cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6940100.v2
title: Autophagy controls neonatal myogenesis by regulating the GH-IGF1 system through a NFE2L2- and DDIT3-mediated mechanism

description: Macroautophagy/autophagy is emerging as an important process in adult muscle stem cells functions: it regulates metabolic reprogramming during activation from a quiescent state, maintains stemness and prevents senescence. We now show that autophagy is specifically required for neonatal myogenesis and muscle development. Specific deletion of <i>Atg7</i> in PAX7<sup>+</sup> (paired box 7) precursors led in mice to a dwarf phenotype, with an effect restricted to the neonatal phase of muscle development. <i>Atg7</i> knockdown suppressed neonatal satellite cell (nSC) proliferation and differentiation, downregulating the GH-IGF1 functions. When we disrupted autophagy, NFE2L2/NRF2 (nuclear factor, erythroid 2 like 2) accumulated in muscle and nSCs and negatively modulated DDIT3/CHOP (DNA-damage inducible transcript 3) expression. Lower levels of DDIT3 were responsible for reduced GHR expression leading to impaired local production of IGF1. Our results conclusively identify a novel autophagy-dependent pathway that regulates nSC behavior and indicate that autophagy is required for skeletal muscle development in the neonatal phase. <b>Abbreviations:</b> AKT/protein kinase B: Thymoma viral proto-oncogene; ASCs: adult stem cells; ATF4: activating transcription factor 4; ATG7: autophagy related 7; BAT: brown adipose tissue; BMP: bone morphogenetic protein; CEBPB: CCAAT/enhancer binding protein (C/EBP), beta; CSA: cross sectional area; CTNNB1: catenin (cadherin associated protein), beta 1; DDIT3: DNA-damage inducible transcript 3; DM: differentiation medium; E: embryonic stage; EIF2AK3/PERK; EIF4EBP1: eukaryotic translation initiation factor 2 alpha kinase 3; eukaryotic translation initiation factor 4E binding protein 1; ER: endoplasmic reticulum; FGF21: fibroblast growth factor 21; GH: growth hormone; GHR: growth hormone receptor; HSCs: hematopoietic stem cells; IGF1: insulin-like growth factor 1; ITGAM: integrin alpha M; KEAP1: kelch-like ECH-associated protein 1; LY6A/Sca-1; MAP1LC3: lymphocyte antigen 6 complex, locus A; microtubule-associated protein 1 light chain 3; MAPK1/ERK2: mitogen-activated protein kinase 1; MAPK3/ERK1: mitogen-activated protein kinase 3; miRNAs: microRNAs; MSCs: mesenchymal stem cells; MTOR: mechanistic target of rapamycin kinase; mtUPR: mitochondrial unfolded protein response; MYF5: myogenic factor 5; MYH: myosin, heavy polypeptide; MYOD1: myogenic differentiation 1; MYOG: myogenin; NFE2L2: nuclear factor, erythroid derived 2, like 2; nSC: neonatal satellite cells; NSCs: neuronal stem cells; P: postnatal day; PAX7: paired box 7; PECAM1: platelet/endothelial cell adhesion molecule 1; PPARG: peroxisome proliferator activated receptor gamma; PTPRC: protein tyrosine phosphatase, receptor type, C; ROS: reactive oxygen species; RPS6: ribosomal protein S6; SCs: adult satellite cells; SQSTM1: sequestosome 1; STAT5: signal transducer and activator of transcription 5; TGFB1: transforming growth factor beta 1; WAT: white adipose tissue; WT: wild type.
DOI: 10.6084/m9.figshare.6940100.v1
title: Autophagy controls neonatal myogenesis by regulating the GH-IGF1 system through a NFE2L2- and DDIT3-mediated mechanism

description: Macroautophagy/autophagy is emerging as an important process in adult muscle stem cells functions: it regulates metabolic reprogramming during activation from a quiescent state, maintains stemness and prevents senescence. We now show that autophagy is specifically required for neonatal myogenesis and muscle development. Specific deletion of <i>Atg7</i> in PAX7<sup>+</sup> (paired box 7) precursors led in mice to a dwarf phenotype, with an effect restricted to the neonatal phase of muscle development. <i>Atg7</i> knockdown suppressed neonatal satellite cell (nSC) proliferation and differentiation, downregulating the GH-IGF1 functions. When we disrupted autophagy, NFE2L2/NRF2 (nuclear factor, erythroid 2 like 2) accumulated in muscle and nSCs and negatively modulated DDIT3/CHOP (DNA-damage inducible transcript 3) expression. Lower levels of DDIT3 were responsible for reduced GHR expression leading to impaired local production of IGF1. Our results conclusively identify a novel autophagy-dependent pathway that regulates nSC behavior and indicate that autophagy is required for skeletal muscle development in the neonatal phase. <b>Abbreviations:</b> AKT/protein kinase B: Thymoma viral proto-oncogene; ASCs: adult stem cells; ATF4: activating transcription factor 4; ATG7: autophagy related 7; BAT: brown adipose tissue; BMP: bone morphogenetic protein; CEBPB: CCAAT/enhancer binding protein (C/EBP), beta; CSA: cross sectional area; CTNNB1: catenin (cadherin associated protein), beta 1; DDIT3: DNA-damage inducible transcript 3; DM: differentiation medium; E: embryonic stage; EIF2AK3/PERK; EIF4EBP1: eukaryotic translation initiation factor 2 alpha kinase 3; eukaryotic translation initiation factor 4E binding protein 1; ER: endoplasmic reticulum; FGF21: fibroblast growth factor 21; GH: growth hormone; GHR: growth hormone receptor; HSCs: hematopoietic stem cells; IGF1: insulin-like growth factor 1; ITGAM: integrin alpha M; KEAP1: kelch-like ECH-associated protein 1; LY6A/Sca-1; MAP1LC3: lymphocyte antigen 6 complex, locus A; microtubule-associated protein 1 light chain 3; MAPK1/ERK2: mitogen-activated protein kinase 1; MAPK3/ERK1: mitogen-activated protein kinase 3; miRNAs: microRNAs; MSCs: mesenchymal stem cells; MTOR: mechanistic target of rapamycin kinase; mtUPR: mitochondrial unfolded protein response; MYF5: myogenic factor 5; MYH: myosin, heavy polypeptide; MYOD1: myogenic differentiation 1; MYOG: myogenin; NFE2L2: nuclear factor, erythroid derived 2, like 2; nSC: neonatal satellite cells; NSCs: neuronal stem cells; P: postnatal day; PAX7: paired box 7; PECAM1: platelet/endothelial cell adhesion molecule 1; PPARG: peroxisome proliferator activated receptor gamma; PTPRC: protein tyrosine phosphatase, receptor type, C; ROS: reactive oxygen species; RPS6: ribosomal protein S6; SCs: adult satellite cells; SQSTM1: sequestosome 1; STAT5: signal transducer and activator of transcription 5; TGFB1: transforming growth factor beta 1; WAT: white adipose tissue; WT: wild type.
DOI: 10.6084/m9.figshare.6940091
title: Bmp2/4/16 alignment (nucleotides)

description: This alignment has been used as input file for RRTree and PAML analysis.
DOI: 10.6084/m9.figshare.6940091.v1
title: Bmp2/4/16 alignment (nucleotides)

description: This alignment has been used as input file for RRTree and PAML analysis.
DOI: 10.6084/m9.figshare.6940088
title: Supplementary Material for: Examining the Cascade of Participant Attrition in a Genomic Medicine Research Study: Barriers and Facilitators to Achieving Diversity

description: <b><i>Background/Aims:</i></b> Recent genomic medicine initiatives underscore the importance of including diverse participants in research. Considerable literature has identified barriers to and facilitators of increasing diversity, yet disparities in recruiting and retaining adequate numbers of participants from diverse groups continue to limit the generalizability of clinical genomic research. <b><i>Methods:</i></b> The North Carolina Clinical Genomic Evaluation by Next-gen Exome Sequencing study employed evidence-based strategies to enhance the participation of under-represented minority patients. In this study, we evaluate the impact of our efforts by systematically analyzing the “cascade” of attrition of participants throughout study interactions. <b><i>Results:</i></b> Although successful in recruiting a cohort that included ~30% non-Caucasian patients overall, the study still enrolled and retained a lower proportion of minorities compared to the pool of eligible patients who were nominated. We evaluated sociodemographic characteristics and related variables as potential factors associated with attrition throughout these phases of the study. <b><i>Conclusions:</i></b> These results suggest that varied approaches will be needed to increase participation in genomic medicine research. Our findings highlight factors to consider when developing strategies to address this critical need. Failing to include a broad range of populations in research studies will exacerbate existing disparities in the translation of genomic sequencing to medical care.
DOI: 10.6084/m9.figshare.6940088.v1
title: Supplementary Material for: Examining the Cascade of Participant Attrition in a Genomic Medicine Research Study: Barriers and Facilitators to Achieving Diversity

description: <b><i>Background/Aims:</i></b> Recent genomic medicine initiatives underscore the importance of including diverse participants in research. Considerable literature has identified barriers to and facilitators of increasing diversity, yet disparities in recruiting and retaining adequate numbers of participants from diverse groups continue to limit the generalizability of clinical genomic research. <b><i>Methods:</i></b> The North Carolina Clinical Genomic Evaluation by Next-gen Exome Sequencing study employed evidence-based strategies to enhance the participation of under-represented minority patients. In this study, we evaluate the impact of our efforts by systematically analyzing the “cascade” of attrition of participants throughout study interactions. <b><i>Results:</i></b> Although successful in recruiting a cohort that included ~30% non-Caucasian patients overall, the study still enrolled and retained a lower proportion of minorities compared to the pool of eligible patients who were nominated. We evaluated sociodemographic characteristics and related variables as potential factors associated with attrition throughout these phases of the study. <b><i>Conclusions:</i></b> These results suggest that varied approaches will be needed to increase participation in genomic medicine research. Our findings highlight factors to consider when developing strategies to address this critical need. Failing to include a broad range of populations in research studies will exacerbate existing disparities in the translation of genomic sequencing to medical care.
DOI: 10.6084/m9.figshare.6939923
title: Data from: Biological motion as an innate perceptual mechanism driving social affiliation

description: This data set contains the raw data needed to reproduce the figures presented in the paper. Analysis code and a bioRxiv preprint of this work are also available.<br>
DOI: 10.6084/m9.figshare.6939914
title: Using social networking sites for language learning to develop intercultural competence in language education programs

description: This article examines the ways a social networking site for language learning (SNSLL) enhances or hinders intercultural communicative competence (ICC). The study identifies the components of intercultural competence that emerge from students’ interactions and reflections about the SNSLL Livemocha. The research was conducted with second-year students of an English class in a Colombian university. Data were collected through screen recordings, students’ logs, surveys, and a focus group. Findings indicate that, of the five dimensions of ICC, the components of Attitudes, Knowledge, Skills of Interpreting and Relating, and Skills of Discovery and Interaction featured strongly on students’ exchanges and reflections. SNSLLs hold potential to enhance intercultural skills; however, pedagogical adjustment and refocusing of some of their activities are required to expand opportunities for intercultural engagement.
DOI: 10.6084/m9.figshare.6939914.v1
title: Using social networking sites for language learning to develop intercultural competence in language education programs

description: This article examines the ways a social networking site for language learning (SNSLL) enhances or hinders intercultural communicative competence (ICC). The study identifies the components of intercultural competence that emerge from students’ interactions and reflections about the SNSLL Livemocha. The research was conducted with second-year students of an English class in a Colombian university. Data were collected through screen recordings, students’ logs, surveys, and a focus group. Findings indicate that, of the five dimensions of ICC, the components of Attitudes, Knowledge, Skills of Interpreting and Relating, and Skills of Discovery and Interaction featured strongly on students’ exchanges and reflections. SNSLLs hold potential to enhance intercultural skills; however, pedagogical adjustment and refocusing of some of their activities are required to expand opportunities for intercultural engagement.
DOI: 10.6084/m9.figshare.6939797
title: Approach to local thermodynamic equilibrium and the evolution to a glassy core following neutron/ion radiation impact

description: Using molecular dynamics simulations and statistical-mechanical metrics, we make quantitative predictions on the local thermodynamic and dynamic states following an ion or neutron impact in three materials – copper, silicon and solid argon. Through a two-energy distribution, we first capture the non-equilibrium temperature evolution and the approach to the local thermal equilibrium in three generic stages. By examining the time-resolved van Hove self-correlator, we then demonstrate that the impact core of all the three materials shows the dynamic characteristics of a jammed or glassy state. We delineate a dynamic atom-hopping mechanism that attests to a rapid defect recovery stage in copper; silicon, on the contrary, accommodates only small displacements which resist recovery. The dissimilitude between copper with a close-packed structure and silicon with an open network structure is further drawn out through an isoconfigurational analysis of displacements, which shows a compact dendritic-like condensation front for the mobile atoms in copper through atom hopping. In contrast, silicon portrays larger-scale spatial oscillations of dynamically separated regions, which appear to be a precursor to dynamic lattice instability and eventual amorphisation.
DOI: 10.6084/m9.figshare.6939797.v1
title: Approach to local thermodynamic equilibrium and the evolution to a glassy core following neutron/ion radiation impact

description: Using molecular dynamics simulations and statistical-mechanical metrics, we make quantitative predictions on the local thermodynamic and dynamic states following an ion or neutron impact in three materials – copper, silicon and solid argon. Through a two-energy distribution, we first capture the non-equilibrium temperature evolution and the approach to the local thermal equilibrium in three generic stages. By examining the time-resolved van Hove self-correlator, we then demonstrate that the impact core of all the three materials shows the dynamic characteristics of a jammed or glassy state. We delineate a dynamic atom-hopping mechanism that attests to a rapid defect recovery stage in copper; silicon, on the contrary, accommodates only small displacements which resist recovery. The dissimilitude between copper with a close-packed structure and silicon with an open network structure is further drawn out through an isoconfigurational analysis of displacements, which shows a compact dendritic-like condensation front for the mobile atoms in copper through atom hopping. In contrast, silicon portrays larger-scale spatial oscillations of dynamically separated regions, which appear to be a precursor to dynamic lattice instability and eventual amorphisation.
DOI: 10.5281/zenodo.4006040
title: SGB.Sep19

description: PhyloPhlAn metagenomic database "SGB.Sep19"
DOI: 10.5281/zenodo.4006039
title: SGB.Sep19

description: PhyloPhlAn metagenomic database "SGB.Sep19"
DOI: 10.6084/m9.figshare.6939437
title: Additional file 6: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Results of secondary assay, excel file format. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6939437.v1
title: Additional file 6: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Results of secondary assay, excel file format. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6939431
title: Additional file 9: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S6. List of subset of differentially expressed genes (DEGs) related to ROS detoxification. (XLSX 470 kb)
DOI: 10.6084/m9.figshare.6939431.v1
title: Additional file 9: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S6. List of subset of differentially expressed genes (DEGs) related to ROS detoxification. (XLSX 470 kb)
DOI: 10.6084/m9.figshare.6939422
title: Additional file 5: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Results of secondary screen, excel file format. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.6939416
title: Additional file 8: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S5. List of subset of differentially expressed genes (DEGs) related with defense genes. (XLSX 484 kb)
DOI: 10.6084/m9.figshare.6939422.v1
title: Additional file 5: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Results of secondary screen, excel file format. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.6939416.v1
title: Additional file 8: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S5. List of subset of differentially expressed genes (DEGs) related with defense genes. (XLSX 484 kb)
DOI: 10.6084/m9.figshare.6939401
title: Additional file 7: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S4. List of subset of differentially expressed genes (DEGs) related with PRRs genes. (XLSX 505 kb)
DOI: 10.6084/m9.figshare.6939401.v1
title: Additional file 7: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S4. List of subset of differentially expressed genes (DEGs) related with PRRs genes. (XLSX 505 kb)
DOI: 10.6084/m9.figshare.6939395
title: Additional file 3: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Genes selected for follow-up, excel file format. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6939395.v1
title: Additional file 3: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Genes selected for follow-up, excel file format. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6939383
title: Additional file 2: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Uncorrected and seed-corrected logP values from RSA analysis, excel file format. (XLSX 1121 kb)
DOI: 10.6084/m9.figshare.6939383.v1
title: Additional file 2: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle

description: Uncorrected and seed-corrected logP values from RSA analysis, excel file format. (XLSX 1121 kb)
DOI: 10.6084/m9.figshare.6939374
title: Additional file 4: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S3. List of all differentially expressed genes (DEGs) of Actinidia chinensis var. chinensis modulated in response to Pseudomonas syringae pv. actinidiae inoculation both in acibenzolar-S-methyl treated and untreated plants. (XLSX 1256 kb)
DOI: 10.6084/m9.figshare.6939374.v1
title: Additional file 4: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl

description: Table S3. List of all differentially expressed genes (DEGs) of Actinidia chinensis var. chinensis modulated in response to Pseudomonas syringae pv. actinidiae inoculation both in acibenzolar-S-methyl treated and untreated plants. (XLSX 1256 kb)
DOI: 10.6084/m9.figshare.6939359
title: Additional file 8: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Genotyping-by-Sequencing derived SNP markers of 101 synthetic hexaploid wheats used in this study. (XLSX 15100Â kb)
DOI: 10.6084/m9.figshare.6939359.v1
title: Additional file 8: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Genotyping-by-Sequencing derived SNP markers of 101 synthetic hexaploid wheats used in this study. (XLSX 15100Â kb)
DOI: 10.6084/m9.figshare.6939350
title: Additional file 7: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Details of 12 bread wheat cultivars used in this study. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6939350.v1
title: Additional file 7: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Details of 12 bread wheat cultivars used in this study. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6939341
title: Additional file 6: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Kinship relationship matrix of 101 Aegilops tauschii. (XLSX 117Â kb)
DOI: 10.6084/m9.figshare.6939341.v1
title: Additional file 6: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Kinship relationship matrix of 101 Aegilops tauschii. (XLSX 117Â kb)
DOI: 10.6084/m9.figshare.6939332
title: Additional file 5: of Unlocking the novel genetic diversity and population structure of synthetic Hexaploid wheat

description: Kinship relationship matrix of 101 Durum wheat. (XLSX 116Â kb)
DOI: 10.6084/m9.figshare.6939329
title: Additional file 4: of Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium

description: Table S4. Summary of IPA of proteins upregulated on P3 relative P14. Table S5. Summary of IPA of proteins downregulated on P3 relative P14. Table S6. Summary of IPA of proteins exclusively expressed on P3 relative P14. Table S7. Summary of IPA of proteins exclusively expressed on P14 relative to P3. Table S8. Summary of IPA of proteins upregulated on P3 relative P30. Table S9. Summary of IPA of proteins downregulated on P3 relative P30. Table S10. Summary of IPA of exclusively expressed on P3 relative to P30. Table S11. Summary of IPA of proteins exclusively expressed on P30 relative to P3. (XLSX 25 kb)