cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.sh2z9u
title: Occurrence Download

description: A dataset containing 514326 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sedum L."
 ]
}

 The dataset includes 514326 records from 1058 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063823-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2xz4mv
title: Occurrence Download

description: A dataset containing 6837 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-10.50293 40.42969,39.77051 46.40625,42.49512 70.40039,24.65332 72.68555,2.85645 62.92969,-10.85449 58.0957,-10.50293 40.42969))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "MediaType is Image",
 {
 "or" : [
 "Month is April",
 "Month is July",
 "Month is August",
 "Month is September",
 "Month is May",
 "Month is June"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Lupinus polyphyllus Lindl."
 ]
}

 The dataset includes 6837 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048397-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hmehmj
title: Occurrence Download

description: A dataset containing 285 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Avicennia bicolor Standl."
 ]
}

 The dataset includes 285 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062435-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y4zf4k
title: Occurrence Download

description: A dataset containing 1293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythroxylum mucronatum Benth."
 ]
}

 The dataset includes 1293 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069301-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3e6enu
title: Occurrence Download

description: A dataset containing 591 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anolis gemmosus O'Shaughnessy, 1875"
 ]
}

 The dataset includes 591 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068104-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfzuwf
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Zamia meermanii Calonje",
 "DecimalLatitude is greater than or equal to -90",
 "DecimalLongitude is greater than or equal to -180"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026360-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5rbkqp
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Calycanthus floridus L.",
 "Year 1990-2020"
 ]
}

 The dataset includes 76 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032539-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9u4s5g
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-70.18633 -17.86034,-70.19251 -17.82017,-70.26873 -17.81296,-70.27456 -17.84695,-70.23336 -17.92763,-70.19354 -17.94411,-70.18393 -17.91698,-70.1465 -17.88609,-70.14376 -17.85622,-70.18633 -17.86034))"
 ]
}

 The dataset includes 49 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030295-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsxmgg
title: Occurrence Download

description: A dataset containing 3644 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Bromus rigidus Roth",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3644 records from 184 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033053-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spcuxm
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alstroemeria piauhyensis Gardner ex Baker"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032553-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcbq81
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hopea nigra Burck"
 ]
}

 The dataset includes 41 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000967-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nh23wt
title: Occurrence Download

description: A dataset containing 1619 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Triatoma infestans (Klug, 1834)"
 ]
}

 The dataset includes 1619 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062445-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vkj27p
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "Year 1950-2020",
 {
 "or" : [
 "DatasetKey is CSIC-Real Jardín Botánico-Colección de Plantas Vasculares (MA)",
 "DatasetKey is Herbario de la Universidad de Sevilla",
 "DatasetKey is Jardín Botánico de Córdoba: Herbarium COA",
 "DatasetKey is Colección de plantas vasculares del herbario de la Universitat de València (VAL)",
 "DatasetKey is Herbario COFC de la Universidad de Córdoba: colección general de plantas vasculares",
 "DatasetKey is Herbario HSS Finca La Orden-Valdesequera (CICYTEX). Junta de Extremadura",
 "DatasetKey is Herbario de la Universidad de Granada: Colección GDA-Fanerogamia",
 "DatasetKey is Herbario MAIA, colección Manuel Martín Bolaños",
 "DatasetKey is SANT Herbarium vascular plants collection",
 "DatasetKey is MGC Herbarium of University of Malaga (Spain): MGC-Cormof dataset",
 "DatasetKey is Colección de plantas vasculares del Herbario \"Jaime Andrés Rodríguez\". LEB",
 "DatasetKey is Herbarium JACA. Instituto Pirenaico de Ecología-CSIC"
 ]
 },
 "TaxonKey is Gleditsia triacanthos L."
 ]
}

 The dataset includes 63 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048934-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h2czs7
title: Occurrence Download

description: A dataset containing 761 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudococcus viburni (Signoret, 1875)"
 ]
}

 The dataset includes 761 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021099-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6078/d14s3k
title: The Evolution of Function within the Nudix Superfamily: Reconciled tree of the entire Nudix clan

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Reconciled tree of the entire Nudix clan. The files in Dendroscope format have the same tree topologies as the Newick format, and additionally contain rich information such as reconciliation, bootstrap and so on; these files can be opened by earlier version of Dendroscope (v3.2.8 or earlier).
DOI: 10.6078/d18g6v
title: The Evolution of Function within the Nudix Superfamily: Phylogenetic tree of the entire Nudix clan

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Phylogenetic tree of the entire Nudix clan. It can be opened by most phylogeny visualization software such as Dendroscope v3.2.8 (Huson & Scornavacca 2012 doi:10.1093/sysbio/sys062).
DOI: 10.6078/d1d594
title: The Evolution of Function within the Nudix Superfamily: Reconciled tree of proteins in the 347-select set

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Reconciled tree of proteins in the 347-select set. The files in Dendroscope format have the same tree topologies as the Newick format, and additionally contain rich information such as reconciliation, bootstrap and so on; these files can be opened by earlier version of Dendroscope (v3.2.8 or earlier) (doi:10.1093/sysbio/sys062).
DOI: 10.6078/d1j01m
title: The Evolution of Function within the Nudix Superfamily: Phylogenetic tree of the 347-select proteins

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Phylogenetic tree of the 347-select proteins. It can be opened by most phylogeny visualization software such as Dendroscope v3.2.8 (Huson & Scornavacca 2012 doi:10.1093/sysbio/sys062).
DOI: 10.6084/m9.figshare.28813342
title: Additional file 2 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 2: Table S1 All 5hmC peaks.
DOI: 10.6084/m9.figshare.28813342.v1
title: Additional file 2 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 2: Table S1 All 5hmC peaks.
DOI: 10.6078/d1np4k
title: The Evolution of Function within the Nudix Superfamily: Full Nudix clan alignment in FASTA format

description: The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205 Nudix proteins collected from the literature. We corrected erroneous functions or provided more appropriate descriptions for 53 annotations described in the Gene Ontology Annotation database in this family, and propose 275 new experimentally-based annotations. We manually constructed structure-guided sequence alignment of 78 Nudix proteins. Using the structural alignment as a seed, we then made an alignment of 347 “select” Nudix domains, curated from structurally determined, functionally characterized, or phylogenetically important Nudix domains. Based on our review of Nudix pyrophosphohydrolase structures and specificities, we further analyzed a loop region downstream of the Nudix hydrolase motif previously shown to contact the substrate molecule and possess known functional motifs. This loop region provides a potential structural basis for the functional radiation and evolution of substrate specificity within the hydrolase family. Finally, phylogenetic analyses of the 347 select protein domains and of the complete Nudix clan revealed general monophyly with regard to function and a few instances of probable homoplasy.
description: Full Nudix clan alignment in FASTA format; can be opened by most sequence alignment visualization software such as Jalview (Waterhouse et al. 2009 doi:10.1093/bioinformatics/btp033).
DOI: 10.6084/m9.figshare.28813345
title: Additional file 3 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 3: Table S2 TC_LT 5hmC, differential expression and DNA methylation.
DOI: 10.6084/m9.figshare.28813345.v1
title: Additional file 3 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 3: Table S2 TC_LT 5hmC, differential expression and DNA methylation.
DOI: 10.6084/m9.figshare.28813348
title: Additional file 4 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 4: Table S3 High DGE and 5hmC gain in LT.
DOI: 10.6084/m9.figshare.28813348.v1
title: Additional file 4 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 4: Table S3 High DGE and 5hmC gain in LT.
DOI: 10.6084/m9.figshare.28813354
title: Additional file 5 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 5: Table S4 5hmC recover and spread peaks.
DOI: 10.6084/m9.figshare.28813354.v1
title: Additional file 5 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 5: Table S4 5hmC recover and spread peaks.
DOI: 10.6084/m9.figshare.28813357
title: Additional file 6 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 6: Supporting data files.
DOI: 10.6084/m9.figshare.28813357.v1
title: Additional file 6 of Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation

description: Additional file 6: Supporting data files.