cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.52ugds
title: Occurrence Download

description: A dataset containing 3332 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate accuracy invalid, Coordinate precision invalid, Coordinate uncertainty meters invalid, Coordinate precision/uncertainty mismatch, Footprint SRS invalid, Footprint WKT mismatch, Footprint WKT invalid, Country coordinate mismatch, Country mismatch, Country invalid, Country derived from coordinates, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Continent derived from country, Continent derived from coordinates, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Recorded date mismatch, Recorded date invalid, Recorded date unlikely, Taxon match fuzzy, Taxon match higher rank, Taxon match aggregate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, The scientific name differs on the record from that found in the checklist, Taxon match none, The backbone match found using the taxon IDs differs from what would be found if using the scientific names , Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Identified date invalid, Basis of record invalid, Type status invalid, Multimedia date invalid, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status unparsable, Occurrence status inferred from individual count, ccurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy, Institution collection mismatch, Possibly on loan, Different owner institution)",
 "OccurrenceStatus is Present",
 "TaxonKey is Alnus Mill."
 ]
}

 The dataset includes 3332 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107981-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfkh2z
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ageratina saxorum (Standl. & Steyerm.) H.Rob."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107982-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvs3v3
title: Occurrence Download

description: A dataset containing 5391 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Echinargus isola (Reakirt, 1866)"
 ]
}

 The dataset includes 5391 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107984-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffb9vp
title: Occurrence Download

description: A dataset containing 12819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Issue is one of (Zero coordinate, Coordinate out of range, Coordinate invalid, Coordinate rounded, Geodetic datum invalid, Geodetic datum assumed WGS84, Coordinate reprojected, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate accuracy invalid, Coordinate precision invalid, Coordinate uncertainty meters invalid, Coordinate precision/uncertainty mismatch, Footprint SRS invalid, Footprint WKT mismatch, Footprint WKT invalid, Country coordinate mismatch, Country mismatch, Country invalid, Country derived from coordinates, Continent coordinate mismatch, Continent country mismatch, Continent invalid, Continent derived from country, Continent derived from coordinates, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Recorded date mismatch, Recorded date invalid, Recorded date unlikely, Taxon match fuzzy, Taxon match higher rank, Taxon match aggregate, The scientific name ID was not used in backbone matching, The taxon concept ID was not used in backbone matching, The taxon ID was not used in backbone matching, The scientific name ID was not found in the checklist, The taxon concept ID was not found in the checklist, The taxon ID was not found in the checklist, The scientific name differs on the record from that found in the checklist, Taxon match none, The backbone match found using the taxon IDs differs from what would be found if using the scientific names , Depth not metric, Depth unlikely, Depth min max swapped, Depth non numeric, Elevation unlikely, Elevation min max swapped, Elevation not metric, Elevation non numeric, Modified date invalid, Modified date unlikely, Identified date unlikely, Identified date invalid, Basis of record invalid, Type status invalid, Multimedia date invalid, Multimedia URI invalid, References URI invalid, Error during interpretation, Individual count invalid, Individual count conflicts with occurrence status, Occurrence status unparsable, Occurrence status inferred from individual count, ccurrence status inferred from basis of record, Georeferenced date unlikely, Georeferenced date invalid, Ambiguous institution, Ambiguous collection, Institution match none, Collection match none, Institution match fuzzy, Collection match fuzzy, Institution collection mismatch, Possibly on loan, Different owner institution)",
 "OccurrenceStatus is Present",
 "TaxonKey is Anadenanthera Speg."
 ]
}

 The dataset includes 12819 records from 284 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107983-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phgrx9
title: Occurrence Download

description: A dataset containing 130839 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ceratophyllum demersum L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 130839 records from 1083 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107978-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fkc4hu
title: Occurrence Download

description: A dataset containing 5985 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Virgin Islands (British)",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 5985 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107985-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.84f4sd
title: Occurrence Download

description: A dataset containing 1003886 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Loxia curvirostra Linnaeus, 1758",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 1003886 records from 639 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107979-240626123714530/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.7679504.v1
title: Additional file 3: of Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: Table S2. Mean gene copy-number ratios of cancer associated genes across the cancer cell line panel. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.22883856
title: The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper (<i>Capsicum annuum</i>)

description: The red colouration of ripe chilli pepper fruit is due to the presence of the carotenoid capsanthin. 1-D-deoxy-xylulose 5-phosphate synthase (DXS) and phytoene synthase(s) (PSY) are influential biosynthetic steps in the carotenoid pathway. A panel of chilli accessions for varying fruit colour intensity revealed the correlation of carotenoid content with PSY and DXS transcript levels. The PSY and DXS genes were sequenced from high and low carotenoid genotypes to deduce potential allelic variation. PSY-1 and -2 showed tissue-specific expression, with PSY-1 and -2 expressed in chromoplast and chloroplast containing tissues, respectively. Protein modelling, phylogenetic analysis and transcription factor analysis were conducted to understand how the allelic variation identified could affect carotenoid biosynthesis and regulation, and subsequently colour intensity phenotype. A candidate mutation located in the transit peptide of the PSY-1 protein sequence was identified in the low colour intensity genotype. Sequence variation within the promoter region of the DXS gene present in the high colour intensity genotype was determined in the glyceraldehyde 3-phosphate binding motif (GAPF). These data can be exploited to develop tools and resources for the breeding of high colour intensity chilli pepper fruit.
DOI: 10.6084/m9.figshare.24456751
title: Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research

description: Background: Elucidating epigenetic mechanisms could provide new biomarkers for disease diagnosis and prognosis. Technological advances allow genome-wide profiling of 5-hydroxymethylcytosines (5hmC) in liquid biopsies. 5hmC-Seal followed by NGS is a highly sensitive technique for 5hmC biomarker discovery in cfDNA. Currently, 5hmC Seal is optimized for EDTA blood collection. We asked whether heparin was compatible with 5hmC Seal as many clinical and biobanked samples are stored in heparin. Methods: We obtained 60 samples in EDTA matched to 60 samples in heparin from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Samples were comprised of 30 controls and 30 individuals who were later diagnosed with colon cancer. We profiled genome-wide 5hmC in cfDNA using 5hmC-Seal assay followed by NGS. The 5hmC profiling data from samples collected in EDTA were systematically compared to those in heparin across various genomic features. Results: cfDNA isolation and library construction appeared comparable in heparin vs. EDTA. Typical genomic distribution patterns of 5hmC, including gene bodies and enhancer markers, were comparable in heparin vs. EDTA. 5hmC analysis of cases and controls yielded highly correlated differential features suggesting that both anticoagulants were compatible with 5hmC Seal assay. Conclusions: While not currently recommended for the 5hmC-Seal protocol, blood samples stored in heparin were successfully used to generate analysable and biologically relevant genome-wide 5hmC profiling. Our findings are the first to support opportunities to expand the biospecimen resource to heparin samples for 5hmC Seal and perhaps other PCR-based technologies in epigenetic research.
DOI: 10.6084/m9.figshare.24456751.v1
title: Analysis of genome-wide 5-hydroxymethylation of blood samples stored in different anticoagulants: opportunities for the expansion of clinical resources for epigenetic research

description: Background: Elucidating epigenetic mechanisms could provide new biomarkers for disease diagnosis and prognosis. Technological advances allow genome-wide profiling of 5-hydroxymethylcytosines (5hmC) in liquid biopsies. 5hmC-Seal followed by NGS is a highly sensitive technique for 5hmC biomarker discovery in cfDNA. Currently, 5hmC Seal is optimized for EDTA blood collection. We asked whether heparin was compatible with 5hmC Seal as many clinical and biobanked samples are stored in heparin. Methods: We obtained 60 samples in EDTA matched to 60 samples in heparin from the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial. Samples were comprised of 30 controls and 30 individuals who were later diagnosed with colon cancer. We profiled genome-wide 5hmC in cfDNA using 5hmC-Seal assay followed by NGS. The 5hmC profiling data from samples collected in EDTA were systematically compared to those in heparin across various genomic features. Results: cfDNA isolation and library construction appeared comparable in heparin vs. EDTA. Typical genomic distribution patterns of 5hmC, including gene bodies and enhancer markers, were comparable in heparin vs. EDTA. 5hmC analysis of cases and controls yielded highly correlated differential features suggesting that both anticoagulants were compatible with 5hmC Seal assay. Conclusions: While not currently recommended for the 5hmC-Seal protocol, blood samples stored in heparin were successfully used to generate analysable and biologically relevant genome-wide 5hmC profiling. Our findings are the first to support opportunities to expand the biospecimen resource to heparin samples for 5hmC Seal and perhaps other PCR-based technologies in epigenetic research.
DOI: 10.6084/m9.figshare.9776699
title: MOESM1 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 1: Table S1. Expression level of 167 driven genes.
DOI: 10.6084/m9.figshare.9776699.v1
title: MOESM1 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 1: Table S1. Expression level of 167 driven genes.
DOI: 10.6084/m9.figshare.11873859
title: Integrating Multidimensional Data for Clustering Analysis With Applications to Cancer Patient Data

description: Advances in high-throughput genomic technologies coupled with large-scale studies including The Cancer Genome Atlas (TCGA) project have generated rich resources of diverse types of omics data to better understand cancer etiology and treatment responses. Clustering patients into subtypes with similar disease etiologies and/or treatment responses using multiple omics data types has the potential to improve the precision of clustering than using a single data type. However, in practice, patient clustering is still mostly based on a single type of omics data or ad hoc integration of clustering results from individual data types, leading to potential loss of information. By treating each omics data type as a different informative representation from patients, we propose a novel multi-view spectral clustering framework to integrate different omics data types measured from the same subject. We learn the weight of each data type as well as a similarity measure between patients via a nonconvex optimization framework. We solve the proposed nonconvex problem iteratively using the ADMM algorithm and show the convergence of the algorithm. The accuracy and robustness of the proposed clustering method is studied both in theory and through various synthetic data. When our method is applied to the TCGA data, the patient clusters inferred by our method show more significant differences in survival times between clusters than those inferred from existing clustering methods. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.9776708
title: MOESM2 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 2: Table S2. Methylation level of 167 driven genes.
DOI: 10.6084/m9.figshare.9776708.v1
title: MOESM2 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 2: Table S2. Methylation level of 167 driven genes.
DOI: 10.6084/m9.figshare.9776714
title: MOESM3 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 3: Table S3. Metascape functional analysis results.
DOI: 10.6084/m9.figshare.9776714.v1
title: MOESM3 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 3: Table S3. Metascape functional analysis results.
DOI: 10.6084/m9.figshare.19211527
title: Additional file 1 of Comparison of porcine ALG and rabbit ATG on outcomes of HLA-haploidentical hematopoietic stem cell transplantation for patients with acquired aplastic anemia

description: Additional file 1. Institution and years for the patients who were treated with haplo-HSCT
DOI: 10.34683/sr566
title: StoneRounds Case: SR566
title: Type 2 Usher Syndrome

description: StoneRounds Case SR566 was diagnosed with Type 2 Usher Syndrome likely caused by mutations in the gene: USH2A.
DOI: 10.6084/m9.figshare.16590741.v1
title: Additional file 2 of Inferring SARS-CoV-2 functional genomics from viral transcriptome with identification of potential antiviral drugs and therapeutic targets

description: Additional file 2: Table S1. The differentially expressed human genes and SR genes in SARS-CoV-2-infected human cells. Table S2. TFs that significantly associated with viral genes. Table S3. The co-expression relationships between ncRNAs and SR genes in COVID-19. Table S4. Potential host-targeted antiviral drugs associated with SR genes.
DOI: 10.6084/m9.figshare.9776720
title: MOESM4 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 4: Table S4. Clinical signatures, mRNA types and mutational signatures of all patients.
DOI: 10.6084/m9.figshare.9776720.v1
title: MOESM4 of A six-gene prognostic model predicts overall survival in bladder cancer patients

description: Additional file 4: Table S4. Clinical signatures, mRNA types and mutational signatures of all patients.
DOI: 10.11583/dtu.21756236
title: data for: Mixed-stock analysis of Atlantic herring (Clupea harengus): a tool for identifying management units and complex migration dynamics

description: The file is a comma-separated file, where each row gives a list of 59 SNP genotypes in Atlantic herring; one row per individual (3690 total). Each individual is denoted by its number ('Fish_no'), followed by collection location or scientific cruise ID ('Location_Cruise') following Tables 1-2 in Bekkevold et al. (DOI:10.1093/icesjms/fsac223), followed by collection year ('Collection_year'). Individual SNP locus names are given in the top row. Genotypes are given as the two alleles separated by commas. Missing genotypes are given as 'NA'.
<br>
<br>
DOI: 10.11583/dtu.21756236.v1
title: data for: Mixed-stock analysis of Atlantic herring (Clupea harengus): a tool for identifying management units and complex migration dynamics

description: The file is a comma-separated file, where each row gives a list of 59 SNP genotypes in Atlantic herring; one row per individual (3690 total). Each individual is denoted by its number ('Fish_no'), followed by collection location or scientific cruise ID ('Location_Cruise') following Tables 1-2 in Bekkevold et al. (DOI:10.1093/icesjms/fsac223), followed by collection year ('Collection_year'). Individual SNP locus names are given in the top row. Genotypes are given as the two alleles separated by commas. Missing genotypes are given as 'NA'.
<br>
<br>
DOI: 10.6084/m9.figshare.21308682
title: Additional file 3 of Evaluate the immune-related eRNA models and signature score to predict the response to immunotherapy in thyroid carcinoma

description: Additional file 3: Table S1. Premier sequences for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.19211783
title: Additional file 1 of Transcriptomic comparison of ovarian granulosa cells between adult sheep and prepubertal lambs

description: Additional file 1: Table S1. The results of original data filtering.
DOI: 10.6084/m9.figshare.9776750
title: Additional file 1 of Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes

description: Table S1. Breast cancer patient sample characteristics. MpBC: metaplastic breast cancer. TNBC: triple negative breast cancer. FFPE: formalin-fixed paraffin-embedded. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.9776750.v1
title: Additional file 1 of Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes

description: Table S1. Breast cancer patient sample characteristics. MpBC: metaplastic breast cancer. TNBC: triple negative breast cancer. FFPE: formalin-fixed paraffin-embedded. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.16590624
title: Additional file 10 of Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

description: Additional file 10: Table S4. The degree of fold change under drought at the phylum level.
DOI: 10.6084/m9.figshare.21308682.v1
title: Additional file 3 of Evaluate the immune-related eRNA models and signature score to predict the response to immunotherapy in thyroid carcinoma

description: Additional file 3: Table S1. Premier sequences for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.16590627
title: Additional file 11 of Strategies and Structure Feature of the Aboveground and Belowground Microbial Community Respond to Drought in Wild Rice (Oryza longistaminata)

description: Additional file 11: Table S5. The degree of fold change under drought at ASV level.
DOI: 10.6084/m9.figshare.21308685
title: Additional file 4 of Evaluate the immune-related eRNA models and signature score to predict the response to immunotherapy in thyroid carcinoma

description: Additional file 4: Table S2. The differentially expressed genes between high and low-risk group.
DOI: 10.6084/m9.figshare.9776765
title: Additional file 3 of Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes

description: Table S2. Custom NanoString panel gene list. (PNG 415 kb) (XLSX 19 kb)
DOI: 10.6084/m9.figshare.9776765.v1
title: Additional file 3 of Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes

description: Table S2. Custom NanoString panel gene list. (PNG 415 kb) (XLSX 19 kb)
DOI: 10.6084/m9.figshare.16590494.v1
title: Additional file 2 of Xanthine dehydrogenase as a prognostic biomarker related to tumor immunology in hepatocellular carcinoma

description: Additional file 2: Immunostaining score.
DOI: 10.6084/m9.figshare.25244395
title: 171717

description: raw data set
DOI: 10.6084/m9.figshare.25244395.v1
title: 171717

description: raw data set
DOI: 10.5281/zenodo.10646991
title: Almorox Crown Dataset - Crown Instance Segmentation Data & Dieback Estimates

description: COCO, imagery & inventory data for manucsript provisionally entitled "Low-Cost Tree Crown Dieback Estimation Using Deep Learning-Based Segmentation". Archive split into parts to aid uploading.