

See Non-indigenous marine macroalgae in native communities: A case study in the British Isles. Journal of the Marine Biological Association of the United Kingdom, 2008, 88(4), 693–698. DOI: 10.1017/S0025315408001409 for original source
DOI: 10.5281/zenodo.12621660
title: Düsseldorf Pfalz Apotheke

description: Historical questionnaire/s 1924/1948 and index cards, partly selected enclosures regarding the history of a German pharmacy, catalogued via Kalliope portal (Historischer Fragebogen 1924/1948 und Karteikarten, ggf. gemeinfreie Anlagen zur Apothekengeschichte; als Katalog dient das Nachlassportal Kalliope): https://kalliope-verbund.info/DE-611-BF-70963[Funktion: Im Findbuch anzeigen]Please note: The Kalliope catalogue entry might indicate related material in the archival folder which cannot be published due to copyright or other legal restrictions (NB: Das Katalogisat bei Kalliope kann auch auf Materialien - teils erheblichen Umfangs - verweisen, die aus archiv- oder urheberrechtlichen Gründen nicht veröffentlicht werden dürfen).