cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7639967
title: Baseline-Covariate Adjusted Confidence Interval for Proportional Difference Between Two Treatment Groups in Clinical Trials

description: The treatment effect of a therapeutic product on a binary endpoint is often expressed as the difference in proportions of subjects with the outcome of interest between the treated and control groups of a clinical trial. Analysis of the proportional difference and construction of the associated confidence interval (CI) is often complicated due to the baseline covariate(s) being associated with the primary endpoint. Analysis adjusting for such baseline covariate(s) generally improves efficiency of hypothesis testing and precision of treatment effect estimation, and avoids possible bias caused by baseline covariate imbalances. Most existing literatures focus on constructing unadjusted or categorical covariate(s) adjusted only CI, which provides very limited advice on how different statistical methods perform and which method is optimal in terms of constructing both categorical and continuous baseline covariate(s) adjusted CI for proportional difference. We review and compare the performance of three commonly used model-based methods as well as the traditional nonparametric weighted-difference methods for the construction of covariate-adjusted CI for proportional difference via a real data application and simulations. The coverage of 95% CI, Type I error control, and power are examined. We also examine the factors leading to the model convergence failure in different scenarios via simulations.
DOI: 10.6084/m9.figshare.8164238
title: Additional file 1: of Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome

description: Table S1. The complete list of annotated MTB HPs. Table S2. The 67 annotated proteins identified by searching against genomes of other MTB strains. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.20222936
title: Evaluation model of downhole vortex tools drainage and gas recovery effects according to TOPSIS method

description: A new index for the evaluation of the effect of vortex tools is proposedAn evaluation model (SCORE model) was developed to more intuitively predict the effectiveness of using vortex toolsThe effect of the vortex tools in the actual wells is consistent with the SCORE model prediction points.The SCORE model can predict the effects of vortex tools and provides reference values for determining whether vortex tools are suitable for actual gas field production. A new index for the evaluation of the effect of vortex tools is proposed An evaluation model (SCORE model) was developed to more intuitively predict the effectiveness of using vortex tools The effect of the vortex tools in the actual wells is consistent with the SCORE model prediction points. The SCORE model can predict the effects of vortex tools and provides reference values for determining whether vortex tools are suitable for actual gas field production.
DOI: 10.6084/m9.figshare.8164316.v1
title: MOESM1 of Analysis of the SNP rs3747333 and rs3747334 in NLGN4X gene in autism spectrum disorder: a meta-analysis

description: Additional file 1. Supplementary material.
DOI: 10.6084/m9.figshare.8164337.v1
title: Additional file 10: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S6. Differentially expressed miRNA and target gene expression in peanut embryos. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.8164343
title: Additional file 11: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S7. KEGG pathways of the targets of differentially expressed miRNAs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8164346
title: Additional file 12: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S8. Specific primer sequences used for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8164388
title: Additional file 9: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S5. Summary of miRNA candidates identified in peanut. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.20222889
title: Autophagy and its mediated mitochondrial quality control maintain pollen tube growth and male fertility in Arabidopsis

description: Macroautophagy/autophagy, a major catabolic pathway in eukaryotes, participates in plant sexual reproduction including the processes of male gametogenesis and the self-incompatibility response. Rapid pollen tube growth is another essential reproductive process that is metabolically highly demanding to drive the vigorous cell growth for delivery of male gametes for fertilization in angiosperms. Whether and how autophagy operates to maintain the homeostasis of pollen tubes remains unknown. Here, we provide evidence that autophagy is elevated in growing pollen tubes and critically required during pollen tube growth and male fertility in Arabidopsis. We demonstrate that SH3P2, a critical non-ATG regulator of plant autophagy, colocalizes with representative ATG proteins during autophagosome biogenesis in growing pollen tubes. Downregulation of <i>SH3P2</i> expression significantly disrupts Arabidopsis pollen germination and pollen tube growth. Further analysis of organelle dynamics reveals crosstalk between autophagosomes and prevacuolar compartments following the inhibition of phosphatidylinositol 3-kinase. In addition, time-lapse imaging and tracking of ATG8e-labeled autophagosomes and depolarized mitochondria demonstrate that they interact specifically <i>via</i> the ATG8-family interacting motif (AIM)-docking site to mediate mitophagy. Ultrastructural identification of mitophagosomes and two additional forms of autophagosomes imply that multiple types of autophagy are likely to function simultaneously within pollen tubes. Altogether, our results suggest that autophagy is functionally crucial for mediating mitochondrial quality control and canonical cytoplasm recycling during pollen tube growth. <b>Abbreviations:</b> AIM: ATG8-family interacting motif; ATG8: autophagy related 8; ATG5: autophagy related 5; ATG7: autophagy related 7; BTH: acibenzolar-S-methyl; DEX: dexamethasone; DNP: 2,4-dinitrophenol; GFP: green fluorescent protein; YFP: yellow fluorescent protein; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; PVC: prevacuolar compartment; SH3P2: SH3 domain-containing protein 2.
DOI: 10.6084/m9.figshare.6591464.v1
title: The development of a decision aid for tinnitus

description: <b>Objective:</b> To develop a decision aid for tinnitus care that would meet international consensus for decision aid quality. <b>Design:</b> A mixed methods design that included qualitative in-depth interviews, literature review, focus groups, user testing and readability checking. <b>Study sample:</b> Patients and clinicians who have clinical experience of tinnitus. <b>Results:</b> A decision aid for tinnitus care was developed. This incorporates key evidence of efficacy for the most frequently used tinnitus care options, together with information derived from patient priorities when deciding which choice to make. <b>Conclusion:</b> The decision aid has potential to enable shared decision making between clinicians and patients in audiology. The decision aid meets consensus standards.
DOI: 10.6084/m9.figshare.8164316
title: MOESM1 of Analysis of the SNP rs3747333 and rs3747334 in NLGN4X gene in autism spectrum disorder: a meta-analysis

description: Additional file 1. Supplementary material.
DOI: 10.6084/m9.figshare.24942342
title: Start Learning Coding without a Computer A Case Study on Children’s Gamified Coding Education Tool with Explanatory Sequential Mixed Method-DATA.xlsx

description: The survey data for the paper “Start Learning Coding without a Computer? A Case Study on Children’s Gamified Coding Education Tool with Explanatory Sequential Mixed Method”.
DOI: 10.6084/m9.figshare.7639967.v1
title: Baseline-covariate adjusted confidence interval for proportional difference between two treatment groups in clinical trials

description: The treatment effect of a therapeutic product on a binary endpoint is often expressed as the difference in proportions of subjects with the outcome of interest between the treated and control groups of a clinical trial. Analysis of the proportional difference and construction of the associated confidence interval (CI) is often complicated due to the baseline covariate(s) being associated with the primary endpoint. Analysis adjusting for such baseline covariate(s) generally improves efficiency of hypothesis testing and precision of treatment effect estimation, and avoids possible bias caused by baseline covariate imbalances. Most existing literatures focus on constructing unadjusted or categorical covariate(s) adjusted only CI, which provides very limited advice on how different statistical methods perform and which method is optimal in terms of constructing both categorical and continuous baseline covariate(s) adjusted CI for proportional difference. We review and compare the performance of three commonly used model-based methods as well as the traditional non-parametric weighted-difference methods for the construction of covariate-adjusted CI for proportional difference via a real data application and simulations. The coverage of 95% CI, type I error control, and power are examined. We also examine the factors leading to the model convergence failure in different scenarios via simulations.
DOI: 10.6084/m9.figshare.8164238.v1
title: Additional file 1: of Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome

description: Table S1. The complete list of annotated MTB HPs. Table S2. The 67 annotated proteins identified by searching against genomes of other MTB strains. (XLSX 141 kb)
DOI: 10.6084/m9.figshare.8164373.v1
title: Additional file 5: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S1. Summary of data from the sequencing of peanut sRNA libraries. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8164382
title: Additional file 7: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S3. Size distribution of sRNA sequences. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7639967.v2
title: Baseline-Covariate Adjusted Confidence Interval for Proportional Difference Between Two Treatment Groups in Clinical Trials

description: The treatment effect of a therapeutic product on a binary endpoint is often expressed as the difference in proportions of subjects with the outcome of interest between the treated and control groups of a clinical trial. Analysis of the proportional difference and construction of the associated confidence interval (CI) is often complicated due to the baseline covariate(s) being associated with the primary endpoint. Analysis adjusting for such baseline covariate(s) generally improves efficiency of hypothesis testing and precision of treatment effect estimation, and avoids possible bias caused by baseline covariate imbalances. Most existing literatures focus on constructing unadjusted or categorical covariate(s) adjusted only CI, which provides very limited advice on how different statistical methods perform and which method is optimal in terms of constructing both categorical and continuous baseline covariate(s) adjusted CI for proportional difference. We review and compare the performance of three commonly used model-based methods as well as the traditional nonparametric weighted-difference methods for the construction of covariate-adjusted CI for proportional difference via a real data application and simulations. The coverage of 95% CI, Type I error control, and power are examined. We also examine the factors leading to the model convergence failure in different scenarios via simulations.
DOI: 10.6084/m9.figshare.8164385.v1
title: Additional file 8: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S4. Distribution of the identity of the first nucleotide of different lengths of novel sRNAs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6591464
title: The development of a decision aid for tinnitus

description: <b>Objective:</b> To develop a decision aid for tinnitus care that would meet international consensus for decision aid quality. <b>Design:</b> A mixed methods design that included qualitative in-depth interviews, literature review, focus groups, user testing and readability checking. <b>Study sample:</b> Patients and clinicians who have clinical experience of tinnitus. <b>Results:</b> A decision aid for tinnitus care was developed. This incorporates key evidence of efficacy for the most frequently used tinnitus care options, together with information derived from patient priorities when deciding which choice to make. <b>Conclusion:</b> The decision aid has potential to enable shared decision making between clinicians and patients in audiology. The decision aid meets consensus standards.
DOI: 10.6084/m9.figshare.8164379
title: Additional file 6: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S2. Mapping results of sRNA sequences and the peanut genome. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8164388.v1
title: Additional file 9: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S5. Summary of miRNA candidates identified in peanut. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8164337
title: Additional file 10: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S6. Differentially expressed miRNA and target gene expression in peanut embryos. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.8164382.v1
title: Additional file 7: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S3. Size distribution of sRNA sequences. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8164385
title: Additional file 8: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S4. Distribution of the identity of the first nucleotide of different lengths of novel sRNAs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.11834379
title: Additional file 2 of Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)

description: Additional file 2: Table S1. Names, origin, population structure, haplotypes of Rf genes and fertility traits of 337 O. sativa accessions. ‘New’ in the columns of the three Rf genes haplotype indicates that the paternal line carries a novel allele, which does not belong to any main haplotypes in this study. Table S2. Primers used in this study. Table S3. Haplotype classification of Rf4. Red numbers in the Position column indicate selected SNPs to differentiate different haplotypes in the partial sequencing of Rf4. Table S4. Haplotype classification of Rf5. Red numbers in the Position column indicate selected SNPs to differentiate different haplotypes in the partial sequencing of Rf5.
DOI: 10.6084/m9.figshare.8164346.v1
title: Additional file 12: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S8. Specific primer sequences used for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.11834379.v1
title: Additional file 2 of Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.)

description: Additional file 2: Table S1. Names, origin, population structure, haplotypes of Rf genes and fertility traits of 337 O. sativa accessions. ‘New’ in the columns of the three Rf genes haplotype indicates that the paternal line carries a novel allele, which does not belong to any main haplotypes in this study. Table S2. Primers used in this study. Table S3. Haplotype classification of Rf4. Red numbers in the Position column indicate selected SNPs to differentiate different haplotypes in the partial sequencing of Rf4. Table S4. Haplotype classification of Rf5. Red numbers in the Position column indicate selected SNPs to differentiate different haplotypes in the partial sequencing of Rf5.
DOI: 10.6084/m9.figshare.8164343.v1
title: Additional file 11: of Integrated microRNA and transcriptome profiling reveals a miRNA-mediated regulatory network of embryo abortion under calcium deficiency in peanut (Arachis hypogaea L.)

description: Table S7. KEGG pathways of the targets of differentially expressed miRNAs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.11834613
title: Additional file 11 of A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

description: Additional file 11: Table S7. Primer sequences for qRT-PCR and the transformation of rice protoplasts.
DOI: 10.6084/m9.figshare.11834619
title: Additional file 5 of Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napusÂ L.)

description: Additional file 5: Table S1. The phenotypic variation for RRLs in this natural rapeseed population. SE, Standard Error; CV, Coefficient of variation; RRL1, RRL2, RRL3 represent the relative RRL in replication 1, 2 and 3 respectively. RRL_Means was the average value of three RRLs; ** indicate significant correlation at the 1% level.
DOI: 10.6084/m9.figshare.11834649.v1
title: Additional file 9 of Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

description: Additional file 9: Table S5. The primer sequences of qRT – PCR.
DOI: 10.6084/m9.figshare.11834604
title: Additional file 10 of A combined microRNA and transcriptome analyses illuminates the resistance response of rice against brown planthopper

description: Additional file 10: Table S6. Integrated analysis of BPH resistance related miRNAs and their target genes.
DOI: 10.6084/m9.figshare.19698942.v1
title: Circular RNA CircSHKBP1 accelerates the proliferation, invasion, angiogenesis, and stem cell-like properties via modulation of microR-766-5p/high mobility group AT-hook 2 axis in laryngeal squamous cell carcinoma

description: Laryngeal squamous cell carcinoma (LSCC) is a common malignancy in head and neck. Circular SHKBP1 (circSHKBP) exerts momentous functions in the occurrence of many cancers including LSCC. Thus, we investigated the oncogenic capacities of circSHKBP1 in LSCC, and revealed the underlying mechanism as a competing endogenous RNA. The expression levels of circSHKBP1, miR-766-5p, and high mobility group AT-hook 2 (HMGA2) were examined by quantitative real-time PCR and their influences on the overall survival were measured by Kaplan–Meier method. The correlations between circSHKBP1 and miR-766-5p or HMGA2 were detected by Spearman’s rank correlation analysis. <i>In vitro</i>, the influences of circSHKBP1/miR-766-5p/HMGA2 axis on the tumorigenesis of LSCC were examined by CCK-8, transwell, sphere formation, and angiogenesis assays, respectively. circSHKBP1 expression was up-regulated in the LSCC specimens and cell lines. And elevated circSHKBP1 expression was closely linked to poor prognosis. Silencing circSHKBP1 expression restrained cell proliferation, invasion, angiogenesis, stem cell-like properties and tumor growth. We observed that miR-766-5p was down-regulated and negatively correlated to circSHKBP1 in LSCC samples. However, HMGA2 was highly expressed and positively associated with circSHKBP1 in these specimens. Importantly, the levels of circSHKBP1, miR-766-5p, and HMGA2 were closely associated with patients’ clinical parameters including lymph nodes metastasis and TNM stages. Mechanistic analysis clarified that circSHKBP1 sponged miR-766-5p to regulate HMGA2, the target of miR-766-5p. Moreover, miR-766-5p inhibition and overexpression of HMGA2 rescued the tumor-suppressing roles of circSHKBP1 downregulation in LSCC. In conclusion, circSHKBP1 accelerated the tumorigenesis of LSCC via modulating HMGA2 by targeting miR-766-5p.
DOI: 10.6084/m9.figshare.8164403
title: Additional file 4: of Both chronic HBV infection and naturally acquired HBV immunity confer increased risks of B-cell non-Hodgkin lymphoma

description: Table S2. Main characteristics of the case-control studies evaluating the association between HBV infection and NHL. Abbreviations: ICD-O3 = International Classification of Disease for Oncology 3rd edition; SEER = Surveillance, Epidemiology, and Results; ICD-10 = International Classification of Diseases-10th revision. (XLS 41 kb)
DOI: 10.6084/m9.figshare.11834649
title: Additional file 9 of Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

description: Additional file 9: Table S5. The primer sequences of qRT – PCR.
DOI: 10.6084/m9.figshare.8164406
title: Additional file 5: of Both chronic HBV infection and naturally acquired HBV immunity confer increased risks of B-cell non-Hodgkin lymphoma

description: Table S3. Main characteristics of the cohort studies evaluating the association between HBV infection and NHL. Abbreviations: NSW = New South Wales; RCIPD = Registry for Catastrophic Illness Patient Database. (XLS 30 kb)
DOI: 10.6084/m9.figshare.11834637
title: Additional file 7 of Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napusÂ L.)

description: Additional file 7: Table S3. The information for top 20 enriched pathways for genes in the associated regions.
DOI: 10.6084/m9.figshare.20222554
title: Additional file 3 of Sequence, structure, and function of the Dps DNA-binding protein from Deinococcus wulumuqiensis R12

description: Additional file 3. MS_identified_information.
DOI: 10.6084/m9.figshare.8164406.v1
title: Additional file 5: of Both chronic HBV infection and naturally acquired HBV immunity confer increased risks of B-cell non-Hodgkin lymphoma

description: Table S3. Main characteristics of the cohort studies evaluating the association between HBV infection and NHL. Abbreviations: NSW = New South Wales; RCIPD = Registry for Catastrophic Illness Patient Database. (XLS 30 kb)