cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fuda8f
title: Occurrence Download

description: A dataset containing 209000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Glycaspis australoraria Moore, 1961, Abantiades latipennis Tindale, 1932, Glycaspis planitecta Moore, 1970, Cardiaspina bilobata Taylor, 1989, Glycaspis cellula Moore, 1970, Brentiscerus putoni (White, 1878), Petauroides volans (Kerr, 1792), Quadrastichodella nova Girault, 1922, Ophelimus listzi (Girault, 1934), Nascio simillima van de Poll, 1886, Glycaspis baileyi Moore, 1961, Glycaspis siliciflava Moore, 1961, Creiis viridis (Froggatt, 1900), Creiis lituratus (Froggatt, 1900), Ophelimus nuptus (Girault, 1928), Platyobria brevifoliae Taylor, 1987, Thaumastocoris majeri Noack, Cassis & Rose, 2011, Glycaspis confinis Moore, 1970, Putoniessa variegata Stevens, 1994, Glycaspis mirabilis Moore, 1961, Glycaspis sudicola Moore, 1970, Ageletha hemiteles Meyrick, 1883, Pseudodirphia regia Draudt, 1930, Melithreptus albogularis Gould, 1848, Eucalyptus tereticornis Sm., Anoplognathus boisduvali Boisduval, 1835, Chionaspis formosa Green, 1904, Glycaspis pratensis Moore, 1961, Glycaspis struicis Moore, 1961, Ipoella brunnea (Evans, 1934), Ctenarytaina bipartita Burckhardt, Farnier, Queiroz, Taylor & Steinbauer, Cardiaspina squamula Taylor, 1962, Eurymeloides lineata (Signoret, 1850), Eurymeloides marmorata (Burmeister, 1838), Glycaspis mannifera (Froggatt, 1900), Glycaspis dobsoni Moore, 1970, Glycaspis eucalypti (Dobson, 1851), Schedotrioza serrata Taylor, 1990, Glycaspis salebrosa Moore, 1961, Glycaspis planaria Moore, 1961, Glycaspis cyrtoma Moore, 1961, Lepidosaphes eucalypti (Froggatt, 1914), Ledracotis gunnensis Evans, 1937, Phellopsylla formicosa (Froggatt, 1900), Ramphastos vitellinus ariel Vigors, 1826, Morpho anaxibia (Esper, 1798), Phocides polybius (Fabricius, 1793), Malocampa punctata Stoll, 1780, Euselasia euboea (Hewitson, 1852), Siculodes falcata C.Felder, R.Felder & Rogenhofer, 1875)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 209000 records from 288 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016903-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e8yuvp
title: Occurrence Download

description: A dataset containing 5216455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Accipiter cooperii (Bonaparte, 1828), Lanius ludovicianus Linnaeus, 1766, Agkistrodon laticinctus Gloyd & Conant, 1934, Ricinus carolynae Nelson, 1972, Menacanthus alaudae (Schrank, 1776), Dendrolimus tabulaeformis Tsai & Liu, 1962, Leptographium sinense M.L.Yin, Z.W.de Beer & M.J.Wingf., Leptographium wushanense Y.Pan, J.Lu & H.Ye, Tomicus armandii Li & Zhang, 2010, Pissodes punctatus Langor & Zhang, 1999, Dendroctonus armandi Tsai & Li, 1959, Conophthorus teocotum Wood, 1980, Conophthorus michoacanae Wood, 1980, Zadiprion ojedae, Dendroctonus rhizophagus J.B.Thomas & D.E.Bright, 1970, Eutrichillus biguttatus (LeConte, 1852), Prionus pocularis Dalman, 1817, Pseudanaphothrips araucariae Mound & Palmer, 1990, Pineus boerneri Annand, 1928, Phytocoris fenestratus Reuter, 1909, Limenitis pratti Leech, 1890, Neotibicen canicularis (Harris, 1841), Cinara costata (Zetterstedt, 1828), Eulachnus thunbergii Wilson, 1919, Essigella californica (Essig, 1909), Sirex juvencus (Linnaeus, 1758), Zale lunifera Hübner, 1818, Lepidosaphes pini (Maskell, 1897), Dendrolimus spectabilis (Butler, 1877), Neodiprion excitans Rohwer, Arceuthobium bicarinatum Urb., Nosema fumiferanae (H.M.Thomson) Percy, 1973, Lypha setifacies (West, 1925), Madremyia saundersii (Williston, 1889), Actia interrupta Curran, 1933, Hemisturmia tortricis (Coquillett, 1897), Nemorilla pyste (Walker, 1849), Phryxe pecosensis (Townsend, 1926), Dioryctria albovittella (Hulst, 1890), Leptographium procerum (W.B.Kendr.) M.J.Wingf., Trigonoderus longipilis Yang, 1996, Allocricellius tabulaeformisi Yang, 1996, Macromesus huanglongnicus Yang, 1996, Pycnetron curculionidis Gahan, 1925, Rhynchopsitta pachyrhyncha (Swainson, 1827), Ricinus picturatus (Carriker, 1902), Gloveria medusa (Strecker, 1898), Chiasmia pumila (Kuznetzov, 1929), Hemisarcoptes malus (Shimer, 1868), Xanthisthisa niveifrons (Prout, 1922))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5216455 records from 390 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016902-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6qssj7
title: Occurrence Download

description: A dataset containing 6903 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 Pseudosasa Makino ex Nakai"
 ]
}

 The dataset includes 6903 records from 241 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016912-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.frce78
title: Occurrence Download

description: A dataset containing 217 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pelusios gabonensis"
 ]
}

 The dataset includes 217 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023910-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58j3qg
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((80.43951 13.51076,179.45827 13.51076,179.45827 53.06744,80.43951 53.06744,80.43951 13.51076))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Diphyscium suzukii"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023909-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2mj6uz
title: Occurrence Download

description: A dataset containing 452 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Musa ornata Roxb.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 452 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092661-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b36e2y
title: Occurrence Download

description: A dataset containing 1001 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mushroom (KIDR-MR)"
 ]
}

 The dataset includes 1001 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092663-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mcb4zz
title: Occurrence Download

description: A dataset containing 23916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, Svalbard and Jan Mayen, Portugal, Spain, France, Germany, Belgium, Netherlands, Denmark, Estonia, Latvia, Lithuania, Italy, Greece, Cyprus, Türkiye, Russian Federation, Ukraine, Romania, Bulgaria, Albania, Croatia, Austria, Slovakia, Poland)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Trientalis europaea L."
 ]
}

 The dataset includes 23916 records from 123 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092665-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpjpxc
title: Occurrence Download

description: A dataset containing 502 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ensete ventricosum (Welw.) Cheesman)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 502 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092666-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jjxkbz
title: Occurrence Download

description: A dataset containing 88713 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lamium galeobdolon subsp. argentatum (Smejkal) J.Duvign.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 88713 records from 225 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092645-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xna7sh
title: Occurrence Download

description: A dataset containing 6029 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Gyrinophilus porphyriticus (Green, 1827))"
 ]
}

 The dataset includes 6029 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092669-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/4atv-nz4r
title: Measurement of Inorganics in air and particle phase and ozone at Aliartos

description: Measurement of Inorganics in air and particle phase and ozone at Aliartos
DOI: 10.48597/s8t2-azcm
title: Measurement of Sulphur_dioxide at Aliartos

description: Measurement of Sulphur_dioxide at Aliartos
DOI: 10.48597/ytq5-whdx
title: Measurement of Ozone at Aliartos

description: Measurement of Ozone at Aliartos
DOI: 10.48597/gf5g-bt2t
title: Measurement of Inorganics in air and particle phase and ozone at Aliartos

description: Measurement of Inorganics in air and particle phase and ozone at Aliartos
DOI: 10.6084/m9.figshare.26096800
title: PlantVillage Dataset

description: PlantVillage dataset is a public dataset that contains a set of labeled leaf images. It includes 3171 diseased and healthy apple plant leaf images collected under controlled conditions. The images of apple leaves are categorized into four groups: "Healthy", "Scab", "Black Rot", and "Cedar Rust". All the original images in the dataset are 256x256 pixels with RGB color space.
DOI: 10.5281/zenodo.12530258
title: Reproductive and vegetative phenology database of two progenies of Euterpe oleracea Mart. planted in the Amazon estuary

description: During the period from May/2009 to April/2013, we monitored the reproductive and vegetative phenophases of two progenies of Euterpe oleracea Mart., planted in the floodplain forest of the Amazon estuary. We carried out prospecting on the east and west coast of the Amazon estuary with the aim of selecting native açaí palm matrices with phenotypic production characteristics during the period of low natural production of this palm.
DOI: 10.5281/zenodo.12530259
title: Reproductive and vegetative phenology database of two progenies of Euterpe oleracea Mart. planted in the Amazon estuary

description: During the period from May/2009 to April/2013, we monitored the reproductive and vegetative phenophases of two progenies of Euterpe oleracea Mart., planted in the floodplain forest of the Amazon estuary. We carried out prospecting on the east and west coast of the Amazon estuary with the aim of selecting native açaí palm matrices with phenotypic production characteristics during the period of low natural production of this palm.
DOI: 10.15468/dl.ff5czw
title: Occurrence Download

description: A dataset containing 411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ravenala madagascariensis Sonn.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 411 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092671-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ud6xs5
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is The Lepidopterists' Society Season Summary",
 "TaxonKey is Catocala texanae French, 1902"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092674-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11257222
title: AMIA Pipeline Test Data

description: The first datasets in the HIV-1C_ZA folder contains the initial Human Immuniodefeciency Virus 1C (HIV-1C) Integrase (IN) amino acid mutations associated with patient sequence data extrapoloated in a previous research project conducted by R. Chitongo (DOI: 10.1371/journal.pone.0223464). This dataset is curated in a standard Comma Separated Variable (.csv) file with each of the mutations associated with a particular patient listed benath a random identifier with no direct or indirect patient information present. These random identifiers do not correlate to a specific patient either and have just been assigned for differential purposes between which mutations were present in a particular patient. This also includes the protein homology model generated in our study present in the standar Protein Data Bank (PDB) format of the HIV-1C IN. The second variant_ouputs folder contains the various datasets and files generated from the initial phase of the AMIA pipeline which is further elaborated upon in the published literature.
DOI: 10.5281/zenodo.11257223
title: AMIA Pipeline Test Data

description: The first datasets in the HIV-1C_ZA folder contains the initial Human Immuniodefeciency Virus 1C (HIV-1C) Integrase (IN) amino acid mutations associated with patient sequence data extrapoloated in a previous research project conducted by R. Chitongo (DOI: 10.1371/journal.pone.0223464). This dataset is curated in a standard Comma Separated Variable (.csv) file with each of the mutations associated with a particular patient listed benath a random identifier with no direct or indirect patient information present. These random identifiers do not correlate to a specific patient either and have just been assigned for differential purposes between which mutations were present in a particular patient. This also includes the protein homology model generated in our study present in the standar Protein Data Bank (PDB) format of the HIV-1C IN. The second variant_ouputs folder contains the various datasets and files generated from the initial phase of the AMIA pipeline which is further elaborated upon in the published literature.
DOI: 10.15468/dl.ehry7x
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Strelitzia alba (L.f.) Skeels)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 42 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092675-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jccxy
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "TaxonKey is Gastrodia elata Blume"
 ]
}

 The dataset includes 190 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092679-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdeb47
title: Occurrence Download

description: A dataset containing 2166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Strelitzia nicolai Regel & Körn.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2166 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092680-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11143197
title: Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility

description: Abstract

The pachynema progression, a crucial meiotic process, contributes to the completion of prophase I. Nevertheless, the regulation of this significant meiotic process remains poorly understood. In this study, we identified a novel testis-specific protein HSF5, which regulates pachynema progression during male meiosis in a chromatin-binding manner. Deficiency of HSF5 results in meiotic arrest and male infertility, characterized as unconventionally accumulated pachynema halting at the mid-to-late stage, with extensive spermatocyte apoptosis. Our scRNA-seq data confirmed consistent expressional alterations of certain driver genes(Sycp1, Msh4, Meiob, etc.) crucial for pachynema progression in Hsf5-/- individuals. Ulteriorly, HSF5 was revealed to primarily bind to promoter regions of such key divers by CUT&Tag analysis. Also, our results demonstrated that HSF5 biologically interacted with the chromatin-remodeling SWI/SNF complex, and it could function as a transcriptional factor for pachynema progression during meiosis. Therefore, our study underscores the importance of the chromatin-associated HSF5 for the differentiation of spermatocytes, improving the protein regulatory network of the pachynema progression.

Instructions for this dataset

The source code required to reproduce the single-cell analysis results of the article is provided, and intermediate files in the analysis are also provided. The intermediate file is a filtered and manually annotated Seurat object that can be read directly by R. Raw reads of the single-cell data can be found at NCBI SRA repository PRJNA1098350.
DOI: 10.5281/zenodo.11143196
title: Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility

description: Abstract

The pachynema progression, a crucial meiotic process, contributes to the completion of prophase I. Nevertheless, the regulation of this significant meiotic process remains poorly understood. In this study, we identified a novel testis-specific protein HSF5, which regulates pachynema progression during male meiosis in a chromatin-binding manner. Deficiency of HSF5 results in meiotic arrest and male infertility, characterized as unconventionally accumulated pachynema halting at the mid-to-late stage, with extensive spermatocyte apoptosis. Our scRNA-seq data confirmed consistent expressional alterations of certain driver genes(Sycp1, Msh4, Meiob, etc.) crucial for pachynema progression in Hsf5-/- individuals. Ulteriorly, HSF5 was revealed to primarily bind to promoter regions of such key divers by CUT&Tag analysis. Also, our results demonstrated that HSF5 biologically interacted with the chromatin-remodeling SWI/SNF complex, and it could function as a transcriptional factor for pachynema progression during meiosis. Therefore, our study underscores the importance of the chromatin-associated HSF5 for the differentiation of spermatocytes, improving the protein regulatory network of the pachynema progression.

Instructions for this dataset

The source code required to reproduce the single-cell analysis results of the article is provided, and intermediate files in the analysis are also provided. The intermediate file is a filtered and manually annotated Seurat object that can be read directly by R. Raw reads of the single-cell data can be found at NCBI SRA repository PRJNA1098350. The two tables are the raw data of the mass spectrometry-based proteomics.



Seurat_analysis.R: R code to reproduce the single cell analysis results in the article.

scvelo_analysis.py: Python code to reproduce the single-cell RNA velocity analysis results in the article.

Whole_testis.rds, Germ_cells.rds: Seurat objects stored in rds format contain whole testis cells and sperm cells respectively.
DOI: 10.5281/zenodo.11159366
title: Meiotic chromatin-associated HSF5 is indispensable for pachynema progression and male fertility

description: Abstract

The pachynema progression, a crucial meiotic process, contributes to the completion of prophase I. Nevertheless, the regulation of this significant meiotic process remains poorly understood. In this study, we identified a novel testis-specific protein HSF5, which regulates pachynema progression during male meiosis in a chromatin-binding manner. Deficiency of HSF5 results in meiotic arrest and male infertility, characterized as unconventionally accumulated pachynema halting at the mid-to-late stage, with extensive spermatocyte apoptosis. Our scRNA-seq data confirmed consistent expressional alterations of certain driver genes(Sycp1, Msh4, Meiob, etc.) crucial for pachynema progression in Hsf5-/- individuals. Ulteriorly, HSF5 was revealed to primarily bind to promoter regions of such key divers by CUT&Tag analysis. Also, our results demonstrated that HSF5 biologically interacted with the chromatin-remodeling SWI/SNF complex, and it could function as a transcriptional factor for pachynema progression during meiosis. Therefore, our study underscores the importance of the chromatin-associated HSF5 for the differentiation of spermatocytes, improving the protein regulatory network of the pachynema progression.

Instructions for this dataset

The source code required to reproduce the single-cell analysis results of the article is provided, and intermediate files in the analysis are also provided. The intermediate file is a filtered and manually annotated Seurat object that can be read directly by R. Raw reads of the single-cell data can be found at NCBI SRA repository PRJNA1098350. The two tables are the raw data of the mass spectrometry-based proteomics.



Seurat_analysis.R: R code to reproduce the single cell analysis results in the article.

scvelo_analysis.py: Python code to reproduce the single-cell RNA velocity analysis results in the article.

Whole_testis.rds, Germ_cells.rds: Seurat objects stored in rds format contain whole testis cells and sperm cells respectively.

Mass spectrometry results.xlsx, Mass spectrometry proteins.xlsx: Mass spectrometry-based proteomics data provides original results for peptides and proteins.