cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.ketu35
title: Occurrence Download

description: A dataset containing 1714213 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Pl@ntNet observations"
 ]
}

 The dataset includes 1714213 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060069-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uoru6x
title: Occurrence Download

description: A dataset containing 1239122 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is A global database for the distributions of crop wild relatives",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1239122 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000514-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bv5fv
title: Occurrence Download

description: A dataset containing 17747 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pomatoschistus microps (Krøyer, 1838)"
 ]
}

 The dataset includes 17747 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013451-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.amcmst
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhytidoconcha"
 ]
}

 The dataset includes 24 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004510-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25625/r10aab
title: Human and macaque pairs employ different coordination strategies in a transparent decision game

description: Behavioral data: choice sequences, reward outcomes and the reaction and movement times, in human-human, rhesus macaque-macaque, and human-macaque dyads
DOI: 10.6084/m9.figshare.c.3596783_d3
title: Additional file 2 of Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)

description: Differentially expressed gonad development and germ cell-related genes in ovary vs. testis cells. ORF – Open reading frame. Blast hit species, e-value, Bit Score – Blast best hit details. Log2FC – Fold change values (log2 transformed) as determined by edgeR, positive values represent over-expression in testis cells, negative values are over-expressed in the ovary cells. p-value, FDR (false discovery rate adjusted p-value) – edgeR differential expression analysis statistics. KEGG – Kyoto encyclopedia of genes and genomes function. (XLSX 35.7 kb)
DOI: 10.6084/m9.figshare.c.3596792_d1
title: Additional file 1: of Usage of gloves for hair shampooing in German hairdressing salons

description: Figure “Occupational dermatitis in German hairdressers. Number of suspected and recognised cases and compensation payments (1999-2014; BGW data)”. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3596795_d1
title: Additional file 1: Table S4. of Phase II clinical trial of sorafenib plus interferon-alpha treatment for patients with metastatic renal cell carcinoma in Japan

description: Comparison of the current study with other sorafenib-interferon combination studies and with single-agent sorafenib studies [25]. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3596783_d4
title: Additional file 4 of Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)

description: Differentially expressed gonad development and germ cell-related genes in crude vs. Percoll-enriched testis cells. ORF – Open reading frame. Blast hit species, e-value, Bit Score – Blast best hit details. Log2FC – Fold change values (log2 transformed) as determined by edgeR, positive values represent over-expression in testis cells, negative values are over-expressed in the ovary cells. p-value, FDR (false discovery rate adjusted p-value) – edgeR differential expression analysis statistics. KEGG – Kyoto encyclopedia of genes and genomes function. (XLSX 26.5 kb)
DOI: 10.6084/m9.figshare.c.3596804_d1
title: Additional file 1: Table S1. of Effects of capecitabine treatment on the uptake of thymidine analogs using exploratory PET imaging agents: 18F-FAU, 18F-FMAU, and 18F-FLT

description: Additional Patient Information. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3596801_d3
title: MOESM2 of Functional inclusion bodies produced in the yeast Pichia pastoris

description: Additional file 2. Raw experimental data.
DOI: 10.6084/m9.figshare.c.3596816_d1
title: Additional file 4: Table S4. of Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night

description: Spreadsheet listing all differentially expressed gene s between male and female mosquitoes. GeneID = gene ID; base Mean = the mean of the normalized counts for all samples;log2FoldChange = Log 2 fold change in expression low-light relative to control; lfcMLE = unshrunken maximum likelihood estimates of Log2 fold change in expression; lfcSE = Standard Error of log2FoldChange; Stat = Wald statisic; pvalue; padj = p value adjusted after Benjamini-Hochberg; Annotation = functional annotation of the gene; Domain(s) = Interpro domain annotations. Genes with an absolute fold change of two are shown in bold. (XLS 2665 kb)
DOI: 10.6084/m9.figshare.c.3596804_d2
title: Additional file 2: Table S2. of Effects of capecitabine treatment on the uptake of thymidine analogs using exploratory PET imaging agents: 18F-FAU, 18F-FMAU, and 18F-FLT

description: Patient Image Data. (XLSX 19Â kb)
DOI: 10.6084/m9.figshare.c.3596816_d2
title: Additional file 3: Table S3. of Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night

description: Spreadsheet listing all overrepresented gene ontology terms associated with genes exhibiting decreased expression in males exposed to the ALAN treatment. GOBIP, gene ontology biological process identifier. (XLS 18Â kb)
DOI: 10.35110/50eef03f-5314-409a-a5b8-4b50bed68363
title: Jeu de données drone du marais Breton

description: Acquisition de données multisources sur le marais Breton par drone et capteurs multisources (RGB,Multispectral). Recherche.
DOI: 10.6084/m9.figshare.c.3597740_d1
title: MOESM1 of Comparison of the specificity of antibodies to VAR2CSA in Cameroonian multigravidae with and without placental malaria: a retrospective caseâ  control study

description: Additional file 1. Cut-off values for DBL domains and FV2.
DOI: 10.6084/m9.figshare.c.3597740_d3
title: MOESM2 of Comparison of the specificity of antibodies to VAR2CSA in Cameroonian multigravidae with and without placental malaria: a retrospective caseâ  control study

description: Additional file 2. Testing mouse anti-human monoclonal antibodies for cross-reactivity (median fluorescent intensities tabulated).
DOI: 10.6084/m9.figshare.c.3597656_d14
title: Additional file 19: of A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

description: Title: The 105 Upland cotton cultivars used for finding the efficacy of deletion marker allele CFBid0004 in this study. Description of data: This table contains 105 NCVT cultivars name. The historic phenotypic data of those 105 cultivars were used to find out the practical efficacy of the InDel marker CFBid0004 in Upland cotton breeding. (XLSX 11Â kb)
DOI: 10.35110/24c7721e-cd9e-4c73-929b-1d5008721381
title: Jeu de données Drone du marais poitevin

description: Acquisition de données multisources sur le marais Poitevin par drone et capteurs multisources (RGB,Multispectral). Recherche.
DOI: 10.6084/m9.figshare.27636132
title: DNA methylation analysis of multiple genes in thymic epithelial tumors

description: <b>Aim:</b> To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs). <b>Materials & methods:</b> We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples. <b>Results:</b> thymic carcinomas (TCs) showed hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with thymomas (TMs) and healthy thymic tissues. <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes. <b>Conclusion:</b> The present study confirms <i>GHSR, ELF3, IL1RN</i> and <i>RAG1</i> as TET epigenetic biomarkers. Tumors arising from the epithelium of the thymus gland (TETs), including thymomas (TMs) and thymic carcinomas (TCs), are rare malignancies whose etiology remains almost unknown. Recent studies are suggesting that altered epigenetic mechanisms, such as DNA methylation, contribute to TETs pathogenesis. Altered DNA methylation levels of specific genes have been associated with the severity of TETs, potentially providing biomarkers of these conditions. In the current study methylation levels of 15 genes among the most promising epigenetic biomarkers of TETs were evaluated in a cohort of 71 bioptic TET samples, including 64 TMs and 7 TCs. We observed that TCs were characterized by hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with TMs and healthy thymic tissues. Moreover, <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. Since almost 20–40% of TM patients have myasthenia gravis, we also searched for differences between patients with and without MG. None of the 15 investigated genes showed mean methylation differences between the two TMs groups. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes, and between primary tumors and recurrences. No changes in blood methylation levels of the investigated genes were observed among TET subtypes.
DOI: 10.6084/m9.figshare.27901623
title: CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells

description: Mammalian genomes encode 12 proteins that contain a CXXC zinc finger domain. Most members of this family are large multi-domain proteins that function in the control of DNA methylation and histone methylation patterns. CXXC5 is a smaller member of the family, along with its closest homologue CXXC4. These two proteins lack known catalytic domains. Here, we have characterized CXXC5 in mouse embryonic stem (ES) cells. We used gene knockouts, RNA sequencing, and DNA methylation analysis by whole-genome bisulfite sequencing. We show that CXXC5 is a nuclear protein that interacts with 5-methylcytosine oxidases (TET proteins). Removal of CXXC5 from ES cells leads to very few changes in gene expression. CXXC5 extensively colocalizes with TET1 and TET2 at CpG islands. CXXC5 inactivation leads to a substantial reduction of DNA methylation levels that affects all genomic compartments including genic and intergenic regions and CpG island shores. We propose a model in which CXXC5 serves as an anchor for TET proteins at CpG islands. In the absence of CXXC5, the 5-methylcytosine oxidases become dislodged from CpG islands and are enabled to induce genome-scale DNA demethylation. Thus, CXXC5 serves as a stabilizer of DNA methylation patterns.
DOI: 10.6084/m9.figshare.27901623.v1
title: CXXC5 stabilizes DNA methylation patterns in mouse embryonic stem cells

description: Mammalian genomes encode 12 proteins that contain a CXXC zinc finger domain. Most members of this family are large multi-domain proteins that function in the control of DNA methylation and histone methylation patterns. CXXC5 is a smaller member of the family, along with its closest homologue CXXC4. These two proteins lack known catalytic domains. Here, we have characterized CXXC5 in mouse embryonic stem (ES) cells. We used gene knockouts, RNA sequencing, and DNA methylation analysis by whole-genome bisulfite sequencing. We show that CXXC5 is a nuclear protein that interacts with 5-methylcytosine oxidases (TET proteins). Removal of CXXC5 from ES cells leads to very few changes in gene expression. CXXC5 extensively colocalizes with TET1 and TET2 at CpG islands. CXXC5 inactivation leads to a substantial reduction of DNA methylation levels that affects all genomic compartments including genic and intergenic regions and CpG island shores. We propose a model in which CXXC5 serves as an anchor for TET proteins at CpG islands. In the absence of CXXC5, the 5-methylcytosine oxidases become dislodged from CpG islands and are enabled to induce genome-scale DNA demethylation. Thus, CXXC5 serves as a stabilizer of DNA methylation patterns.
DOI: 10.6084/m9.figshare.27636132.v2
title: DNA methylation analysis of multiple genes in thymic epithelial tumors

description: <b>Aim:</b> To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs). <b>Materials & methods:</b> We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples. <b>Results:</b> thymic carcinomas (TCs) showed hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with thymomas (TMs) and healthy thymic tissues. <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes. <b>Conclusion:</b> The present study confirms <i>GHSR, ELF3, IL1RN</i> and <i>RAG1</i> as TET epigenetic biomarkers. Tumors arising from the epithelium of the thymus gland (TETs), including thymomas (TMs) and thymic carcinomas (TCs), are rare malignancies whose etiology remains almost unknown. Recent studies are suggesting that altered epigenetic mechanisms, such as DNA methylation, contribute to TETs pathogenesis. Altered DNA methylation levels of specific genes have been associated with the severity of TETs, potentially providing biomarkers of these conditions. In the current study methylation levels of 15 genes among the most promising epigenetic biomarkers of TETs were evaluated in a cohort of 71 bioptic TET samples, including 64 TMs and 7 TCs. We observed that TCs were characterized by hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with TMs and healthy thymic tissues. Moreover, <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. Since almost 20–40% of TM patients have myasthenia gravis, we also searched for differences between patients with and without MG. None of the 15 investigated genes showed mean methylation differences between the two TMs groups. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes, and between primary tumors and recurrences. No changes in blood methylation levels of the investigated genes were observed among TET subtypes.
DOI: 10.6084/m9.figshare.27316629
title: The mystique of epigenetic regulation: the remarkable case of a human noncoding RNA, nc886

description: nc886 is a regulatory noncoding RNA that is transcribed by RNA polymerase III (Pol III), is variably expressed in different biological contexts, and plays roles in inflammation and cancer. Epigenetic mechanisms play an intriguing role in regulating nc886 expression. As a maternally imprinted gene and metastable epiallele, nc866 exhibits polymorphic imprinting, with a methylation status that is influenced by environmental and biological factors. Consequently, the promoter DNA methylation status and the different resulting RNA expression levels of nc886 are associated with physiological and pathological conditions. In this review, we summarize the literature and explore the significance in relation to diverse roles of nc886. nc886 is transcribed by RNA polymerase III. nc886 binds to target proteins such as Protein Kinase R and Dicer to control their activities. nc886 has CpG islands in the promoter region, whose hypermethylation suppresses nc886 expression. CpG DNA methylation of nc886 is allele-specific. nc886 is a maternally imprinted gene. Imprinting of nc886 CpG DNA methylation is polymorphic; nc886 is imprinted in 75% of individuals but has both alleles unmethylated in the remaining 25%. nc886 is a metastable epiallele, whose CpG DNA methylation status is stochastically established and largely maintained during development. nc886 CpG DNA methylation in offspring is influenced by maternal factors including nutritional status, folic acid supplementation, age at conception and environmental factors. nc886 CpG DNA methylation is associated with several health traits. nc886 CpG DNA methylation is dysregulated in pathological conditions, with cancer being the most prominent example.
DOI: 10.6084/m9.figshare.27636132.v1
title: DNA methylation analysis of multiple genes in thymic epithelial tumors

description: <b>Aim:</b> To investigate DNA methylation levels of a panel of genes in thymic epithelial tumors (TETs). <b>Materials & methods:</b> We selected 15 genes among the most promising epigenetic biomarkers of TETs and evaluated their methylation levels in 71 TET samples. <b>Results:</b> thymic carcinomas (TCs) showed hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with thymomas (TMs) and healthy thymic tissues. <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes. No changes in blood methylation levels of the investigated genes were seen among TET subtypes. <b>Conclusion:</b> The present study confirms <i>GHSR, ELF3, IL1RN</i> and <i>RAG1</i> as TET epigenetic biomarkers. Tumors arising from the epithelium of the thymus gland (TETs), including thymomas (TMs) and thymic carcinomas (TCs), are rare malignancies whose etiology remains almost unknown. Recent studies are suggesting that altered epigenetic mechanisms, such as DNA methylation, contribute to TETs pathogenesis. Altered DNA methylation levels of specific genes have been associated with the severity of TETs, potentially providing biomarkers of these conditions. In the current study methylation levels of 15 genes among the most promising epigenetic biomarkers of TETs were evaluated in a cohort of 71 bioptic TET samples, including 64 TMs and 7 TCs. We observed that TCs were characterized by hypermethylation of <i>GHSR</i> and <i>ELF3</i> genes and reduced <i>IL1RN</i> methylation levels compared with TMs and healthy thymic tissues. Moreover, <i>RAG1</i> was hypomethylated in TMs compared with healthy thymic tissues. Since almost 20–40% of TM patients have myasthenia gravis, we also searched for differences between patients with and without MG. None of the 15 investigated genes showed mean methylation differences between the two TMs groups. No difference in the methylation levels of the investigated genes was seen among TM stages and subtypes, and between primary tumors and recurrences. No changes in blood methylation levels of the investigated genes were observed among TET subtypes.
DOI: 10.6084/m9.figshare.27316629.v2
title: The mystique of epigenetic regulation: the remarkable case of a human noncoding RNA, nc886

description: nc886 is a regulatory noncoding RNA that is transcribed by RNA polymerase III (Pol III), is variably expressed in different biological contexts, and plays roles in inflammation and cancer. Epigenetic mechanisms play an intriguing role in regulating nc886 expression. As a maternally imprinted gene and metastable epiallele, nc866 exhibits polymorphic imprinting, with a methylation status that is influenced by environmental and biological factors. Consequently, the promoter DNA methylation status and the different resulting RNA expression levels of nc886 are associated with physiological and pathological conditions. In this review, we summarize the literature and explore the significance in relation to diverse roles of nc886. nc886 is transcribed by RNA polymerase III. nc886 binds to target proteins such as Protein Kinase R and Dicer to control their activities. nc886 has CpG islands in the promoter region, whose hypermethylation suppresses nc886 expression. CpG DNA methylation of nc886 is allele-specific. nc886 is a maternally imprinted gene. Imprinting of nc886 CpG DNA methylation is polymorphic; nc886 is imprinted in 75% of individuals but has both alleles unmethylated in the remaining 25%. nc886 is a metastable epiallele, whose CpG DNA methylation status is stochastically established and largely maintained during development. nc886 CpG DNA methylation in offspring is influenced by maternal factors including nutritional status, folic acid supplementation, age at conception and environmental factors. nc886 CpG DNA methylation is associated with several health traits. nc886 CpG DNA methylation is dysregulated in pathological conditions, with cancer being the most prominent example.
DOI: 10.6084/m9.figshare.27604598
title: Gastric microbiome composition accompanied with the <i>Helicobacter pylori</i> related DNA methylation anomaly

description: <b>Aim:</b> DNA methylation is associated with gastric cancer and <i>Helicobacter pylori</i> (<i>H. pylori</i>) infection, while increasing evidence indicated involvement of other microbes reside in gastric mucosa during gastric tumorigenesis. We investigated bacterial communities in the gastric mucosa accompanied with <i>H. pylori</i> related methylation anomaly. <b>Materials & methods:</b> Gastric mucosa samples from antrum were obtained from 182 cancer-free patients. Bacterial communities were evaluated using 16S rRNA sequencing. The result was correlated with <i>H. pylori</i> related promoter CpG island (CGI) methylation of five genes (<i>IGF2, SLC16A12, SOX11, P2RX7 and MYOD1</i>), LINE1 hypomethylation and telomere length. <b>Results & conclusion:</b> We showed correlation between lower bacterial alpha diversity and higher CGI methylation. Multivariate analysis demonstrated older age (t = 3.46, <i>p</i> = 0.0007), <i>H. pylori</i> infection (t = 9.99, <i>p</i> &lt; 0.0001) and lower bacterial alfa diversity (Shannon index: t = -2.34, <i>p</i> = 0.02) were significantly associated with CGI hypermethylation. In genus or family levels, increased abundance of <i>Helicobacter</i> was associated with hyper CGI methylation with strongest correlation, while decreased abundance of four bacteria (<i>Intrasporangiaceae family, Macellibacteroides</i>, <i>Peptostreptococcus</i> and <i>Dietziaceae family</i>) was also associated with hyper CGI methylation. Our findings suggest the potential correlation between CGI methylation induction and lower bacterial alpha diversity in the gastric mucosa accompanied by <i>H. pylori</i> infection. DNA methylation is associated with gastric cancer and <i>H. pylori</i> infection related gastritis, while increasing evidence has indicated the substantial involvement of other microbes that reside in the gastric mucosa during gastric tumorigenesis. We investigated the bacterial communities in the non-neoplastic gastric mucosa accompanied with the <i>H. pylori</i> related methylation anomaly. Our findings showed potential correlation between methylation induction and change in bacterial communities characterized as lower bacterial alpha diversity in the gastric mucosa accompanied by <i>H. pylori</i> infection.