cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30876674
title: <b>Benchmarking Denoising Strategies and Nucleic Acid Templates for ITS2 Amplicon Sequencing of Gut Microbiome</b>

description: Background: The human gut mycobiome plays a critical role in host immunity, yet standardized workflows for fungal internal transcribed spacer (ITS) amplicon sequencing remain elusive. Unlike the bacterial 16S rRNA gene, where the impact of DNA versus RNA templates is well-documented, such comparative benchmarks are lacking for fungal studies. Furthermore, fungal ITS regions exhibit significant length heterogeneity, posing unique challenges for denoising algorithms that were originally designed for conserved bacterial amplicons.Methods: We performed ITS2 sequencing on paired DNA and RNA (cDNA) from fecal samples of healthy controls and patients with acute gastrointestinal injury (AGI). We systematically benchmarked three pipelines: DADA2 (ASV), Deblur (ASV), and VSEARCH (OTU). We then evaluated genomic (DNA) vs. transcriptomic (RNA) concordance and used ANCOM to compare disease-associated signatures within each template.Results: DADA2 outperformed VSEARCH and Deblur by resolving biological length heterogeneity without the artifacts introduced by rigid trimming. Direct comparison between DNA and RNA profiles revealed high concordance: Alpha and Beta diversity showed no significant differences, and ANCOM identified no differentially abundant taxa between the two nucleic acid templates. However, intra-template clinical analysis (AGI vs. Healthy) revealed distinct biomarker profiles. While DNA and RNA analyses both identified <i>Glomeromycota</i> as a key disease marker, they each detected unique sets of additional differentially abundant taxa.Conclusions: DADA2 is the optimal denoising strategy for ITS2 data due to its ability to handle length polymorphism. Regarding nucleic acid templates, we propose a tiered strategy: for routine community profiling, DNA sequencing is sufficient as it accurately captures the dominant, stable mycobiome structure. However, for in-depth clinical investigations targeting the active rare biosphere or specific metabolic shifts, RNA-based sequencing provides necessary complementary insight.
DOI: 10.6084/m9.figshare.30876674.v1
title: <b>Benchmarking Denoising Strategies and Nucleic Acid Templates for ITS2 Amplicon Sequencing of Gut Microbiome</b>

description: Background: The human gut mycobiome plays a critical role in host immunity, yet standardized workflows for fungal internal transcribed spacer (ITS) amplicon sequencing remain elusive. Unlike the bacterial 16S rRNA gene, where the impact of DNA versus RNA templates is well-documented, such comparative benchmarks are lacking for fungal studies. Furthermore, fungal ITS regions exhibit significant length heterogeneity, posing unique challenges for denoising algorithms that were originally designed for conserved bacterial amplicons.Methods: We performed ITS2 sequencing on paired DNA and RNA (cDNA) from fecal samples of healthy controls and patients with acute gastrointestinal injury (AGI). We systematically benchmarked three pipelines: DADA2 (ASV), Deblur (ASV), and VSEARCH (OTU). We then evaluated genomic (DNA) vs. transcriptomic (RNA) concordance and used ANCOM to compare disease-associated signatures within each template.Results: DADA2 outperformed VSEARCH and Deblur by resolving biological length heterogeneity without the artifacts introduced by rigid trimming. Direct comparison between DNA and RNA profiles revealed high concordance: Alpha and Beta diversity showed no significant differences, and ANCOM identified no differentially abundant taxa between the two nucleic acid templates. However, intra-template clinical analysis (AGI vs. Healthy) revealed distinct biomarker profiles. While DNA and RNA analyses both identified <i>Glomeromycota</i> as a key disease marker, they each detected unique sets of additional differentially abundant taxa.Conclusions: DADA2 is the optimal denoising strategy for ITS2 data due to its ability to handle length polymorphism. Regarding nucleic acid templates, we propose a tiered strategy: for routine community profiling, DNA sequencing is sufficient as it accurately captures the dominant, stable mycobiome structure. However, for in-depth clinical investigations targeting the active rare biosphere or specific metabolic shifts, RNA-based sequencing provides necessary complementary insight.
DOI: 10.15468/dl.9r9jq8
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dasysphaera hyposericea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009572-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18429482
title: Supporting Information for: The temporal evolution of volcanic ash fingers and their effect on particle sedimentation in laboratory experiments and field observations

description: This repositery contains supporting information accompanying the submission of the manuscript entitled: "The temporal evolution of volcanic ash fingers and their effect on particle sedimentation in laboratory experiments and field observations" by Fries, Lemus, Jarvis, Simionato, Díaz-Vecino, Clarke, Phillips, Manzella and Bonadonna. The manuscript has been submitted on 02 December 2024 to the Journal of Geophysical Research - Solid Earth. All the files present in this repositery are described in the file "Supporting_Information_Friesetal.pdf". Please refer to that file for additional information on the data present in the repositery.
DOI: 10.5281/zenodo.14261311
title: Supporting Information for: The temporal evolution of volcanic ash fingers and their effect on particle sedimentation in laboratory experiments and field observations

description: This repositery contains supporting information accompanying the submission of the manuscript entitled: "The temporal evolution of volcanic ash fingers and their effect on particle sedimentation in laboratory experiments and field observations" by Fries, Lemus, Jarvis, Simionato, Díaz-Vecino, Clarke, Phillips, Manzella and Bonadonna. The manuscript has been submitted on 02 December 2024 to the Journal of Geophysical Research - Solid Earth. All the files present in this repositery are described in the file "Supporting_Information_Friesetal.pdf". Please refer to that file for additional information on the data present in the repositery.
DOI: 10.15468/dl.43h8hn
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ocenebra paddeui",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009573-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.48y3qy
title: Occurrence Download

description: A dataset containing 236 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((5.07276 45.87142,5.07017 45.87018,5.06634 45.86691,5.06294 45.8645,5.06436 45.86006,5.0655 45.84975,5.06659 45.84333,5.07023 45.84042,5.07658 45.83889,5.07876 45.84005,5.08808 45.84282,5.08857 45.85011,5.08579 45.85721,5.08036 45.86314,5.07943 45.86382,5.07635 45.87037,5.07276 45.87142))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Plantae",
 "Year 2016-2026"
 ]
}

 The dataset includes 236 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009574-260129131611470/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.30094057
title: Swedish Primary Forest Map 2025

description: Vector-based product of Swedish primary forest ecosystems (e.i. includes forest land but also, lakes, wetlands, rivers etc...)Variables:<br>FID and FID_save:identifiers<br>NewNat: Naturalness score of forest<br>Namn: Name of forest<br>For further information on how the map was created and the naturalness was assigned please see: Volle et al. 2026. Swedish primary forests: factors behind their persistence and their potential suitability as natural baselines. <i>Landscape Ecology. </i>DOI: 10.1007/s10980-026-02296-0
DOI: 10.6084/m9.figshare.30094057.v1
title: Swedish Primary Forest Map 2025

description: Vector-based product of Swedish primary forest ecosystems (e.i. includes forest land but also, lakes, wetlands, rivers etc...)Variables:<br>FID and FID_save:identifiers<br>NewNat: Naturalness score of forest<br>Namn: Name of forest<br>For further information on how the map was created and the naturalness was assigned please see: Volle et al. 2026. Swedish primary forests: factors behind their persistence and their potential suitability as natural baselines. <i>Landscape Ecology. </i>DOI: 10.1007/s10980-026-02296-0
DOI: 10.5281/zenodo.18418764
title: Chemical Analysis of Commercial Functionalized Graphene Nanoplatelets along the Production Process with Raman and XPS

description: The raw data of the aforementioned publication are given as ascii-files
DOI: 10.5281/zenodo.18418765
title: Chemical Analysis of Commercial Functionalized Graphene Nanoplatelets along the Production Process with Raman and XPS

description: The raw data of the aforementioned publication are given as ascii-files
DOI: 10.15468/dl.7mtg56
title: Occurrence Download

description: A dataset containing 1893942 records in GBIF matching the query:
SELECT kingdom, phylum, class, "order", family, genus, species, taxonRank, scientificName, speciesKey, eventdate, "year", decimalLongitude, decimalLatitude
FROM occurrence
WHERE hasCoordinate = TRUE
 AND decimalLongitude &gt; 14.16751398 AND decimalLongitude &lt; 14.55440852
 AND decimalLatitude &gt; 47.67898893 AND decimalLatitude &lt; 47.85659594
 AND BasisOfRecord = 'HUMAN_OBSERVATION'


 The dataset's 1893942 records were derived from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009535-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5sdhq9
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vicia parviflora, Vicia parviflora, Vicia parviflora, Vicia parviflora, Vicia parviflora, Vicia parviflora, Ervum gracile, Ervum gracile, Vicia tenuissima)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009575-260129131611470/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.30617513
title: <b>A Comparative Analysis of Denoising Methods and Nucleic Acid Templates for 16S rRNA Amplicon Sequencing of the Gut Microbiome</b>

description: Of the three bioinformatics pipelines (DADA2, Deblur, VSEARCH) evaluated for analyzing paired 16S rRNA DNA and RNA amplicons from human fecal samples, DADA2 demonstrated superior performance by producing more biologically coherent community profiles and a better-balanced feature table. Employing this optimized DADA2 workflow, we found no significant differences between DNA and RNA-derived microbial communities across composition (phylum and genus levels), alpha and beta diversity, or predicted metagenomic function, with only sporadic genus-level biomarkers and functional differences detected. Based on these findings and the practical advantages of DNA regarding cost and stability, we recommend a standardized DADA2-based DNA amplicon sequencing workflow for gut microbiome profiling to enhance reproducibility and cross-study comparability.
DOI: 10.6084/m9.figshare.30617513.v1
title: <b>A Comparative Analysis of Denoising Methods and Nucleic Acid Templates for 16S rRNA Amplicon Sequencing of the Gut Microbiome</b>

description: Of the three bioinformatics pipelines (DADA2, Deblur, VSEARCH) evaluated for analyzing paired 16S rRNA DNA and RNA amplicons from human fecal samples, DADA2 demonstrated superior performance by producing more biologically coherent community profiles and a better-balanced feature table. Employing this optimized DADA2 workflow, we found no significant differences between DNA and RNA-derived microbial communities across composition (phylum and genus levels), alpha and beta diversity, or predicted metagenomic function, with only sporadic genus-level biomarkers and functional differences detected. Based on these findings and the practical advantages of DNA regarding cost and stability, we recommend a standardized DADA2-based DNA amplicon sequencing workflow for gut microbiome profiling to enhance reproducibility and cross-study comparability.
DOI: 10.15468/74ysms
title: Selezione di campioni dall'Erbario Giorgio Jan - Flora Italiae Superioris | Giorgio Jan's herbarium selected specimens

description: The dataset contains 200 occurrence records of plant specimens stored in two different parcels. The first folder (series XXIII, no. III) contains species belonging to 7 botanical families (Caryophyllaceae, Hypericaceae, Linaceae, Malvaceae, Parnassiceae, Polygalaceae, and Resedaceae), while the second (series XXIII, no. V) contains species belonging to 13 families (Caryophyllaceae, Crassulaceae, Cucurbitaceae, Grossulariaceae, Haloragaceae, Hydrangeaceae, Lythraceae, Myrtaceae, Onagraceae, Plantaginaceae, Saxifragaceae and Tamaricaceae).
DOI: 10.15468/dl.4rh26e
title: Occurrence Download

description: A dataset listing the 676 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "OccurrenceStatus is Present",
 "StateProvince is MINAS GERAIS, MG"
 ]
}

 The dataset's 676 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009559-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60893/figshare.pof.31017925
title: Data

description: Raw data of figures in maintext
DOI: 10.60893/figshare.pof.31017925.v1
title: Data

description: Raw data of figures in maintext
DOI: 10.15468/dl.4y36sd
title: Occurrence Download

description: A dataset containing 554814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cervus elaphus",
 "Continent is Europe",
 "HasCoordinate is true"
 ]
}

 The dataset includes 554814 records from 1179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009457-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpz2xn
title: Occurrence Download

description: A dataset containing 82631 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fagus grandifolia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 82631 records from 223 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009523-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.reuy2a
title: Occurrence Download

description: A dataset containing 13672 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vicia sativa, Vicia sativa, Vicia sativa)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 13672 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009576-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/emv-gm3-t9p
title: Acanthonyx petiverii H. Milne Edwards, 1834

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x2h-0q0-gsg
title: Latreutes parvulus (Stimpson, 1871)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tfk-yjj-gzm
title: Ozius reticulatus (Desbonne in Desbonne & Schramm, 1867)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3bz-98z-46p
title: Pilumnus spinulosus Kessler, 1861

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sa5-xkk-xmj
title: Jaxea nocturna Nardo, 1847

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e0b-fxa-vel
title: Alpheus rapacida De Man, 1908

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xxy-zf8-gnb
title: Pilumnus spinifer H. Milne Edwards, 1834

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/faq-1wn-ja3
title: Pilumnus hirtellus (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/faq-dqb-z29
title: Systellaspis debilis (A. Milne-Edwards, 1881)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d1s-ac5-wp2
title: Polybius pusillus (Leach, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/70y-zxq-qcg
title: Eualus cranchii (Leach, 1817)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wej-6ak-j7m
title: Alpheus dentipes Guérin, 1832

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0mf-8mp-x1v
title: Machaerus atlanticus (Miers, 1881)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vlg-yg4-h0e
title: Upogebia Leach, 1814

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kj1-hfw-0fk
title: Macrobrachium crenulatum Holthuis, 1950

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ya8-lq1-gs9
title: Cuapetes americanus (Kingsley, 1878)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/43v-dbm-641
title: Heptacarpus sitchensis (Brandt, 1851)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1h5-7d2-cpa
title: Catapaguroides A. Milne-Edwards & Bouvier, 1892

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mfk-3fv-c7z
title: Pisidia longicornis (Linnaeus, 1767)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fxd-k36-pbs
title: Eualus pusiolus (Krøyer, 1841)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qkg-mb2-xrd
title: Crangon crangon (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7d6-fzm-25r
title: Crangon crangon (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hn4-9wd-1t8
title: Eualus cranchii (Leach, 1817)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ybg-11m-n3a
title: Atya scabra (Leach, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/53p-6lq-d4s
title: Plesionika richardi (Coutière, 1905)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8sp-aq8-ghj
title: Atya intermedia Bouvier, 1904

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5sa-ldy-5hh
title: Plesionika richardi (Coutière, 1905)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h0f-2bs-thn
title: Pagurus prideaux Leach, 1815

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/x0y-dbc-7h2
title: Portunus sanguinolentus (Herbst, 1783)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bfa-hz6-j6p
title: Pugettia foliata (Stimpson, 1860)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z4s-836-f1x
title: Hexapanopeus paulensis Rathbun, 1930

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3yw-c9w-pwh
title: Clibanarius erythropus (Latreille, 1818)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/peb-8fr-wle
title: Atlantotlos rhombifer Doflein, 1904

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9qp-z17-rlt
title: Pagurus alatus Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qtp-8hq-t16
title: Caridina nilotica (P. Roux, 1833)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/fjl-yl7-wtq
title: Ethusa mascarone (Herbst, 1785)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3t6-dct-7lw
title: Goneplax rhomboides (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jf6-jzx-sx1
title: Pagurus pubescens Krøyer, 1838

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/16w-40e-5fg
title: Hyas lyratus Dana, 1851

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3r6-61p-g79
title: Kingsleya latifrons (Randall, 1840)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c8v-z5d-zfg
title: Goneplax barnardi (Capart, 1951)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mcc-8eh-14h
title: Pagurus cuanensis Bell, 1846

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mfp-pzf-ts1
title: Atlantotlos rhombifer Doflein, 1904

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wm4-yzz-b9x
title: Grimothea quadrispina (J. E. Benedict, 1902)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.