cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wstqjq2sz
title: Drp1 controls Complex II assembly and skeletal muscle metabolism by Sdhaf2 action on mitochondria

description: The Dynamin-related GTPase, Drp1 (encoded by Dnm1l) plays a central role
 in mitochondrial fission and is requisite for numerous cellular processes
 however its role in muscle metabolism remains unclear. Herein, we show
 that among human tissues, the highest number of gene correlations with
 DNM1L  are in skeletal muscle. Knockdown of Drp1 (Drp1-KD)
 promoted mitochondrial hyperfusion in the muscle of male mice. Reduced
 fatty acid oxidation and impaired insulin action along with increased
 muscle succinate was observed in Drp1-KD muscle. Muscle Drp1-KD reduced
 Complex II assembly and activity as a consequence of diminished
 mitochondrial translocation of succinate dehydrogenase assembly factor 2
 (Sdhaf2). Restoration of Sdhaf2 normalized Complex II activity, lipid
 oxidation, and insulin action in Drp1-KD myocytes. Drp1 is critical in
 maintaining mitochondrial Complex II assembly, lipid oxidation, and
 insulin sensitivity, suggesting a mechanistic link between mitochondrial
 morphology and skeletal muscle metabolism, which is clinically relevant in
 combatting metabolic-related diseases.
description: <strong>RNAseq: </strong>A homogenous portion of
 frozen skeletal muscle samples was homogenized using a tissue homogenizer
 in Trizol. RNA was isolated using the Qiagen RNeasy Mini QIAcube Kit
 following the manufacturer’s instructions. Libraries were prepared using
 the TruSeq Stranded Total RNA Library Prep Kit and RiboZero Gold following
 the manufacturer’s instructions. The resulting libraries were combined
 into two pools and sequenced on an Illumina HiSeq 4000 within the UCLA
 Neuroscience Genomics core facility following in-house established
 protocols. For metabolomics, muscle samples were processed and analyzed by
 Metabolon Inc.
description: # Drp1 controls Complex II assembly and skeletal muscle metabolism by
 Sdhaf2 action on mitochondria
 [https://doi.org/10.5061/dryad.wstqjq2sz](https://doi.org/10.5061/dryad.wstqjq2sz) Table S4 contains the raw metabolomics data and Table S5 contains the raw RNA-sequencing data of gastrocnemius muscle from normal chow-fed male mDrp1HET vs. Control f/f mice. ## Description of the data and file structure These data are in Excel files. Table S4 includes Biochemical, mouse ID, and Fold change. Table S5 includes gene ID, baseMean (the mean of normalized count of all samples), log2Foldchange, IfcSE (standard error of the log2FoldChange estimate), stat (statistics), pvalue (p value), and padj (adjusted p value).
DOI: 10.15468/dl.ka2u9b
title: Occurrence Download

description: A dataset containing 466 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hoita macrostachya",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 466 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003725-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c8y574
title: Occurrence Download

description: A dataset containing 213 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-79.95644 -4.12661,-75.97087 -4.12661,-75.97087 0.38315,-79.95644 0.38315,-81.11096 -0.99877,-79.95644 -4.12661))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Danaus plexippus",
 "Year 2000-2026"
 ]
}

 The dataset includes 213 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003726-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q6ch5k
title: Occurrence Download

description: A dataset containing 3026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Prunus serotina"
 ]
}

 The dataset includes 3026 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003724-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wu3z56
title: Occurrence Download

description: A dataset containing 1905 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nemadactylus bergi",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 1905 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003727-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0k6djhb5w
title: Prebiotic galactooligosaccharide (GOS) effects on suckling and weaned pigs

description: Galactooligosaccharides were supplemented to gruel creep diets during
 farrowing and/or in phase 1 nursery diets.  Growth performance,
 intestinal health parameters (such as GI morphology, short-chain fatty
 acids & microbial community) and plasma cytokins were evaluated
 under the hypothesis that GOS would improve piglet growth through its
 prebiotic effects as it is fermented in the intestine.
description: Detailed methods are reported in the published paper
description: # Prebiotic galactooligosaccharide (GOS) effects on suckling and weaned
 pigs
 [https://doi.org/10.5061/dryad.0k6djhb5w](https://doi.org/10.5061/dryad.0k6djhb5w) The data represent growth performance, intestinal short chain fatty acids and histology together with systemic cytokine concentrations from pre- and post-weaning pigs fed diets with or without prebiotic galactooligosaccharides. A full peer-reviewed manuscript is being published that describes various methods in full detail. [https://doi.org/10.1186/s40104-024-01047-y](https://doi.org/10.1186/s40104-024-01047-y) ## Description of the data and file structure The excel workbook contains multiple sheets that report raw data collected for various dependent variables. Each sheet identifies the independent variables to which each experimental unit was assigned. The first sheet includes a list of abbreviations used in subsequent sheets. These data were statistically analyzed and reported in the associated journal publication. | Abbreviations | Meaning | | :--------------- | :----------------------------------------------- | | trt | treatment | | ftrt | farrowing treatment | | ntrt | nursery treatment | | ADG | average daily gain | | ADFI | average daily feed intake | | FC | Farrowing control | | FG- | Farrowing creep without GOS | | FG+ | Farrowing creep with GOS | | NG- | Nursery diet without GOS | | NG+ | Nursery diet with GOS | | prop | propionate | | buty | butyrate | | val | valerate | | BCA | branched chain acids | | GM-CSF | granulocyte macrophage colony-stimulating factor | | IFN | interferon | | IL | interluekin | | TNF | tumor necrosis factor | | d… | day… | | F or M (for Sex) | Female or Male | | . | missing data point |
DOI: 10.5061/dryad.x95x69pr5
title: Data from: Exceptionally preserved stomach contents of a young tyrannosaurid reveal an ontogenetic dietary shift in an iconic extinct predator (TMP 2009.12.14 Citipes tail segment)

description: Tyrannosaurids were large carnivorous dinosaurs that underwent major
 changes in skull robusticity and body proportions as they grew, suggesting
 they occupied different ecological niches during their lifespan. Although
 adults commonly fed on dinosaurian megaherbivores, the diet of juvenile
 tyrannosaurids is largely unknown. Here we describe a remarkable specimen
 of a juvenile Gorgosaurus libratus that preserves the articulated
 hindlimbs of two yearling caenagnathid dinosaurs inside its abdominal
 cavity. The prey were selectively dismembered and consumed in two separate
 feeding events. This predator-prey association provides direct evidence of
 an ontogenetic dietary shift in tyrannosaurids. Juvenile tyrannosaurids
 may have hunted small and young dinosaurs until they reached a size when,
 to satisfy energetic requirements, they transitioned to feeding on
 dinosaurian megaherbivores. Tyrannosaurids thus occupied both mesopredator
 and apex predator roles during their lifespan, a factor that may have been
 key to their evolutionary success.
description: The matrix block containing the Citipes caudal vertebrae was
 subjected to computed tomography (CT) on a Toshiba Aquilion medical CT
 scanner at the Drumheller Health Centre in Drumheller, Alberta, Canada. CT
 scanning was conducted at a voltage of 120 kV, an X-ray tube current of
 300 mA, and with contiguous slices of a thickness of 0.5 mm.
description: # TMP 2009.12.14 Citipes tail segment
 The matrix block
 containing the Citipes caudal vertebrae was subjected to computed
 tomography (CT) on a Toshiba Aquilion medical CT scanner at the Drumheller
 Health Centre in Drumheller, Alberta, Canada. CT scanning was conducted at
 a voltage of 120 kV, an X-ray tube current of 300 mA, and with contiguous
 slices of a thickness of 0.5 mm. ## Description of the data and file
 structure Raw dicom files for Citipes tail segment found in the stomach of
 juvenile Gorgosaurus libratus (TMP 2009.12.14) curated at the Royal
 Tyrrell Museum of Palaeontology, Drumheller, Alberta, Canada. ##
DOI: 10.5061/dryad.51c59zwfd
title: Gene prediction for: A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides

description: Wildlife diseases, such as the sea star wasting (SSW) epizootic that
 outbroke in the mid-2010s, appear to be associated with acute and/or
 chronic abiotic environmental change; dissociating the effects of
 different drivers can be difficult. The sunflower sea star, Pycnopodia
 helianthoides, was the species most severely impacted during the SSW
 outbreak, which overlapped with periods of anomalous atmospheric and
 oceanographic conditions, and there is not yet a consensus on the
 cause(s). Genomic data may reveal underlying molecular signatures that
 implicate a subset of factors and, thus, clarify past events while also
 setting the scene for effective restoration efforts. To advance this goal,
 we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C
 proximity reads to generate a highly contiguous genome assembly that was
 then annotated using RNA-seq-informed gene prediction. The genome assembly
 is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO
 completeness score 96.1%, and 22 major scaffolds consistent with prior
 evidence that sea star genomes comprise 22 autosomes. These statistics
 generally fall between those of other recently assembled chromosome-scale
 assemblies for two species in the distantly related asteroid genus
 Pisaster. These novel genomic resources for Pycnopodia helianthoides will
 underwrite population genomic, comparative genomic, and phylogenomic
 analyses — as well as their integration across scales — of SSW and
 environmental stressors. This data resource contains the files associated
 with gene prediction.
description: # Gene prediction for: A reference genome for ecological restoration of
 the sunflower sea star, Pycnopodia helianthoides
 [https://doi.org/10.5061/dryad.51c59zwfd](https://doi.org/10.5061/dryad.51c59zwfd) The files contained here represent the results of gene prediction for the sunflower star, *Pycnopodia helianthoides*. ## Description of the data files * interproscan.tsv.gz : table with function assignment to transcript IDs * interproscan.gff3 : functional annotation in gff3 format, annotations for all the predicted coding genes in the genome based on the protein translation * augustus.hints.codingseq : nucleotide sequences for all the predicted genes, gene set delivered by bioinformatics@greifswald as coding sequences in fasta format; this file can be used for transcriptome quantification * augustus.hints.aa : protein sequences for all the predicted genes, gene set delivered by bioinformatics@greifswald as protein sequences in fasta format * augustus.hints.gtf : coordinates for all genomic features, gene set delivered by bioinformatics@greifswald in gtf format ## Authors Lars Gabriel, Katharina J. Hoff
DOI: 10.5061/dryad.dncjsxm5j
title: Bacterial traits, N deposition and mycorrhiza. qSIP Aspartic Acid

description: Nitrogen (N) deposition increases soil carbon (C) storage by reducing
 microbial activity.  These effects vary in soil beneath trees
 that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi.
 Variation in carbon C and N uptake traits among microbes may explain
 differences in soil nutrient cycling between mycorrhizal associations in
 response to high N loads, a mechanism not previously examined due to
 methodological limitations. Here, we used quantitative Stable Isotope
 Probing (qSIP) to measure bacterial C and N assimilation rates from an
 added organic compound, which we conceptualize as functional
 traits.  As such, we applied a trait-based approach to explore
 whether variation in assimilation rates of bacterial taxa can inform
 shifts in soil function under chronic N deposition. We show taxon-specific
 and community-wide declines of bacterial C and N uptake under chronic N
 deposition in both AM and ECM soils. N deposition-induced reductions in
 microbial activity were mirrored by declines in soil organic matter
 mineralization rates in AM but not ECM soils. Our findings suggest C and N
 uptake traits of bacterial communities can predict C cycling feedbacks to
 N deposition in AM soils but additional data, for instance on the traits
 of fungi, may be needed to connect microbial traits with soil C and N
 cycling in ECM systems. Our study also highlights the potential of
 employing qSIP in conjunction with trait–based approaches to inform how
 ecological processes of microbial communities influence soil functioning
description: The methods used to collect the data are detailed in the article.
 Metadata and units for each variable are given in the dataset
 itself. 
description: # Bacterial Traits, N deposition and Mycorrhiza. QSIP Aspartic Acid
 [https://doi.org/10.5061/dryad.dncjsxm5j](https://doi.org/10.5061/dryad.dncjsxm5j) Dataset provides the soil functions measured in the study and serves to support the results we present in the main text ## Description of the data and file structure The methods used to collect the data are detailed in the article. Metadata and units for each variable are given in the dataset itself. ## Sharing/Access information This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any. Links to other publicly accessible locations of the data: [https://www.ncbi.nlm.nih.gov/sra/PRJNA995554](https://www.ncbi.nlm.nih.gov/sra/PRJNA995554)
DOI: 10.15468/hdxz2b
title: Two new species of Microglanis (Siluriformes: Pseudopimelodidae) from the upper-middle rio Araguaia basin, Central Brazil

description: This dataset contains the digitized treatments in Plazi based on the original journal article Ruiz, William Benedito Gotto, Shibatta, Oscar Akio (2011): Two new species of Microglanis (Siluriformes: Pseudopimelodidae) from the upper-middle rio Araguaia basin, Central Brazil. Neotropical Ichthyology 9 (4): 697-707, DOI: 10.1590/S1679-62252011000400002, URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252011000400002&lng=en&tlng=enTwo new species of Microglanis are described from tributaries of upper-middle rio Araguaia, States of Mato Grosso and Goiás, Brazil. Microglanis oliveirai differs from its congeners by the short supraoccipital process not reaching the small anterior nuchal plate, and reduced number of gill rakers, lateral line pores, ribs, vertebrae, and caudal-fin rays. Microglanis xylographicus differs from its congeners by the presence of melanophores surrounding the neuromasts of the superficial lines, snout length 11.4-12.9% SL and body color pattern consisting of horizontal brown stripes similar to a wooden bark pattern. An identification key of Microglanis species from the Amazon basin is presented.Duas espécies novas de Microglanis são descritas de tributários do alto-médio rio Araguaia, estados do Mato Grosso e Goiás, Brasil. Microglanis oliveirai difere de seus congêneres pelo processo supraoccipital curto não atingindo a pequena placa nucal anterior, e número reduzido de rastros branquiais, poros da linha lateral, costelas, vértebras e raios da nadadeira caudal. Microglanis xylographicus difere de seus congêneres pela presença de melanóforos ao redor dos neuromastos alinhados superficialmente, comprimento do focinho 11,4-12,9% CP e padrão de colorido do corpo, formado por listras horizontais castanhas como marcas de casca de madeira. Uma chave de identificação de espécies de Microglanis da bacia Amazônica é apresentada.
DOI: 10.15468/dl.cexr45
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myotis diminutus"
 ]
}

 The dataset includes 82 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003730-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fxpnvx0zj
title: Supplemental dataset 1 for: Ediacaran palaeobiology and biostratigraphy of the Nama Group, Namibia, with emphasis on the erniettomorphs, tubular and trace fossils, and a new sponge, Arimasia germsi gen. et sp. nov.

description: Ediacaran fossils, obtained in stratigraphic context in 1993, 1995 and
 1996, with the assistance of A. Seilacher, IGCP project 320 scientists and
 the Geological Survey of Namibia, are described for the first time. Most
 are from the Kliphoek and Buchholzbrunn members of the Dabis Formation and
 the Huns and Spitskop members of the Urusis Formation, Witputs subbasin,
 but a significant number, including Pteridinium, are from the Kliphoek
 Member, Zaris Formation and the Neiderhagen Member, Nudaus Formation north
 of the Osis arch, which separates the two subbasins. We extend the
 stratigraphic ranges and geographic distributions of several important
 taxa, including Archaeichnium, Ernietta, Pteridinium and Swartpuntia,
 provide reassessments of the paleobiology of these and other organisms,
 and describe a new sponge—possibly an unmineralized archaeocyath—Arimasia
 germsi gen. et sp. nov. We also describe and illustrate various
 ichnofossils, including the oldest known traces from the Nama Group,
 narrow down the first appearance of Treptichnus in the Nama succession,
 and reinforce the idea that there was a prolific infauna of micrometazoans
 during the latest Ediacaran by naming and describing previously reported
 microburrows found on the surfaces of gutter casts as Ariichnus vagus
 igen. et isp. nov.
description: Carbonate hand samples, spaced 1 m apart where possible, were
 collected by MRS and BR from limestone sections measured by them and/or
 JGG from the Mooifontein Member on Aar, Mamba, Mooifontein and Twyfel
 farms; from the Omkyk Member at Swartmodder on Omkyk; from the Urikos,
 Neiderhagen and Vingerbreek members on Saurus; and from the Huns Member on
 Arimas and Swartkloofberg; but samples from only some of those sections
 were processed because of funding constraints. All isotopic data are
 tabulated in Supplemental dataset 1 and plotted against stratigraphic
 heights in Figure 2.
description: # Supplemental dataset 1
 [https://doi.org/10.5061/dryad.fxpnvx0zj](https://doi.org/10.5061/dryad.fxpnvx0zj) An Excel file that contains lists of carbon isotope samples and analyses. ## Description of the data and file structure Supplemental dataset 1 is an Excel file that tabulates carbon and oxygen isotopic analyses (in parts per thousand versus the VPDB standard) from the Namibian farms Aar (16), Arimas (83), Mamba (125) and Mooifontein (50). Any unfilled cells are there for clarity of because the relevant data were unavailable.
DOI: 10.5061/dryad.z08kprrkc
title: Seasonal roost selection of wild turkeys at their northern range edge

description: Wild turkeys (Meleagris gallopavo) are diurnally active birds that spend
 the dark hours roosting in trees. We tested the hypothesis that multiple
 benefits exist for roost tree selection by wild turkeys, including
 thermoregulation, resource acquisition, and protection from predators. We
 compared 48 roost trees used by eastern wild turkeys (M. g. silvestris) in
 Ontario, Canada to 48 non-roost trees sampled contemporaneously during
 2017-2019 to determine roost site selection between seasons. Mean (± SE)
 roost tree height (21.4 ± 0.8 m) was taller than non-roost trees (18.2 ±
 0.8 m), and roost trees were also larger in diameter at breast height
 (58.1 ± 5.5 cm versus 38.7 ± 3.1 cm). Using ibuttons to collect
 microclimate temperatures at the tree, we found that mean temperature (±
 SE) of a deciduous roost (14.5 ± 0.1°C) was higher than temperature at
 either a coniferous roost (13.9 ± 0.1°C) or ambient temperature (13.2 ±
 0.1°C) during the summer months. In winter however, we did not find any
 relationship between temperature and tree type. Roosts were closer to
 buildings (150.8 ± 26.0 m) in the winter compared to summer and year-round
 roosts, and winter roosts were also farther away from crops (395.2 ± 63.7
 m) compared to roost sites used year-round. Summer roosts were closer to
 roads (143 ± 36.3 m) than the roosts in the winter and roosts used
 year-round. Our data suggest that thermoregulation is not the driving
 force behind roost selection; instead, predator avoidance appears to play
 the most important role, with some weaker evidence in support of proximity
 to resources.
description: # Seasonal roost selection of wild turkeys at their northern range edge.
 [https://doi.org/10.5061/dryad.z08kprrkc](https://doi.org/10.5061/dryad.z08kprrkc) The dataset consists of a workbook containing data on characteristics of wild turkey (*Meleagris gallopavo*) tree roosts from Ontario, Canada. Sheet 1 of the workbook consists of tree and site characteristics measured at roosts and associated random trees to evaluate characteristics associated with roosts used by turkeys. These are empirical measurements taken from trees and sites associated with the trees. Field names are descriptive of the contents. Sheets 2 and 3 of the workbook contain mean temperature data collected over time using ibuttons placed on a single coniferous and a single deciduous roost compared to ambient temperature (in summer and winter, respectively).
DOI: 10.15468/dl.4z3wkk
title: Occurrence Download

description: A dataset listing the 13910 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "OccurrenceStatus is Present",
 "StateProvince is Maryland",
 "TaxonKey is Arthropoda"
 ]
}

 The dataset's 13910 records were derived from 217 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003688-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.