cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8274305.v1
title: Additional file 2: of Difficulty in inferring microbial community structure based on co-occurrence network approaches

description: R source codes for generating datasets and for evaluating co-occurrence network performance. (ZIP 5 kb)
DOI: 10.6084/m9.figshare.8274248
title: Additional file 7: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: miRNA targets prediction. Section 1: miRNA targets detected in the Paspalum transcriptome reference and annotated after blastx on a rice peptide database (E-valâ â 50). Section 2: miRNA targets with or without differential expression between sexual and apomictic libraries, as detected in the Paspalum transcriptome reference: read coverage analysis and annotation. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8274248.v1
title: Additional file 7: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: miRNA targets prediction. Section 1: miRNA targets detected in the Paspalum transcriptome reference and annotated after blastx on a rice peptide database (E-valâ â 50). Section 2: miRNA targets with or without differential expression between sexual and apomictic libraries, as detected in the Paspalum transcriptome reference: read coverage analysis and annotation. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8274230
title: Additional file 4: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of miRNA detected in floral samples of sexual and apomictic P. notatum genotypes. Section 1. List of clusters harboring miRNAs detected in four references (P. notatum floral transcriptome, O. sativa genome, S. italica genome, S. bicolor genome) with ShortStack v.3.8.5. Section 2. BLAST SSEARCH of mature miRNAs sequences of P. notatum against MirBase. Section 3. edgeR expression analysis of clusters harbouring miRNAs detected using the above-mentioned four references. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8274224
title: Additional file 3: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of P. notatum floral transcripts harboring sRNA derived from apomictic and sexual libraries. Section 1: Number of small RNA reads from apomictic (Apo) and sexual (Sex) libraries mapping onto the Paspalum transcriptome reference. Section 2: List of the 1000 P. notatum transcripts with highest small RNA coverage. Section 3: Classification of the Paspalum annotated small RNA targets into ontology classes, according to Plant Structure Development Stage Ontologies ( www.planteome.org ). Section 4. Functional classification and PANTHER overrepresentation test for annotated small RNA targets. Section 5: edgeR analysis of small RNA reads mapped over the P. notatum reference transcriptome. (XLSX 6165 kb)
DOI: 10.6084/m9.figshare.8274230.v1
title: Additional file 4: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of miRNA detected in floral samples of sexual and apomictic P. notatum genotypes. Section 1. List of clusters harboring miRNAs detected in four references (P. notatum floral transcriptome, O. sativa genome, S. italica genome, S. bicolor genome) with ShortStack v.3.8.5. Section 2. BLAST SSEARCH of mature miRNAs sequences of P. notatum against MirBase. Section 3. edgeR expression analysis of clusters harbouring miRNAs detected using the above-mentioned four references. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8274224.v1
title: Additional file 3: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of P. notatum floral transcripts harboring sRNA derived from apomictic and sexual libraries. Section 1: Number of small RNA reads from apomictic (Apo) and sexual (Sex) libraries mapping onto the Paspalum transcriptome reference. Section 2: List of the 1000 P. notatum transcripts with highest small RNA coverage. Section 3: Classification of the Paspalum annotated small RNA targets into ontology classes, according to Plant Structure Development Stage Ontologies ( www.planteome.org ). Section 4. Functional classification and PANTHER overrepresentation test for annotated small RNA targets. Section 5: edgeR analysis of small RNA reads mapped over the P. notatum reference transcriptome. (XLSX 6165 kb)
DOI: 10.6084/m9.figshare.8274206
title: Additional file 1: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of annotated Paspalum floral transcripts involved in sRNA-directed pathways. Section 1. List of key rice genes involved in small RNA-directed pathways and their P. notatum homologs expressed in floral tissues. Section 2: Expression levels of floral P. notatum transcripts homologous to key genes involved in small RNA-directed pathways. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8274206.v1
title: Additional file 1: of Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum

description: Lists of annotated Paspalum floral transcripts involved in sRNA-directed pathways. Section 1. List of key rice genes involved in small RNA-directed pathways and their P. notatum homologs expressed in floral tissues. Section 2: Expression levels of floral P. notatum transcripts homologous to key genes involved in small RNA-directed pathways. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.8274158
title: Additional file 4: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S4. List of genes that were down regulated in Wt in ID as compared to IR growth conditions. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8274158.v1
title: Additional file 4: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S4. List of genes that were down regulated in Wt in ID as compared to IR growth conditions. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8274149
title: Additional file 3: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S3. List of genes that were upregulated in Wt in ID as compared to IR growth conditions. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8274146
title: Additional file 2: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S2. List of genes that were down regulated in TC in ID as compared to IR growth conditions. (XLSX 4349 kb)
DOI: 10.6084/m9.figshare.8274149.v1
title: Additional file 3: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S3. List of genes that were upregulated in Wt in ID as compared to IR growth conditions. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8274140
title: Additional file 1: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S1. List of genes that were upregulated in TC in ID as compared to IR growth conditions. (XLSX 4483 kb)
DOI: 10.6084/m9.figshare.8274146.v1
title: Additional file 2: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S2. List of genes that were down regulated in TC in ID as compared to IR growth conditions. (XLSX 4349 kb)
DOI: 10.6084/m9.figshare.8274140.v1
title: Additional file 1: of Global transcriptomic analyses of Salmonella enterica in Iron-depleted and Iron-rich growth conditions

description: Table S1. List of genes that were upregulated in TC in ID as compared to IR growth conditions. (XLSX 4483 kb)
DOI: 10.6084/m9.figshare.8274056
title: Additional file 9: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpGs differently methylated between Duroc and PiNN and the transcripts close to these CpGs (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8274056.v1
title: Additional file 9: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpGs differently methylated between Duroc and PiNN and the transcripts close to these CpGs (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8274050
title: Additional file 8: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between PiNN and PiPP (XLSX 89 kb)
DOI: 10.6084/m9.figshare.8274044
title: Additional file 7: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Duroc and PiPP (XLSX 179 kb)
DOI: 10.6084/m9.figshare.8274050.v1
title: Additional file 8: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between PiNN and PiPP (XLSX 89 kb)
DOI: 10.6084/m9.figshare.8274044.v1
title: Additional file 7: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Duroc and PiPP (XLSX 179 kb)
DOI: 10.6084/m9.figshare.8274038
title: Additional file 6: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Duroc and PiNN (XLSX 180 kb)
DOI: 10.6084/m9.figshare.8274032
title: Additional file 5: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and PiNN (XLSX 123 kb)
DOI: 10.6084/m9.figshare.8274038.v1
title: Additional file 6: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Duroc and PiNN (XLSX 180 kb)
DOI: 10.6084/m9.figshare.8274023
title: Additional file 4: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and PiPP (XLSX 111 kb)
DOI: 10.6084/m9.figshare.8274032.v1
title: Additional file 5: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and PiNN (XLSX 123 kb)
DOI: 10.6084/m9.figshare.8274023.v1
title: Additional file 4: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and PiPP (XLSX 111 kb)
DOI: 10.6084/m9.figshare.8274017
title: Additional file 3: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and Duroc (XLSX 108 kb)
DOI: 10.6084/m9.figshare.8274011
title: Additional file 2: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Primers sequence for pyrosequence and qPCR (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8274017.v1
title: Additional file 3: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: CpG sites significant at FDR 25% between Dupi and Duroc (XLSX 108 kb)
DOI: 10.6084/m9.figshare.8274005
title: Additional file 1: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Phenotype of the animals used in the study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8274011.v1
title: Additional file 2: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Primers sequence for pyrosequence and qPCR (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8274005.v1
title: Additional file 1: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Phenotype of the animals used in the study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8273996
title: Additional file 10: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Genes annotated from the selected CpG (different methylation level &gt; 25% and significant at FDR
DOI: 10.6084/m9.figshare.8273996.v1
title: Additional file 10: of Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

description: Genes annotated from the selected CpG (different methylation level &gt; 25% and significant at FDR
DOI: 10.6084/m9.figshare.8273960
title: Additional file 3: of Unravelling the sex- and age-specific impact of poaching mortality with multievent modeling

description: Dataset (.csv) used for analysis. (CSV 4 kb)
DOI: 10.6084/m9.figshare.8273951
title: Additional file 6: of Deferasirox drives ROS-mediated differentiation and induces interferon-stimulated gene expression in human healthy haematopoietic stem/progenitor cells and in leukemia cells

description: Table S2. List of up- and downregulated genes in DFO-treated compared to DFX-untreated cells. (XLS 12 kb)
DOI: 10.6084/m9.figshare.8273960.v1
title: Additional file 3: of Unravelling the sex- and age-specific impact of poaching mortality with multievent modeling

description: Dataset (.csv) used for analysis. (CSV 4 kb)
DOI: 10.6084/m9.figshare.8273945
title: Additional file 5: of Deferasirox drives ROS-mediated differentiation and induces interferon-stimulated gene expression in human healthy haematopoietic stem/progenitor cells and in leukemia cells

description: Table S1. List of up- and downregulated genes in DFX-treated compared to DFX-untreated cells. (XLS 24 kb)
DOI: 10.6084/m9.figshare.8273951.v1
title: Additional file 6: of Deferasirox drives ROS-mediated differentiation and induces interferon-stimulated gene expression in human healthy haematopoietic stem/progenitor cells and in leukemia cells

description: Table S2. List of up- and downregulated genes in DFO-treated compared to DFX-untreated cells. (XLS 12 kb)
DOI: 10.6084/m9.figshare.8273945.v1
title: Additional file 5: of Deferasirox drives ROS-mediated differentiation and induces interferon-stimulated gene expression in human healthy haematopoietic stem/progenitor cells and in leukemia cells

description: Table S1. List of up- and downregulated genes in DFX-treated compared to DFX-untreated cells. (XLS 24 kb)
DOI: 10.6084/m9.figshare.8273891
title: MOESM1 of Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data

description: Additional file 1. Listing of derivatives that were predicted by PROXIMAL and had a chemical ID in PubChem.
DOI: 10.6084/m9.figshare.8273891.v1
title: MOESM1 of Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data

description: Additional file 1. Listing of derivatives that were predicted by PROXIMAL and had a chemical ID in PubChem.
DOI: 10.6084/m9.figshare.8273864
title: Identification of mechanisms defining resistance and susceptibility of Camellia plants to necrotrophic petal blight disease

description: Supplementary files for the PhD thesis: Kondratev N. (2019) "Identification of mechanisms defining resistance and susceptibility of <i>Camellia</i> plants to necrotrophic petal blight disease". Massey University, New Zealand<br>Supplementary File 1 | Assembled <i>Camellia lutchuensis</i> transcriptomeSupplementary File 2 | Assembled <i>Camellia</i> ‘Nicky Crisp’ transcriptomeSupplementary File 3 | Assembled <i>Ciborinia</i> camelliae transcriptomeSupplementary File 4 | Annotation and cluster analysis results of <i>C. lutchuensis</i> differentially expressed transcriptsSupplementary File 5 | Results of GO enrichment analysis of <i>C. lutchuensis</i> expression clustersSupplementary File 6 | STRING mapping results of <i>C. lutchuensis</i> upregulated transcript clustersSupplementary File 7 | Differentially-expressed phenylpropanoid genes of <i>C. lutchuensis</i>Supplementary File 8 | Secreted proteins of <i>C. camelliae</i> and <i>Camellia ‘Nicky Crisp’</i>Supplementary File 9 | List of <i>C. camelliae</i> transcripts upregulated at 6 hpi of incompatible interaction with <i>C. lutchuensis</i><br>
DOI: 10.6084/m9.figshare.8273876
title: SNP.rar

description: SNP raw data <i></i><i></i><br><i></i>
DOI: 10.6084/m9.figshare.8273864.v1
title: Identification of mechanisms defining resistance and susceptibility of Camellia plants to necrotrophic petal blight disease

description: Supplementary files for the PhD thesis: Kondratev N. (2019) "Identification of mechanisms defining resistance and susceptibility of <i>Camellia</i> plants to necrotrophic petal blight disease". Massey University, New Zealand<br>Supplementary File 1 | Assembled <i>Camellia lutchuensis</i> transcriptomeSupplementary File 2 | Assembled <i>Camellia</i> ‘Nicky Crisp’ transcriptomeSupplementary File 3 | Assembled <i>Ciborinia</i> camelliae transcriptomeSupplementary File 4 | Annotation and cluster analysis results of <i>C. lutchuensis</i> differentially expressed transcriptsSupplementary File 5 | Results of GO enrichment analysis of <i>C. lutchuensis</i> expression clustersSupplementary File 6 | STRING mapping results of <i>C. lutchuensis</i> upregulated transcript clustersSupplementary File 7 | Differentially-expressed phenylpropanoid genes of <i>C. lutchuensis</i>Supplementary File 8 | Secreted proteins of <i>C. camelliae</i> and <i>Camellia ‘Nicky Crisp’</i>Supplementary File 9 | List of <i>C. camelliae</i> transcripts upregulated at 6 hpi of incompatible interaction with <i>C. lutchuensis</i><br>
DOI: 10.6084/m9.figshare.8273774
title: Individuals have unique muscle activation signatures as revealed during gait and pedaling

description: Raw electromyographic (EMG) data collected during walking on a treadmill (1.11 m/s) and pedalling on a cycloergometer (four different submaximal intensities: 10% and 15% of maximal power output; 80 and 150 Watts).Data are available for 80 participants (day 1). Reproducibility data (day 2) are available for 53 of these 80 participants.<br>
DOI: 10.6084/m9.figshare.8273816
title: A soil phosphorus dynamics (SPD) model

description: The dynamics of soil phosphorus (P) control its bioavailability. Yet, it remains a challenge to quantify soil P dynamics. Here, we developed a soil P dynamics (SPD) model. We then assimilated eight datasets of 426-day changes in Hedley P fractions into the SPD model, to quantify the dynamics of six major P pools in eight soil samples that are representative of a wide type of soils. The performance of our SPD model was better for labile P, secondary mineral P, and occluded P than for non-occluded organic P (Po) and primary mineral P. All parameters describing soil P dynamics were approximately constrained by the datasets. The average turnover rates were labile P 0.040 g g<sup>-1</sup> d<sup>-1</sup>, non-occluded Po 0.051 g g<sup>-1</sup> d<sup>-1</sup>, secondary mineral P 0.023 g g<sup>-1</sup> d<sup>-1</sup>, primary mineral P 0.00088 g g<sup>-1</sup> d<sup>-1</sup>, occluded Po 0.0066 g g<sup>-1</sup> d<sup>-1</sup>, and occluded inorganic P 0.0065 g g<sup>-1</sup> d<sup>-1</sup>, in the greenhouse environment studied. Labile P was transferred on average more to non-occluded Po (transfer coefficient of 0.42) and secondary mineral P (0.38) than to plants (0.20). Soil pH and organic C concentration were the key soil properties regulating the competition for P between plants and soil secondary minerals. The turnover rate of labile P was positively correlated with that of non-occluded Po and secondary mineral P. The pool size of labile P was most sensitive to its turnover rate. Overall, we suggest data assimilation can contribute significantly to an improved understanding of soil P dynamics.<br>Paper on this data and model is published as follows: Hou, E., Lu, X., Jiang, L., Wen, D. & Luo, Y. Quantifying soil phosphorus dynamics: a data assimilation approach. Journal of Geophysical Research: Biogeosciences 124, 2159-2173 (2019).
DOI: 10.6084/m9.figshare.8273765
title: Biotin attenuation of oxidative stress, mitochondrial dysfunction, lipid metabolism alteration and 7β-hydroxycholesterol-induced cell death in 158N murine oligodendrocytes

description: Mitochondrial dysfunction and oxidative stress are involved in neurodegenerative diseases associated with an enhancement of lipid peroxidation products such as 7β-hydroxycholesterol (7β-OHC). It is, therefore, important to study the ability of 7β-OHC to trigger mitochondrial defects, oxidative stress, metabolic dysfunctions and cell death, which are hallmarks of neurodegeneration, and to identify cytoprotective molecules. The effects of biotin were evaluated on 158N murine oligodendrocytes, which are myelin synthesizing cells, exposed to 7β-OHC (50 µM) with or without biotin (10 and 100 nM) or α-tocopherol (positive control of cytoprotection). The effects of biotin on 7β-OHC activities were determined using different criteria: cell adhesion; plasma membrane integrity; redox status. The impact on mitochondria was characterized by the measurement of transmembrane mitochondrial potential (ΔΨm), reactive oxygen species (ROS) overproduction, mitochondrial mass, quantification of cardiolipins and organic acids. Sterols and fatty acids were also quantified. Cell death (apoptosis, autophagy) was characterized by the enumeration of apoptotic cells, caspase-3 activation, identification of autophagic vesicles, and activation of LC3-I into LC3-II. Biotin attenuates 7β-OHC-induced cytotoxicity: loss of cell adhesion was reduced; antioxidant activities were normalized. ROS overproduction, protein and lipid oxidation products were decreased. Biotin partially restores mitochondrial functions: attenuation of the loss of ΔΨm; reduced levels of mitochondrial O<sub>2</sub><sup>•−</sup> overproduction; normalization of cardiolipins and organic acid levels. Biotin also normalizes cholesterol and fatty acid synthesis, and prevents apoptosis and autophagy (oxiapoptophagy). Our data support that biotin, which prevents oligodendrocytes damages, could be useful in the treatment of neurodegeneration and demyelination.