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

description: A dataset containing 37672 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Misgurnus anguillicaudatus (Cantor, 1842)"
 ]
}

 The dataset includes 37672 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107923-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sutb6n
title: Occurrence Download

description: A dataset containing 18114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Catharanthus roseus (L.) G.Don)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 18114 records from 361 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107928-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5883/bold:aaj0394
title: Overview of Barcode Index Number - BOLD:AAJ0394

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.15468/dl.bbxqbg
title: Occurrence Download

description: A dataset containing 4409 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "PublishingCountry is one of (Colombia)",
 "BasisOfRecord is one of (Specimen, Fossil)",
 "Country is one of (French Polynesia, Gabon, Gambia, Georgia, Germany, Ghana, Gibraltar, Greece, Greenland, Grenada, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Honduras, Hong Kong, Hungary, Iceland, India, Indonesia, Iran (Islamic Republic of), Iraq, Ireland, Isle of Man, Israel, Italy, Côte d’Ivoire, Jamaica, Japan, Jersey, Jordan, Kazakhstan, Kenya, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Lao People’s Democratic Republic, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macao, North Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Mauritania, Mauritius, Mayotte, Mexico, Micronesia (Federated States of), Moldova, Republic of, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Nepal, Netherlands, New Caledonia, New Zealand)"
 ]
 }
 ]
}

 The dataset includes 4409 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107929-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13453392
title: ZentralGut.ch-Datensatz: Postkartensammlung der Bibliothek Zug

description: Metadaten-Datensätze der Postkartensammlung der Bibliothek Zug. Die Bibliothek Zug ist im Besitz einer Sammlung von rund 2'000 historischer Postkarten mit zugerischen Motiven. Die Postkarten beinhalten grösstenteils
DOI: 10.5281/zenodo.13453393
title: ZentralGut.ch-Datensatz: Postkartensammlung der Bibliothek Zug

description: Metadaten-Datensätze der Postkartensammlung der Bibliothek Zug. Die Bibliothek Zug ist im Besitz einer Sammlung von rund 2'000 historischer Postkarten mit zugerischen Motiven. Die Postkarten beinhalten grösstenteils
DOI: 10.15468/dl.u8aem8
title: Occurrence Download

description: A dataset containing 19194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ceiba pentandra (L.) Gaertn.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 19194 records from 497 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107931-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j63ey2
title: Occurrence Download

description: A dataset containing 15078 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "PublishingCountry is one of (Colombia)",
 "BasisOfRecord is one of (Specimen, Fossil)",
 "Country is one of (Nicaragua, Niger, Nigeria, Niue, Korea (Democratic People’s Republic of), Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palestine, State of, Panama, Papua New Guinea, Paraguay, Peru, Philippines, Pitcairn, Poland, Portugal, Puerto Rico, Qatar, Congo, Réunion, Romania, Russian Federation, Rwanda, Saint Barthélemy, Saint Helena, Ascension and Tristan da Cunha, Saint Kitts and Nevis, Saint Lucia, Saint Martin (French part), Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten (Dutch part), Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, Korea, Republic of, South Sudan, Spain, Sri Lanka, Sudan, Suriname, Svalbard and Jan Mayen, Eswatini, Sweden, Switzerland, Syrian Arab Republic, Chinese Taipei, Tajikistan, Tanzania, United Republic of, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tunisia, Türkiye, Turkmenistan, Turks and Caicos Islands, Tuvalu, Virgin Islands (U.S.), Uganda, Ukraine, United Arab Emirates, United Kingdom of Great Britain and Northern Ireland, United States of America, Uruguay, Uzbekistan, Vanuatu, Holy See, Venezuela (Bolivarian Republic of), Viet Nam, Wallis and Futuna, Western Sahara, Yemen, Zambia, Zimbabwe)"
 ]
 }
 ]
}

 The dataset includes 15078 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107933-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/aad43af87a1d404a8ab94b3ca327dc12
title: Groundwater, soil moisture, light and weather data in Brownsville forest, Nassawadox, VA, 2019-2023

description: This dataset includes groundwater, soil moisture, weather and light data collected in eight study sites in the Brownsville forested area (VA). In particular, sites H5 and H7 characterize the high forest where healthy Pinus taeda dominate, sites L1 and L6 characterize the low forest, where barren or dead Pinus taeda are present, sites M1 and M2 characterize the medium forest, representing transition between high and low forest, transition site where dead trees and saltmarsh vegetation live together and marsh site dominated by saltmarsh vegetation. Data collection, started in January 2019, is done for VCR-LTER and CCZN (Coastal Critical Zone Network) long term projects. CTD-Diver are used to measure groundwater pressure, specific conductance and temperature. They hang from a cable in six wells, one for each study site. Water pressure is compensated using barometric pressure data collected by the weather station nearby. Water levels are georeferenced to NAVD 88. Two soil moisture sensors for each site are placed 7-10 cm and 30 cm below the ground surface to detect water content, specific conductance and temperature of the first soil layer. Two weather stations are always installed in different sites. Their position is periodically changed to cover all sites. 
 This material is based upon work supported by the National Science Foundation under Grant No. 2012322, Collaborative Research: Network Cluster: The Coastal Critical Zone: Processes that transform landscapes and fluxes between land and sea.
DOI: 10.15468/dl.444zrz
title: Occurrence Download

description: A dataset containing 5654 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cenchrus alopecuroides (L.) Thunb.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5654 records from 181 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107935-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10677930
title: Data/results associated with the publication: "Dense seismic node arrays for enhanced understanding and monitoring of geothermal systems"

description: Contained in this repository are the data associated with the results presented in the work:T.S. Hudson, T. Kettlety, JM. Kendall, T. O’Toole, A. Jupe, R. Shail, G. Grand. "Dense seismic node arrays for enhanced understanding and monitoring of geothermal systems".Submitted to: The Seismic Record.

The following data are included in this repository:1. An earthquake catalogue (in directory earthquake_catalogue). All data are labelled in the corresponding text file.2. Earthquake magnitude results. These are contained in the directory magnitude_results, and are bundled in a python pickle format. To read, use the command "import pickle ; mag_dict = pickle.load(open("mags_dict_filt.pkl", 'rb'))".3. Earthquake source mechanism results (in directory source_mechanism_results). These are DC-constrained solutions, with the polarity observations used in the inversion contained in the csv files and the pdf files showing the best fitting solution (labelled by event origin time). Note that we only include solutions for which we have any confidence in the solution, in line with those included in the main manuscript. See main manuscript for further details.4. Anisotropy results, in the directory anisotropy_results. All results are in a single txt file, each labelled by an event unique id, followed by SWSPy outputs of anisotropy measurements. See SWSPy documentation for further details on parameters.
DOI: 10.6084/m9.figshare.11342192
title: Molecular phylogeny suggests the affinity of the planktonic diatoms <i>Climacodium</i> and <i>Bellerochea</i> (Lithodesmiales, Mediophyceae)

description: <i>Climacodium frauenfeldianum</i> is a planktonic chain-forming diatom able to proliferate in severely oligotrophic waters of tropical seas. In this study, a strain of <i>C. frauenfeldianum</i>, the type of <i>Climacodium</i>, was established in culture from the tropical southwestern Atlantic Ocean off Brazil. SEM observations showed weakly silicified cells, without visible surface sculpturing. In the small subunit (SSU) rRNA and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (<i>rbc</i>L) gene phylogeny, <i>C. frauenfeldianum</i> clustered with sequences of <i>Bellerochea malleus</i> (the type of <i>Bellerochea</i>) and <i>B. horologicalis</i>. Contrary to previous classifications that placed <i>Climacodium</i> in the Hemiaulaceae, <i>Climacodium</i> and <i>Bellerochea</i> should be placed in the same family, Bellerocheaceae. The species <i>Bellerochea yucatanensis</i> needs further research because sequences of the single strain available clustered with the genus <i>Lithodesmioides</i>. In adaptation to the oligotrophic open ocean environment, <i>C. frauenfeldianum</i> seems to have evolved an appearance closer to <i>Hemiaulus</i>, i.e. very lightly silicified flat cells with long elevations, and with diazotrophic cyanobionts.
DOI: 10.6084/m9.figshare.11342192.v1
title: Molecular phylogeny suggests the affinity of the planktonic diatoms <i>Climacodium</i> and <i>Bellerochea</i> (Lithodesmiales, Mediophyceae)

description: <i>Climacodium frauenfeldianum</i> is a planktonic chain-forming diatom able to proliferate in severely oligotrophic waters of tropical seas. In this study, a strain of <i>C. frauenfeldianum</i>, the type of <i>Climacodium</i>, was established in culture from the tropical southwestern Atlantic Ocean off Brazil. SEM observations showed weakly silicified cells, without visible surface sculpturing. In the small subunit (SSU) rRNA and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (<i>rbc</i>L) gene phylogeny, <i>C. frauenfeldianum</i> clustered with sequences of <i>Bellerochea malleus</i> (the type of <i>Bellerochea</i>) and <i>B. horologicalis</i>. Contrary to previous classifications that placed <i>Climacodium</i> in the Hemiaulaceae, <i>Climacodium</i> and <i>Bellerochea</i> should be placed in the same family, Bellerocheaceae. The species <i>Bellerochea yucatanensis</i> needs further research because sequences of the single strain available clustered with the genus <i>Lithodesmioides</i>. In adaptation to the oligotrophic open ocean environment, <i>C. frauenfeldianum</i> seems to have evolved an appearance closer to <i>Hemiaulus</i>, i.e. very lightly silicified flat cells with long elevations, and with diazotrophic cyanobionts.
DOI: 10.6084/m9.figshare.7672223
title: Additional file 10: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S8. Performance of error correction methods on correcting bases at heterozygous positions. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7672229
title: Additional file 11: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S9. Memory usage performance statistics by the preprocessing modules of five error correction methods (unit: G). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7672247
title: Additional file 3: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S1. Performance statistics on sensitivity. a. Sensitivity performance statistics on PacBio data of ten methods using five SR coverages. b. Sensitivity performance statistics on ONT data of ten methods using five SR coverages. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7672247.v1
title: Additional file 3: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S1. Performance statistics on sensitivity. a. Sensitivity performance statistics on PacBio data of ten methods using five SR coverages. b. Sensitivity performance statistics on ONT data of ten methods using five SR coverages. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7672253
title: Additional file 4: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S2. Performance statistics on accuracy. a. Accuracy performance statistics on PacBio data of ten methods using five SR coverages. b. Accuracy performance statistics on ONT data of ten methods using five SR coverages. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7672253.v1
title: Additional file 4: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S2. Performance statistics on accuracy. a. Accuracy performance statistics on PacBio data of ten methods using five SR coverages. b. Accuracy performance statistics on ONT data of ten methods using five SR coverages. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7672256
title: Additional file 5: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S3. Performance statistics on output rate. a. Output rate (%) performance statistics on PacBio data of ten methods using five SR coverages. b. Output rate (%) performance statistics on ONT data of ten methods using five SR coverages. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7672256.v1
title: Additional file 5: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S3. Performance statistics on output rate. a. Output rate (%) performance statistics on PacBio data of ten methods using five SR coverages. b. Output rate (%) performance statistics on ONT data of ten methods using five SR coverages. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8196539
title: Additional file 1: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: GO enrichment analysis of P. radiata genes up-regulated in the presence of spruce wood. Statistically significant up-regulation (p-value &lt; 0.05, log2 FC ≥ 1) was analyzed previously [26] as compared with malt extract cultivation at the two week (2w up-regulated) and/or four week (4w up-regulated) time points of cultivation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8196539.v1
title: Additional file 1: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: GO enrichment analysis of P. radiata genes up-regulated in the presence of spruce wood. Statistically significant up-regulation (p-value &lt; 0.05, log2 FC ≥ 1) was analyzed previously [26] as compared with malt extract cultivation at the two week (2w up-regulated) and/or four week (4w up-regulated) time points of cultivation. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7672262
title: Additional file 6: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S4. Performance statistics on alignment rate. a. Alignment rate (%) performance statistics on PacBio data of ten methods using five SR coverages. b. Alignment rate (%) performance statistics on ONT data of ten methods using five SR coverages. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8196548
title: Additional file 2: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: P. radiata gene models encoding CAZymes, their locations in the genome assembly together with transcriptome data and proteome data from spruce wood cultivations [26]. 2w, two week time point of the spruce wood cultivation; 4w, four week time point of the spruce wood cultivation; up, up-regulated; down, down-regulated. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7672262.v1
title: Additional file 6: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S4. Performance statistics on alignment rate. a. Alignment rate (%) performance statistics on PacBio data of ten methods using five SR coverages. b. Alignment rate (%) performance statistics on ONT data of ten methods using five SR coverages. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8196548.v1
title: Additional file 2: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: P. radiata gene models encoding CAZymes, their locations in the genome assembly together with transcriptome data and proteome data from spruce wood cultivations [26]. 2w, two week time point of the spruce wood cultivation; 4w, four week time point of the spruce wood cultivation; up, up-regulated; down, down-regulated. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.8196557
title: Additional file 3: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: P. radiata gene models encoding plant cell wall attacking CAZymes and located in clusters in the genome assembly. Fold change of expression of the genes in spruce wood cultivations as compared with malt extract cultivations at the two week (2w) and four week (4w) time points of cultivation was analyzed previously [26]. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8196557.v1
title: Additional file 3: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: P. radiata gene models encoding plant cell wall attacking CAZymes and located in clusters in the genome assembly. Fold change of expression of the genes in spruce wood cultivations as compared with malt extract cultivations at the two week (2w) and four week (4w) time points of cultivation was analyzed previously [26]. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7672268
title: Additional file 7: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S5. Performance statistics on run time. a. Run time performance statistics on PacBio data of ten methods using five SR coverages (Unit: second). b. Run time performance statistics on ONT data of ten methods using five SR coverages (Unit: second). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8196566
title: Additional file 4: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: Putative secondary metabolism genes identified from the P. radiata genome assembly. Fold change of expression of the genes in spruce wood cultivations as compared with malt extract cultivations at the two week (2w) and four week (4w) time points of cultivation was analyzed previously [26]. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7672277
title: Additional file 8: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S6. Performance statistics on memory usage. a. Memory usage performance statistics on PacBio data of ten methods using five SR coverages (unit: G). b. Memory usage performance statistics on ONT data of ten methods using five SR coverages (unit: G). (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8196566.v1
title: Additional file 4: of Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

description: Putative secondary metabolism genes identified from the P. radiata genome assembly. Fold change of expression of the genes in spruce wood cultivations as compared with malt extract cultivations at the two week (2w) and four week (4w) time points of cultivation was analyzed previously [26]. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7672277.v1
title: Additional file 8: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S6. Performance statistics on memory usage. a. Memory usage performance statistics on PacBio data of ten methods using five SR coverages (unit: G). b. Memory usage performance statistics on ONT data of ten methods using five SR coverages (unit: G). (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7672280
title: Additional file 9: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S7. Performance statistics on improving de novo assembly. a. Genome assembly performance statistics of ten methods on E. coli PacBio dataset using five SR coverages. b. Genome assembly performance statistics of ten methods on S. cerevisae PacBio datasets using five SR coverages. c. Genome assembly performance statistics of five methods on D. melanogaster PacBio dataset using five SR coverages. d. Genome assembly performance statistics of five methods on A. thaliana PacBio dataset using five SR coverages. e. Genome assembly performance statistics of ten methods on E. coli ONT dataset using five SR coverages. f. Genome assembly performance statistics of ten methods on S. cerevisae ONT dataset using five SR coverages. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7672280.v1
title: Additional file 9: of A comparative evaluation of hybrid error correction methods for error-prone long reads

description: Table S7. Performance statistics on improving de novo assembly. a. Genome assembly performance statistics of ten methods on E. coli PacBio dataset using five SR coverages. b. Genome assembly performance statistics of ten methods on S. cerevisae PacBio datasets using five SR coverages. c. Genome assembly performance statistics of five methods on D. melanogaster PacBio dataset using five SR coverages. d. Genome assembly performance statistics of five methods on A. thaliana PacBio dataset using five SR coverages. e. Genome assembly performance statistics of ten methods on E. coli ONT dataset using five SR coverages. f. Genome assembly performance statistics of ten methods on S. cerevisae ONT dataset using five SR coverages. (XLSX 48 kb)