cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12586705
title: Additional file 9 of Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam)

description: Additional file 9: Table S3. Transcription factor statistics.
DOI: 10.6084/m9.figshare.12586705.v1
title: Additional file 9 of Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam)

description: Additional file 9: Table S3. Transcription factor statistics.
DOI: 10.6084/m9.figshare.17305299
title: Additional file 8 of Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks

description: Additional file 8: Table S5. The KEGG enrichment results of genes annotated by the top 2000 SNPs in GWAS.
DOI: 10.6084/m9.figshare.17305299.v1
title: Additional file 8 of Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks

description: Additional file 8: Table S5. The KEGG enrichment results of genes annotated by the top 2000 SNPs in GWAS.
DOI: 10.6084/m9.figshare.14683880
title: Monitoring Heterogeneous Multivariate Profiles Based on Heterogeneous Graphical Model

description: Process monitoring using profile data remains an important and challenging problem in various manufacturing industries. Motivated by an application case of motherboard testing processes, we develop a novel modeling and monitoring framework for heterogeneous multivariate profiles. In this framework, a heterogeneous graphical model is constructed to depict the complicated heterogeneous relationship among profile channels. Then monitoring the heterogeneous relationship among profile channels can be reduced to monitoring the graphical networks. Besides, we investigate several theoretical results concerning the accuracy of the estimated graphical structure. Finally, we demonstrate the proposed method through extensive simulations and a real case study.
DOI: 10.6084/m9.figshare.14683880.v1
title: Monitoring Heterogeneous Multivariate Profiles Based on Heterogeneous Graphical Model

description: Process monitoring using profile data remains an important and challenging problem in various manufacturing industries. Motivated by an application case of motherboard testing processes, we develop a novel modeling and monitoring framework for heterogeneous multivariate profiles. In this framework, a heterogeneous graphical model is constructed to depict the complicated heterogeneous relationship among profile channels. Then monitoring the heterogeneous relationship among profile channels can be reduced to monitoring the graphical networks. Besides, we investigate several theoretical results concerning the accuracy of the estimated graphical structure. Finally, we demonstrate the proposed method through extensive simulations and a real case study.
DOI: 10.6084/m9.figshare.12586742
title: Additional file 1 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 1: Table S1. Sequences of oligonucleotides used in this study.
DOI: 10.6084/m9.figshare.12586742.v1
title: Additional file 1 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 1: Table S1. Sequences of oligonucleotides used in this study.
DOI: 10.6084/m9.figshare.12586745
title: Additional file 2 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 2: Table S2. Primers used in qRT-PCR experiments.
DOI: 10.6084/m9.figshare.12586745.v1
title: Additional file 2 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 2: Table S2. Primers used in qRT-PCR experiments.
DOI: 10.6084/m9.figshare.12586748
title: Additional file 3 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 3: Table S3. Clinicodemographic characteristics of tibial fracture enrollees (n = 10).
DOI: 10.6084/m9.figshare.12586748.v1
title: Additional file 3 of miR-1323 suppresses bone mesenchymal stromal cell osteogenesis and fracture healing via inhibiting BMP4/SMAD4 signaling

description: Additional file 3: Table S3. Clinicodemographic characteristics of tibial fracture enrollees (n = 10).
DOI: 10.6084/m9.figshare.17305353
title: Additional file 3 of m6A target microRNAs in serum for cancer detection

description: Additional file 3: Table S1. Functional annotation for m6A target miRNAs. Table S2. Differential expression analysis of the m6A target miRNAs between cancer and non-cancer control in serum. Table S3. Identification of eighteen candidate m6A target miRNAs used for constructing diagnostic signature. Table S4. The median value of m6A-miRNAs signature in the 12 cancer types. Table S5. Spearman correlation between the m6A-miRNAs signature and 18 candidate miRNAs.
DOI: 10.6084/m9.figshare.17305353.v1
title: Additional file 3 of m6A target microRNAs in serum for cancer detection

description: Additional file 3: Table S1. Functional annotation for m6A target miRNAs. Table S2. Differential expression analysis of the m6A target miRNAs between cancer and non-cancer control in serum. Table S3. Identification of eighteen candidate m6A target miRNAs used for constructing diagnostic signature. Table S4. The median value of m6A-miRNAs signature in the 12 cancer types. Table S5. Spearman correlation between the m6A-miRNAs signature and 18 candidate miRNAs.
DOI: 10.6084/m9.figshare.22548285
title: Redo Total Aortic Arch Replacement in Patients with Aortic Dissection After Open-Heart Surgery and Long-Term Follow-Up Results

description: ABSTRACT Introduction: The objectives of this study were to investigate the main treatment strategies and long-term follow-up results of aortic dissection surgery after open-heart surgery (ADSOHS) and to analyze the risk factors that cause ADSOHS. Methods: One hundred thirty-seven patients with ADSOHS hospitalized in our hospital from January 2009 to December 2018 were selected as the research object. Long-term follow-up results, complications, mortality, and changes of cardiac function before and after operation were used to explore the value of Sun’s operation. Results: The length of stay in intensive care unit of these 137 patients ranged from 9.5 to 623.75 hours (average of 76.41±97.29 hours), auxiliary ventilation time ranged from 6.0 to 259.83 hours (average of 46.16±55.59 hours), and hospital stay ranged from six to 85 days (average of 25.06±13.04 days). There were seven cases of postoperative low cardiac output, 18 cases of coma and stroke, and six cases of transient neurological dysfunction. A total of 33 patients died; 19 patients died during the perioperative period, 18 died during Sun’s operation and one died during other operation; and 14 patients died during follow-up (January 2021), 12 cases of Sun’s operation and two cases of other operations. Conclusion: ADSOHS treatment strategy is of high application value, and the risk of neurological complications and mortality is low. The main risk factors are postoperative low cardiac output, coma, stroke, and transient neurological dysfunction. The extracorporeal circulation time is relatively long. Short- and long-term follow-up effects are good, and it is worthy of clinical promotion.
DOI: 10.6084/m9.figshare.22548285.v1
title: Redo Total Aortic Arch Replacement in Patients with Aortic Dissection After Open-Heart Surgery and Long-Term Follow-Up Results

description: ABSTRACT Introduction: The objectives of this study were to investigate the main treatment strategies and long-term follow-up results of aortic dissection surgery after open-heart surgery (ADSOHS) and to analyze the risk factors that cause ADSOHS. Methods: One hundred thirty-seven patients with ADSOHS hospitalized in our hospital from January 2009 to December 2018 were selected as the research object. Long-term follow-up results, complications, mortality, and changes of cardiac function before and after operation were used to explore the value of Sun’s operation. Results: The length of stay in intensive care unit of these 137 patients ranged from 9.5 to 623.75 hours (average of 76.41±97.29 hours), auxiliary ventilation time ranged from 6.0 to 259.83 hours (average of 46.16±55.59 hours), and hospital stay ranged from six to 85 days (average of 25.06±13.04 days). There were seven cases of postoperative low cardiac output, 18 cases of coma and stroke, and six cases of transient neurological dysfunction. A total of 33 patients died; 19 patients died during the perioperative period, 18 died during Sun’s operation and one died during other operation; and 14 patients died during follow-up (January 2021), 12 cases of Sun’s operation and two cases of other operations. Conclusion: ADSOHS treatment strategy is of high application value, and the risk of neurological complications and mortality is low. The main risk factors are postoperative low cardiac output, coma, stroke, and transient neurological dysfunction. The extracorporeal circulation time is relatively long. Short- and long-term follow-up effects are good, and it is worthy of clinical promotion.
DOI: 10.6084/m9.figshare.6819674
title: Li H, Mishra M, Ding S, Miyamoto MM (2018) Diversity and dynamics of “Candidatus Endobugula” and other symbiotic bacteria in Chinese populations of the bryozoan, Bugula neritina. Microb Ecol: in press

description: The metagenomics datasets for the geographic and life cycle samples of Li et al. (2018) are presented here in four separate folders: (OR_GEO) original reads for the geographic samples; (FFS_GEO) final filtered sequences for the geographic samples; (OR_LC) original reads for the life cycle samples; and (FFS_LC) final filtered sequences for the life cycle samples. Each separate dataset is labelled with the abbreviation of its sample (see Table 2 and Figure 1 of Li et al., 2018) followed by either “OR” or “FFS” (for original reads or final filtered sequences, respectively). For example, the “SY3_OR” dataset includes the original reads for the SY<sub>3</sub> geographic sample, whereas the “S6_FFS” dataset contains the final filtered sequences for the S6 life cycle collection.
DOI: 10.6084/m9.figshare.22548324
title: Effects of Remote Ischemic Preconditioning on Decreasing Troponin Release in Patients Not Taking Sulfonylureas After Cardiac Surgery – A Meta-Analysis

description: ABSTRACT Introduction: Remote ischemic preconditioning (RIPC) is a new noninvasive myocardial protection strategy that uses blood pressure cuf inflation to simulate transient non-fatal ischemia to protect the myocardium and reduce ischemia-reperfusion injury. Sulfonylureas may mask the effects of RIPC due to their cardioprotec-tive effect. This meta-analysis aimed to evaluate whether RIPC, in the absence of sulfonylureas, reduces troponin release in patients undergoing cardiac surgery. Methods: We conducted a meta-analysis of randomized controlled clinical trials to determine whether RIPC can reduce postoperative troponin release in cardiac surgery patients undergoing cardiopulmonary bypass without treatment with sulfonylureas. The data were normalized to equivalent units prior to the analysis. A random-effects model was used to provide more conservative estimate of the effects in the presence of known or unknown heterogeneity. Results: Six studies with a total of 570 participants were included. The analysis showed that troponin release was lower in the RIPC group than in the control group at six hours (test of standardized mean differences = 0, Z=3.64, P&lt;0.001) and 48 hours (Z=2.72, P=0.007) postoperatively. When the mean of cross-clamping time was &gt; 60 minutes, RIPC reduced troponin release at six hours (Z=2.84, P=0.005), 24 hours (Z=2.64, P=0.008), and 48 hours (Z=2.87, P=0.004) postoperatively. Conclusion: In cardiac surgery patients who are not taking sulfonylureas, RIPC can reduce troponin release at six and 48 hours postoperatively; hence, RIPC may serve significant benefits in certain cardiac surgery patients.
DOI: 10.6084/m9.figshare.22548324.v1
title: Effects of Remote Ischemic Preconditioning on Decreasing Troponin Release in Patients Not Taking Sulfonylureas After Cardiac Surgery – A Meta-Analysis

description: ABSTRACT Introduction: Remote ischemic preconditioning (RIPC) is a new noninvasive myocardial protection strategy that uses blood pressure cuf inflation to simulate transient non-fatal ischemia to protect the myocardium and reduce ischemia-reperfusion injury. Sulfonylureas may mask the effects of RIPC due to their cardioprotec-tive effect. This meta-analysis aimed to evaluate whether RIPC, in the absence of sulfonylureas, reduces troponin release in patients undergoing cardiac surgery. Methods: We conducted a meta-analysis of randomized controlled clinical trials to determine whether RIPC can reduce postoperative troponin release in cardiac surgery patients undergoing cardiopulmonary bypass without treatment with sulfonylureas. The data were normalized to equivalent units prior to the analysis. A random-effects model was used to provide more conservative estimate of the effects in the presence of known or unknown heterogeneity. Results: Six studies with a total of 570 participants were included. The analysis showed that troponin release was lower in the RIPC group than in the control group at six hours (test of standardized mean differences = 0, Z=3.64, P&lt;0.001) and 48 hours (Z=2.72, P=0.007) postoperatively. When the mean of cross-clamping time was &gt; 60 minutes, RIPC reduced troponin release at six hours (Z=2.84, P=0.005), 24 hours (Z=2.64, P=0.008), and 48 hours (Z=2.87, P=0.004) postoperatively. Conclusion: In cardiac surgery patients who are not taking sulfonylureas, RIPC can reduce troponin release at six and 48 hours postoperatively; hence, RIPC may serve significant benefits in certain cardiac surgery patients.
DOI: 10.6084/m9.figshare.24499726
title: <b>Collaborative Software Exploration with Multimedia </b><b>Note </b><b>Taking in Virtual Reality</b> - Online Appendix

description: Structure of this PackageTechnical Implementation (pre-packed portable installation)Eclipse-backendVR-frontendDemonstration VideoExperiment Procedure: structure of the experimentVR SessionsVR Session Script: instructions from the experiment instructor to participantsTutorial: explanation of toolExperiment instructions: task for the studyResultsVR Sessions Activity Timeline: shows for each participant what activity they performed and for how long next to a soundwave illustration of their recorded voice and highlights for time intervals in which they were actively speakingCreated Whiteboards - Session 1Whiteboard 1 (as interactive HTML or as static PNG)Whiteboard 2 (as interactive HTML or as static PNG)Whiteboard 3 (as interactive HTML or as static PNG)Whiteboard 4 (as interactive HTML or as static PNG)Created Whiteboards - Session 2Whiteboard 1 (as interactive HTML or as static PNG)Whiteboard 2 (as interactive HTML or as static PNG)Whiteboard 3 (as interactive HTML or as static PNG)Post-Session Questionnaire: individually filled in by each participant directly after the sessionResults as raw table (including free-text comments)Results as stacked bar chartFeedback from the subject system's original developersResults for Original Developer #1 (includes complete questionnaire)Results for Original Developer #2 (includes complete questionnaire)Results as stacked bar chart<br>
DOI: 10.6084/m9.figshare.5771181.v1
title: Quadratic Majorization for Nonconvex Loss with Applications to the Boosting Algorithm

description: Classical robust statistical methods dealing with noisy data are often based on modifications of convex loss functions. In recent years, nonconvex loss-based robust methods have been increasingly popular. A nonconvex loss can provide robust estimation for data contaminated with outliers. The significant challenge is that a nonconvex loss can be numerically difficult to optimize. This article proposes quadratic majorization algorithm for nonconvex (QManc) loss. The QManc can decompose a nonconvex loss into a sequence of simpler optimization problems. Subsequently, the QManc is applied to a powerful machine learning algorithm: quadratic majorization boosting algorithm (QMBA). We develop QMBA for robust classification (binary and multi-category) and regression. In high-dimensional cancer genetics data and simulations, the QMBA is comparable with convex loss-based boosting algorithms for clean data, and outperforms the latter for data contaminated with outliers. The QMBA is also superior to boosting when directly implemented to optimize nonconvex loss functions. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5771181
title: Quadratic Majorization for Nonconvex Loss with Applications to the Boosting Algorithm

description: Classical robust statistical methods dealing with noisy data are often based on modifications of convex loss functions. In recent years, nonconvex loss-based robust methods have been increasingly popular. A nonconvex loss can provide robust estimation for data contaminated with outliers. The significant challenge is that a nonconvex loss can be numerically difficult to optimize. This article proposes quadratic majorization algorithm for nonconvex (QManc) loss. The QManc can decompose a nonconvex loss into a sequence of simpler optimization problems. Subsequently, the QManc is applied to a powerful machine learning algorithm: quadratic majorization boosting algorithm (QMBA). We develop QMBA for robust classification (binary and multi-category) and regression. In high-dimensional cancer genetics data and simulations, the QMBA is comparable with convex loss-based boosting algorithms for clean data, and outperforms the latter for data contaminated with outliers. The QMBA is also superior to boosting when directly implemented to optimize nonconvex loss functions. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.22548441
title: Cerebral cortex swelling in V180I genetic Creutzfeldt–Jakob disease: comparative imaging study between sporadic and V180I genetic Creutzfeldt–Jakob disease in the early stage

description: The most common genetic Creutzfeldt-Jakob disease (gCJD) in Japan is caused by a point mutation in which isoleucine replaces valine at codon 180 of the prion protein (<i>PrP</i>) gene (V180I gCJD). Evidence suggests that cerebral cortex swelling, which appears as abnormal hyperintensities on diffusion-weighted imaging (DWI), is a characteristic magnetic resonance imaging (MRI) finding of V180I gCJD. However, no study has directly compared the MRI findings between V180I gCJD and sporadic CJD (sCJD). The current study, therefore, aims to clarify the imaging features of V180I gCJD, which would lead to prompt genetic counselling and analysis of the <i>PrP</i> gene, particularly focusing on cerebral cortex swelling. We included 35 patients with sCJD (<i>n</i> = 23) or V180I gCJD (<i>n</i> = 12). Cerebral cortex swelling on T2-weighted imaging (T2WI) or fluid-attenuated inversion recovery (FLAIR) wherein abnormal cortical hyperintensities were observed on DWI, and the distribution of grey matter hyperintensities on DWI were visually evaluated. V180I gCJD patients had significantly more cerebral cortex swelling (100% vs. 13.0%, <i>p</i> &lt; 0.001), an overall correct classification of 91.4%, and parahippocampal gyrus hyperintensities on DWI (100% vs. 39.1%, <i>q</i> = 0.019) than sCJD patients. Cerebral cortical hyperintensities on DWI with swelling on T2WI or FLAIR are characteristic imaging findings of V180I gCJD and are useful for differentiating it from sCJD.
DOI: 10.6084/m9.figshare.22548441.v1
title: Cerebral cortex swelling in V180I genetic Creutzfeldt–Jakob disease: comparative imaging study between sporadic and V180I genetic Creutzfeldt–Jakob disease in the early stage

description: The most common genetic Creutzfeldt-Jakob disease (gCJD) in Japan is caused by a point mutation in which isoleucine replaces valine at codon 180 of the prion protein (<i>PrP</i>) gene (V180I gCJD). Evidence suggests that cerebral cortex swelling, which appears as abnormal hyperintensities on diffusion-weighted imaging (DWI), is a characteristic magnetic resonance imaging (MRI) finding of V180I gCJD. However, no study has directly compared the MRI findings between V180I gCJD and sporadic CJD (sCJD). The current study, therefore, aims to clarify the imaging features of V180I gCJD, which would lead to prompt genetic counselling and analysis of the <i>PrP</i> gene, particularly focusing on cerebral cortex swelling. We included 35 patients with sCJD (<i>n</i> = 23) or V180I gCJD (<i>n</i> = 12). Cerebral cortex swelling on T2-weighted imaging (T2WI) or fluid-attenuated inversion recovery (FLAIR) wherein abnormal cortical hyperintensities were observed on DWI, and the distribution of grey matter hyperintensities on DWI were visually evaluated. V180I gCJD patients had significantly more cerebral cortex swelling (100% vs. 13.0%, <i>p</i> &lt; 0.001), an overall correct classification of 91.4%, and parahippocampal gyrus hyperintensities on DWI (100% vs. 39.1%, <i>q</i> = 0.019) than sCJD patients. Cerebral cortical hyperintensities on DWI with swelling on T2WI or FLAIR are characteristic imaging findings of V180I gCJD and are useful for differentiating it from sCJD.