cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19933079.v1
title: Additional file 1 of Gut microbiome mediates the protective effects of exercise after myocardial infarction

description: Additional file 1: Table S1. Data production of 49 samples in Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S2. Alpha Diversity index among Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S3. The difference of Alpha Diversity index among Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S4. Relative abundance profile at the phylum level among Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S5. Relative abundance profile at the genus level among Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S6. Detailed information of genera differently enriched across Sham+Control and MI+Control. Table S7. Detailed information of genera differently enriched across MI+Control and MI+Run. Table S8. Alpha Diversity index among MI+ABX, MI+ABX+Control, MI+1/4ABX+Control and MI+Untreated+Control. Table S9. The difference of Alpha Diversity index among MI+ABX, MI+ABX+Control, MI+1/4ABX+Control and MI+Untreated+Control. Table S10. Alpha Diversity index among MI+ABX+Run, MI+1/4ABX+Run and MI+Untreated+Run. Table S11. The difference of Alpha Diversity index among MI+ABX+Run, MI+1/4ABX+Run and MI+Untreated+Run. Table S12. Relative abundance profile at the phylum level among MI+ABX, MI+ABX+Control, MI+1/4ABX+Control and MI+Untreated+Control. Table S13. Relative abundance profile at the phylum level among MI+ABX+Run, MI+1/4ABX+Run and MI+Untreated+Run. Table S14. Detailed information of genera differently enriched across MI+ABX+Run, MI+1/4ABX+Run and MI+Untreated+Run. Table S15. Relative abundance profile at the phylum level among MI+ABX+PBS, MI+ABX+FMT(MI+Control) and MI+ABX+FMT(MI+Run). Table S16. Relative abundance profile at the genus level among MI+ABX+PBS, MI+ABX+FMT(MI+Control) and MI+ABX+FMT(MI+Run). Table S17. Quantitative data of 116 metabolites in Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S18. The relative abundance of each metabolite classes in Sham+Control, MI+Control, Sham+Run, and MI+Run. Table S19. Detailed information of Univariate Statistics across Sham+Control and MI+Control. Table S20..Detailed information of Univariate Statistics across Sham+Control and Sham+RUN. Table S21. Detailed information of 42 metabolites differently enriched across Sham+Control and MI+Control. Table S22. Detailed information of 37 metabolites differently enriched across MI+Control and MI+Run. Table S23. Detailed information of metabolites pathways analysis across MI+Control and MI+Run. Table S24. Detailed information of metabolites pathways on network across MI+Control and MI+Run. Table S25. Detailed information of pathways analysis across Sham+Control and MI+Control. Table S26. Detailed information of metabolites metabolites pathways on network across Sham+Control and MI+Control. Table S27. Detailed information of pathways analysis across Sham+Control and Sham+Run. Table S28. Detailed information of metabolites metabolites pathways on network across Sham+Control and Sham+Run. Table S29. Detailed information of the relationship between metabolites and the top 50 genera
DOI: 10.6084/m9.figshare.19933125
title: Additional file 10 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 10: Table S6. GO terms associated with genes with increased expression in the mutant versus WT at day 5 and H3K27me3 at day 0. Enriched biological processes, cellular components, molecular functions, and MeSH disease terms are shown with the p-value/adj. p-value (FDR), genes observed versus expected, and term-associated genes.
DOI: 10.6084/m9.figshare.19933128
title: Additional file 11 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 11: Table S7. GO terms associated with genes with increased expression in the mutant versus WT at day 5, H3K27me3 at day 0, and loss of DNA methylation in the mutant at day 5. Enriched biological processes, cellular components, molecular functions, and MeSH disease terms are shown with the p-value/adj. p-value (FDR), genes observed versus expected, and term-associated genes.
DOI: 10.6084/m9.figshare.19933125.v1
title: Additional file 10 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 10: Table S6. GO terms associated with genes with increased expression in the mutant versus WT at day 5 and H3K27me3 at day 0. Enriched biological processes, cellular components, molecular functions, and MeSH disease terms are shown with the p-value/adj. p-value (FDR), genes observed versus expected, and term-associated genes.
DOI: 10.6084/m9.figshare.19933131
title: Additional file 12 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 12: Table S8. Concordance in gene expression patterns between our human embryonic stem cells with H3K27M mutation and DIPG tumors involving H3K27M mutation. (A) Pathway enrichment analysis for concordant differentially regulated genes in H3K27M versus WT cells at day 5 and DIPG tumor versus normal brain tissue samples. (B) List of concordant differentially regulated genes (139 genes) in H3K27M versus WT cells at day 5 and DIPG tumor versus normal brain tissue samples.
DOI: 10.6084/m9.figshare.19933128.v1
title: Additional file 11 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 11: Table S7. GO terms associated with genes with increased expression in the mutant versus WT at day 5, H3K27me3 at day 0, and loss of DNA methylation in the mutant at day 5. Enriched biological processes, cellular components, molecular functions, and MeSH disease terms are shown with the p-value/adj. p-value (FDR), genes observed versus expected, and term-associated genes.
DOI: 10.6084/m9.figshare.19933131.v1
title: Additional file 12 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 12: Table S8. Concordance in gene expression patterns between our human embryonic stem cells with H3K27M mutation and DIPG tumors involving H3K27M mutation. (A) Pathway enrichment analysis for concordant differentially regulated genes in H3K27M versus WT cells at day 5 and DIPG tumor versus normal brain tissue samples. (B) List of concordant differentially regulated genes (139 genes) in H3K27M versus WT cells at day 5 and DIPG tumor versus normal brain tissue samples.
DOI: 10.6084/m9.figshare.19933137
title: Additional file 2 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 2: Table S1. Biological replicates and clonal lines used. (A) Biological replicate experiments performed, and clones used for each biological replicate experiment are shown. Results obtained for the wild type (WT) H1 hESC line were compared with at least two different clonal H1 derivatives with CRISPR-mediated introduction of the H3K27M mutation, across 3-6 biological replicate experiments, except for ChIP-seq, which involved H3K27M clone 1 versus WT comparisons. (B) ELDA assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (C) Titer-Glo assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (D-L) Protein assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (M-O) Scorecard assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (P) RT-qPCR assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (Q) Positive and negative control primer pairs used for DNA methylation analysis.
DOI: 10.6084/m9.figshare.19933137.v1
title: Additional file 2 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 2: Table S1. Biological replicates and clonal lines used. (A) Biological replicate experiments performed, and clones used for each biological replicate experiment are shown. Results obtained for the wild type (WT) H1 hESC line were compared with at least two different clonal H1 derivatives with CRISPR-mediated introduction of the H3K27M mutation, across 3-6 biological replicate experiments, except for ChIP-seq, which involved H3K27M clone 1 versus WT comparisons. (B) ELDA assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (C) Titer-Glo assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (D-L) Protein assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (M-O) Scorecard assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (P) RT-qPCR assay: biological replicate experiments performed, and clones used for each biological replicate experiment as well as individual data values are shown. (Q) Positive and negative control primer pairs used for DNA methylation analysis.
DOI: 10.6084/m9.figshare.19933143
title: Additional file 4 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 4: Table S2. Transcriptomic analysis of differential gene expression in the K27M (mutant) versus wild type cells. Differentially expressed genes in clusters a-e are shown, with their fold changes and p-value/adjusted p-value. Final sheet shows differential gene expression (log2 fold change) and adjusted p-values for each pairwise sample comparison.
DOI: 10.6084/m9.figshare.19933143.v1
title: Additional file 4 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 4: Table S2. Transcriptomic analysis of differential gene expression in the K27M (mutant) versus wild type cells. Differentially expressed genes in clusters a-e are shown, with their fold changes and p-value/adjusted p-value. Final sheet shows differential gene expression (log2 fold change) and adjusted p-values for each pairwise sample comparison.
DOI: 10.6084/m9.figshare.19933155.v1
title: Additional file 8 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 8: Table S4. ChIP-seq analysis demonstrates widespread loss of H3K27me3 in H3K27M mutant cells. (A) Numbers of peaks meeting each criterion, (B) all peaks obtained in either H3K27M mutant or WT cells, and those peaks that were unique (non-intersecting) between the two sample types. (C) Genes associated with H3K27me3 peaks that were unique to the WT sample. (D-F) GO terms associated with genes that were unique to the WT sample. (G) Genes associated with H3K27me3 peaks that were unique to the H3K27M mutant sample. (H-J) GO terms associated with genes that were unique to the mutant sample.
DOI: 10.6084/m9.figshare.19933155
title: Additional file 8 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 8: Table S4. ChIP-seq analysis demonstrates widespread loss of H3K27me3 in H3K27M mutant cells. (A) Numbers of peaks meeting each criterion, (B) all peaks obtained in either H3K27M mutant or WT cells, and those peaks that were unique (non-intersecting) between the two sample types. (C) Genes associated with H3K27me3 peaks that were unique to the WT sample. (D-F) GO terms associated with genes that were unique to the WT sample. (G) Genes associated with H3K27me3 peaks that were unique to the H3K27M mutant sample. (H-J) GO terms associated with genes that were unique to the mutant sample.
DOI: 10.6084/m9.figshare.19933158
title: Additional file 9 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 9: Table S5. Analysis of differential DNA methylation in H3K27M mutant versus WT cells. (A) DNA methylation peaks gained in the H3K27M mutant versus WT samples at day 0. (B-D) GO terms associated with day 0 H3K27M mutant gained peak-associated genes. (E) DNA methylation peaks lost in the mutant vs WT samples at day 0. (F-H) GO terms associated with day 0 mutant lost peak-associated genes. (I) DNA methylation peaks gained in the mutant vs WT samples at day 5. (J-L) GO terms associated with day 5 mutant gained peak-associated genes. (M) DNA methylation peaks lost in the mutant vs WT samples at day 5. (N-P) GO terms associated with day 5 mutant lost peak-associated genes.
DOI: 10.6084/m9.figshare.19933158.v1
title: Additional file 9 of The H3K27M mutation alters stem cell growth, epigenetic regulation, and differentiation potential

description: Additional file 9: Table S5. Analysis of differential DNA methylation in H3K27M mutant versus WT cells. (A) DNA methylation peaks gained in the H3K27M mutant versus WT samples at day 0. (B-D) GO terms associated with day 0 H3K27M mutant gained peak-associated genes. (E) DNA methylation peaks lost in the mutant vs WT samples at day 0. (F-H) GO terms associated with day 0 mutant lost peak-associated genes. (I) DNA methylation peaks gained in the mutant vs WT samples at day 5. (J-L) GO terms associated with day 5 mutant gained peak-associated genes. (M) DNA methylation peaks lost in the mutant vs WT samples at day 5. (N-P) GO terms associated with day 5 mutant lost peak-associated genes.
DOI: 10.6084/m9.figshare.17012411
title: Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

description: <br> For more details see DOI: 10.1080/19490976.2022.2083419 <br> 16S rRNA gene amplicon V3-V4 sequencing performed on Illumina Mi-Seq with Nextera XT kit, processed with QIIME pipeline. Gut mucosa samples at 6 positions along the gut of adult, treatment-naive IBD and IBS patients.<br>
DOI: 10.6084/m9.figshare.17012558
title: Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

description: <br> For more details see DOI: 10.1080/19490976.2022.2083419 <br> 16S rRNA gene amplicon V3-V4 sequencing performed on Illumina Mi-Seq with Nextera XT kit, processed with QIIME pipeline. Faecal and gut mucosa samples of adult, treatment-naive IBD and IBS patients, as well as faecal samples of healthy volunteers.<br>
DOI: 10.6084/m9.figshare.17012411.v1
title: Mucosal Microbiota is Stable along the Gut and Independent of Localized Inflammation Status in Newly Diagnosed, Treatment-naïve Adult Inflammatory Bowel Disease Patients

description: 16S rRNA gene amplicon V3-V4 sequencing performed on Illumina Mi-Seq with Nextera XT kit, processed with QIIME pipeline. Gut mucosa samples at 6 positions along the gut of adult, treatment-naive IBD and IBS patients. <br><br>For more details see DOI: XXX<br>
DOI: 10.6084/m9.figshare.17012558.v1
title: Newly Diagnosed, Treatment-naïve Adult Crohn’s Disease, Ulcerative Colitis and Irritable Bowel Syndrome Patients are Better Differentiated by Mucosal than Fecal Microbiota

description: 16S rRNA gene amplicon V3-V4 sequencing performed on Illumina Mi-Seq with Nextera XT kit, processed with QIIME pipeline. Faecal and gut mucosa samples of adult, treatment-naive IBD and IBS patients, as well as faecal samples of healthy volunteers. <br><br>For more details see DOI: XXX
DOI: 10.6084/m9.figshare.19698352
title: Data and R scripts used in Pouta et al. 2022. Partitioning of space among trees in an old-growth spruce forest in subarctic Fennoscandia. Front. For. Glob. Change 5:817248.

description: Data from a large (8.8 ha) fully mapped plot in a Norway spruce dominated old-growth forest, and R scripts used in the analyses of the data.
DOI: 10.6084/m9.figshare.19933388
title: Evaluation of project promoting health in adolescents

description: OBJECTIVE Evaluate a program promoting exercise and healthy eating among adolescents. METHODS This was a cross-sectional study of 911 adolescents aged 13 to 18 years old in public schools in Goiania, Midwestern Brazil, 2010. The participants were divided into two groups: intervention (schools taking part in the Healthy Living, project) and control. The following were deemed to be exercise: displacement, physical education classes in school, physical activity outside school, and leisure-time physical activity. Pupils who totaled 300 or more minutes per week were defined as active. Consuming protective foods five or more days a week was classified as adequate intake. Statistical analyses made using the Chi-square test. RESULTS Most adolescents were identified as inactive or insufficiently active, 65.7% in the Intervention Group and 65.2% Control Group, showing no significant differences between groups, and with higher prevalence among girls. Slightly more than half of adolescents consumed health protective foods 5 or more days a week, 56.6% in the Intervention Group and 50.4% in the Control Group (p = 0.373). CONCLUSIONS There were no differences between schools in the Intervention Group and Control Group with regard to food choices and physical activity. This indicates that the Healthy Living project needs to be reevaluated to improve the effectiveness in achieving its objectives.
DOI: 10.6084/m9.figshare.19933388.v1
title: Evaluation of project promoting health in adolescents

description: OBJECTIVE Evaluate a program promoting exercise and healthy eating among adolescents. METHODS This was a cross-sectional study of 911 adolescents aged 13 to 18 years old in public schools in Goiania, Midwestern Brazil, 2010. The participants were divided into two groups: intervention (schools taking part in the Healthy Living, project) and control. The following were deemed to be exercise: displacement, physical education classes in school, physical activity outside school, and leisure-time physical activity. Pupils who totaled 300 or more minutes per week were defined as active. Consuming protective foods five or more days a week was classified as adequate intake. Statistical analyses made using the Chi-square test. RESULTS Most adolescents were identified as inactive or insufficiently active, 65.7% in the Intervention Group and 65.2% Control Group, showing no significant differences between groups, and with higher prevalence among girls. Slightly more than half of adolescents consumed health protective foods 5 or more days a week, 56.6% in the Intervention Group and 50.4% in the Control Group (p = 0.373). CONCLUSIONS There were no differences between schools in the Intervention Group and Control Group with regard to food choices and physical activity. This indicates that the Healthy Living project needs to be reevaluated to improve the effectiveness in achieving its objectives.
DOI: 10.6084/m9.figshare.19933389
title: Vitamin A deficiency and associated factors in children in urban areas

description: OBJECTIVE To estimate the prevalence of vitamin A deficiency and its associated factors in children. METHODS A cross-sectional population-based study, involving 1,211 children of both sexes, aged between six and 59 months old, was carried out in the urban zone of 9 cities in the state of Paraiba, Northeastern Brazil. Vitamin A status was assessed by serum retinol levels (high performance liquid chromatography – HPLC) and subclinical infection was assessed by C-reactive protein concentrations. Socioeconomic, demographic and sanitation conditions, as well as vitamin A supplement intake, were also evaluated. Children with serum retinol concentrations RESULTS The prevalence of vitamin A deficiency was 21.8% (95%CI 19.6;24.2), showing an association with subclinical infection and lack of indoor plumbing. The prevalence of vitamin A deficiency was 21.8% (95%CI 19.6;24.2). After adjustment, vitamin A deficiency was found to be linked with subclinical infection and lack of indoor plumbing. Vitamin A deficiency was four times higher (CI95% 1.49;10.16) in children with subclinical infection whose homes were without indoor plumbing, compared to children who were not infected and with indoor plumbing in their homes. CONCLUSIONS Despite activities aimed at the prevention and control of vitamin A deficiency, hypovitaminosis A, remains a public health concern among children under five.
DOI: 10.6084/m9.figshare.19933389.v1
title: Vitamin A deficiency and associated factors in children in urban areas

description: OBJECTIVE To estimate the prevalence of vitamin A deficiency and its associated factors in children. METHODS A cross-sectional population-based study, involving 1,211 children of both sexes, aged between six and 59 months old, was carried out in the urban zone of 9 cities in the state of Paraiba, Northeastern Brazil. Vitamin A status was assessed by serum retinol levels (high performance liquid chromatography – HPLC) and subclinical infection was assessed by C-reactive protein concentrations. Socioeconomic, demographic and sanitation conditions, as well as vitamin A supplement intake, were also evaluated. Children with serum retinol concentrations RESULTS The prevalence of vitamin A deficiency was 21.8% (95%CI 19.6;24.2), showing an association with subclinical infection and lack of indoor plumbing. The prevalence of vitamin A deficiency was 21.8% (95%CI 19.6;24.2). After adjustment, vitamin A deficiency was found to be linked with subclinical infection and lack of indoor plumbing. Vitamin A deficiency was four times higher (CI95% 1.49;10.16) in children with subclinical infection whose homes were without indoor plumbing, compared to children who were not infected and with indoor plumbing in their homes. CONCLUSIONS Despite activities aimed at the prevention and control of vitamin A deficiency, hypovitaminosis A, remains a public health concern among children under five.
DOI: 10.6084/m9.figshare.19933409
title: Brazilian adaptation of the questionnaire to assess adherence to treatment for arterial hypertension

description: OBJECTIVE To describe the cross-cultural adaptation of the questionnaire evaluating adhesion to treatment for arterial hypertension from its original Spanish version to a Portuguese version, to be applied in Brazil. METHODS In order to establish conceptual, semantic and operational equivalents of the items, two independent translations to Portuguese, and two back-translations into Spanish were performed. The translations and back-translations were assessed for changes in referential and general meanings. The synthesis of the translations was applied in pre-tests with patients with arterial hypertension and/or diabetes, which were important to identify different problems and confirm earlier decisions. RESULTS In general, the second translation and back translation were evaluated more positively because the translation process did not affect the meanings in five of the twelve items of the questionnaire. Operational changes were made and a vignette with response options and an example included in the instrument facilitated application in interviews. CONCLUSIONS The results obtained in the process of evaluating the items’ conceptual, semantic and operational equivalence allowed the construction of a Portuguese version of the MBG questionnaire to assess adherence to treatment which can be applied in the Brazilian context.