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

description: A dataset containing 213179 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos L.f., Arthurdendyus triangulatus (Dendy, 1895), Cabomba caroliniana A.Gray, Callosciurus finlaysonii (Horsfield, 1823), Cherax destructor Clark, 1936, Corvus splendens Vieillot, 1817, Crassula helmsii (Kirk) Cockayne, Elodea densa (Planch.) Casp., Eriocheir sinensis H.Milne Edwards, 1853, Erythranthe guttata (DC.) G.L.Nesom, Faxonius immunis (Hagen, 1870), Faxonius juvenilis (Hagen, 1870), Faxonius rusticus (Girard, 1852), Faxonius virilis (Hagen, 1870), Gambusia affinis (Baird & Girard, 1853), Heracleum mantegazzianum Sommier & Levier, Heracleum persicum Desf. ex Fisch., C.A.Mey. & Avé-Lall., Heracleum pubescens (Hoffm.) M.Bieb., Houttuynia cordata Thunb., Hydrocotyle ranunculoides L.f., Impatiens glandulifera Royle, Koenigia polystachya (Wall. ex Meisn.) T.M.Schust. & Reveal, Lagarosiphon major (Ridl.) Moss, Lepomis gibbosus (Linnaeus, 1758), Limnoperna fortunei (Dunker, 1857), Ludwigia grandiflora (Michx.) Greuter & Burdet, Ludwigia peploides (Kunth) P.H.Raven, Lysichiton americanus Hultén & H.St.John, Morone americana (Gmelin, 1789), Muntiacus reevesi (Ogilby, 1839), Myriophyllum aquaticum (Vell.) Verdc., Myriophyllum heterophyllum Michx., Pacifastacus leniusculus (Dana, 1852), Petasites japonicus (Siebold & Zucc.) Maxim., Pontederia cordata L., Procambarus acutus (Girard, 1852), Procambarus clarkii (Girard, 1852), Procambarus virginalis Lyko, 2017, Pseudorasbora parva (Temminck & Schlegel, 1846), Pycnonotus cafer (Linnaeus, 1766), Saururus cernuus L., Sciurus carolinensis Gmelin, 1788, Sciurus niger Linnaeus, 1758, Solenopsis invicta Buren, 1972, Solenopsis richteri Forel, 1909, Threskiornis aethiopicus (Latham, 1790), Vespa velutina Lepeletier, 1836, Zizania latifolia (Griseb.) Hance ex F.Muell.)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 213179 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031636-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ut565a
title: Occurrence Download

description: A dataset containing 1074489 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Belgium, Germany, Netherlands)",
 "TaxonKey is one of (Ondatra zibethicus (Linnaeus, 1766), Myocastor coypus (Molina, 1782))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1074489 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031635-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26103115
title: Coss-sectional Study on Awareness and Atitudes towards Posthumous Organ Donation among residents of Al Riyadh, Khartoum, 2020

description: This study explores the awareness and attitudes towards posthumous organ donation among citizens in Al Riyadh, Khartoum, Sudan. A total of 200 participants were surveyed through structured interviews and self-administered questionnaires. The results indicate that 84% of respondents were willing to donate their organs after death, with the main reasons for acceptance being beneficence and charity. Religious beliefs and concerns about the body's integrity were the primary reasons for refusal. The study concludes that gender, higher educational levels, and increased knowledge are crucial factors influencing the decision to donate. The findings suggest the need for public campaigns, further research, and the establishment of organ donation registration centers in Sudan.
DOI: 10.6084/m9.figshare.26103115.v4
title: Coss-sectional Study on Awareness and Atitudes towards Posthumous Organ Donation among residents of Al Riyadh, Khartoum, 2020

description: This study explores the awareness and attitudes towards posthumous organ donation among citizens in Al Riyadh, Khartoum, Sudan. A total of 200 participants were surveyed through structured interviews and self-administered questionnaires. The results indicate that 84% of respondents were willing to donate their organs after death, with the main reasons for acceptance being beneficence and charity. Religious beliefs and concerns about the body's integrity were the primary reasons for refusal. The study concludes that gender, higher educational levels, and increased knowledge are crucial factors influencing the decision to donate. The findings suggest the need for public campaigns, further research, and the establishment of organ donation registration centers in Sudan.
DOI: 10.15468/dl.s7z6t7
title: Occurrence Download

description: A dataset containing 366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 "TaxonKey is Physeter macrocephalus Linnaeus, 1758"
 ]
}

 The dataset includes 366 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031654-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gz2u78
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Apis nuluensis Tingek, Koeniger & Koeniger, 1996"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031655-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fq3kmm
title: Occurrence Download

description: A dataset containing 9686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((112.54839 24.79583,112.59363 24.80422,112.61091 24.86757,112.67426 24.87102,112.73992 24.85835,112.77677 24.8238,112.74913 24.78348,112.75489 24.72359,112.78368 24.666,112.83552 24.66254,112.89887 24.64872,112.94149 24.62799,112.94724 24.57961,112.93227 24.53008,112.91845 24.47249,112.953 24.43563,112.99332 24.42642,113.02557 24.39762,113.07164 24.37574,113.13154 24.38035,113.19258 24.36307,113.25593 24.35846,113.35351 24.36761,113.41686 24.38719,113.51707 24.41599,113.54241 24.49661,113.44796 24.50237,113.48252 24.55766,113.40765 24.56572,113.44796 24.65787,113.35812 24.71892,113.26367 24.68667,113.19456 24.66939,113.19226 24.62562,113.17153 24.57379,113.12776 24.55651,113.11393 24.52311,113.07708 24.54614,113.0598 24.50583,112.98263 24.49201,112.98263 24.5496,113.01142 24.61871,112.98493 24.69588,113.03215 24.7051,113.10357 24.73619,113.16116 24.76729,113.17844 24.803,113.17728 24.8675,113.13352 24.89054,113.11624 24.9274,113.07247 24.94237,113.06095 24.96195,113.01603 25.00227,112.9377 25.0541,112.91697 25.00227,112.90315 24.97347,112.86284 24.97347,112.811 24.96771,112.77875 24.95043,112.7154 24.94237,112.67854 24.93892,112.69237 24.96195,112.69237 24.97693,112.67854 25.00803,112.64284 25.01814,112.64284 25.05269,112.62902 25.06997,112.59331 25.07573,112.53111 25.03772,112.53917 25.02159,112.51959 25.02159,112.51959 25.00086,112.5219 24.98128,112.50692 24.98013,112.51614 24.9663,112.53111 24.9663,112.53572 24.95133,112.51614 24.94557,112.51038 24.92599,112.51614 24.90871,112.52996 24.89374,112.52535 24.87646,112.51614 24.85342,112.54839 24.79583))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9686 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031656-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14209959
title: Accelerating the Conjugate Gradient Method on Distributed-Memory Computers: Software and Experiment Data

description: This Zenodo record consists of supplementary material for journal article 'Accelerating the Conjugate Gradient Method on Distributed-Memory Computers' by Kozický, Šimeček and Rúra. Archive 'software.zip' contains the source code of the software we used to perform the experiments in our article, archive 'data-experiments.zip' contains the raw data from our experiments and archive 'data-manuscript.zip' contains the result data presented in our article.
DOI: 10.5281/zenodo.14209960
title: Accelerating the Conjugate Gradient Method on Distributed-Memory Computers: Software and Experiment Data

description: This Zenodo record consists of supplementary material for journal article 'Accelerating the Conjugate Gradient Method on Distributed-Memory Computers' by Kozický, Šimeček and Rúra. Archive 'software.zip' contains the source code of the software we used to perform the experiments in our article, archive 'data-experiments.zip' contains the raw data from our experiments and archive 'data-manuscript.zip' contains the result data presented in our article.
DOI: 10.5281/zenodo.14213222
title: Production and evolution of granitic regolith under cold temperate climate in northeast China: a perspective from 238U-234U-230Th disequilibrium
DOI: 10.5281/zenodo.14213223
title: Production and evolution of granitic regolith under cold temperate climate in northeast China: a perspective from 238U-234U-230Th disequilibrium
DOI: 10.15468/dl.6jegfc
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma flavipiperatum Dixon, 1963"
 ]
}

 The dataset includes 299 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031657-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rhvfk5
title: Occurrence Download

description: A dataset containing 2566 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Base de dados da Coleção Ictiológica do LEP-UFRRJ",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2566 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031659-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xk72hn
title: Occurrence Download

description: A dataset containing 353 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ambystoma amblycephalum Taylor, 1940"
 ]
}

 The dataset includes 353 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031660-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14213238
title: Artigos da RSL
DOI: 10.5281/zenodo.14213239
title: Artigos da RSL
DOI: 10.15468/dl.bnfkhx
title: Occurrence Download

description: A dataset containing 4073 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "DatasetKey is one of (Canadian Museum of Nature Mammal Collection, iNaturalist Research-grade Observations, AMNH Mammal Collections, NHMD Mammalogy Collection, Marine mammal aerial surveys in the Bering, Chukchi and Beaufort Seas 1979-2010, UAM Mammal Collection (Arctos), USGS Alaska Science Center Polar Bear Maternal Dens, Macaulay Library Audio and Video Collection, NHMD Quaternary Zoology Collection, NMNH Extant Specimen Records (USNM, US))",
 "TaxonKey is Ursus maritimus Phipps, 1774"
 ]
}

 The dataset includes 4073 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031663-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cahugq
title: Occurrence Download

description: A dataset containing 356 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 one of (Sinocrassula indica (Decne.) A.Berger)"
 ]
}

 The dataset includes 356 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031664-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fpphs
title: Occurrence Download

description: A dataset containing 267 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Haiti",
 "DatasetKey is University of Vermont Zadock Thompson Zoological Collection-Invertebrates",
 "OccurrenceStatus is Present",
 "TaxonKey is Coleoptera"
 ]
}

 The dataset includes 267 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031665-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2z42gc
title: Occurrence Download

description: A dataset containing 2 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 one of (Sinocrassula jiaozishanensis Chao Chen, J.Guan Wang & Z.R.He)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031666-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.76ny86
title: Occurrence Download

description: A dataset containing 8 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 one of (Sinocrassula longistyla (Praeger) S.H.Fu)"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031667-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11557420
title: GENEActiv accelerometer file related to the #120 OxWearables / stepcount issue

description: An example of .bin file that have an IndexError when processing.

Consider #120 OxWearables / stepcount issue for more details.

The .csv files are 1-second epoch conversions from the .bin file and contain time, x, y, z columns. The conversion was done by: 



reading the .bin with the GENEAread R package.

keeping only the time, x, y and z columns.

saving the data.frame into a .csv file.


The only difference between the .csv files is the column format used for the time column before saving:



time column in XXXXXX_....csv had a string class

time column in XXXXXT....csv had a "POSIXct" "POSIXt" class
DOI: 10.5281/zenodo.11557421
title: GENEActiv accelerometer file related to the #120 OxWearables / stepcount issue

description: An example of .bin file that have an IndexError when processing.

Consider #120 OxWearables / stepcount issue for more details.
DOI: 10.5281/zenodo.14213237
title: GENEActiv accelerometer file related to the #120 OxWearables / stepcount issue

description: An example of .bin file that have an IndexError when processing.

Consider #120 OxWearables / stepcount issue for more details.

The .csv files are 1-second epoch conversions from the .bin file and contain time, x, y, z columns. The conversion was done by: 



reading the .bin with the GENEAread R package.

keeping only the time, x, y and z columns.

saving the data.frame into a .csv file.


The only difference between the .csv files is the column format used for the time column before saving:



time column in XXXXXX_....csv had a string class

time column in XXXXXT....csv had a "POSIXct" "POSIXt" class
DOI: 10.15151/esrf-es-1897081240
title: Structural Biology at EMBL Grenoble, IBS-CIBB and IAB

description: This proposal clusters crystallography and bioSAXS projects at the EMBL Grenoble, IBS-CIBB and IAB. It combines groups working on different topics with a major focus on cell signaling proteins, drug discovery, long non-coding RNAs, nucleic acid-protein complexes, and host-pathogen interactions. The proposers have long-standing experience in the use, as well as the development of beam lines for macromolecular crystallography and biological small angle X-ray scattering and have participated in successive BAG applications over the years, mostly at the ESRF but also at other synchrotrons. The BAG responsible is Andrew McCarthy (EMBL Grenoble) for this application round.
DOI: 10.15468/dl.rv2843
title: Occurrence Download

description: A dataset containing 1 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 one of (Sinocrassula papillosa Jankalski)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031668-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4d5cqx
title: Occurrence Download

description: A dataset containing 100 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 one of (Meterostachys sikokianus (Makino) Nakai)"
 ]
}

 The dataset includes 100 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031669-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4kt9fu
title: Occurrence Download

description: A dataset containing 0 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 one of (Sinocrassula parvifoliana S.S.Ying)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031670-241107131044228/datasets/export for details.
DOI: 10.5281/zenodo.14000489
title: BBS phase 1 & phase 2 high quality E. coli bin assembled genomes

description: 1,402 Escherichia coli bin assembled genomes derived from the metagenome data collected as part of the BabyBiome study (BBS) phase 1 & phase 2.

The data in this upload was first published as part of "Group 2 and 3 ABC-transporter dependant K-antigen loci contribute significantly to variation in the invasive potential of Escherichia coli"  (Gladstone et al. 2024, to be released).

Files

Assembly data:



BBS_E_coli_BAGs.tar: Archive containing sequences of the 1,402 bin assembled genomes.

BBS_E_coli_metadata.tsv: Table linking the sequence assemblies to the subject data.


Capsule predictions:



BBS_E_coli_Kaptive_output.csv: Capsule predictions for all sequence data.

BBS_E_coli_deduplicated_sequences_IDs.txt: Filenames for assemblies that constitute the 873 deduplicated sequences analysed in Gladstone et al. 2024.


Quality control data:



BBS_E_coli_demix_check_scores.tsv: Output from demix_check for the sequence assemblies.

BBS_E_coli_checkm_results.tsv: Output from checkm.

BBS_E_coli_gunc_results.tsv: Output from gunc.


Methods

Bin assembled genomes

Source data:



BBS phase 1: Shao et al. 2019

BBS phase 2: Shao et al. 2024


The data was produced using the mSWEEP and mGEMS pipeline (Mäklin et al. 2020 & Mäklin et al. 2021) following the steps described in Khawaja, Mäklin, Kallonen, et al. 2024.

Quality control

The BAGs in this upload were filtered with demix_check (https://github.com/harry-thorpe/demix_check) and only those with a quality score 1 or 2 are included. For the capsule type annotations, contigs shorter than 5,000bp were removed but the short contigs are still present in the uploaded files). Further QC data is available from checkm (Parks et al. 2015) and gunc (Orakov et al. 2022) results.

Multilocus sequence typing

Sequence type (ST) was determined using fastmlst (Guerrero-Araya et al. 2021) with the `ecoli#1` database.

PopPUNK  clustering

Sequence clusters (SC) correspond to the database available from https://zenodo.org/records/12528310 and were created using PopPUNK (Lees et al. 2019). Construction is described in Khawaja, Mäklin, Kallonen, et al. 2024.

Capsule type annotations

The capsule type annotations were created using Kaptive (Lam et al. 2022) with an E. coli specific database available from https://github.com/rgladstone/EC-K-typing and described in Gladstone et al. 2024.
DOI: 10.5281/zenodo.14051467
title: BBS phase 1 & phase 2 high quality E. coli bin assembled genomes

description: 1,402 Escherichia coli bin assembled genomes derived from the metagenome data collected as part of the BabyBiome study (BBS) phase 1 & phase 2.

The data in this upload was first published as part of "Group 2 and 3 ABC-transporter dependant K-antigen loci contribute significantly to variation in the invasive potential of Escherichia coli"  (Gladstone et al. 2024, to be released).

Files

Assembly data:



BBS_E_coli_BAGs.tar: Archive containing sequences of the 1,402 bin assembled genomes.

BBS_E_coli_metadata.tsv: Table linking the sequence assemblies to the subject data.


Capsule predictions:



BBS_E_coli_Kaptive_output.csv: Capsule predictions for all sequence data.

BBS_E_coli_deduplicated_sequences_IDs.txt: Filenames for assemblies that constitute the 873 deduplicated sequences analysed in Gladstone et al. 2024.


Quality control data:



BBS_E_coli_demix_check_scores.tsv: Output from demix_check for the sequence assemblies.

BBS_E_coli_checkm_results.tsv: Output from checkm.

BBS_E_coli_gunc_results.tsv: Output from gunc.


Methods

Bin assembled genomes

Source data:



BBS phase 1: Shao et al. 2019

BBS phase 2: Shao et al. 2024


The data was produced using the mSWEEP and mGEMS pipeline (Mäklin et al. 2020 & Mäklin et al. 2021) following the steps described in Khawaja, Mäklin, Kallonen, et al. 2024.

Quality control

The BAGs in this upload were filtered with demix_check (https://github.com/harry-thorpe/demix_check) and only those with a quality score 1 or 2 are included. For the capsule type annotations, contigs shorter than 5,000bp were removed but the short contigs are still present in the uploaded files). Further QC data is available from checkm (Parks et al. 2015) and gunc (Orakov et al. 2022) results.

Multilocus sequence typing

Sequence type (ST) was determined using fastmlst (Guerrero-Araya et al. 2021) with the `ecoli#1` database.

PopPUNK  clustering

Sequence clusters (SC) correspond to the database available from https://zenodo.org/records/12528310 and were created using PopPUNK (Lees et al. 2019). Construction is described in Khawaja, Mäklin, Kallonen, et al. 2024.

Capsule type annotations

The capsule type annotations were created using Kaptive (Lam et al. 2022) with an E. coli specific database available from https://github.com/rgladstone/EC-K-typing and described in Gladstone et al. 2024.