cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8133843
title: Databases for NEXT-RSV-SEQ (RSV, HMPV, PIV)

description: Here, we provide databases ready for use in sequencing read decontamination with our Next-RSV-SEQ pipeline (https://gitlab.com/rki_bioinformatics/next-rsv-seq), designed for viral genome assembly using Illumina data.

Available Databases:



Human orthopneumovirus / Human respiratory syncytial virus (RSV): [RSV_GRCh38_2022-04-06.zip]

Human metapneumovirus (HMPV): [HMPV_2022-05-28.zip]

Parainfluenza virus (PIV): [PIV_2022-05-28.zip]


These databases were created using Kraken2 and are based on all complete viral genome sequences available on NCBI Reference Sequence Database (RefSeq) as of April 6, 2022 (for RSV), and May 28, 2022 (for HMPV and PIV). The RSV database also includes the human genome sequence GRCh38 (Genome Reference Consortium Human Build 38). The databases have been compressed into zip format for easy downloading. Before use, please unpack the respective zip archive.
DOI: 10.5281/zenodo.8133844
title: Databases for NEXT-RSV-SEQ (RSV, HMPV, PIV)

description: Here, we provide databases ready for use in sequencing read decontamination with our Next-RSV-SEQ pipeline (https://gitlab.com/rki_bioinformatics/next-rsv-seq), designed for viral genome assembly using Illumina data.

Available Databases:



Human orthopneumovirus / Human respiratory syncytial virus (RSV): [RSV_GRCh38_2022-04-06.zip]

Human metapneumovirus (HMPV): [HMPV_2022-05-28.zip]

Parainfluenza virus (PIV): [PIV_2022-05-28.zip]


These databases were created using Kraken2 and are based on all complete viral genome sequences available on NCBI Reference Sequence Database (RefSeq) as of April 6, 2022 (for RSV), and May 28, 2022 (for HMPV and PIV). The RSV database also includes the human genome sequence GRCh38 (Genome Reference Consortium Human Build 38). The databases have been compressed into zip format for easy downloading. Before use, please unpack the respective zip archive.
DOI: 10.15468/dl.ekma8b
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (ARG, CHL, PRY, URY, FLK, BRA.21_1, BRA.16_1, BRA.24_1)",
 "TaxonKey is Chiliophyllum densifolium Phil."
 ]
}

 The dataset includes 26 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020621-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/aqahtf
title: Collection Maurice GAIGNON

description: Maurice Gaignon fut ingénieur chimiste à Rhône-Poulenc à Lyon. Il mena de front sa carrière et ses recherches en mycologie. Spécialiste des Heterobasidiomycetes, il a été membre actif de la Société Linnéenne de Lyon et président de la section Mycologie. Son fungarium, donné à l'Herbier LY, contient plus de 6500 spécimens. Les notes et documents de travail associés sont conservés par la famille.
DOI: 10.6084/m9.figshare.25848820
title: Phenotypic characterization of Histoplasma species

description: <b>Evaluation of extracellular proteolytic activity:</b> To evaluate extracellular proteolytic activity in different species of <i>Histoplasma</i>, we grew the 27 <i>Histoplasma</i> strains (Table S1) in HMM plates supplemented with 1.5% skim milk. Strains with a proteolytic activity show a clear halo around their yeast colonies.<b>Optical density and growth curves of</b><b> </b><b><i>Histoplasma</i></b><b> </b><b>yeast cultures:</b> We mixed 600 μl of liquid culture with 300 μl of 3M NaOH in a plastic cuvette, which was covered with Parafilm and vortexed for 10 seconds to separate yeast clumps and measure optical density (OD) in a GENESYS 10vis spectrophotometer (Thermo Spectronic) starting at day 0, and at every 24 hours after that until day 11.<b>Yeast Area:</b> We mixed 10 μl from a yeast culture that had large yeast clumps removed with 10 μl of Lactophenol Cotton Blue on a glass slide. Differential interference contrast (DIC) images were obtained using 100X/1.4 Oil UPlan S Apo PSF quality objective on an Olympus BX-61 microscope and collected using a QImaging RETIGA 4000R color camera and Volocity 6.3 acquisition software.Description of the data and file structureWe are including four files: Three of them are experimental observations, and one of them is the code required to analyze the data.halo_radius_miss.csv: ratio sizes of H. mississipiense cultures in .5% skim milk media. The variable halo is in cms and reflects the ratio of the lysis halo. Isolate refers to the name of the Histoplasma strain.od_cells_histo.csv: rates of growth of different species of Histoplasma in liquid media. Strain refers to the name of the Histoplasma strain. OD refers to the turbidity of the culture (reported in Absorbance Units). Cells is the number of cells in the culture.Cell_Size_df.csv: cell size for different species of Histoplasma. Line refers to the name of the Histoplasma strain. Replicate refers to the number of the experimental batch. Area is the ellipse area of the cell (in micrometers^2).histoplasma_morphology_code.R: Analytical code to generate linear models.<br>
DOI: 10.6084/m9.figshare.25848820.v1
title: Phenotypic characterization of Histoplasma species

description: <b>Evaluation of extracellular proteolytic activity:</b> To evaluate extracellular proteolytic activity in different species of <i>Histoplasma</i>, we grew the 27 <i>Histoplasma</i> strains (Table S1) in HMM plates supplemented with 1.5% skim milk. Strains with a proteolytic activity show a clear halo around their yeast colonies.<b>Optical density and growth curves of</b><b> </b><b><i>Histoplasma</i></b><b> </b><b>yeast cultures:</b> We mixed 600 μl of liquid culture with 300 μl of 3M NaOH in a plastic cuvette, which was covered with Parafilm and vortexed for 10 seconds to separate yeast clumps and measure optical density (OD) in a GENESYS 10vis spectrophotometer (Thermo Spectronic) starting at day 0, and at every 24 hours after that until day 11.<b>Yeast Area:</b> We mixed 10 μl from a yeast culture that had large yeast clumps removed with 10 μl of Lactophenol Cotton Blue on a glass slide. Differential interference contrast (DIC) images were obtained using 100X/1.4 Oil UPlan S Apo PSF quality objective on an Olympus BX-61 microscope and collected using a QImaging RETIGA 4000R color camera and Volocity 6.3 acquisition software.Description of the data and file structureWe are including four files: Three of them are experimental observations, and one of them is the code required to analyze the data.halo_radius_miss.csv: ratio sizes of H. mississipiense cultures in .5% skim milk media. The variable halo is in cms and reflects the ratio of the lysis halo. Isolate refers to the name of the Histoplasma strain.od_cells_histo.csv: rates of growth of different species of Histoplasma in liquid media. Strain refers to the name of the Histoplasma strain. OD refers to the turbidity of the culture (reported in Absorbance Units). Cells is the number of cells in the culture.Cell_Size_df.csv: cell size for different species of Histoplasma. Line refers to the name of the Histoplasma strain. Replicate refers to the number of the experimental batch. Area is the ellipse area of the cell (in micrometers^2).histoplasma_morphology_code.R: Analytical code to generate linear models.<br>
DOI: 10.15468/dl.txwyfd
title: Occurrence Download

description: A dataset containing 13394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Elephantopus mollis Kunth"
 ]
}

 The dataset includes 13394 records from 442 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020623-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/me31w4
title: Supplemental Material (3tables 1figure).pdf

description: :unav
DOI: 10.15468/dl.sg7x9w
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (ARG, CHL, PRY, URY, FLK, BRA.21_1, BRA.16_1, BRA.24_1)",
 "TaxonKey is one of (Chiliotrichiopsis ledifolia (Griseb.) Cabrera, Chiliotrichiopsis keidelii Cabrera)"
 ]
}

 The dataset includes 150 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020626-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5285/ec659b31a8ca40918e58ec6d03af07a6
title: ESA Sea Surface Temperature Climate Change Initiative (SST_cci): Advanced Very High Resolution Radiometer (AVHRR) Level 2 Pre-processed (L2P) product, version 3.0

description: This dataset provides global sea surface temperatures (SST) from Advanced Very High Resolution Radiometers (AVHRR), presented on the native geometry of observation, and spanning 1980 to 2021. 

The SST CCI AVHRR product contains two different SST estimates. The first is the skin temperature of the water at the time it was observed. The second is an estimate of the temperature at 20 cm depth at either 1030h or 2230h local time, which closely approximates the daily mean SST. Each SST value has an associated total uncertainty estimate, and uncertainty estimates for various contributions to that total. 

The dataset has been produced as part of the version 3 Climate Data Record (CDR) produced by the European Space Agency (ESA) Climate Change Initiative Sea Surface Temperature project (ESA SST_cci). The CDR accurately maps the surface temperature of the global oceans over the period 1980 to 2021 using observations from many satellites, with a high degree of independence from in situ measurements. The data provide independently quantified SSTs to a quality suitable for climate research. 

This CDR Version 3.0 product supersedes the CDR v2.1 product. Compared to the previous version the major changes are: 

* Longer time series: 1980 to 2021 (previous CDR was Sept 1981 to 2016) 

* Improved retrieval to reduce systematic biases using bias-aware optimal methods (for single view sensors) 

* Improved retrieval with respect to desert-dust aerosols 

* Addition of early AVHRR/1 data in 1980s, and improved AVHRR processing to reduce data gaps in 1980s 

* Use of full-resolution MetOp AVHRR data (previously used ‘global area coverage’ Level 1 data) 

Data are made freely and openly available under a Creative Commons License by Attribution (CC By 4.0) https://creativecommons.org/licenses/by/4.0/ 

When citing this dataset please also cite the associated data paper: 

Embury, O., Merchant, C.J., Good, S.A., Rayner, N.A., Høyer, J.L., Atkinson, C., Block, T., Alerskans, E., Pearson, K.J., Worsfold, M., McCarroll, N., Donlon, C. Satellite-based time-series of sea-surface temperature since 1980 for climate applications. Scientific Data 11, 326 (2024). https://doi.org/10.1038/s41597-024-03147-w
DOI: 10.17632/jt2ppwr62p.2
title: Instances for Weapon Target Assignment Problem

description: This dataset corresponds to the Static Weapon Target Problem (WTA), the WTA Problem aims to find best assignment of weapons to targets, to minimize the expected damage of the defended area in order to increase chances of survival. 

This supports the paper: Emrullah Sonuc, Baha Sen, Safak Bayir (2017) A Parallel Simulated Annealing Algorithm For Weapon-Target Assignment Problem
DOI: 10.5281/zenodo.11204238
title: Xenium Breast Cancer Factor Analysis

description: Xenium Breast Cancer Factor Analysis (TSV format)
DOI: 10.5281/zenodo.11204239
title: Xenium Breast Cancer Factor Analysis

description: Xenium Breast Cancer Factor Analysis (TSV format)
DOI: 10.17632/b64wrvdyk4.1
title: Targeted National Suicide Prevention Strategies

description: Targeted National Suicide Prevention Strategies
DOI: 10.15468/dl.ba4svy
title: Occurrence Download

description: A dataset containing 348872 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Trifolium dubium Sibth.)"
 ]
}

 The dataset includes 348872 records from 2428 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020617-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpk4py
title: Occurrence Download

description: A dataset containing 2065 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "CoordinateUncertaintyInMeters 0.0-100.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cerambyx cerdo Linnaeus, 1758",
 "Year 2014-2024"
 ]
}

 The dataset includes 2065 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048950-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lgroqa
title: Occurrence Download

description: A dataset containing 201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pterygoplichthys pardalis (Castelnau, 1855)",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 201 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012975-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.usttbm
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Porophyllum macrocephalum DC."
 ]
}

 The dataset's 1 records were derived from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035742-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fbj4rw
title: Occurrence Download

description: A dataset containing 75552 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-4.94705 36.21907,-4.58539 36.83125,-4.96244 37.38355,-5.4934 37.58506,-6.34754 37.42023,-6.55531 36.7203,-6.4168 36.16939,-5.56527 35.91678,-4.94705 36.21907))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 75552 records from 364 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048949-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xldkqd
title: Occurrence Download

description: A dataset containing 10062 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Campephilus guatemalensis (Hartlaub, 1844)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10062 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012976-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dqv8ag
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gasteranthus mutabilis L.E.Skog & L.P.Kvist"
 ]
}

 The dataset includes 33 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0164238-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xprfux
title: Occurrence Download

description: A dataset containing 1035920 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coenonympha Hübner, 1819"
 ]
}

 The dataset includes 1035920 records from 1052 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0285527-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cegafp
title: Occurrence Download

description: A dataset containing 652169 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is New York City Street Tree Census - 2015"
 ]
}

 The dataset includes 652169 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048955-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hs4rrj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fleischmannia hammelii H.Rob."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0164237-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2qxs5z
title: Occurrence Download

description: A dataset containing 428 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ipomoea digitata L."
 ]
}

 The dataset includes 428 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0164240-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7hyb6s
title: Occurrence Download

description: A dataset containing 824 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plethodon dorsalis Cope, 1889",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 2000",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 824 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022087-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfum9n
title: Occurrence Download

description: A dataset containing 517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "TaxonKey is Bombus magnus Vogt, 1911"
 ]
}

 The dataset includes 517 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214966-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2yjv4y
title: Occurrence Download

description: A dataset containing 270895 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "PublishingCountry is Colombia",
 "StateProvince is one of (Meta, MEta, Meta ?, Meta Department, San Martin, Meta Prov, Meta Intendencia, Meta Dept)",
 "Year 2021-2022"
 ]
}

 The dataset includes 270895 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0427062-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g5iqri
title: Occurrence Download

description: A dataset containing 293 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 2000-2020",
 "Geometry POLYGON((-7.57507 51.84935,-5.4657 51.84935,-5.4657 53.06763,-7.57507 53.06763,-7.57507 51.84935))",
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Numenius arquata (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 293 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017393-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x8792x
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ceropegia rupicola Deflers"
 ]
}

 The dataset includes 30 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0133304-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.262mcs
title: Occurrence Download

description: A dataset listing the 838 species recorded in GBIF matching the query:
{
 "and" : [
 "PublishingOrg is e8eada63-4a33-44aa-b2fd-4f71efb222a0",
 "TaxonKey is Mammalia"
 ]
}

 The dataset's 838 records were derived from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069240-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7hxcej
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Geophis pyburni Campbell & Murphy, 1977"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0279829-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yjxf2f
title: Occurrence Download

description: A dataset containing 234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plethodon yonahlossee Dunn, 1917",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 2000",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 234 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022086-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ejd6nh
title: Occurrence Download

description: A dataset containing 19134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rhodophyta"
 ]
}

 The dataset includes 19134 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069245-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.js8vcy
title: Occurrence Download

description: A dataset containing 19245 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Papilio cresphontes Cramer, 1777"
 ]
}

 The dataset includes 19245 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0133303-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.