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

description: A dataset containing 63907 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycadales"
 ]
}

 The dataset includes 63907 records from 660 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047634-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10642000
title: Excel data of the 106 Tunisian post-graduate dental students
DOI: 10.5281/zenodo.10642001
title: Excel data of the 106 Tunisian post-graduate dental students
DOI: 10.5281/zenodo.13163574
title: Excel data of the 106 Tunisian post-graduate dental students
DOI: 10.6084/m9.figshare.14363568
title: Up-regulation of LINC00619 promotes apoptosis and inhibits proliferation, migration and invasion while promoting apoptosis of osteosarcoma cells through inactivation of the HGF-mediated PI3K-Akt signalling pathway

description: This study is performed to evaluate the role of long noncoding RNA (lncRNA) LINC00619 in osteosarcoma through the PI3K-Akt signalling pathway by binding to HGF. Osteosarcoma and osteochondroma tissues from patients were collected. The relationship between lncRNA LINC00619 and HGF was proved by the dual-luciferase reporter gene assay. The expression patterns of lncRNA LINC00619 as well as the levels of proliferating cell nuclear antigen (PCNA), hepatocyte growth factor (HGF), phosphoinositide 3-kinase (PI3K), protein kinase B (Akt), Bax, Bcl-2, alkaline phosphatase (ALP), and osteopontin (OPN) were detected by RT-qPCR and Western blot analysis. In addition, MTT assay, flow cytometry, scratch test, and Transwell assay were performed to assess the cell proliferation, cell cycle distribution, apoptosis, cell migration, and invasion in each group, respectively. Osteosarcoma tissues presented with elevated positive expression rate of HGF, up-regulated expression levels of PCNA, HGF, PI3K, Akt, Bcl-2, ALP and OPN, and down-regulated expressions of Bax and LINC00619. HGF was verified as a target gene of lncRNA LINC00619. LINC00619 was found to down-regulate the expressions of PCNA, HGF, PI3K, Akt, Bcl-2, ALP, and OPN in osteosarcoma cells. Up-regulation of lncRNA LINC00619 decreased cell growth, migration intensity, and invasion ability, but enhanced the apoptosis rate of osteosarcoma cells. Our findings suggest that lncRNA LINC00619 inhibits proliferation, migration and invasion and improves apoptosis of osteosarcoma cells through the inhibition of the activation of the HGF-dependent PI3K-Akt signalling pathway.
DOI: 10.6084/m9.figshare.14332859.v1
title: Cell type-specific chromatin accessibility analysis in the mouse and human brain

description: The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using ATAC-seq include a small amount of material needed, fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. With increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs. Here we tested three protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescence-activated nuclei sorting (FANS) and ATAC-seq. Our study shows that the cryopreservation method impacts the number of open chromatin regions identified from frozen brain tissue using ATAC-seq. However, we show that all protocols generate consistent and robust data and enable the identification of functional regulatory elements in neuronal cells. Our study implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. We also reveal additional challenges of doing chromatin analysis on <i>post-mortem</i> human brain tissue. Overall, ATAC-seq coupled with FANS is a powerful method to capture cell-type-specific chromatin accessibility information in mouse and human brain. Our study provides alternative brain preservation methods that generate high-quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in the brain.
DOI: 10.6084/m9.figshare.14332859
title: Cell type-specific chromatin accessibility analysis in the mouse and human brain

description: The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and pathophysiology of neuropsychiatric disorders. The advantages of using ATAC-seq include a small amount of material needed, fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. With increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs. Here we tested three protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescence-activated nuclei sorting (FANS) and ATAC-seq. Our study shows that the cryopreservation method impacts the number of open chromatin regions identified from frozen brain tissue using ATAC-seq. However, we show that all protocols generate consistent and robust data and enable the identification of functional regulatory elements in neuronal cells. Our study implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. We also reveal additional challenges of doing chromatin analysis on <i>post-mortem</i> human brain tissue. Overall, ATAC-seq coupled with FANS is a powerful method to capture cell-type-specific chromatin accessibility information in mouse and human brain. Our study provides alternative brain preservation methods that generate high-quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in the brain.
DOI: 10.6084/m9.figshare.14046387
title: Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers

description: Genome-wide association studies (GWAS) have identified SNPs linked with lung cancer risk. Our aim was to discover the genes, non-coding RNAs, and regulatory elements within GWAS-identified risk regions that are deregulated in non-small cell lung carcinoma (NSCLC) to identify novel, clinically targetable genes and mechanisms in carcinogenesis. A targeted bisulphite-sequencing approach was used to comprehensively investigate DNA methylation changes occurring within lung cancer risk regions in 17 NSCLC and adjacent normal tissue pairs. We report differences in differentially methylated regions between adenocarcinoma and squamous cell carcinoma. Among the minimal regions found to be differentially methylated in at least 50% of the patients, 7 candidates were replicated in 2 independent cohorts (n = 27 and n = 87) and the potential of 6 as methylation-dependent regulatory elements was confirmed by functional assays. This study contributes to understanding the pathways implicated in lung cancer initiation and progression, and provides new potential targets for cancer treatment.
DOI: 10.6084/m9.figshare.14046387.v2
title: Differentially methylated regions within lung cancer risk loci are enriched in deregulated enhancers

description: Genome-wide association studies (GWAS) have identified SNPs linked with lung cancer risk. Our aim was to discover the genes, non-coding RNAs, and regulatory elements within GWAS-identified risk regions that are deregulated in non-small cell lung carcinoma (NSCLC) to identify novel, clinically targetable genes and mechanisms in carcinogenesis. A targeted bisulphite-sequencing approach was used to comprehensively investigate DNA methylation changes occurring within lung cancer risk regions in 17 NSCLC and adjacent normal tissue pairs. We report differences in differentially methylated regions between adenocarcinoma and squamous cell carcinoma. Among the minimal regions found to be differentially methylated in at least 50% of the patients, 7 candidates were replicated in 2 independent cohorts (n = 27 and n = 87) and the potential of 6 as methylation-dependent regulatory elements was confirmed by functional assays. This study contributes to understanding the pathways implicated in lung cancer initiation and progression, and provides new potential targets for cancer treatment.
DOI: 10.6084/m9.figshare.14363568.v1
title: Up-regulation of LINC00619 promotes apoptosis and inhibits proliferation, migration and invasion while promoting apoptosis of osteosarcoma cells through inactivation of the HGF-mediated PI3K-Akt signalling pathway

description: This study is performed to evaluate the role of long noncoding RNA (lncRNA) LINC00619 in osteosarcoma through the PI3K-Akt signalling pathway by binding to HGF. Osteosarcoma and osteochondroma tissues from patients were collected. The relationship between lncRNA LINC00619 and HGF was proved by the dual-luciferase reporter gene assay. The expression patterns of lncRNA LINC00619 as well as the levels of proliferating cell nuclear antigen (PCNA), hepatocyte growth factor (HGF), phosphoinositide 3-kinase (PI3K), protein kinase B (Akt), Bax, Bcl-2, alkaline phosphatase (ALP), and osteopontin (OPN) were detected by RT-qPCR and Western blot analysis. In addition, MTT assay, flow cytometry, scratch test, and Transwell assay were performed to assess the cell proliferation, cell cycle distribution, apoptosis, cell migration, and invasion in each group, respectively. Osteosarcoma tissues presented with elevated positive expression rate of HGF, up-regulated expression levels of PCNA, HGF, PI3K, Akt, Bcl-2, ALP and OPN, and down-regulated expressions of Bax and LINC00619. HGF was verified as a target gene of lncRNA LINC00619. LINC00619 was found to down-regulate the expressions of PCNA, HGF, PI3K, Akt, Bcl-2, ALP, and OPN in osteosarcoma cells. Up-regulation of lncRNA LINC00619 decreased cell growth, migration intensity, and invasion ability, but enhanced the apoptosis rate of osteosarcoma cells. Our findings suggest that lncRNA LINC00619 inhibits proliferation, migration and invasion and improves apoptosis of osteosarcoma cells through the inhibition of the activation of the HGF-dependent PI3K-Akt signalling pathway.
DOI: 10.6084/m9.figshare.14038464
title: Saliva cell type DNA methylation reference panel for epidemiological studies in children

description: Saliva is a widely used biological sample, especially in pediatric research, containing a heterogenous mixture of immune and epithelial cells. Associations of exposure or disease with saliva DNA methylation can be influenced by cell-type proportions. Here, we developed a saliva cell-type DNA methylation reference panel to estimate interindividual cell-type heterogeneity in whole saliva studies. Saliva was collected from 22 children (7–16 years) and sorted into immune and epithelial cells, using size exclusion filtration and magnetic bead sorting. DNA methylation was measured using the Illumina MethylationEPIC BeadChip. We assessed cell-type differences in DNA methylation profiles and tested for enriched biological pathways. Immune and epithelial cells differed at 181,577 (22.8%) DNA methylation sites (t-test p &lt; 6.28 × 10<sup>−8</sup>). Immune cell hypomethylated sites are mapped to genes enriched for immune pathways (p &lt; 3.2 × 10<sup>−5</sup>). Epithelial cell hypomethylated sites were enriched for cornification (p = 5.2 × 10<sup>−4</sup>), a key process for hard palette formation. Saliva immune and epithelial cells have distinct DNA methylation profiles which can drive whole-saliva DNA methylation measures. A primary saliva DNA methylation reference panel, easily implemented with an R package, will allow estimates of cell proportions from whole saliva samples and improve epigenetic epidemiology studies by accounting for measurement heterogeneity by cell-type proportions.
DOI: 10.6084/m9.figshare.14038464.v1
title: Saliva cell type DNA methylation reference panel for epidemiological studies in children

description: Saliva is a widely used biological sample, especially in pediatric research, containing a heterogenous mixture of immune and epithelial cells. Associations of exposure or disease with saliva DNA methylation can be influenced by cell-type proportions. Here, we developed a saliva cell-type DNA methylation reference panel to estimate interindividual cell-type heterogeneity in whole saliva studies. Saliva was collected from 22 children (7–16 years) and sorted into immune and epithelial cells, using size exclusion filtration and magnetic bead sorting. DNA methylation was measured using the Illumina MethylationEPIC BeadChip. We assessed cell-type differences in DNA methylation profiles and tested for enriched biological pathways. Immune and epithelial cells differed at 181,577 (22.8%) DNA methylation sites (t-test p &lt; 6.28 × 10<sup>−8</sup>). Immune cell hypomethylated sites are mapped to genes enriched for immune pathways (p &lt; 3.2 × 10<sup>−5</sup>). Epithelial cell hypomethylated sites were enriched for cornification (p = 5.2 × 10<sup>−4</sup>), a key process for hard palette formation. Saliva immune and epithelial cells have distinct DNA methylation profiles which can drive whole-saliva DNA methylation measures. A primary saliva DNA methylation reference panel, easily implemented with an R package, will allow estimates of cell proportions from whole saliva samples and improve epigenetic epidemiology studies by accounting for measurement heterogeneity by cell-type proportions.
DOI: 10.6084/m9.figshare.14169970
title: DNA-methylation for the detection and distinction of 19 human malignancies

description: The contribution of DNA-methylation based gene silencing to carcinogenesis is well established. Increasingly, DNA-methylation is examined using genome-wide techniques, with recent public efforts yielding immense data sets of diverse malignancies representing the vast majority of human cancer related disease burden. Whereas mutation events may group preferentially or in high frequency with a given histology, mutations are poor classifiers of tumour type. Here we examine the hypothesis that cancer-specific DNA-methylation reflects the tissue of origin or carcinogenic risk factor, and these methylation abnormalities may be used to faithfully classify tumours according to histology. We present an analysis of 7427 tumours representing 19 human malignancies and 708 normal samples demonstrating that specific tumour changes in methylation can correctly determine site of origin and tumour histology with 86% overall accuracy. Examination of misclassified tumours reveals underlying shared biology as the source of misclassifications, including common cell of origin or risk factors.
DOI: 10.6084/m9.figshare.14169970.v1
title: DNA-methylation for the detection and distinction of 19 human malignancies

description: The contribution of DNA-methylation based gene silencing to carcinogenesis is well established. Increasingly, DNA-methylation is examined using genome-wide techniques, with recent public efforts yielding immense data sets of diverse malignancies representing the vast majority of human cancer related disease burden. Whereas mutation events may group preferentially or in high frequency with a given histology, mutations are poor classifiers of tumour type. Here we examine the hypothesis that cancer-specific DNA-methylation reflects the tissue of origin or carcinogenic risk factor, and these methylation abnormalities may be used to faithfully classify tumours according to histology. We present an analysis of 7427 tumours representing 19 human malignancies and 708 normal samples demonstrating that specific tumour changes in methylation can correctly determine site of origin and tumour histology with 86% overall accuracy. Examination of misclassified tumours reveals underlying shared biology as the source of misclassifications, including common cell of origin or risk factors.
DOI: 10.15468/dl.qvutmf
title: Occurrence Download

description: A dataset containing 470638 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "StateProvince is La Guajira",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 470638 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047635-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/9104993
title: Balochi Language to English Translation Dataset
DOI: 10.15468/dl.ep2ugy
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "MediaType is Image",
 "OccurrenceStatus is Present",
 "Sex is one of (Male, Female)",
 "TaxonKey is Samaris spinea Mihara & Amaoka, 2004"
 ]
}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047636-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yvzg9t
title: Occurrence Download

description: A dataset containing 6000 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is INC PAS Plants of Cemeteries of Southern Poland"
 ]
}

 The dataset includes 6000 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047637-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nkws5
title: Occurrence Download

description: A dataset containing 1118 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Univ. of Białystok - Vascular Plants of NE Poland"
 ]
}

 The dataset includes 1118 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047638-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xz2jfy
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Coordinate rounded",
 "TaxonKey is Cassia grandis L.f."
 ]
}

 The dataset includes 87 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047639-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m67d7k
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "TaxonKey is Cassia grandis L.f."
 ]
}

 The dataset includes 171 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047641-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ybnzu9
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Geodetic datum assumed WGS84",
 "TaxonKey is Cassia grandis L.f."
 ]
}

 The dataset's 1 records were derived from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047640-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2j1f67
title: CCDC 2325068: Experimental Crystal Structure Determination

description: Related Article: Minami Nakamura, Yukiyasu Kashiwagi, Mitsuhiko Morisue|2024|CrystEngComm|26|3964|doi:10.1039/D4CE00495G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.5qhcth
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 570 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047643-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7ntvd
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 570 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047644-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ebfz4
title: Occurrence Download

description: A dataset containing 5089 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-104 4,-78.3 4,-78.3 23,-104 23,-104 4))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cycadopsida"
 ]
}

 The dataset includes 5089 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047645-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mggdbh
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Prostephanus truncatus (Horn, 1878)"
 ]
}

 The dataset includes 70 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047646-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qx2x4
title: Occurrence Download

description: A dataset containing 407 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "Country is one of (Brazil, Australia)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Delphinidae"
 ]
}

 The dataset includes 407 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047647-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.