cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0215166.10fu
title: SH0215166.10FU

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: 10.15156/bio/sh0215167.10fu
title: SH0215167.10FU

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: 10.15156/bio/sh0215168.10fu
title: SH0215168.10FU

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: 10.15156/bio/sh0215169.10fu
title: SH0215169.10FU

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: 10.15156/bio/sh0215170.10fu
title: SH0215170.10FU

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: 10.15156/bio/sh0215171.10fu
title: SH0215171.10FU

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: 10.15156/bio/sh0215172.10fu
title: SH0215172.10FU

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: 10.17044/scilifelab.28211678
title: nf-core/metatdenovo taxonomy

description: The data in this repository can be used to assign taxonomy to sequences with Diamond [Buchfink et al. 2015], particularly using the --diamond_dbs parameter in nf-core/metatdenovo, release 1.1 or later.Currently, the data available represents species-representative genomes from the Genome Taxonomy Database (GTDB), release R09-RS220 [Parks et al. 2018].File preparationAll species-representative genomes from GTDB were downloaded from the National Center for Biotechnology Information (NCBI) and annotated with Prokka [v. 1.14.6; Seemann 2014], and the sequences for all resulting proteins were used for this data. The taxonomy dump files (in NCBI taxonomy dump format) were created from the GTDB metadata with TaxonKit [v. 0.18.0; Shen and Ren 2021] and the Diamond database with Diamond [v. 2.1.10; Buchfink et al. 2015] in "taxonomy mode", i.e. using the taxonomy dump created with TaxonKit. (See below for commands used.)File descriptionsThere are five files:gtdb-r220.faa.gz: Fasta file with protein sequences. Not used by nf-core/metatdenovo but can be used to create the Diamond database below.gtdb-r220.taxonomy.dmnd: Diamond database with taxonomy information.gtdb-r220.names.dmp: Taxonomy dump file.gtdb-r220.nodes.dmp: Nodes dump file.gtdb-r220.seqid2taxid.tsv.gz: Mapping from protein accession to taxon.The Diamond database and taxonomy dump files can be used with nf-core/metatdenovo (Version &gt;1.1) by providing a csv file like below to the --diamond_dbs parameter. (Although Nextflow can use https-urls for paths, it is usually better to download the very large files and keep local copies.)db,dmnd_path,taxdump_names,taxdump_nodes,ranks,parse_with_taxdumpgtdb,gtdb_r220_repr.dmnd,gtdb_taxdump/names.dmp,gtdb_taxdump/nodes.dmp,domain;phylum;class;order;genus;species;strain,Commands used to prepare taxonomy dump files and the Diamond databaseTaxonomy dump: cut -f 1,19-20 *metadata.tsv | grep -v 'accession' | awk 'BEGIN { FS="\t" } { if ( $2 == "t" ) { print $1 "\t" $3 } }' | taxonkit create-taxdump --gtdb -O .Diamond database: gunzip -c gtdb-r220.faa.gz | sed '/^&gt;/s/ .*//' | diamond makedb --taxonmap gtdb-r220.seqid2taxid.tsv.gz --taxonnames gtdb-r220.names.dmp --taxonnodes gtdb-r220.nodes.dmp --db gtdb-r220.taxonomy.dmnd --no-parse-seqidsRevision history20250211 First version<br><br>
DOI: 10.17044/scilifelab.28211678.v1
title: nf-core/metatdenovo taxonomy

description: The data in this repository can be used to assign taxonomy to sequences with Diamond [Buchfink et al. 2015], particularly using the --diamond_dbs parameter in nf-core/metatdenovo, release 1.1 or later.Currently, the data available represents species-representative genomes from the Genome Taxonomy Database (GTDB), release R09-RS220 [Parks et al. 2018].File preparationAll species-representative genomes from GTDB were downloaded from the National Center for Biotechnology Information (NCBI) and annotated with Prokka [v. 1.14.6; Seemann 2014], and the sequences for all resulting proteins were used for this data. The taxonomy dump files (in NCBI taxonomy dump format) were created from the GTDB metadata with TaxonKit [v. 0.18.0; Shen and Ren 2021] and the Diamond database with Diamond [v. 2.1.10; Buchfink et al. 2015] in "taxonomy mode", i.e. using the taxonomy dump created with TaxonKit. (See below for commands used.)File descriptionsThere are five files:gtdb-r220.faa.gz: Fasta file with protein sequences. Not used by nf-core/metatdenovo but can be used to create the Diamond database below.gtdb-r220.taxonomy.dmnd: Diamond database with taxonomy information.gtdb-r220.names.dmp: Taxonomy dump file.gtdb-r220.nodes.dmp: Nodes dump file.gtdb-r220.seqid2taxid.tsv.gz: Mapping from protein accession to taxon.The Diamond database and taxonomy dump files can be used with nf-core/metatdenovo (Version &gt;1.1) by providing a csv file like below to the --diamond_dbs parameter. (Although Nextflow can use https-urls for paths, it is usually better to download the very large files and keep local copies.)db,dmnd_path,taxdump_names,taxdump_nodes,ranks,parse_with_taxdumpgtdb,gtdb_r220_repr.dmnd,gtdb_taxdump/names.dmp,gtdb_taxdump/nodes.dmp,domain;phylum;class;order;genus;species;strain,Commands used to prepare taxonomy dump files and the Diamond databaseTaxonomy dump: cut -f 1,19-20 *metadata.tsv | grep -v 'accession' | awk 'BEGIN { FS="\t" } { if ( $2 == "t" ) { print $1 "\t" $3 } }' | taxonkit create-taxdump --gtdb -O .Diamond database: gunzip -c gtdb-r220.faa.gz | sed '/^&gt;/s/ .*//' | diamond makedb --taxonmap gtdb-r220.seqid2taxid.tsv.gz --taxonnames gtdb-r220.names.dmp --taxonnodes gtdb-r220.nodes.dmp --db gtdb-r220.taxonomy.dmnd --no-parse-seqidsRevision history20250211 First version<br><br>
DOI: 10.15468/dl.39pps4
title: Occurrence Download

description: A dataset containing 159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Elaphodus cephalophus Milne-Edwards, 1872"
 ]
}

 The dataset includes 159 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002715-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24416/uu01-s0mhdm
title: Molecular simulation data package on the dielectric permittivity of nanoconfined geofluids with various salt concentrations

description: To determine the effect of salinity on the dielectric permittivity of nanoconfined geofluids, we employed molecular dynamics (MD) simulations of saline water confined in calcite slit nanochannels. This data package includes data points, figures, and MD input files to simulate the behaviour of saline water with various NaCl concentrations confined in calcite nanopores at ambient conditions. The dielectric behaviour of nanoconfined saline water deviates significantly compared to the bulk. However, the dielectric properties are weakly dependent on salinity for both the perpendicular and parallel dielectric permittivity components. The data is organized into nine folders referred to as Figure X, where X corresponds to the figure number in the primary publication and a Simulations folder containing the MD input files. All MD simulations were conducted using the LAMMPS package. Detailed information about the files and methods employed can be found in the accompanying readme file.
DOI: 10.15468/dl.73w2r5
title: Occurrence Download

description: A dataset containing 14237 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Scaevola taccada (Gaertn.) Roxb."
 ]
}

 The dataset includes 14237 records from 227 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002714-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13980957
title: Gedminiene_ea_Dukstelis_paleolake_climate reconstructions

description: Supplementary dataset related to the Gedminiene et al. manuscript, describing multiproxy analyses from a Late Glacial- Holocene core sequence from Dukštelis paleolake, SE Lithuania. This file includes:



Palynological data (pollen, using calibration data taxonomy, in percentages, for Ensemble of six calibrations models and for  calibration with Modern analogue technique (MAT)

Pollen-based reconstructions (temperatures and precipitation)
DOI: 10.5281/zenodo.13980956
title: Gedminiene_ea_Dukstelis_paleolake_climate reconstructions

description: Supplementary dataset related to the Gedminiene et al. manuscript, describing multiproxy analyses from a Late Glacial- Holocene core sequence from Dukštelis paleolake, SE Lithuania. This file includes:



Palynological data (pollen, using calibration data taxonomy, in percentages, for Ensemble of six calibrations models and for  calibration with Modern analogue technique (MAT)

Pollen-based reconstructions (temperatures and precipitation)
DOI: 10.34658/rdb.szdizg/7s6aza
title: Control of Mitochondrial Electron Transport Chain Flux and Apoptosis by Retinoic Acid Raman Imaging In Vitro Human Bronchial and Lung Cancerous Cells.pptx

description: Experimental data results used and discussed in the publication: "Control of Mitochondrial Electron Transport Chain Flux and Apoptosis by Retinoic Acid Raman Imaging In Vitro Human Bronchial and Lung Cancerous Cells."
DOI: 10.34658/rdb.szdizg/co9jnw
title: Confocal Raman imaging reveals the impact of retinoids on human breast cancer via monitoring the redox status of cytochrome c.pptx

description: Experimental data results used and discussed in the publication: "Confocal Raman imaging reveals the impact of retinoids on human breast cancer via monitoring the redox status of cytochrome c."
DOI: 10.34658/rdb.szdizg/pquh7i
title: Raman imaging and chemometric methods in human normal bronchial and cancer lung cells Raman biomarkers of lipid reprogramming.pptx

description: Experimental data results used and discussed in the publication: "Raman imaging and chemometric methods in human normal bronchial and cancer lung cells Raman biomarkers of lipid reprogramming."
DOI: 10.34658/rdb.szdizg
title: Abramczyk H. - OPUS-22 - The triangle: carotenoids-retinoids-cytochromes plays a key role in development and progress of cancer

description: The results of the research obtained as part of the OPUS-22 (NCN, UMO-2021/43/B/ST4/01547) scientific activity in the Laboratory of Laser Molecular Spectroscopy, Faculty of Chemistry, Lodz University of Technology. www.mitr.p.lodz.pl/raman
DOI: 10.34658/rdb.szdizg/21ecgr
title: Hemoglobin and cytochrome c reinterpreting the origins of oxygenation and oxidation in erytocytes and in vivo cancer lung cells.pptx

description: Experimental data results used and discussed in the publication: "Hemoglobin and cytochrome c reinterpreting the origins of oxygenation and oxidation in erytocytes and in vivo cancer lung cells."
DOI: 10.34658/rdb.szdizg/3hpzr4
title: Metabolism changes caused by glucose in normal and cancer human brain cell lines by Raman imaging and chemometric methods.pptx

description: Experimental data results used and discussed in the publication: "Metabolism changes caused by glucose in normal and cancer human brain cell lines by Raman imaging and chemometric methods."
DOI: 10.34658/rdb.szdizg/73yt2h
title: The role of cardiolipin and cytochrome c in mitochondrial metabolism of cancer cells determined by Raman imaging in vitro study on the brain glioblastoma U-87 MG cell line.pptx

description: Experimental data results used and discussed in the publication: "The role of cardiolipin and cytochrome c in mitochondrial metabolism of cancer cells determined by Raman imaging: in vitro study on the brain glioblastoma U-87 MG cell line."
DOI: 10.34658/rdb.szdizg/9rdvsl
title: Monitoring alterations of all-trans-retinal in human brain cancer cells by label-free confocal Raman imaging regulation of the redox status of cytochrome c.pptx

description: Experimental data results used and discussed in the publication: " Monitoring alterations of all-trans-retinal in human brain cancer cells by label-free confocal Raman imaging regulation of the redox status of cytochrome c."
DOI: 10.34658/rdb.szdizg/jjk6ft
title: The role of glucose and fructose on lipid droplet metabolism in human normal bronchial and cancer lung cells by Raman spectroscopy.pptx

description: Experimental data results used and discussed in the publication: "The role of glucose and fructose on lipid droplet metabolism in human normal bronchial and cancer lung cells by Raman spectroscopy."
DOI: 10.34658/rdb.szdizg/xormre
title: A Novel HER2 Protein Identification Methodology in Breast Cancer Cells Using Raman Spectroscopy and Raman Imaging An Analytical Validation Study.pptx

description: Experimental data results used and discussed in the publication: "A Novel HER2 Protein Identification Methodology in Breast Cancer Cells Using Raman Spectroscopy and Raman Imaging: An Analytical Validation Study."
DOI: 10.34658/rdb.szdizg/yiw2kk
title: Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging.pptx

description: Experimental data results used and discussed in the publication: "Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging."
DOI: 10.34658/rdb.szdizg/ykiypa
title: Biochemical changes in lipid and protein metabolism caused by mannose-Raman spectroscopy studies.pptx

description: Experimental data results used and discussed in the publication: "Biochemical changes in lipid and protein metabolism caused by mannose-Raman spectroscopy studies."
DOI: 10.15468/dl.6bz644
title: Occurrence Download

description: A dataset containing 3599 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Diversity of the cladocerans (Crustacea, Branchiopoda) in Republic of Tyva, Russian Federation"
 ]
}

 The dataset includes 3599 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002716-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3az4wm
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Artocarpus altilis (Parkinson) Fosberg",
 "Year 1990-2010"
 ]
}

 The dataset includes 309 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002718-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/ex5ang
title: Research on early fault detection of current sensors operating in a closed-loop control structure using transfer learning

description: This research is focussed on transfer learning used to develop universal algorithms to detect various faults of current sensors in the AC drive system. It presents the possibility of using the idea of deep convolutional network transfer learning in fault diagnosis of current sensors of induction motors operating in a closed control structure. The versatility of the approach includes the possibility, as demonstrated in the article, of expanding the range of current sensor faults to be analyzed. In the study, a drive system simulation model was used as a source of diagnostic information. Particularly notable is the very high level of precision of the developed system (more than 98.3%) at the same time as the possibility of extending the types and levels of considered faults. Furthermore, the response time to an emerging fault was less than 0.0125 seconds.
DOI: 10.15468/dl.c448ym
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Muntiacus gongshanensis Ma, 1990"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002719-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gm2htb
title: Occurrence Download

description: A dataset containing 19732 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 Lutra lutra (Linnaeus, 1758)",
 "Year is greater than or equal to 1900",
 "Country is Norway",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 19732 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002720-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.