cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/j5krtjfj6y.1
title: DNA methylation data of hematopoietic transplantation patients

description: The analysis was performed to decide if the age of the recipient body affects epigenetic aging in the donor cells.

All raw data was processed starting from .idat files with R for this analysis. Based on a recent study that compared different DNA methylation raw data processing pipelines for epigenetic clocks 3 we decided on using ENmix with the suggested optimal parameters for epigenetic clocks from the comparison: Out-of-bag background correction, RELIC dye-bias correction, quantile normalization separately for methylated and unmethylated intensities and RCP correction of probe design type bias. The folder with raw .idat files was first loaded with ENmix::readidat() then profiled by ENmix:qcinfo() with default settings. Loaded data was then sequentially applied to ENmix::preprocessENmix(), ENmix::norm.quantile() and ENmix::rcp() with the above described parameters. ENmix::qcfilter() was then applied, removing very low quality CpGs and samples detected by the qcinfo() function and imputing missing values. The result from this pipeline is a table of DNA methylation beta values. This pipeline was run separately for each batch of measurements.

Included in this Mendeley Data collection is the processed and normalized (as described above) DNA methlation beta values for all samples. The batches are exported as separate files. The comRand.csv file contains a table where the "randID" column corresponds to columns in the batchX.csv files. This table also has all the required information about the ages of the donors and recipients of the hematopoietic transplantation (at time of transplantation) and the age of the measured cells at the time of measurement (column ageCells).
DOI: 10.6084/m9.figshare.14935439.v2
title: Morphological and molecular characterization of the new aethaloid species <i>Didymium yulii</i>

description: Five specimens, initially presumed to be <i>Fuligo septica</i> or <i>Mucilago crustacea</i>, were collected from Jilin Province and the Inner Mongolia Autonomous Region in China, but all five turned out to represent a new aethaloid species, <i>Didymium yulii</i>. This new species is characterized by pseudocapillitia without capillitia and an aethalioid fruiting body, features that are morphologically distinct from those of any other species of <i>Didymium</i>. To assess the phylogenetic relationships between <i>D. yulii</i> and other members of <i>Didymium</i> and in the Didymiaceae, sequences from two nonoverlapping targeted portions of nuc 18S rDNA (~450 bp and ~1050 bp) and translation elongation factor 1-alpha (<i>tef1</i>) were obtained and analyzed. The results indicate that <i>D. yulii</i> forms a single clade separate from other species of <i>Didymium</i> and the clade that contains <i>M. crustacea</i>, which strongly supports the identification of the five specimens as a new species.
DOI: 10.6084/m9.figshare.17032469.v1
title: 45-45.mat

description: The electric field signal amplitude distribution of the diametrically loaded disk.when the direction of polarizer is 45 Deg..
DOI: 10.6084/m9.figshare.7070981.v1
title: Additional file 3: of Weipixiao attenuate early angiogenesis in rats with gastric precancerous lesions

description: HIF-1alpha (IHC-IOD). Raw data for Fig.Â 7. (XLS 21 kb)
DOI: 10.6084/m9.figshare.13346440
title: Additional file 3 of Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa)

description: Additional file 3: Table S3. The up- and down-regulated transcirpts bewteen Resting and Male libraries.
DOI: 10.6084/m9.figshare.7070978.v1
title: Additional file 1: of Endothelial cells promote metastasis of prostate cancer by enhancing autophagy

description: Table S1. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.14935474.v2
title: <i>Leptosphaerulina</i> species isolated from golf turfgrass in China, with description of <i>L. macrospora</i>, sp. nov.

description: Leptosphaerulina leaf blight occurs on most turfgrasses. Hitherto, <i>Leptosphaerulina</i> species associated with this disease include <i>L. americana, L. argentinensis, L. australis</i>, and <i>L. trifolii</i>. However, following Koch’s postulates, <i>L. australis</i> was confirmed as saprobes but not pathogens, and the other three species have not been tested. The pathogenicity of <i>Leptosphaerulina</i> spp. is still questionable. In this study, we isolated 19 <i>Leptosphaerulina</i> strains from diseased golf turfgrasses in China, and they were identified as <i>L. gaeumannii, L. saccharicola</i>, and a new species, <i>L. macrospora</i>, through multilocus (ITS, 28S, <i>rpb2</i>, and <i>tub2</i>) phylogenetic analyses and morphological observations. Pathogenicity test revealed that the three <i>Leptosphaerulina</i> species identified in this study cannot infect live/healthy turfgrass tissues of <i>Poa pratensis</i> and <i>Agrostis stolonifera</i> and only produced pseudothecia on the dead leaves of stressed seedlings. Considering the results of pathogenicity tests in this and previous studies, we speculate that most <i>Leptosphaerulina</i> species isolated from diseased turfgrass are not pathogens but saprobes. Applying proper management practices to prevent severe turfgrass stress is a key measure to reduce or eliminate the effects of <i>Leptosphaerulina</i> on golf turfgrass.
DOI: 10.6084/m9.figshare.7070999
title: Additional file 4: of Weipixiao attenuate early angiogenesis in rats with gastric precancerous lesions

description: VEGF (IHC-IOD). Raw data for Fig.Â 8. (XLS 23 kb)
DOI: 10.6084/m9.figshare.7071023.v1
title: Additional file 5: of Weipixiao attenuate early angiogenesis in rats with gastric precancerous lesions

description: ERK1 (PCR). Raw data for Fig.Â 9. (XLS 23 kb)
DOI: 10.17632/3k2tpx9ssr.2
title: Redefined indel taxonomy reveals insights into mutational signatures

description: Despite their deleterious effects, small insertions and deletions (indels) have received far less attention than substitutions1,2. Recent computational advances have surmounted previous technical challenges, enabling the study of mutational processes driving indel formation. Here we generated isogenic CRISPR-edited human cellular models of post-replicative repair dysfunction (PRRd), including individual and combined gene-edits of mismatch repair (MMR) and replicative polymerases (POLE and POLD1). Unique, diverse mutational footprints of MMR deficiency and polymerase dysfunction were revealed. However, the prevailing indel classification framework1 falls short in discriminating these indel signatures from background mutagenesis and among each other, as it condenses important biological signals into predominantly two indel subclasses, limiting signature analyses. To address this, we propose a novel classification system that considers the 5’ and 3’ nucleobases flanking an indel, as with substitution signatures, resulting in 89 indel subclasses. Our new indel classification enhances the disambiguation of experimental signatures, and through analysis of 4,775 cancer whole genomes from the 100,000 Genomes Project3, we uncover 37 indel signatures (InDs); 27 are new. Further, we develop a classifier – PRRDetect, which outperforms approved biomarkers, such as Tumor Mutational Burden (TMB), for immunotherapy. This re-defined indel taxonomy advances our understanding of mutagenesis and heralds potential clinical applications.

Deposited here are the de novo mutation lists from the experimental samples included in the study. Whole-genome sequencing short reads were aligned to GRCh38/hg38 using BWA-MEM. Post-processing filters were applied to improve the specificity of mutation-calling. Specifically, for single nucleotide variant calls by CaVEMan, we used CLPM == 0 and ASMD &gt;= 140. To reduce false positive calls by Pindel, we used QUAL &gt;= 250 and REP &lt; 10. Rearrangements were not assessed as they were too few to be informative. De novo substitutions and indels in subclones were obtained by subtracting from respective parental clone whenever available, or by removing mutations shared among subclones.
DOI: 10.6084/m9.figshare.13346440.v1
title: Additional file 3 of Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa)

description: Additional file 3: Table S3. The up- and down-regulated transcirpts bewteen Resting and Male libraries.
DOI: 10.15468/dl.h2d822
title: Occurrence Download

description: A dataset containing 461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bufo bufo (Linnaeus, 1758)",
 "Country is Norway",
 "Year is greater than or equal to 2023",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 461 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083248-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y69pur
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abies pinsapo Boiss.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083252-240321170329656/datasets/export for details.
DOI: 10.15468/dl.3dg9w4
title: Occurrence Download

description: A dataset containing 831 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus adenopoda Maxim."
 ]
}

 The dataset includes 831 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083250-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rwq99z
title: Occurrence Download

description: A dataset containing 1160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cotoneaster adpressus Bois",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1160 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083251-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7ar2p3
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria nubicola G.Taylor"
 ]
}

 The dataset includes 46 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083253-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yakj6n
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuduvaria beccarii (Scheff.) J.Sinclair"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083256-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pmzta6
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula chartacea Franch."
 ]
}

 The dataset includes 32 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083255-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6jjw3r
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteronia rangei Muschl."
 ]
}

 The dataset includes 22 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083257-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g549c3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abies sibirica Ledeb.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083260-240321170329656/datasets/export for details.
DOI: 10.15468/dl.c4vqqx
title: Occurrence Download

description: A dataset containing 3466 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Houttuynia cordata Thunb.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3466 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083258-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8fggzy
title: Occurrence Download

description: A dataset containing 15708 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "TaxonKey is Schizachyrium scoparium (Michx.) Nash"
 ]
}

 The dataset includes 15708 records from 195 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083259-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21338/essmd2024_cntry_e01
title: ESS Multilevel Data 2024, country, edition 1.0
DOI: 10.15468/dl.uwa7fa
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria nubisylvae O.Lachenaud"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083262-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wyr5u
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus alaschanica Kom."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083261-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vmhp3p
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuduvaria borneensis Y.C.F.Su & R.M.K.Saunders"
 ]
}

 The dataset includes 26 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083264-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e99tm9
title: Occurrence Download

description: A dataset containing 749 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus potaninii Maxim.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 749 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083263-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ef8gz
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula chasmophila (Balf.fil. ex Hutch.) Balf.fil. ex Hutch."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083266-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xf8phs
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is EDP Foz-Tua: Pyrenean Desman (Galemys pyrenaicus) - Ecological Monitoring Program (2017-2020)"
 ]
}

 The dataset includes 105 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083265-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wdmac
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abietinella abietina (Hedw.) M.Fleisch.",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083268-240321170329656/datasets/export for details.
DOI: 10.15468/dl.hr5kmk
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteronia scabra Harv."
 ]
}

 The dataset includes 21 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083267-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.42ks2q
title: Occurrence Download

description: A dataset containing 187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Calamus viminalis Willd.)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 187 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083269-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.57m9fy
title: Occurrence Download

description: A dataset containing 216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Viburnum macrocephalum Fortune",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 216 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083270-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kw5auv
title: Occurrence Download

description: A dataset containing 338 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aristolochia contorta Bunge",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 338 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083271-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j3sd69
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria nudiflora Wight & Arn."
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083273-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pk4zuq
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseuduvaria brachyantha Y.C.F.Su & R.M.K.Saunders"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083275-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eh3uqk
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula chienii W.P.Fang"
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083276-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uut4e4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acacia karroo Hayne",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083277-240321170329656/datasets/export for details.
DOI: 10.15468/dl.7ucker
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteronia scariosa L.fil."
 ]
}

 The dataset includes 60 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083278-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5v2c2h
title: Occurrence Download

description: A dataset containing 34174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "FamilyKey is Passeridae",
 "Country is Norway",
 "Year is greater than or equal to 2023",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 34174 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083274-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s8fqfy
title: Occurrence Download

description: A dataset containing 522 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Actinidia arguta (Siebold & Zucc.) Planch. ex Miq.",
 "Country is China",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 522 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083279-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.am4hhw
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria nummularioides Guillaumin"
 ]
}

 The dataset includes 121 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083281-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.