cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7120841.v3
title: DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy

description: Ionizing radiation (IR) causes DNA double-strand breaks and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation (IR); we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (cathepsins and Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using a protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
DOI: 10.6084/m9.figshare.7120841.v2
title: DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy

description: Ionizing radiation (IR) causes DNA double-strand breaks (DSBs) and activates a versatile cellular response regulating DNA repair, cell-cycle progression, transcription, DNA replication and other processes. In recent years proteomics has emerged as a powerful tool deepening our understanding of this multifaceted response. In this study we use SILAC-based proteomics to specifically investigate dynamic changes in cytoplasmic protein abundance after ionizing radiation; we present in-depth bioinformatics analysis and show that levels of proteins involved in autophagy (cathepsins and other lysosomal proteins), proteasomal degradation (Ubiquitin-related proteins), energy metabolism (mitochondrial proteins) and particularly translation (ribosomal proteins and translation factors) are regulated after cellular exposure to ionizing radiation. Downregulation of no less than 68 ribosomal proteins shows rapid changes in the translation pattern after IR. Additionally, we provide evidence of compartmental cytosol-nuclear translocation of numerous DNA damage related proteins using protein correlation profiling. In conclusion, these results highlight unexpected cytoplasmic processes actively orchestrated after genotoxic insults and protein translocation from the cytoplasm to the nucleus as a fundamental regulatory mechanism employed to aid cell survival and preservation of genome integrity.
DOI: 10.6084/m9.figshare.7120808
title: MW WX ZH Manuscript Data

description: This file contains the minimum dataset for Wu et al. accepted to PLoS-One in September, 2018, titled "Similar Image Retrieval in Large-scale Trademark Databases based on Regional and Boundary Fusion Feature".The design of the experiment is fully explained in the manuscript. The database of trademark images including 5 image dataset folders : 1.CE-Shape-1, 2.100Class,3.geometry defor, 4.TrademarkAffine, and 5.TrademarkTransform. <br>1.CE-SHAPE-1 dataset containing 1400 MPEG-7 core experimental shape.2.100Class dataset containing 100 trademark images which were used as query samples. 3.geometry defor dataset was used for trademark geometry deformation experiment in this study, and the geometric transformations include shrinkage, spheroidization, torsion, and corrugation. 4.TrademarkAffine dataset was used for trademark affine transformation experiments in this study. Each image is processed with any combination of the transformations (Translation, Scaling, Rotate) to obtain 50 similar images of the original image respectively. 5.TrademarkTransform dataset was used for trademark geometry deformation experiment in this study.
DOI: 10.6084/m9.figshare.7120778
title: Identification of key genes and functional coexpression modules in ulcerative colitis by gene datasets analysis

description: Robust rank aggregation method is a kind of bioinformatics analysis,which is used to obtain significant differentially expressed genes in ulcerative colitis datasets. (<b>T</b><b>able</b><b> </b><b>S1</b>);Weighted gene coexpression network analysis was used to explore the functional modules involved in ulcerative colitis pathogenesis.(<b>T</b><b>able</b><b> </b><b>S</b><b>2</b>)<b></b><i></i><sub></sub><sup></sup><br><b></b><i></i><sub></sub><sup></sup><b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.7120808.v1
title: MW WX ZH Manuscript Data

description: This file contains the minimum dataset for Wu et al. accepted to PLoS-One in September, 2018, titled "Similar Image Retrieval in Large-scale Trademark Databases based on Regional and Boundary Fusion Feature".The design of the experiment is fully explained in the manuscript. The database of trademark images including 5 image dataset folders : 1.CE-Shape-1, 2.100Class,3.geometry defor, 4.TrademarkAffine, and 5.TrademarkTransform. <br>1.CE-SHAPE-1 dataset containing 1400 MPEG-7 core experimental shape.2.100Class dataset containing 100 trademark images which were used as query samples. 3.geometry defor dataset was used for trademark geometry deformation experiment in this study, and the geometric transformations include shrinkage, spheroidization, torsion, and corrugation. 4.TrademarkAffine dataset was used for trademark affine transformation experiments in this study. Each image is processed with any combination of the transformations (Translation, Scaling, Rotate) to obtain 50 similar images of the original image respectively. 5.TrademarkTransform dataset was used for trademark geometry deformation experiment in this study.
DOI: 10.6084/m9.figshare.7120769
title: Data.csv

description: Daily Korea Stock Price Index (KOSPI) for January 2000–December 2016. The total number of cases comprises 4,203 trading days. Each sample contains daily price information including the low price, high price, opening price, closing price, and trading volume.
DOI: 10.6084/m9.figshare.7120730
title: Additional file 7: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Foods sorted according to their nutritive content. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7120727
title: Additional file 6: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Metabolite pathway enrichment analysis results for each selected microbes. (XLSX 108 kb)
DOI: 10.6084/m9.figshare.7120730.v1
title: Additional file 7: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Foods sorted according to their nutritive content. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.7120724
title: Additional file 5: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Data for support, complementarity and competition. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.7120727.v1
title: Additional file 6: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Metabolite pathway enrichment analysis results for each selected microbes. (XLSX 108 kb)
DOI: 10.6084/m9.figshare.7120724.v1
title: Additional file 5: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Data for support, complementarity and competition. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.7120718
title: Additional file 4: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Nutrient profile of each microbes in the community in exam as resulted from NetSeed. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7120718.v1
title: Additional file 4: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Nutrient profile of each microbes in the community in exam as resulted from NetSeed. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.7120709
title: Additional file 8: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S5. Detail information about DEGs for wandering stage and white puparium stage in Bactrocera dorsalis. (XLSX 683 kb)
DOI: 10.6084/m9.figshare.7120709.v1
title: Additional file 8: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S5. Detail information about DEGs for wandering stage and white puparium stage in Bactrocera dorsalis. (XLSX 683 kb)
DOI: 10.6084/m9.figshare.7120703
title: Additional file 2: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Relevant co-mention for PubMed IDs. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7120703.v1
title: Additional file 2: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Relevant co-mention for PubMed IDs. (XLSX 109 kb)
DOI: 10.6084/m9.figshare.7120694
title: Additional file 7: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S4. Detail information about DEGs for wandering stage and late wandering stage in Bactrocera dorsalis. (XLSX 634 kb)
DOI: 10.6084/m9.figshare.7120694.v1
title: Additional file 7: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S4. Detail information about DEGs for wandering stage and late wandering stage in Bactrocera dorsalis. (XLSX 634 kb)
DOI: 10.6084/m9.figshare.7120688
title: Additional file 1: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Relevant relationship for PubMed IDs. (XLSX 225 kb)
DOI: 10.6084/m9.figshare.7120688.v1
title: Additional file 1: of A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space

description: Relevant relationship for PubMed IDs. (XLSX 225 kb)
DOI: 10.6084/m9.figshare.12356810
title: Analysis: unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

description: This collection contains data received during the reconstruction of magnetotactic bacteria genomes and their further analysis.
DOI: 10.6084/m9.figshare.12356810.v1
title: Analysis: unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases

description: This collection contains data received during the reconstruction of magnetotactic bacteria genomes and their further analysis.
DOI: 10.6084/m9.figshare.7120646
title: Additional file 4: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S3. All genes FPKM value during the pupariation in Bactrocera dorsalis. (XLSX 1346 kb)
DOI: 10.6084/m9.figshare.7120646.v1
title: Additional file 4: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S3. All genes FPKM value during the pupariation in Bactrocera dorsalis. (XLSX 1346 kb)
DOI: 10.6084/m9.figshare.7120592
title: Additional file 12: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S6. The detail FPKM value of 20-hydroxyecdysone biosynthesis and signaling related genes during the pupariation in Bactrocera dorsalis. (XLSX 12 kb)
DOI: 10.5281/zenodo.4002021
title: Test Scene Dataset for Physically Based Rendering

description: A test scene data set for physically based rendering.<br> The scenes include different geometries, materials and illumination setups of varying complexity to facilitate the evaluation and testing of Monte-Carlo rendering algorithms.<br> The source files are provided in the Blender file format for easy editing and additional exports to the Mitsuba XML format are included.
DOI: 10.6084/m9.figshare.7120592.v1
title: Additional file 12: of RNA-seq analysis of gene expression changes during pupariation in Bactrocera dorsalis (Hendel) (Diptera: Tephritidae)

description: Table S6. The detail FPKM value of 20-hydroxyecdysone biosynthesis and signaling related genes during the pupariation in Bactrocera dorsalis. (XLSX 12 kb)
DOI: 10.5281/zenodo.4002020
title: Test Scene Dataset for Physically Based Rendering

description: A test scene data set for physically based rendering.<br> The scenes include different geometries, materials and illumination setups of varying complexity to facilitate the evaluation and testing of Monte-Carlo rendering algorithms.<br> The source files are provided in the Blender file format for easy editing and additional exports to the Mitsuba XML format are included.
DOI: 10.6084/m9.figshare.7120583
title: Additional file 5: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S4. Summary statistics for the phenotypic traits evaluated in the A0514 population. Number of clones (N), Mean, standard deviation (S.D.), minimum (Min), and maximum (Max) values. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7120586
title: Additional file 2: of Overlapping group screening for detection of gene-gene interactions: application to gene expression profiles with survival trait

description: An R package â OGSâ , which is a Windows binaries zip file. (ZIP 29 kb)
DOI: 10.6084/m9.figshare.7120583.v1
title: Additional file 5: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S4. Summary statistics for the phenotypic traits evaluated in the A0514 population. Number of clones (N), Mean, standard deviation (S.D.), minimum (Min), and maximum (Max) values. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7120586.v1
title: Additional file 2: of Overlapping group screening for detection of gene-gene interactions: application to gene expression profiles with survival trait

description: An R package â OGSâ , which is a Windows binaries zip file. (ZIP 29 kb)
DOI: 10.6084/m9.figshare.7120565
title: Additional file 4: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S3. Least square means of the phenotypic traits evaluated in the A0514 population. Glucose values are based on squared root transformation. (XLS 73Â kb) (XLSX 31 kb)
DOI: 10.6084/m9.figshare.7120565.v1
title: Additional file 4: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S3. Least square means of the phenotypic traits evaluated in the A0514 population. Glucose values are based on squared root transformation. (XLS 73Â kb) (XLSX 31 kb)
DOI: 10.6084/m9.figshare.7120544
title: Additional file 3: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S2. Order of the mapped SNPs on chromosomes 1â 12 (Chr, Overall map) and corresponding homologs (H1-H8). (XLSX 110 kb)
DOI: 10.6084/m9.figshare.7120544.v1
title: Additional file 3: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S2. Order of the mapped SNPs on chromosomes 1â 12 (Chr, Overall map) and corresponding homologs (H1-H8). (XLSX 110 kb)
DOI: 10.6084/m9.figshare.7120526
title: Additional file 1: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S1. Parent and F1 offspring genotype configurations in the A05141 tetraploid. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7120523
title: Additional file 10: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S5. Description of phenotypic traits. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120526.v1
title: Additional file 1: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S1. Parent and F1 offspring genotype configurations in the A05141 tetraploid. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7120523.v1
title: Additional file 10: of Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato

description: Table S5. Description of phenotypic traits. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120520
title: Additional file 9: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S8. Average identity-by-descent-segment share in Central and East European populations. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7120520.v1
title: Additional file 9: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S8. Average identity-by-descent-segment share in Central and East European populations. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7120511
title: Additional file 8: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S7. Average identity-by-descent-segment share in Northeast European populations. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.7120511.v1
title: Additional file 8: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S7. Average identity-by-descent-segment share in Northeast European populations. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.7120496
title: Additional file 7: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S6. Correlation analysis of k9 ancestral component and chromosome Y haplogroup N sub-haplogroups. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7120496.v1
title: Additional file 7: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S6. Correlation analysis of k9 ancestral component and chromosome Y haplogroup N sub-haplogroups. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7120472
title: Additional file 6: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S5. Y chromosome haplogroup frequencies in Eurasia. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7120472.v1
title: Additional file 6: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S5. Y chromosome haplogroup frequencies in Eurasia. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.7120457
title: Additional file 5: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S4. Mitochondrial DNA haplogroup frequencies in Eurasia. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.7120457.v1
title: Additional file 5: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S4. Mitochondrial DNA haplogroup frequencies in Eurasia. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.7120439
title: Additional file 4: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S3. Mitochondrial DNA data of Uralic speakers. (XLSX 541 kb)
DOI: 10.6084/m9.figshare.7120439.v1
title: Additional file 4: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S3. Mitochondrial DNA data of Uralic speakers. (XLSX 541 kb)
DOI: 10.6084/m9.figshare.7120391
title: Additional file 1: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S1. Autosomal data used in the study. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7120391.v1
title: Additional file 1: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S1. Autosomal data used in the study. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7120385
title: Additional file 17: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S16. Y chromosomal hg Q STR data. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7120385.v1
title: Additional file 17: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S16. Y chromosomal hg Q STR data. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7120373
title: Additional file 2: of Effects of repurposed drug candidates nitroxoline and nelfinavir as single agents or in combination with erlotinib in pancreatic cancer cells

description: Table S2. Mean percentages of cells identified as sub-G1 population. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120373.v1
title: Additional file 2: of Effects of repurposed drug candidates nitroxoline and nelfinavir as single agents or in combination with erlotinib in pancreatic cancer cells

description: Table S2. Mean percentages of cells identified as sub-G1 population. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120364
title: Additional file 16: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S15. Mantel test results. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120364.v1
title: Additional file 16: of Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations

description: Table S15. Mantel test results. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7120358
title: Additional file 1: of Effects of repurposed drug candidates nitroxoline and nelfinavir as single agents or in combination with erlotinib in pancreatic cancer cells

description: Table S1. Effects of erlotinib, nelfinavir and nitroxoline as single agents versus drug combinations on cell viability. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7120358.v1
title: Additional file 1: of Effects of repurposed drug candidates nitroxoline and nelfinavir as single agents or in combination with erlotinib in pancreatic cancer cells

description: Table S1. Effects of erlotinib, nelfinavir and nitroxoline as single agents versus drug combinations on cell viability. (XLSX 12 kb)