cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0141037.10fu
title: SH0141037.10FU

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: 10.13145/bacdive154080.20251217.10
title: Capnocytophaga canis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154081.20241212.9.2
title: Escherichia coli

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141038.10fu
title: SH0141038.10FU

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: 10.13145/bacdive154081.20251217.10
title: Escherichia coli

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141039.10fu
title: SH0141039.10FU

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: 10.13145/bacdive154082.20241212.9.2
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154082.20251217.10
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141040.10fu
title: SH0141040.10FU

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: 10.13145/bacdive154083.20241212.9.2
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154083.20251217.10
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154084.20241212.9.2
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154084.20251217.10
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141041.10fu
title: SH0141041.10FU

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: 10.13145/bacdive154085.20241212.9.2
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154085.20251217.10
title: Haematobacter massiliensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154086.20241212.9.2
title: Haematobacter missouriensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141042.10fu
title: SH0141042.10FU

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: 10.3535/hfn-0fb-bgm
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/t7f-xh7-xw0
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xva-f6f-w8c
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.13145/bacdive154086.20251217.10
title: Haematobacter missouriensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive154087.20241212.9.2
title: Haematobacter missouriensis

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15156/bio/sh0141043.10fu
title: SH0141043.10FU

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: 10.3535/2mm-aqt-906
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/2ts-ea2-6jf
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/73h-mgy-ap6
title: Lypusidae Herrich-Schäffer, 1857

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.34740/kaggle/dsv/11212016
title: T-Física Postulates by Tiberius
DOI: 10.15468/dl.zxc86t
title: Occurrence Download

description: A dataset containing 1025 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-97.01994 28.79528,-89.83946 28.79528,-89.83946 30.78928,-97.01994 30.78928,-97.01994 28.79528))",
 "TaxonKey is Myocastor coypus (Molina, 1782)"
 ]
}

 The dataset includes 1025 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006529-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15107478
title: Toy input dataset for "snrnaseq-step2-cell-typing" code, from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667)

description: This is a toy dataset that can be used to run code step #2 from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667), which performs likelihood-based cell typing of single-nucleus RNA sequencing data (Github: https://github.com/amwilson149/snrnaseq-step2-cell-typing/tree/main).

To test the code on this dataset, place these files in the 'data' directory of the code repository, and unzip the compressed files. Then run the script.

 

A description of the study using this code follows:

For people with HIV (PWH), substance use disorders (SUDs) are a prominent neurological risk factor, and the impacts of both on dopaminergic pathways are a potential point of deleterious convergence. Here, we profile, at single nucleus resolution, the substantia nigra (SN) transcriptomes of 90 postmortem donors in the context of chronic HIV and opioid/cocaine SUD, including 67 prospectively characterized PWH. We report altered microglial expression for hundreds of pro- and anti-inflammatory regulators attributable to HIV, and separately, to SUD. Stepwise, progressive microglial dysregulation, coupled to altered SN dopaminergic and GABAergic signaling, was associated with SUD/HIV dual diagnosis and further with lack of viral suppression in blood. In virologically suppressed donors, SUD comorbidity was associated with microglial transcriptional changes permissive for HIV infection. We report HIV-related downregulation of monoamine reuptake transporters specifically in dopaminergic neurons regardless of SUD status or viral load, and additional transcriptional signatures consistent with selective vulnerability of SN dopamine neurons.
DOI: 10.5281/zenodo.15107479
title: Toy input dataset for "snrnaseq-step2-cell-typing" code, from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667)

description: This is a toy dataset that can be used to run code step #2 from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667), which performs likelihood-based cell typing of single-nucleus RNA sequencing data (Github: https://github.com/amwilson149/snrnaseq-step2-cell-typing/tree/main).

To test the code on this dataset, place these files in the 'data' directory of the code repository, and unzip the compressed files. Then run the script.

 

A description of the study using this code follows:

For people with HIV (PWH), substance use disorders (SUDs) are a prominent neurological risk factor, and the impacts of both on dopaminergic pathways are a potential point of deleterious convergence. Here, we profile, at single nucleus resolution, the substantia nigra (SN) transcriptomes of 90 postmortem donors in the context of chronic HIV and opioid/cocaine SUD, including 67 prospectively characterized PWH. We report altered microglial expression for hundreds of pro- and anti-inflammatory regulators attributable to HIV, and separately, to SUD. Stepwise, progressive microglial dysregulation, coupled to altered SN dopaminergic and GABAergic signaling, was associated with SUD/HIV dual diagnosis and further with lack of viral suppression in blood. In virologically suppressed donors, SUD comorbidity was associated with microglial transcriptional changes permissive for HIV infection. We report HIV-related downregulation of monoamine reuptake transporters specifically in dopaminergic neurons regardless of SUD status or viral load, and additional transcriptional signatures consistent with selective vulnerability of SN dopamine neurons.
DOI: 10.15468/dl.q3x55f
title: Occurrence Download

description: A dataset containing 2285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-124.96954 26.54627,-60.59628 26.54627,-60.59628 48.20345,-124.96954 48.20345,-124.96954 26.54627))",
 "TaxonKey is Brassica tournefortii Gouan"
 ]
}

 The dataset includes 2285 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006531-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aey6up
title: Occurrence Download

description: A dataset containing 4457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-124.80478 25.16603,-66.4592 25.16603,-66.4592 48.5868,-124.80478 48.5868,-124.80478 25.16603))",
 "TaxonKey is Bromus tectorum L."
 ]
}

 The dataset includes 4457 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006530-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xkr89m
title: Occurrence Download

description: A dataset containing 1985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-1000000.0",
 "Geometry POLYGON((-127.69427 24.39873,-60.42675 24.39873,-60.42675 49.48153,-127.69427 49.48153,-127.69427 24.39873))",
 "TaxonKey is Salsola tragus L."
 ]
}

 The dataset includes 1985 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006532-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nb824c
title: Occurrence Download

description: A dataset containing 31575 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Occurrence evidence)",
 "Country is New Zealand",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi",
 "Year 2023-2024"
 ]
}

 The dataset includes 31575 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006533-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sny34n
title: Occurrence Download

description: A dataset containing 3835 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-122.32131 32.64828,-114.56186 32.64828,-114.56186 37.64508,-122.32131 37.64508,-122.32131 32.64828))",
 "TaxonKey is Linepithema humile (Mayr, 1868)"
 ]
}

 The dataset includes 3835 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006535-250325103851331/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.28691627
title: data.zip

description: This study investigates the impact of China’s construction of high-standard farmland (CHSF) initiatives on grain productivity, focusing on total factor productivity growth of grain (TFPG) from 2000 to 2021. Using a continuous Difference-in-Differences (DID) approach based on balanced panel data from 31 Chinese provinces, this paper identifies significant productivity improvements, with TFPG increasing by an average of 7% post-implementation of CHSF. However, the effects are not uniform across regions—productivity gains are more pronounced in non-major grain-producing and plain areas, emphasizing the role of region-specific infrastructure and adaptive strategies. These findings provide empirical evidence on how large-scale farmland improvement enhances productivity through mechanization and better land use. However, the reliance on provincial-level data may overlook localized variations in CHSF implementation, suggesting the need for further micro-level analysis. Overall, this study highlights the importance of tailored agricultural policies to enhance their effectiveness and promote agricultural sustainability in China and other developing economies.
DOI: 10.15468/dl.4pg3j3
title: Occurrence Download

description: A dataset containing 598 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Fulvetta striaticollis (J.Verreaux, 1870)"
 ]
}

 The dataset includes 598 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006536-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.at6e43
title: Occurrence Download

description: A dataset listing the 31 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "Locality is one of (buriticá, antioquia, co (6.694, -75.898))"
 ]
}

 The dataset's 31 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006534-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xr78rs
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Geometry POLYGON((-124.81013 26.68143,-81.22837 26.68143,-81.22837 49.13768,-124.81013 49.13768,-124.81013 26.68143))",
 "TaxonKey is Salsola kali L."
 ]
}

 The dataset includes 52 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006540-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/b1v4-1k27
title: Alveolar bone density measurements

description: Objective: Oral implant procedures necessitate the assessment of alveolar bone, a vital tooth-supporting structure. While micro-computed tomography (micro-CT) is the gold standard for bone volume fraction measurement for its high spatial resolution and contrast between bone and soft tissue, its substantial radiation exposure limits use to ex vivo specimens. This study evaluates the accuracy of 1.5T magnetic resonance imaging (MRI) in determining bone volume fraction, using micro-CT as the reference. Results: Twenty-one alveolar bone specimens (mean age: 52.9 years; range: 24–82; M/F: 15/6) were subjected to 1.5T MRI. The comparison between 1.5T and 14T MRI demonstrated a statistically significant correlation (r = 0.76, p &lt; 0.0001), similar to the comparison with micro-CT (r = 0.70, p &lt; 0.0001). Consistency in results was affirmed through repeated scans and analytical recalculations. Conclusion