cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5827386.v1
title: Supplementary Material for: Effect of Oridonin on Cytochrome P450 Expression and Activities in HepaRG Cell

description: Oridonin, the major terpene found in <i>Rabdosia rubescens</i>, is widely used as a dietary supplement or therapeutic drug. However, the effects of oridonin on major CYP450s are still unclear. As oridonin can enhance the effect of other clinical drugs, in this study, we investigated the influence of oridonin on CYP450s mRNA expression and its impact on activities in human HepaRG cell to evaluate the safety by studying its potential drug interaction. HepaRG cells were cultured with series concentrations of oridonin (1, 5, 10, and 20 μmol/L), and the major CYP450s mRNA and protein expression, as well as enzyme activities were analyzed by real-time polymerase chain reaction, Western blot analysis and UPLC-MS/MS-based metabolite assay. In general, ordonin has induced effects on the major member of CYP450s mRNA and protein expression, as well as on the enzyme activity in human HepaRG cells, especially on CYP3A4 and CYP2C9. To our knowledge, this is the first systematic research about the inductive effects of oridonin on the major member of CYP450s in human cell line. These results may provide at least partly of the basis for potential drug-drug interactions and oridonin should be used with caution to avoid potential risk.
DOI: 10.6084/m9.figshare.5827380
title: Supplementary Material for: Isoliquiritigenin Ameliorates Indomethacin-Induced Small Intestinal Damage by Inhibiting NOD-Like Receptor Family, Pyrin Domain-Containing 3 Inflammasome Activation

description: Activation of the NOD-Like Receptor Family, Pyrin Domain-Containing 3 (NLRP3) inflammasome, which consists of NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and pro-caspase-1, triggers pro-caspase-1 cleavage promoting the processing of pro-interleukin (IL)-1β into mature IL-1β, which is critical for the development of non-steroidal anti-inflammatory drug (NSAID)-induced enteropathy. We investigated the effects of isoliquiritigenin, a flavonoid derived from the roots of <i>Glycyrrhiza</i> species, on NSAID-induced small intestinal damage and the inflammasome activation. To induce enteropathy, mice were administered indomethacin by gavage with or without isoliquiritigenin pretreatment. Some mice received an intraperitoneal injection of recombinant murine IL-1β in addition to isoliquiritigenin and indomethacin. Indomethacin induced small intestinal damage and increased protein levels of cleaved caspase-1 and mature IL-1β in the small intestine. Treatment with 7.5 and 75 mg/kg isoliquiritigenin inhibited indomethacin-induced small intestinal damage by 40 and 56%, respectively. Isoliquiritigenin also inhibited the indomethacin-induced increase in cleaved caspase-1 and mature IL-1β protein levels, whereas it did not affect the mRNA expression of NLRP3, ASC, caspase-1, and IL-1β. Protection against intestinal damage in isoliquiritigenin-treated mice was completely abolished with exogenous IL-1β. NLRP3<sup>–/–</sup> and caspase-1<sup>–/–</sup> mice exhibited resistance to intestinal damage, and isoliquiritigenin treatment failed to inhibit the damage in NLRP3<sup>–/–</sup> and caspase-1<sup>–/–</sup> mice. Isoliquiritigenin prevents NSAID-induced small intestinal damage by inhibiting NLRP3 inflammasome activation.
DOI: 10.6084/m9.figshare.5827380.v1
title: Supplementary Material for: Isoliquiritigenin Ameliorates Indomethacin-Induced Small Intestinal Damage by Inhibiting NOD-Like Receptor Family, Pyrin Domain-Containing 3 Inflammasome Activation

description: Activation of the NOD-Like Receptor Family, Pyrin Domain-Containing 3 (NLRP3) inflammasome, which consists of NLRP3, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and pro-caspase-1, triggers pro-caspase-1 cleavage promoting the processing of pro-interleukin (IL)-1β into mature IL-1β, which is critical for the development of non-steroidal anti-inflammatory drug (NSAID)-induced enteropathy. We investigated the effects of isoliquiritigenin, a flavonoid derived from the roots of <i>Glycyrrhiza</i> species, on NSAID-induced small intestinal damage and the inflammasome activation. To induce enteropathy, mice were administered indomethacin by gavage with or without isoliquiritigenin pretreatment. Some mice received an intraperitoneal injection of recombinant murine IL-1β in addition to isoliquiritigenin and indomethacin. Indomethacin induced small intestinal damage and increased protein levels of cleaved caspase-1 and mature IL-1β in the small intestine. Treatment with 7.5 and 75 mg/kg isoliquiritigenin inhibited indomethacin-induced small intestinal damage by 40 and 56%, respectively. Isoliquiritigenin also inhibited the indomethacin-induced increase in cleaved caspase-1 and mature IL-1β protein levels, whereas it did not affect the mRNA expression of NLRP3, ASC, caspase-1, and IL-1β. Protection against intestinal damage in isoliquiritigenin-treated mice was completely abolished with exogenous IL-1β. NLRP3<sup>–/–</sup> and caspase-1<sup>–/–</sup> mice exhibited resistance to intestinal damage, and isoliquiritigenin treatment failed to inhibit the damage in NLRP3<sup>–/–</sup> and caspase-1<sup>–/–</sup> mice. Isoliquiritigenin prevents NSAID-induced small intestinal damage by inhibiting NLRP3 inflammasome activation.
DOI: 10.6084/m9.figshare.5827368
title: Supplementary Material for: Vascular Endothelial Growth Factor-A<sub>165</sub>b Restores Normal Glomerular Water Permeability in a Diphtheria-Toxin Mouse Model of Glomerular Injury

description: <b><i>Background/Aims:</i></b><i></i> Genetic cell ablation using the human diphtheria toxin receptor (hDTR) is a new strategy used for analysing cellular function. Diphtheria toxin (DT) is a cytotoxic protein that leaves mouse cells relatively unaffected, but upon binding to hDTR it ultimately leads to cell death. We used a podocyte-specific hDTR expressing (Pod-DTR) mouse to assess the anti-permeability and cyto-protective effects of the splice isoform vascular endothelial growth factor (VEGF-A<sub>165</sub>b). <b><i>Methods:</i></b><i></i> The Pod-DTR mouse was crossed with a mouse that over-expressed VEGF-A<sub>165</sub>b specifically in the podocytes (Neph-VEGF-A<sub>165</sub>b). Wild type (WT), Pod-DTR, Neph-VEGF-A<sub>165</sub>b and Pod-DTR X Neph-VEGF-A<sub>165</sub>b mice were treated with several doses of DT (1, 5, 100, and 1,000 ng/g bodyweight). Urine was collected and the glomerular water permeability (L<sub>p</sub>A/V<sub>i</sub>) was measured ex vivo after 14 days. Structural analysis and podocyte marker expression were also assessed. <b><i>Results:</i></b><i></i> Pod-DTR mice developed an increased glomerular L<sub>p</sub>A/V<sub>i</sub> 14 days after administration of DT (all doses), which was prevented when the mice over-expressed VEGF-A<sub>165</sub>b. No major structural abnormalities, podocyte ablation or albuminuria was observed in Pod-DTR mice, indicating this to be a mild model of podocyte disease. However, a change in expression and localisation of nephrin within the podocytes was observed, indicating disruption of the slit diaphragm in the Pod-DTR mice. This was prevented in the Pod-DTR X Neph-VEGF-A<sub>165</sub>b mice. <b><i>Conclusion:</i></b><i></i> Although only a mild model of podocyte injury, over-expression of the anti-permeability VEGF-A<sub>165</sub>b isoform in the podocytes of Pod-DTR mice had a protective effect. Therefore, this study further highlights the therapeutic potential of VEGF-A<sub>165</sub>b in glomerular disease.
DOI: 10.6084/m9.figshare.5827359
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v1
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v2
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v3
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v4
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v5
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v6
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v7
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v8
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v9
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v10
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827359.v11
title: BSDB-Newsletters

description: This is collection of newsletters of the British Society for Developmental Biology. An overview list can be found here: http://bsdb.org/about-us/bsdb-newsletters/<br>
DOI: 10.6084/m9.figshare.5827251
title: supplementary Table II

description: UBE2D4,TUBGCP3 and CENPO module function annotaion
DOI: 10.6084/m9.figshare.5827251.v1
title: supplementary Table II

description: UBE2D4,TUBGCP3 and CENPO module function annotaion
DOI: 10.6084/m9.figshare.5827215
title: Additional file 8: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: qRT-PCR primer sequences. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827215.v1
title: Additional file 8: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: qRT-PCR primer sequences. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827206
title: Additional file 6: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Functional annotation of DE transcripts between NILs. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5827206.v1
title: Additional file 6: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Functional annotation of DE transcripts between NILs. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.5827197
title: Additional file 5: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Transcription factors present in the 5A introgression. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.5827197.v1
title: Additional file 5: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Transcription factors present in the 5A introgression. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.5827188
title: Additional file 4: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Transcription factor binding sites identified in outside 5A DE transcripts. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5827188.v1
title: Additional file 4: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Transcription factor binding sites identified in outside 5A DE transcripts. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5827173
title: Additional file 2: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Enriched GO terms in the across time comparisons. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.5827173.v1
title: Additional file 2: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Enriched GO terms in the across time comparisons. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.5827164
title: Additional file 1: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Comparison of CSS and TGAC gene models. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5827164.v1
title: Additional file 1: of Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

description: Comparison of CSS and TGAC gene models. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.5827152
title: Additional file 9: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the SNP validation comparison results showing the number and percentages of SNPs with same position (POS-CONC) and genotype (GEN-CONC) from broiler and layer chickens of NGS and chip dataset. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827152.v1
title: Additional file 9: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the SNP validation comparison results showing the number and percentages of SNPs with same position (POS-CONC) and genotype (GEN-CONC) from broiler and layer chickens of NGS and chip dataset. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827146
title: Additional file 8: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the intolerant SNPs located within genes under selection (top 1%). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5827146.v1
title: Additional file 8: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the intolerant SNPs located within genes under selection (top 1%). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.5827143
title: Additional file 2: Table S1. of Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

description: List of species included in the reconstruction of the eight phylomes used in this study. Columns indicate, in this order, the species code for each species, the species name, the source for the protein and the coding DNA sequences, and the phylome in which the species was used (O. europaea var. europaea-215, F. excelsior-216, M. guttatus-217, S. indicum-218, U. gibba-219, S. miltiorrhiza-220, O. e. var. europaea-221, and O.e. var. sylvestris-222). Table S2. List of the GO terms enriched in the expanded protein families and at each evolutionary period as described in Fig. 1b. The first column shows the GO term, the second, the term level, the third, the p value, and the fourth, the term name. Table S3. List of parsimony scores for each of the different hypothesis shown in Additional file 9: Figure S8; and considering the two sets of trees with EST data. Nodes are named as shown in Fig. 3. Table S4. Syntenic regions between coffee and olive used in Fig. 4. In the first column, we can see the letter of the graph. The second and sixth columns show the scaffold names used in the graph (names starting with “C” are for coffee and “O” are for olive). The third and seventh columns show the scaffold names of the genome in coffee and olive, respectively. The fourth and fifth columns show the start and end of the region in coffee. The eighth and ninth columns show the start and end of the syntenic region in olive. (XLS 698 kb)
DOI: 10.6084/m9.figshare.5827143.v1
title: Additional file 2: Table S1. of Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

description: List of species included in the reconstruction of the eight phylomes used in this study. Columns indicate, in this order, the species code for each species, the species name, the source for the protein and the coding DNA sequences, and the phylome in which the species was used (O. europaea var. europaea-215, F. excelsior-216, M. guttatus-217, S. indicum-218, U. gibba-219, S. miltiorrhiza-220, O. e. var. europaea-221, and O.e. var. sylvestris-222). Table S2. List of the GO terms enriched in the expanded protein families and at each evolutionary period as described in Fig. 1b. The first column shows the GO term, the second, the term level, the third, the p value, and the fourth, the term name. Table S3. List of parsimony scores for each of the different hypothesis shown in Additional file 9: Figure S8; and considering the two sets of trees with EST data. Nodes are named as shown in Fig. 3. Table S4. Syntenic regions between coffee and olive used in Fig. 4. In the first column, we can see the letter of the graph. The second and sixth columns show the scaffold names used in the graph (names starting with “C” are for coffee and “O” are for olive). The third and seventh columns show the scaffold names of the genome in coffee and olive, respectively. The fourth and fifth columns show the start and end of the region in coffee. The eighth and ninth columns show the start and end of the syntenic region in olive. (XLS 698 kb)
DOI: 10.6084/m9.figshare.5827140
title: Additional file 1: of The progression rate of spinocerebellar ataxia type 2 changes with stage of disease

description: Database on the Brazilian SCA2 cohort, by Monte et al 2018, Orphanet Journal of Rare Diseases. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.5827140.v1
title: Additional file 1: of The progression rate of spinocerebellar ataxia type 2 changes with stage of disease

description: Database on the Brazilian SCA2 cohort, by Monte et al 2018, Orphanet Journal of Rare Diseases. (XLSX 224 kb)
DOI: 10.6084/m9.figshare.5827137
title: Additional file 7: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with enrichment analysis results including the enriched GO terms from genes located in top 1% regions under selection (INDEL dataset). The enrichment analysis was performed with GeneMANIA prediction server considering human database. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827137.v1
title: Additional file 7: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with enrichment analysis results including the enriched GO terms from genes located in top 1% regions under selection (INDEL dataset). The enrichment analysis was performed with GeneMANIA prediction server considering human database. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827125
title: Additional file 6: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with enrichment analysis results including the enriched GO terms from genes located in top 1% regions under selection (SNP dataset). The enrichment analysis was performed with GeneMANIA prediction server considering human database. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827125.v1
title: Additional file 6: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with enrichment analysis results including the enriched GO terms from genes located in top 1% regions under selection (SNP dataset). The enrichment analysis was performed with GeneMANIA prediction server considering human database. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5827122
title: Additional file 9: Tables S7 and S8. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Gene ontology analysis of gene located at proximity of the Trained (S6) or the Detrained (S7) DMRs. GO: Gene ontology term. FDR: False Discovery Rate. (ZIP 61Â kb)
DOI: 10.6084/m9.figshare.5827122.v1
title: Additional file 9: Tables S7 and S8. of Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

description: Gene ontology analysis of gene located at proximity of the Trained (S6) or the Detrained (S7) DMRs. GO: Gene ontology term. FDR: False Discovery Rate. (ZIP 61Â kb)
DOI: 10.6084/m9.figshare.5827110
title: Additional file 5: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the common putative genes under selection from SNP and INDEL based analyses. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.5827110.v1
title: Additional file 5: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the common putative genes under selection from SNP and INDEL based analyses. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.5827095
title: Additional file 3: Table S2. of Exploring traditional aus-type rice for metabolites conferring drought tolerance

description: Log2 ratios of Drought vs Well-Watered conditions per genotype and 2-way ANOVA. (XLSX 138Â kb)
DOI: 10.6084/m9.figshare.5827095.v1
title: Additional file 3: Table S2. of Exploring traditional aus-type rice for metabolites conferring drought tolerance

description: Log2 ratios of Drought vs Well-Watered conditions per genotype and 2-way ANOVA. (XLSX 138Â kb)
DOI: 10.6084/m9.figshare.5827092
title: Additional file 4: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the top six networks from frameshift and non-frameshift INDELs exclusively from the layer or broiler line. QIAGEN’s Ingenuity® Pathway Analysis (IPA®) software ( http://www.ingenuity.com/ ) with default parameters were used to find metabolic pathways of genes with relevant biological functions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.5827092.v1
title: Additional file 4: of Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

description: An excel file with the top six networks from frameshift and non-frameshift INDELs exclusively from the layer or broiler line. QIAGEN’s Ingenuity® Pathway Analysis (IPA®) software ( http://www.ingenuity.com/ ) with default parameters were used to find metabolic pathways of genes with relevant biological functions. (XLSX 10 kb)