cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27316629.v1
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.v2
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.
DOI: 10.15468/dl.mb3kua
title: Occurrence Download

description: A dataset containing 3229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columbellidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3229 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033068-241126133413365/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.27604598.v1
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.
DOI: 10.35110/b2dc5dae-84dd-4f27-b879-65f791799127
title: Suivi des blocs cyclopéens de la côte rocheuse de Pors-Carn (Saint-Guénolé, Finistère) à partir de modèles numériques de terrain (MNT)

description: Etude des changements morphosédimentaires des amas de blocs cyclopéens de la côte rocheuse de Pors-Carn (Saint-Guénolé) à Penmarc'h (Finistère). Modèles Numériques de Terrain disponibles depuis 2012 avec une fréquence annuelle. Objectifs : étudier les changements morphosédimentaires des formes littorales en réponse aux variations climatiques et/ou des conditions météo-marines
DOI: 10.6084/m9.figshare.c.3598673_d3
title: Additional file 5: of SNP-markers in Allium species to facilitate introgression breeding in onion

description: Table S5. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the F2(CxR) population. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3598673_d4
title: Additional file 1: of SNP-markers in Allium species to facilitate introgression breeding in onion

description: Table S1. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in RF cDNA RF_ctgs conducive for genotyping using the KASP platform. (XLSX 244Â kb)
DOI: 10.6084/m9.figshare.c.3598673_d5
title: Additional file 6: of SNP-markers in Allium species to facilitate introgression breeding in onion

description: Table S6. Positions and Chi-square values to expected segregation ratios for SNPs markers segregating in the CCxRF_new population based on RF-SNP markers. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3598661_d12
title: Additional file 5: Table S4. of Genome-wide identification and characterization of auxin response factor (ARF) family genes related to flower and fruit development in papaya (Carica papaya L.)

description: The saw data of the CpARF family during the different flower developmental stages. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3598673_d6
title: Additional file 2: of SNP-markers in Allium species to facilitate introgression breeding in onion

description: Table S2. Results of Blast2Go to obtain functional anotation of RF contigs containing SNPs that were selected for the KASP platform. (XLSX 57Â kb)
DOI: 10.6084/m9.figshare.c.3598661_d13
title: Additional file 9: Table S6. of Genome-wide identification and characterization of auxin response factor (ARF) family genes related to flower and fruit development in papaya (Carica papaya L.)

description: The saw data of the CpARF family during the different fruit developmental stages. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.c.3598673_d7
title: Additional file 3: of SNP-markers in Allium species to facilitate introgression breeding in onion

description: Table S3. Sequences flanking reliable single nucleotide polymorphisms (SNPs) in onion cDNA al_contigs conducive for genotyping using the KASP platform. (XLSX 1413Â kb)
DOI: 10.35110/b375183e-3c3e-46fb-877f-fe20a93b4826
title: Suivi des blocs cyclopéens de l'île Vierge (Plouguerneau, Finistère) à partir de modèles numériques de terrain (MNT)

description: Etude des changements morphosédimentaires des amas de blocs cyclopéens de l'île Vierge (Finistère). Modèles Numériques de Terrain disponibles depuis 2012 avec une fréquence annuelle. Objectifs : étudier les changements morphosédimentaires des formes littorales en réponse aux variations climatiques et/ou des conditions météo-marines
DOI: 10.6084/m9.figshare.c.3598724_d1
title: Additional file 1: of Patch testing in Iranian children with allergic contact dermatitis

description: Data set on gender, and presence of personal or family history of atopy. (SAV 2 kb)
DOI: 10.35110/4dba3ab7-0ea0-4a61-b1d7-8a134f3b4f57
title: Mesures des conditions hydrodynamiques côtières sur la plage du Vougot (Guissény, Finsitère)

description: Mesures de la houle et des niveaux d'eau dans la zone intertidale de la partie orientale de la plage du Vougot (Guissény, Finistère) commencées en septembre 2012 (toujours en cours).
DOI: 10.6084/m9.figshare.c.3599681_d1
title: Additional file 3: Table S3. of miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1

description: Up (A) and Down (B) regulated genes in miR-27b KD neurons (microarray dataset). (XLSX 380Â kb)
DOI: 10.35110/8e37c01f-4cec-4edb-8c01-7047725f7dc4
title: Suivi pluri-décennal de la flèche de galets du Sillon de Talbert (Pleubian, Côtes d'Armor) à partir de modèles numériques de terrain (MNT)

description: Suivi topo-morphologique de la flèche de galets du Sillon de Talbert (Pleubian, Côtes d'Armor) à partir de modèles numériques de terrain (MNT) commencé en 2002 (toujours en cours)
DOI: 10.6084/m9.figshare.c.3599681_d3
title: Additional file 2: Table S2. of miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1

description: Differentially-expressed presynaptic genes in miR-27b KD (A) and Dicer1 cKO (B) neurons. (nCounter dataset). (XLSX 73Â kb)
DOI: 10.6084/m9.figshare.c.3599693_d2
title: Additional file 9: Table S4. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L

description: Heat map illustrating metabolite changes in response to GAc and shade treatments. The abbreviations GAc5d, GAc7d, SH5d and SH7d mean the log2 fold-change between metabolite relative content obtained in treated and control inflorescences, at 5 and 7 days after 100 % cap fall. Red and green shaded cells indicate p-value ≤ 0.05. Light red and light green shaded cells indicate 0.05
DOI: 10.6084/m9.figshare.c.3599693_d3
title: Additional file 12: Table S6. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L

description: List of GO enriched categories in each pair-wise comparison. Enrichment analysis was performed using R bioconductor topGO package with Fisher's exact test and p-value ≤ 0.01. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3599693_d4
title: Additional file 3: Table S1. of Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L

description: Reference library of chemical standard used for LC/MS/MS analysis. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.c.3599699_d3
title: Additional file 12: Table S6. of Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana

description: List of primers and hybridization probes used in the experiments. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3600566_d2
title: Additional file 3 of A correction method for systematic error in 1H-NMR time-course data validated through stochastic cell culture simulation

description: Code used to generate data for loess analysis. R script used in this work for generating loess model data. (R 10.5 KB)
DOI: 10.15468/dl.xem4fa
title: Occurrence Download

description: A dataset containing 1768 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potamididae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1768 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033069-241126133413365/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.c.3600809_d5
title: Additional file 3: of Phylogenetic approaches to microbial community classification

description: Script to produce clade abundance features. (ZIP 788 kb)
DOI: 10.6084/m9.figshare.c.3600764_d8
title: Additional file 12: Table E7. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: Overrepresented Hub30 Genes and module names. (LS) (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.c.3600809_d6
title: Additional file 6: of Phylogenetic approaches to microbial community classification

description: Clade counts raw dataset. (TXT 9,214 kb)
DOI: 10.6084/m9.figshare.c.3600764_d9
title: Additional file 5: Table E2. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: Consensus of re-analyized included datasets (by Probes). (XLSX 60Â kb)
DOI: 10.6084/m9.figshare.c.3600812_d6
title: Additional file 1: Table S1. of Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant

description: Cluster analysis showing fold change values and description of assembled transcripts of SRA database generated from N. benthamiana leaf discs exposed to oxalic acid (20Â mM) for 0, 2, 6, 12 and 24Â h. Headings of the selected clusters (1-16) utilized in the study are highlighted with blue color, while headings of the other clusters (A-Z) are highlighted in gray color. (XLSX 286 kb)
DOI: 10.6084/m9.figshare.c.3600809_d8
title: Additional file 7: of Phylogenetic approaches to microbial community classification

description: Taxonomic composition of samples. The relative abundance of each group in subgingival and supragingival plaque is shown. Taxonomy is displayed from kingdom to species level. (XLSX 492 kb)
DOI: 10.35110/57833b75-9ed7-4e03-8673-4c48ea7d2159
title: Jeu de données Drone de la Timbertière (Zone Atelier Armorique)

description: Suivi multitemporel de la Timbertière (Zone Atelier Armorique) par données multisources (RGB,Multispectral,thermique). Suivi réalisé dans le cadre de la Zone Atelier Armorique par la Plateforme D2T au printemps et fin d'été / automne. Contribution au suivi dans le cadre du SNO Tourbières.
DOI: 10.6084/m9.figshare.c.3600809_d9
title: Additional file 5: of Phylogenetic approaches to microbial community classification

description: OTU counts raw dataset. (TXT 8,494 kb)
DOI: 10.35110/a714d5f8-0807-436a-909a-3c33a55cd4f3
title: Jeu de données Drone des Landes Blanches (Espace Naturel Sensible) - Vallée du Canut

description: Suivi temporel des Landes Blanches (Espace Naturel Sensible - vallée du Canut) par drone et capteurs multisources (RGB,Multispectral). Suivi réalisé dans le cadre du projet MITI LANDMAN et OSUR Interdisciplinaire Blanc "Intéractions sol / plantes / atmosphère dans les Landes bretonnes".
DOI: 10.6084/m9.figshare.c.3601133_d15
title: MOESM18 of Innate immune defects in HIV permissive cell lines

description: Additional file 18: File S4. List of the 110-cluster used as input in Supplemental File 1.
DOI: 10.6084/m9.figshare.c.3601133_d18
title: MOESM12 of Innate immune defects in HIV permissive cell lines

description: Additional file 12: Table S4. Raw read counts per library of the RNA-seq libraries sequenced in this work.
DOI: 10.15468/dl.x5vphk
title: Occurrence Download

description: A dataset containing 3121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nacellidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3121 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033070-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.md4cz9
title: Occurrence Download

description: A dataset containing 215274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mollusca",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 215274 records from 186 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033058-241126133413365/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.c.3601877_d6
title: Additional file 7: of Can baseline serum microRNAs predict response to TNF-alpha inhibitors in rheumatoid arthritis?

description: Cell subsets related to miRNA expression level, as measured by OpenArray or qPCR assay. In this additional analysis, miRNA expression levels are compared with FACS results on PBMC cell subsets. (XLSX 63Â kb)
DOI: 10.6084/m9.figshare.c.3601901_d1
title: Additional file 3: of Attractor landscape analysis of colorectal tumorigenesis and its reversion

description: The Boolean logic tables of nodes in the human signaling network. Each text file contains a logic table for individual signaling component of the human signaling network. The file name of each text file denotes a target molecule. In the files, each column except the last one displays the name of the source nodes and all possible activity conditions. The last column describes the activity state of the target nodes for each regulating condition of the source nodes. For the 197 nodes of the human signalling network, the 184 text files (except 13 input nodes) are included in Additional file 3. (ZIP 102 kb)
DOI: 10.6084/m9.figshare.c.3601904_d1
title: Additional file 1: of The prognostic utility of GRACE risk score in predictive cardiovascular event rate in STEMI patients with successful fibrinolysis and delay intervention in non PCI-capable hospital: a retrospective cohort study

description: Prognostic value of GRACE. The dataset for the prognostic value of GRACE risk score analysis. (XLSX 52 kb)
DOI: 10.35110/f42bf82f-11e9-4ee9-a628-556895dfd23c
title: Jeu de données drone acquises sur la Tourbière de Bernadouze (2016-06-23)

description: Données drones acquises à l'aide d'un drone de type eBee classic avec des capteurs RGB et multispectral (Multispec4). Acquisitions faites dans le cadre de l'OHM du Haut-Vicdessos. Données utilisées dans le cadre de la thèse de Thierry Erudel (2017) afin de valider des traitements de données Lidar et hyperspectrales ERUDEL Thierry,2014-2018 – Thèse en traitement d’image. Caractérisation de la biodiversité végétale en milieu montagnard et de piedmont par télédétection :apport des données hyperspectrales et lidar. Dir. X. Briottet,Co-dir. T. Houet,Institut supérieur de l'aéronautique et de l'espace / ONERA (Toulouse) - http://www.theses.fr/2018ESAE0018/document
DOI: 10.6084/m9.figshare.c.3601901_d2
title: Additional file 1: of Attractor landscape analysis of colorectal tumorigenesis and its reversion

description: The 688 links comprising the human signaling network. (XLS 111 kb)
DOI: 10.6084/m9.figshare.c.3601901_d4
title: Additional file 4: of Attractor landscape analysis of colorectal tumorigenesis and its reversion

description: The Matlab and Python source codes for mathematical simulations. (ZIP 1070 kb)
DOI: 10.6084/m9.figshare.c.3601901_d5
title: Additional file 2: of Attractor landscape analysis of colorectal tumorigenesis and its reversion

description: The Boolean logic descriptions of nodes in the human signaling network. (XLS 3607 kb)
DOI: 10.6084/m9.figshare.c.3601922_d1
title: Additional file 1: Table S1. of Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target

description: lists the top 100 RNAi target genes with their Tribolium iBeetle-numbers, Tc-genes and Drosophila orthologs. Table S2. lists the best 40 RNAi target genes with their Tribolium iBeetle-numbers, Tc-genes and Drosophila orthologs. Table S3. lists the number of surviving animals after injection with non-overlapping dsRNA fragments. Table S4. lists the number of surviving larvae after single and double RNAi treatments (total dsRNA concentration 0,5 ng/μl). Table S5. shows the sequences of the Tribolium orthologs of the RNAi target genes published by Baum et al. [15]. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3602414_d3
title: Additional file 3: of Metabolic characterization of the natural progression of chronic hepatitis B

description: Supplementary Table S2. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3602429_d1
title: MOESM1 of Effects of elevated CO2 on photosynthetic traits of native and invasive C3 and C4 grasses

description: Additional file 1. (a) Mean Âą SE for individual species across CO2 concentrations for responses measured at 7 and 14 weeks, (b) mean Âą SE for individual species across CO2 concentrations for responses measured at 14 weeks only.