cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3x9akd
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pterophylla croftii (H.C.Hopkins) Pillon & H.C.Hopkins"
 ]
}

 The dataset includes 59 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083569-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2yqquk
title: Occurrence Download

description: A dataset containing 3778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Castanea mollissima Blume",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3778 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083568-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3c4fb8
title: Occurrence Download

description: A dataset containing 1409 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Uncaria rhynchophylla (Miq.) Miq."
 ]
}

 The dataset includes 1409 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083562-240321170329656/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.25284700
title: Environmental reservoirs of Pseudomonads Mubassu et al., 2024.xlsx

description: Identification of Pseudomonad water reservoirs in 6 sub locations and a hospital in Kisumu county. samples 297 samplepes and identified 7 species of pseudomonads on Vitek 2. conducted antimicrobial susceptibility for the 42 resultant isolates on Vitek2.
DOI: 10.6084/m9.figshare.25284700.v2
title: Environmental reservoirs of Pseudomonads Mubassu et al., 2024.xlsx

description: Identification of Pseudomonad water reservoirs in 6 sub locations and a hospital in Kisumu county. samples 297 samplepes and identified 7 species of pseudomonads on Vitek 2. conducted antimicrobial susceptibility for the 42 resultant isolates on Vitek2.
DOI: 10.6084/m9.figshare.25284700.v1
title: Environmental reservoirs of Pseudomonads Mubassu et al., 2024.xlsx

description: Identification of Pseudomonad water reservoirs in 6 sub locations and a hospital in Kisumu county. samples 297 samplepes and identified 7 species of pseudomonads on Vitek 2. conducted antimicrobial susceptibility for the 42 resultant isolates on Vitek2.
DOI: 10.5281/zenodo.10892755
title: DELiVR supporting files (training weights, additional components for inference docker container)

description: Initial Release of the supporting data for the DELiVR cleared-brain analysis pipeline, as described in our 2024 publication: 

Virtual reality-empowered deep-learning analysis of brain cells

Kaltenecker, Al-Maskari, Negwer, et al., Nature Methods 2024

https://doi.org/10.1038/s41592-024-02245-2

This repository contains the following datasets:



Training weights for microglia inference

Training weights for c-fos inference (as used in the paper)

The copy of Terastitcher that we used to build the inference container 

The copy of mBrainAligner that we used to build the inference container

The Dockerfile that we used to build the inference container 

The Ilastik version that we used to build the inference container 


Source code for TeraStitcher: https://github.com/abria/TeraStitcher

Source code for mBrainaligner: https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner 

Download for this specific version of the Ilastik binaries: https://files.ilastik.org/ilastik-1.4.0b8-Linux.tar.bz2
DOI: 10.5281/zenodo.10892756
title: DELiVR supporting files (training weights, additional components for inference docker container)

description: Initial Release of the supporting data for the DELiVR cleared-brain analysis pipeline, as described in our 2024 publication: 

Virtual reality-empowered deep-learning analysis of brain cells

Kaltenecker, Al-Maskari, Negwer, et al., Nature Methods 2024

https://doi.org/10.1038/s41592-024-02245-2

This repository contains the following datasets:



Training weights for microglia inference

Training weights for c-fos inference (as used in the paper)

The copy of Terastitcher that we used to build the inference container 

The copy of mBrainAligner that we used to build the inference container

The Dockerfile that we used to build the inference container 

The Ilastik version that we used to build the inference container 


Source code for TeraStitcher: https://github.com/abria/TeraStitcher

Source code for mBrainaligner: https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner 

Download for this specific version of the Ilastik binaries: https://files.ilastik.org/ilastik-1.4.0b8-Linux.tar.bz2
DOI: 10.5281/zenodo.10908579
title: spatula_versicolor_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.10908580
title: spatula_versicolor_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.10892729
title: DELiVR example dataset

description: Example dataset for our DELiVR pipeline, as published in: 

Virtual reality-empowered deep-learning analysis of brain cells

Kaltenecker, Al-Maskari, Negwer, et al., Nature Methods 2024

https://doi.org/10.1038/s41592-024-02245-2

 

This archive contains one stack of 16-bit tiff images, taken from a cleared mouse brain stained for c-Fos and imaged using a light-sheet microscope (voxel resolution 1.625 x 1.625 x 6 µm in X/Y/Z)
DOI: 10.5281/zenodo.10892730
title: DELiVR example dataset

description: Example dataset for our DELiVR pipeline, as published in: 

Virtual reality-empowered deep-learning analysis of brain cells

Kaltenecker, Al-Maskari, Negwer, et al., Nature Methods 2024

https://doi.org/10.1038/s41592-024-02245-2

 

This archive contains one stack of 16-bit tiff images, taken from a cleared mouse brain stained for c-Fos and imaged using a light-sheet microscope (voxel resolution 1.625 x 1.625 x 6 µm in X/Y/Z)
DOI: 10.15468/dl.vd46ay
title: Occurrence Download

description: A dataset containing 558132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHL.11_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 558132 records from 439 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083416-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5063/f1mk6bc7
title: Terrestrial subsidies and light affect an aquatic micro-ecosystem in unexpected ways

description: 1. The effects of resource subsidies on a recipient ecosystem depends on a variety of factors. First, increasing the supply of limiting nutrients tend to increase the accumulation of biomass across different compartments of the recipient food web. Second, in the case of aquatic microorganisms, this accumulation may also be contingent on inputs of energy through light, mediating interactions between heterotrophic bacteria and autotrophic algae. Third, macroscopic consumers feed upon microorganisms and recycle nutrients through excretion and egestion, profoundly affecting nutrient cycling.2. To examine the context-dependency of nutrient cycling in aquatic systems, we performed an experiment in mesocosms where we followed the responses of dissolved nutrients, microorganisms, and larvae of the cosmopolitan mosquito Culex quinquefasciatus (Diptera: Culicidae) to two terrestrial subsidies differing in C:nutrient, in combination with two light levels. 3. We found that the interactions amongst bacteria and algae themselves remained generally unimportant after accounting for treatment effects, and that light did mediate some of the effects of nutrient subsidies on micro-organisms. We also found that the presence of mosquito larvae was associated with altered concentrations of nitrogen in some treatments, ultimately benefitting algae. Finally, we found that low C:nutrient subsidies generally increased the development rate of mosquito larvae, and that increased light exposure led to higher mosquito survival.4. Overall, these patterns may be explained by strong nitrogen limitation in our system, causing both group of microorganisms to respond similarly to variations in nutrient supply without direct covariation, and to the key role of N recycling by mosquito larvae in sustaining algal densities in exposed treatments. 5. The context-dependency in our study may reflect elemental or molecular constraints other than phosphorus. Our experiment thus calls for greater synthesis amongst ecological theories.
DOI: 10.15468/dl.kgkrh3
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula cunninghamii King ex Craib"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083571-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rg573p
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hylotelephium spectabile (Boreau) H.Ohba",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 95 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083575-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p2c4s6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Achillea micrantha Willd.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083576-240321170329656/datasets/export for details.
DOI: 10.15468/dl.bm7gt7
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus liaotungensis Z.Wang & A.K.Skvortsov"
 ]
}

 The dataset includes 28 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083573-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frjn3n
title: Occurrence Download

description: A dataset containing 1107 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong"
 ]
}

 The dataset includes 1107 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083577-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jct7b8
title: Occurrence Download

description: A dataset containing 1560 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dianthus superbus L.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1560 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083578-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2z784v
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria pachygrammata Bremek."
 ]
}

 The dataset includes 131 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083574-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gfw5ax
title: Occurrence Download

description: A dataset containing 11527 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sciurus vulgaris Linnaeus, 1758",
 "Year is 2021",
 "Country is Netherlands"
 ]
}

 The dataset includes 11527 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083579-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ema6x
title: Occurrence Download

description: A dataset containing 743 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Morus nigra L."
 ]
}

 The dataset includes 743 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083570-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hknw45
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuduvaria multiovulata (C.E.C.Fisch.) J.Sinclair"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083582-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fzkd4
title: Occurrence Download

description: A dataset containing 85346 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cakile maritima Scop."
 ]
}

 The dataset includes 85346 records from 638 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083419-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m9u9kk
title: Occurrence Download

description: A dataset containing 131 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pterophylla decora (Tul.) J.Bradford & Z.S.Rogers"
 ]
}

 The dataset includes 131 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083583-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fdutwf
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Inga alba (Sw.) Willd."
 ]
}

 The dataset includes 80 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083581-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gtn7mj
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus robur L.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083585-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fam6va
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Virginia Aquarium Sea Turtle Research (aggregated per 1-degree cell)"
 ]
}

 The dataset includes 30 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083590-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.styd2r
title: Occurrence Download

description: A dataset containing 330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is Lund University Biological Museum - Zoological collections (MZLU)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Talpa europaea Linnaeus, 1758"
 ]
}

 The dataset includes 330 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083589-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.avuyh4
title: Occurrence Download

description: A dataset containing 32632 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (France, Spain, Andorra)",
 "OccurrenceStatus is Present",
 "TaxonKey is Amaranthus hybridus L."
 ]
}

 The dataset includes 32632 records from 563 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083591-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1762888.08fu
title: SH1762888.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh396813.07fu
title: SH396813.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh396814.07fu
title: SH396814.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1762889.08fu
title: SH1762889.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1762890.08fu
title: SH1762890.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.