cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0180008.10fu
title: SH0180008.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0180009.10fu
title: SH0180009.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.su2m88
title: Occurrence Download

description: A dataset containing 35143283 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 35143283 records from 3075 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001656-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nqz99
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grewia lutea Exell",
 "Continent is Africa"
 ]
}

 The dataset includes 35 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000249-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14000488
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: 10.15468/dl.cmr76r
title: Occurrence Download

description: A dataset containing 19436 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidoscelis sexlineatus (Linnaeus, 1766)"
 ]
}

 The dataset includes 19436 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000248-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18167/dvn1/048zrc
title: RACINE : Mesurer les revenus agricoles en Nouvelle-Calédonie et en Guadeloupe

description: Le projet « RACINE » a pour objectif d’apporter des éléments de méthode pour mesurer la diversité et la complexité des revenus des ménages agricoles (y compris les revenus non agricoles de ces ménages), et pour identifier et évaluer, dans deux situations de l’outre-mer français, les déterminants de ces revenus. Le projet développe une approche par les moyens d’existence, qui s’appuie sur les dotations en ressources et capitaux des ménages ruraux (ressources humaines, naturelles, sociales, physiques et financières) et sur les stratégies mises en oeuvre pour les mettre en valeur
DOI: 10.15468/dl.vcsb9k
title: Occurrence Download

description: A dataset containing 1944 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidoscelis communis (Cope, 1878)"
 ]
}

 The dataset includes 1944 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000251-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpeb35
title: Occurrence Download

description: A dataset containing 5222 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidoscelis costatus (Cope, 1878)"
 ]
}

 The dataset includes 5222 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000250-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.db2vcw
title: Occurrence Download

description: A dataset containing 3221 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Distribución geográfica de las lagartijas partenogenéticas del género Aspidoscelis en México"
 ]
}

 The dataset includes 3221 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000254-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.znxyus
title: Occurrence Download

description: A dataset containing 3634526 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-11.35907 46.79341,17.55493 46.79341,17.55493 63.10934,-11.35907 63.10934,-11.35907 46.79341))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Larus fuscus Linnaeus, 1758"
 ]
}

 The dataset includes 3634526 records from 1099 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000189-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gu9u5e
title: Occurrence Download

description: A dataset containing 724444 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 {
 "and" : [
 "StateProvince is one of (Valle del Cauca)",
 "GadmGid is one of (COL.31.32_2)",
 "TaxonKey is one of (Aves [GBIF Backbone Taxonomy])"
 ]
 }
 ]
}

 The dataset includes 724444 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017174-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5qk44k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physa marmorata",
 "Country is Benin",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017231-250920141307145/datasets/export for details.
DOI: 10.15468/dl.5293gj
title: Occurrence Download

description: A dataset containing 405 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Opsariichthys kaopingensis",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 405 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017235-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzeyws
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physa marmorata",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017232-250920141307145/datasets/export for details.
DOI: 10.6084/m9.figshare.29906144
title: Data AHA_CDA.xlsx

description: Mitochondria are the foremost player in ischemia-reperfusion (I/R) injury, which is one of the major contributors to myocardial infarction. Although current therapeutic options provide symptomatic relief, they fail to restore cardiomyocyte function, which represents a key roadblock in the treatment of reperfusion injury. Therefore, the ability to target mitochondrial pathways will likely provide a means to restore cardiomyocyte function, resulting in an effective and enhanced efficacy treatment. Efficient mitochondrial matrix protein quality control (mPQC) by LONP1 is crucial for cardiac bioenergetics. We compared young adult mice with cardiomyocyte-specific (Lonp1CKO-HET) or whole-body (Lonp1GKO-HET) haploinsufficiency and evaluated mitochondrial dynamics, including mitophagy markers, biogenesis markers, and mitochondrial stress markers. Despite similar cardiac Lonp1 reductions, only Lonp1CKO-HET mice showed mild dysfunction with mitochondrial stress response activation, altered dynamics, reduced biogenesis, and Tfam upregulation. Lonp1GKO-HET hearts lacked these changes, suggesting systemic mPQC deficiency can protect the heart via inter-organ signaling, a potential therapeutic strategy.
DOI: 10.6084/m9.figshare.29906144.v1
title: Data AHA_CDA.xlsx

description: Mitochondria are the foremost player in ischemia-reperfusion (I/R) injury, which is one of the major contributors to myocardial infarction. Although current therapeutic options provide symptomatic relief, they fail to restore cardiomyocyte function, which represents a key roadblock in the treatment of reperfusion injury. Therefore, the ability to target mitochondrial pathways will likely provide a means to restore cardiomyocyte function, resulting in an effective and enhanced efficacy treatment. Efficient mitochondrial matrix protein quality control (mPQC) by LONP1 is crucial for cardiac bioenergetics. We compared young adult mice with cardiomyocyte-specific (Lonp1CKO-HET) or whole-body (Lonp1GKO-HET) haploinsufficiency and evaluated mitochondrial dynamics, including mitophagy markers, biogenesis markers, and mitochondrial stress markers. Despite similar cardiac Lonp1 reductions, only Lonp1CKO-HET mice showed mild dysfunction with mitochondrial stress response activation, altered dynamics, reduced biogenesis, and Tfam upregulation. Lonp1GKO-HET hearts lacked these changes, suggesting systemic mPQC deficiency can protect the heart via inter-organ signaling, a potential therapeutic strategy.
DOI: 10.6084/m9.figshare.29906144.v2
title: Data AHA_CDA.xlsx

description: Mitochondria are the foremost player in ischemia-reperfusion (I/R) injury, which is one of the major contributors to myocardial infarction. Although current therapeutic options provide symptomatic relief, they fail to restore cardiomyocyte function, which represents a key roadblock in the treatment of reperfusion injury. Therefore, the ability to target mitochondrial pathways will likely provide a means to restore cardiomyocyte function, resulting in an effective and enhanced efficacy treatment. Efficient mitochondrial matrix protein quality control (mPQC) by LONP1 is crucial for cardiac bioenergetics. We compared young adult mice with cardiomyocyte-specific (Lonp1CKO-HET) or whole-body (Lonp1GKO-HET) haploinsufficiency and evaluated mitochondrial dynamics, including mitophagy markers, biogenesis markers, and mitochondrial stress markers. Despite similar cardiac Lonp1 reductions, only Lonp1CKO-HET mice showed mild dysfunction with mitochondrial stress response activation, altered dynamics, reduced biogenesis, and Tfam upregulation. Lonp1GKO-HET hearts lacked these changes, suggesting systemic mPQC deficiency can protect the heart via inter-organ signaling, a potential therapeutic strategy.
DOI: 10.15468/dl.uarvwy
title: Occurrence Download

description: A dataset containing 46419 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Monticola saxatilis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 46419 records from 280 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017233-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.anuyfa
title: Occurrence Download

description: A dataset containing 1878 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Puma concolor",
 "Year 2000-2025"
 ]
}

 The dataset includes 1878 records from 158 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017237-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m83awh
title: Occurrence Download

description: A dataset containing 11113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Opsariichthys pachycephalus",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11113 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017238-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.24kqa9
title: Occurrence Download

description: A dataset listing the 7127 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-95.88043 16.33073,-94.98854 16.33073,-94.98854 16.87376,-95.88043 16.87376,-95.88043 16.33073))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 7127 records were derived from 397 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017213-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sgqnty
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caladium bicolor",
 "Country is Brunei Darussalam",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017240-250920141307145/datasets/export for details.
DOI: 10.15468/dl.7nhnw3
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caladium bicolor",
 "Country is Benin",
 "HasCoordinate is true"
 ]
}

 The dataset includes 77 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017239-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h64nny
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caladium bicolor",
 "Country is Burkina Faso",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017241-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34847/nkl.02bd2539
title: VOC24_0006_06

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.0cef0937
title: VOC24_0006_01

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.3c4e4ec9
title: VOC24_0006_04

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.409a59ns
title: VOC24_0005_04

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.4ac330rn
title: VOC24_0005_10

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.4f1bnva1
title: unifr18a04d

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.5c1a60g2
title: VOC24_0005_09

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.5e088tl7
title: VOC24_0007_01

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.8f5d8an6
title: VOC24_0005_07

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.ade6p4lm
title: VOC24_0006_05

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.b6a4qwg1
title: VOC24_0005_06

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.bac0c59w
title: VOC24_0006_03

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.c303zh59
title: VOC24_0005_05

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.cd40x3h1
title: VOC24_0005_08

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.ec01ky7s
title: VOC24_0005_03

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.f3f2be8b
title: VOC24_0006_02

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.3a0f5xf7
title: VOC24_0016_01

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.3af498sd
title: VOC24_0009_02

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.b89a53qp
title: VOC24_0021_03

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.d59bwf8n
title: unine17a03d

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.34847/nkl.eb72r077
title: unine09a04m

description: Fichier source (TGD).
description: Fichier source (WAV).
description: Fichier dérivé (TEI).
DOI: 10.15468/dl.rc9hyc
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pararasbora moltrechti",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 43 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017244-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kud8s6
title: Occurrence Download

description: A dataset containing 333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caladium bicolor",
 "Country is Colombia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 333 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017245-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j76wd4
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caladium bicolor",
 "Country is Central African Republic",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017243-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.