cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27304311.v1
title: Causes and consequences of long-term defaunation in multi-species aggregations: Species traits predict freshwater mussel declines and decreases in biogeochemical storage and recycling

description: 1. One of the foremost challenges in contemporary ecology is understanding the rapid loss of animal diversity and biomass, known as defaunation. The causes and consequences of defaunation depend on species traits that regulate which species are vulnerable to particular stressors and the ecosystem-level consequences of declines.2. We used a &gt;30-year long-term monitoring dataset and a trait-based framework to identify defaunation in multi-species freshwater animal aggregations (freshwater mussels). We quantified long-term trends in mussel density, species richness, and mussel-generated ecosystem function, and tested whether these declines were associated with drought—a key driver of freshwater defaunation. Finally, we determined whether defaunation varied among mussel taxa with contrasting ecophysiological (thermal tolerance guild) and life history traits.3. Losses of mussel density were associated with biomass declines, and consequent losses of mussel-generated carbon and nutrient storage. Mussel aggregations became defaunated and lost function in rivers where drought conditions were more severe and/or frequent during the study. Unexpectedly, declines did not differ among species with different thermal tolerances—both thermally sensitive species and thermally tolerant species declined in defaunated streams. Rather, the taxa driving the declines in density and ecosystem function were those with life history traits adapted for stable hydrologic conditions (low fecundity, long lifespans, late age at maturity).4. Our finding that declines differed among species based on life history traits, but not thermal tolerance guilds, contrasted with previous studies conducted at shorter time intervals. We suggest that the ecophysiological traits that impact individual survival may be more important in governing drought-induced defaunation at shorter time scales, while life history traits that govern population recovery may be more important at longer time scales.5. The magnitude of lost biogeochemical storage and recycling associated with mussel declines was substantial when placed in the context of other studies. Given the significant role that river ecosystems play in global biogeochemical processes, freshwater defaunation may have major consequences if it continues unchecked.6. More broadly, trait-based approaches show clear promise for advancing the predictive capacity of animal ecology. The growing availability of species trait databases for animal assemblages should be leveraged to advance the field.
DOI: 10.15468/dl.4r6qcx
title: Occurrence Download

description: A dataset containing 338 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fuchsia ×hybrida hort. ex Vilm."
 ]
}

 The dataset includes 338 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023054-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhzd4c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enteromius amatolicus (Skelton, 1990)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.529 -24.0715,20.509 -24.0455,20.509 -24.0715,20.529 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023103-250525065834625/datasets/export for details.
DOI: 10.15468/dl.mqznne
title: Occurrence Download

description: A dataset containing 2022 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Undaria pinnatifida",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 2022 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001412-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kyvuu4
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tilia dasystyla",
 "Country is Armenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001415-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3hn3v
title: Occurrence Download

description: A dataset containing 12033 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 1000-1899"
 ]
}

 The dataset includes 12033 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001414-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16965985
title: Microbial adaptations underpin metabolic convergence across global shale basins

description: Phylogenetic trees for the manuscript (in prep) titled "Microbial adaptations underpin metabolic convergence across global shale basins" by Amundson et al. 

 

Description of files: 

rhodanase_MAGs_gtdbtk.bac120.rooted.tree: Phylogenetic tree of MAGs encoding rhodanase genes, generated using GTDB-tk. Tree is also shown in Figure S9. 

dsrAB_phsA_MAGs_gtdbtk.bac120.rooted.tree: Phylogenetic tree of MAGs encoding dsrB genes, generated using GTDB-tk. Tree is also shown in Figure S9. 

dsrB_RAxML_tree_bipartitionsBranchLabels: RAxML tree of all dissimilatory sulfite reductase (dsrB) genes encoded in MAGs, in addition to reference reductive dsrB genes. Tree is also shown in Figure S11.

methyNO_RAxML_bipartitionsBranchLabels: RAxML tree of all methyl-N and methy-O methyltransferase genes encoded in MAGs, in addition to reference methyltransferase genes. Tree is also shown in Figure S12.

methylS_RAxML_bipartitionsBranchLabels: RAxML tree of all methyl-S methyltransferase genes encoded in MAGs, in addition to reference methyltransferase genes. Tree is also shown in Figure S13.
DOI: 10.5281/zenodo.16965984
title: Microbial adaptations underpin metabolic convergence across global shale basins

description: Phylogenetic trees for the manuscript (in prep) titled "Microbial adaptations underpin metabolic convergence across global shale basins" by Amundson et al. 

 

Description of files: 

rhodanase_MAGs_gtdbtk.bac120.rooted.tree: Phylogenetic tree of MAGs encoding rhodanase genes, generated using GTDB-tk. Tree is also shown in Figure S9. 

dsrAB_phsA_MAGs_gtdbtk.bac120.rooted.tree: Phylogenetic tree of MAGs encoding dsrB genes, generated using GTDB-tk. Tree is also shown in Figure S9. 

dsrB_RAxML_tree_bipartitionsBranchLabels: RAxML tree of all dissimilatory sulfite reductase (dsrB) genes encoded in MAGs, in addition to reference reductive dsrB genes. Tree is also shown in Figure S11.

methyNO_RAxML_bipartitionsBranchLabels: RAxML tree of all methyl-N and methy-O methyltransferase genes encoded in MAGs, in addition to reference methyltransferase genes. Tree is also shown in Figure S12.

methylS_RAxML_bipartitionsBranchLabels: RAxML tree of all methyl-S methyltransferase genes encoded in MAGs, in addition to reference methyltransferase genes. Tree is also shown in Figure S13.
DOI: 10.15468/dl.qshyxg
title: Occurrence Download

description: A dataset containing 8400 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Bothrops asper"
 ]
}

 The dataset includes 8400 records from 266 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001413-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8mkqzy
title: Occurrence Download

description: A dataset containing 12033 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae",
 "Year 1000-1899"
 ]
}

 The dataset includes 12033 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001416-250827131500795/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.26961913
title: Data and code from "Contrasting microbial assembly patterns in the woody endosphere of hybrid and non-hybrid <i>Populus</i> trees"

description: QIIME2.zip: contains QIIME2 code and associated metadata for processing bacterial and fungal sequences.R_analyses.zip: contains R code and data files to generate figures and perform statistical analyses.Raw_sequences.zip: contains FASTQ files.<br><br>
DOI: 10.6084/m9.figshare.26961913.v1
title: Data and code from "Contrasting microbial assembly patterns in the woody endosphere of hybrid and non-hybrid <i>Populus</i> trees"

description: QIIME2.zip: contains QIIME2 code and associated metadata for processing bacterial and fungal sequences.R_analyses.zip: contains R code and data files to generate figures and perform statistical analyses.Raw_sequences.zip: contains FASTQ files.<br><br>
DOI: 10.15468/dl.89qr5z
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001418-250827131500795/datasets/export for details.
DOI: 10.15468/dl.ssxtc9
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oenothera biennis",
 "Country is Belarus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 136 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001419-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2y9gq8
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calycophyllum spruceanum",
 "HasCoordinate is true",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 51 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001421-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x8svgy
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oenothera biennis",
 "Country is Bosnia and Herzegovina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001420-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ey8fp
title: Occurrence Download

description: A dataset containing 2960 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mnemiopsis leidyi",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 2960 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001422-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9vnkqm
title: Occurrence Download

description: A dataset containing 121434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Guazuma ulmifolia"
 ]
}

 The dataset includes 121434 records from 606 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001309-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvzj96
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001423-250827131500795/datasets/export for details.
DOI: 10.15468/dl.fcvfd6
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oenothera biennis",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001425-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8rkwpk
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001426-250827131500795/datasets/export for details.
DOI: 10.15468/dl.wrtxwq
title: Occurrence Download

description: A dataset containing 548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Eira barbara"
 ]
}

 The dataset includes 548 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001427-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhmh64
title: Occurrence Download

description: A dataset containing 943 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Lachesis muta"
 ]
}

 The dataset includes 943 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001424-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18130/v3/piuriv
title: Spatial analysis yields evidence for combinative natural killer and CD8 T cells role in antitumor immunity despite profound MHC class I loss in human non-small cell lung cancer

description: This dataset comprises IHC and mIF measurements from two human NSCLC cohorts at the University of Virginia Health System.
DOI: 10.15468/dl.vuqpyd
title: Occurrence Download

description: A dataset containing 356963 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Salsola soda, Salsola tragus, Salvia aethiopis, Salvia coccinea, Salvia glutinosa, Salvia misella, Salvia modesta, Salvia occidentalis, Salvia plebeia, Salvia pratensis, Salvia reflexa, Salvia sclarea, Salvia tiliifolia, Salvia verbenaca, Salvinia auriculata, Salvinia cucullata, Salvinia minima, Salvinia molesta, Salvinia natans, Salvinia nymphellula)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 356963 records from 1505 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001398-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vse72f
title: Occurrence Download

description: A dataset containing 451 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de Lycophyta, Monilophyta, Gimnospermas y Angiospermas Monocotiledóneas del Herbario MDQ de Plantas Vasculares del Instituto de Investigaciones Marinas y Costeras (IIMyC, UNMdP-CONICET/FCEyN)."
 ]
}

 The dataset includes 451 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000126-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60952/bccc-v813
title: Przewlekły, zanikowy stan zapalny błony śluzowej żołądka dużego stopnia, aktywny

description: Materiał zdjęciowy powstał w wyniku badania mającego na celu: analizę obrazów endoskopowych żołądka;                              analizę obrazów morfologicznych (histopatologicznych) wycinków błony śluzowej żołądka pobranych  czasie endoskopii  u pacjentów zgłaszających się z powodu dolegliwości dyspeptycznych (w analizie uwzględniono płeć i wiek badanych); ustalenie wpływu w/w czynników na częstotliwość poszczególnych jednostek chorobowych; analizę współwystępowania zakażenia Helicobakter pylori w stanach zapalnych błony śluzowej żołądka. Materiał do badania mikroskopowego stanowiły wycinki błony śluzowej żołądka pobrane w trakcie badania gastroskopowego od 391chorych kobiet i 639 chorych mężczyzn, którzy zgłaszali się do Poradni Gastrologicznych z powodu różnych dolegliwości dyspeptycznych trwających ok. 2,5 lat. Od każdego chorego pobierano rutynowo po dwa wycinki z okolicy podwpustowej, z okolicy trzonu żołądka i z jamy odźwiernikowej (antrum pylori). Analizę przeprowadzano z uwzględnieniem płci i grup wieku (co 10 lat, w zakresie od 10-20 do ponad 80 lat). Preparaty histopatologiczne barwiono metodami rutynowymi H i E. W wycinkach pobranych od 100 chorych wykonano barwienia pozwalające na wykrycie Helicobacter pylori metodami: zmodyfikowana metoda Giemzy, metoda "pół Grama", oraz metodą Warthina-Starry'ego pozwalająca na wykrycie pojedynczych bakterii. Badania endoskopowe wykonano gastrofiberoskopem Olympus GIF D2 i GIF K. Na zdjęciu przewlekły, zanikowy stan zapalny błony śluzowej żołądka dużego stopnia, aktywny. Wycinek pobrany z trzonu żołądka. Obfity naciek zapalny złożony z limfocytów, komórek plazmatycznych i granulocytów obojętnochłonnych. Gruczoły żołądkowe uległy zanikowi. H. E. x 100. Dokumentacja zdjęciowa preparatów histopatologicznych powstała przy użyciu mikroskopu świetlnego. Opracowanie techniczne na kliszy czarno-białej przez pracownię fotograficzną Instytutu Biostruktury Akademii Medycznej w Warszawie.
DOI: 10.15468/dl.2mdgr7
title: Occurrence Download

description: A dataset containing 436254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Oenothera rosea, Oenothera rubricaulis, Oenothera sesitensis, Oenothera stricta, Oenothera stucchii, Oenothera tetraptera, Oenothera villosa, Oldenlandia corymbosa, Oldenlandia pumila, Olea europaea, Oncosiphon piluliferum, Onobrychis viciifolia, Onopordum acanthium, Onopordum illyricum, Onopordum tauricum, Operculina turpethum, Oplismenus compositus, Oplismenus hirtellus, Oplismenus undulatifolius, Opuntia aurantiaca)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 436254 records from 1299 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000079-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/6pvym-tjc22
title: Rhodobacter sphaeroides JPA 1558

description: cryosections of R sphaeroides strain JPA1558 (TlpT-YFP)
description: <strong>Tilt Series Date:</strong> 2013-06-03</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 33000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grow  (1 day) in SUX medium + Naldixic acid (6.25 µl of 20mg/ml stock) + Kanamycin (2.5 µl stock 1000x) + 25 µl 10mM IPTG.*Spin down 5ml per strain, resuspend pellets (barely visible) in SUX medium + Kanamycin (2.5 µl stock 1000x) + 25 µl 10mM IPTG.*grow overnight.</p>
<strong>Sample Preparation:</strong> cryosectioning by MArk LAdinsky</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-06-03-22/rawdata/</p>atlas_grid-2_7x7cryosections0032.mrc,  Tilt Series (Pixel Size 0.38 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-06-03-22/rawdata/atlas_grid-2_7x7cryosections0032.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas_grid-2_7x7cryosections0032_full.rec,  Reconstruction (Pixel Size 0.76 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-06-03-22/3dimage_26935/atlas_grid-2_7x7cryosections0032_full.rec"
        > <i class="download icon"></i> Download </a></p>