cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17056559
title: Additional file 1 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 1. List of the 93 used AYB lines and phenotypic related traits.
DOI: 10.6084/m9.figshare.17056559.v1
title: Additional file 1 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 1. List of the 93 used AYB lines and phenotypic related traits.
DOI: 10.6084/m9.figshare.17056562
title: Additional file 2 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 2. Genetic distance matrix.
DOI: 10.6084/m9.figshare.17056562.v1
title: Additional file 2 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 2. Genetic distance matrix.
DOI: 10.6084/m9.figshare.17056565
title: Additional file 3 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 3. Structure results at K = 2, K = 3 and K = 4.
DOI: 10.6084/m9.figshare.17056565.v1
title: Additional file 3 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 3. Structure results at K = 2, K = 3 and K = 4.
DOI: 10.6084/m9.figshare.17056568
title: Additional file 4 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 4. DAPC analysis results.
DOI: 10.6084/m9.figshare.17056568.v1
title: Additional file 4 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 4. DAPC analysis results.
DOI: 10.6084/m9.figshare.17056574
title: Additional file 5 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 5. STRUCTURE vs DAPC genotypic-phenotypic traits.
DOI: 10.6084/m9.figshare.17056574.v1
title: Additional file 5 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 5. STRUCTURE vs DAPC genotypic-phenotypic traits.
DOI: 10.6084/m9.figshare.17056577
title: Additional file 6 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 6: Figure S1. PCoA results; Figure S2. PCoA at K = 3 using 80% threshold.
DOI: 10.6084/m9.figshare.17056577.v1
title: Additional file 6 of Predictive genotype-phenotype relations using genetic diversity in African yam bean (Sphenostylis stenocarpa (Hochst. ex. A. Rich) Harms)

description: Additional file 6: Figure S1. PCoA results; Figure S2. PCoA at K = 3 using 80% threshold.
DOI: 10.6084/m9.figshare.17056576
title: Additional file 1 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 1. Midnightblue (immune) subnetwork. The list of genes, module membership, the logarithm of fold change, differential analysis. adj-p.value, and gene-significance statistics.
DOI: 10.6084/m9.figshare.17056576.v1
title: Additional file 1 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 1. Midnightblue (immune) subnetwork. The list of genes, module membership, the logarithm of fold change, differential analysis. adj-p.value, and gene-significance statistics.
DOI: 10.6084/m9.figshare.17056579
title: Additional file 2 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 2. Turquoise (EMT) subnetwork. The list of genes, module membership, the logarithm of fold change, differential analysis. adj-p.value, and gene-significance statistics.
DOI: 10.6084/m9.figshare.17056579.v1
title: Additional file 2 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 2. Turquoise (EMT) subnetwork. The list of genes, module membership, the logarithm of fold change, differential analysis. adj-p.value, and gene-significance statistics.
DOI: 10.6084/m9.figshare.17056585
title: Additional file 4 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 4. The preservation statistics. This table includes $${Z}_{summary }$$ Z summary and $${Median}_{rank}$$ Median rank statistics.
DOI: 10.6084/m9.figshare.17056585.v1
title: Additional file 4 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 4. The preservation statistics. This table includes $${Z}_{summary }$$ Z summary and $${Median}_{rank}$$ Median rank statistics.
DOI: 10.6084/m9.figshare.17056588
title: Additional file 5 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 5. Biological pathways in the directed network. We categorized genes of the detected directed network, using ClueGO plugin in Cytoscape. The Biological pathways and p-values were reported.
DOI: 10.6084/m9.figshare.17056588.v1
title: Additional file 5 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 5. Biological pathways in the directed network. We categorized genes of the detected directed network, using ClueGO plugin in Cytoscape. The Biological pathways and p-values were reported.
DOI: 10.6084/m9.figshare.17056591
title: Additional file 6 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 6. The EMT subnetwork cox-PH results. The cox-PH analysis was implemented for the EMT subnetwork genes. The selected genes, coefficients, and p-values were reported.
DOI: 10.6084/m9.figshare.17056591.v1
title: Additional file 6 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 6. The EMT subnetwork cox-PH results. The cox-PH analysis was implemented for the EMT subnetwork genes. The selected genes, coefficients, and p-values were reported.
DOI: 10.6084/m9.figshare.17056594
title: Additional file 7 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 7. The Immune subnetwork cox-PH results. The cox-PH analysis was implemented for the immune subnetwork genes. The selected genes, coefficients, and p-values were reported.
DOI: 10.6084/m9.figshare.17056594.v1
title: Additional file 7 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 7. The Immune subnetwork cox-PH results. The cox-PH analysis was implemented for the immune subnetwork genes. The selected genes, coefficients, and p-values were reported.
DOI: 10.6084/m9.figshare.17056597
title: Additional file 8 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 8. EMT VIF values. To investigate multicollinearity in the cox-PH model, we calculated the Variance Inflation Factor (VIF). The VIF &lt; 10 indicates no multicollinearity. The VIF of immune genes was reported.
DOI: 10.6084/m9.figshare.17056597.v1
title: Additional file 8 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 8. EMT VIF values. To investigate multicollinearity in the cox-PH model, we calculated the Variance Inflation Factor (VIF). The VIF &lt; 10 indicates no multicollinearity. The VIF of immune genes was reported.
DOI: 10.6084/m9.figshare.17056600
title: Additional file 9 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 9. Immune VIF values. To investigate multicollinearity in the cox-PH model, we calculated the Variance Inflation Factor (VIF). The VIF &lt; 10 indicates no multicollinearity. The VIF of immune genes was reported.
DOI: 10.6084/m9.figshare.17056600.v1
title: Additional file 9 of Involvement of immune system and Epithelial–Mesenchymal-Transition in increased invasiveness of clustered circulatory tumor cells in breast cancer

description: Additional file 9. Immune VIF values. To investigate multicollinearity in the cox-PH model, we calculated the Variance Inflation Factor (VIF). The VIF &lt; 10 indicates no multicollinearity. The VIF of immune genes was reported.
DOI: 10.6084/m9.figshare.17056621
title: Additional file 2 of Multiomic analysis on human cell model of wolfram syndrome reveals changes in mitochondrial morphology and function

description: Additional file 1: Table S1. List of genes and proteins generated in omics analyses for the project.
DOI: 10.6084/m9.figshare.17056621.v1
title: Additional file 2 of Multiomic analysis on human cell model of wolfram syndrome reveals changes in mitochondrial morphology and function

description: Additional file 1: Table S1. List of genes and proteins generated in omics analyses for the project.
DOI: 10.6084/m9.figshare.17056625.v1
title: Additional file 1 of The PARADIGHM (physicians advancing disease knowledge in hypoparathyroidism) registry for patients with chronic hypoparathyroidism: study protocol and interim baseline patient characteristics

description: Additional file 1: Figure S1. Number of patients in the analysis population of 737 patients enrolled at each of the 64 participating centers as of 30 June 2019.
DOI: 10.6084/m9.figshare.17056625
title: Additional file 1 of The PARADIGHM (physicians advancing disease knowledge in hypoparathyroidism) registry for patients with chronic hypoparathyroidism: study protocol and interim baseline patient characteristics

description: Additional file 1: Figure S1. Number of patients in the analysis population of 737 patients enrolled at each of the 64 participating centers as of 30 June 2019.
DOI: 10.6084/m9.figshare.17056663
title: Additional file 6 of Methodological issues in economic evaluations of disease prevention and health promotion: an overview of systematic and scoping reviews

description: Additional file 6. Quantitative Synthesis.
DOI: 10.6084/m9.figshare.17056663.v1
title: Additional file 6 of Methodological issues in economic evaluations of disease prevention and health promotion: an overview of systematic and scoping reviews

description: Additional file 6. Quantitative Synthesis.
DOI: 10.6084/m9.figshare.17056681.v1
title: Additional file 4 of Experimental Chlamydia gallinacea infection in chickens does not protect against a subsequent experimental Chlamydia psittaci infection

description: Additional file 4. qPCR data of individual pharyngeal and cloacal swabs.
DOI: 10.6084/m9.figshare.17056681
title: Additional file 4 of Experimental Chlamydia gallinacea infection in chickens does not protect against a subsequent experimental Chlamydia psittaci infection

description: Additional file 4. qPCR data of individual pharyngeal and cloacal swabs.
DOI: 10.6084/m9.figshare.17056684.v1
title: Additional file 1 of Safety and efficacy of intermittent presumptive treatment with sulfadoxine-pyrimethamine using rapid diagnostic test screening and treatment with dihydroartemisinin-piperaquine at the first antenatal care visit (IPTp-SP+): study protocol for a randomized controlled trial

description: Additional file 1. : Supplementary Table S1. SPIRIT figure
DOI: 10.6084/m9.figshare.17056684
title: Additional file 1 of Safety and efficacy of intermittent presumptive treatment with sulfadoxine-pyrimethamine using rapid diagnostic test screening and treatment with dihydroartemisinin-piperaquine at the first antenatal care visit (IPTp-SP+): study protocol for a randomized controlled trial

description: Additional file 1. : Supplementary Table S1. SPIRIT figure
DOI: 10.6084/m9.figshare.17056706
title: Additional file 10 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 10: Supplementary Table 5. List of primers used in this study.
DOI: 10.6084/m9.figshare.17056706.v1
title: Additional file 10 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 10: Supplementary Table 5. List of primers used in this study.
DOI: 10.6084/m9.figshare.17056709
title: Additional file 1 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 1: Supplementary Table S1. Genomic coordinates of NTBS regions discovered in at least three out of five independent ChIP-chip experiments.
DOI: 10.6084/m9.figshare.17056709.v1
title: Additional file 1 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 1: Supplementary Table S1. Genomic coordinates of NTBS regions discovered in at least three out of five independent ChIP-chip experiments.
DOI: 10.6084/m9.figshare.17056715
title: Additional file 3 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 3: Supplementary Table S2. Table defining the NTBS overlap with gene bodies, percentage overlap of NTBS region and the gene and gene function description.
DOI: 10.6084/m9.figshare.17056715.v1
title: Additional file 3 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 3: Supplementary Table S2. Table defining the NTBS overlap with gene bodies, percentage overlap of NTBS region and the gene and gene function description.
DOI: 10.6084/m9.figshare.17056730
title: Additional file 8 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 8: Supplementary Table 3. List of bacterial strains used in this study.
DOI: 10.6084/m9.figshare.17056730.v1
title: Additional file 8 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 8: Supplementary Table 3. List of bacterial strains used in this study.
DOI: 10.6084/m9.figshare.17056733
title: Additional file 9 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 9: Supplementary Table 4. List of yeast strains used in this study.
DOI: 10.6084/m9.figshare.17056733.v1
title: Additional file 9 of Telomerase subunit Est2 marks internal sites that are prone to accumulate DNA damage

description: Additional file 9: Supplementary Table 4. List of yeast strains used in this study.
DOI: 10.6084/m9.figshare.17056738
title: Additional file 1 of Cultural adaptation of mental health first aid guidelines for depression for Sri Lanka: a Delphi expert consensus study

description: Additional file 1.
DOI: 10.6084/m9.figshare.17056738.v1
title: Additional file 1 of Cultural adaptation of mental health first aid guidelines for depression for Sri Lanka: a Delphi expert consensus study

description: Additional file 1.
DOI: 10.6084/m9.figshare.17056739
title: Additional file 6 of Transcatheter aortic valve replacement associated infective endocarditis case series: broadening the criteria for diagnosis is the need of the hour

description: Additional file 6: Table S1.
DOI: 10.6084/m9.figshare.17056739.v1
title: Additional file 6 of Transcatheter aortic valve replacement associated infective endocarditis case series: broadening the criteria for diagnosis is the need of the hour

description: Additional file 6: Table S1.
DOI: 10.5281/zenodo.5716507
title: Distinct and essential roles of bZIP transcription factors in stress response and pathogenesis in Alternaria alternata

description: The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata un- der metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We determined the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A. alternata by analyzing targeted gene deletion mutants. Morphological analysis provides evidence that bZIPs including Gcn4, MeaB, Atf1, Hac1 and Ada1 are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover, the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings identified many crucial transcription factor genes and pathways related to cell development, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.
DOI: 10.5281/zenodo.5716506
title: Distinct and essential roles of bZIP transcription factors in stress response and pathogenesis in Alternaria alternata

description: The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata un- der metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We determined the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A. alternata by analyzing targeted gene deletion mutants. Morphological analysis provides evidence that bZIPs including Gcn4, MeaB, Atf1, Hac1 and Ada1 are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover, the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings identified many crucial transcription factor genes and pathways related to cell development, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.
DOI: 10.6084/m9.figshare.17056753
title: Additional file 12 of Sex and gender considerations in reporting guidelines for health research: a systematic review

description: Additional file 12. Data extraction.
DOI: 10.6084/m9.figshare.17056753.v1
title: Additional file 12 of Sex and gender considerations in reporting guidelines for health research: a systematic review

description: Additional file 12. Data extraction.
DOI: 10.6084/m9.figshare.17056774
title: Additional file 7 of Sex and gender considerations in reporting guidelines for health research: a systematic review

description: Additional file 7. Detailed internal validity assessment.
DOI: 10.6084/m9.figshare.17056774.v1
title: Additional file 7 of Sex and gender considerations in reporting guidelines for health research: a systematic review

description: Additional file 7. Detailed internal validity assessment.