cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7638062
title: Comparative transcriptomic analysis reveals gene expression changes during early stages of <i>Plasmodiophora brassicae</i> infection in cabbage (<i>Brassica oleracea</i> var. <i>capitata</i> L.)

description: Clubroot caused by <i>Plasmodiophora brassicae</i> is an economically important disease of crucifer crops throughout the world and is a major threat to the quality and yield of cabbage (<i>Brassica oleracea</i> var. <i>capitata</i> L.) in China. Host resistance is essential for clubroot management. Although two cabbage lines (clubroot-resistant line CR21 and clubroot-susceptible line CS54) have been identified through screening 80 cabbage accessions, the molecular mechanisms underlying differential responses to clubroot remain elusive. Herein, RNA-seq analysis was performed to characterize the transcriptomic changes in CR21 and CS54 at 3 days after <i>P. brassicae</i> inoculation (DAI). In total, 1057 and 4741 differentially expressed genes (DEGs) were found in CR21 and CS54, respectively. Moreover, 541 genes were up-regulated in CR21, but showed either no significant change or were down-regulated in CS54. Gene Ontology (GO) analysis showed that most DEGs were involved in metabolism, transport, signal transduction and defence. Compared with the identified putative defence response genes in <i>Arabidopsis thaliana</i>, 165 resistance-related DEGs were obtained, including PAMPs-triggered immunity (PTI)-related genes and Effector-triggered-immunity (ETI)-related genes. Interestingly, the co-supported defence response DEGs contained the defence-related genes, wound response genes, <i>RBOHB, WRKY28</i>, TIR-NBS-LRR class (<i>RPS4</i> etc.), pathogenesis-related (PR) gene (<i>Bo7g005050</i>), lipid transfer protein class (<i>LTP1</i> etc.), plant hormone-related genes, ethylene signalling transduction (<i>HRE1</i>-like gene and <i>EIN3</i>), ABA signalling (<i>PP2C</i> and <i>PYL13</i>), and cell wall modification related genes (<i>EXP17</i> and <i>PME44</i>, beta-1,3-glucanase and cytochrome P450 genes). Taken together, this study provided a comprehensive insight into transcriptomic responses to <i>P. brassicae</i> infection in two different cabbage lines, and identified several candidate genes that might contribute to clubroot resistance in cabbage and other <i>Brassica</i> crops.
DOI: 10.6084/m9.figshare.7638062.v1
title: Comparative transcriptomic analysis reveals gene expression changes during early stages of <i>Plasmodiophora brassicae</i> infection in cabbage (<i>Brassica oleracea</i> var. <i>capitata</i> L.)

description: Clubroot caused by <i>Plasmodiophora brassicae</i> is an economically important disease of crucifer crops throughout the world and is a major threat to the quality and yield of cabbage (<i>Brassica oleracea</i> var. <i>capitata</i> L.) in China. Host resistance is essential for clubroot management. Although two cabbage lines (clubroot-resistant line CR21 and clubroot-susceptible line CS54) have been identified through screening 80 cabbage accessions, the molecular mechanisms underlying differential responses to clubroot remain elusive. Herein, RNA-seq analysis was performed to characterize the transcriptomic changes in CR21 and CS54 at 3 days after <i>P. brassicae</i> inoculation (DAI). In total, 1057 and 4741 differentially expressed genes (DEGs) were found in CR21 and CS54, respectively. Moreover, 541 genes were up-regulated in CR21, but showed either no significant change or were down-regulated in CS54. Gene Ontology (GO) analysis showed that most DEGs were involved in metabolism, transport, signal transduction and defence. Compared with the identified putative defence response genes in <i>Arabidopsis thaliana</i>, 165 resistance-related DEGs were obtained, including PAMPs-triggered immunity (PTI)-related genes and Effector-triggered-immunity (ETI)-related genes. Interestingly, the co-supported defence response DEGs contained the defence-related genes, wound response genes, <i>RBOHB, WRKY28</i>, TIR-NBS-LRR class (<i>RPS4</i> etc.), pathogenesis-related (PR) gene (<i>Bo7g005050</i>), lipid transfer protein class (<i>LTP1</i> etc.), plant hormone-related genes, ethylene signalling transduction (<i>HRE1</i>-like gene and <i>EIN3</i>), ABA signalling (<i>PP2C</i> and <i>PYL13</i>), and cell wall modification related genes (<i>EXP17</i> and <i>PME44</i>, beta-1,3-glucanase and cytochrome P450 genes). Taken together, this study provided a comprehensive insight into transcriptomic responses to <i>P. brassicae</i> infection in two different cabbage lines, and identified several candidate genes that might contribute to clubroot resistance in cabbage and other <i>Brassica</i> crops.
DOI: 10.6084/m9.figshare.11308082
title: MOESM1 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

description: Additional file 1. Proportion of total bacterial (A) and fungal (B) reads assigned to taxonomic ranks.
DOI: 10.6084/m9.figshare.11308082.v1
title: MOESM1 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

description: Additional file 1. Proportion of total bacterial (A) and fungal (B) reads assigned to taxonomic ranks.
DOI: 10.6084/m9.figshare.11308085
title: MOESM6 of Microarray and metabolome analysis of hepatic response to fasting and subsequent refeeding in zebrafish (Danio rerio)

description: Additional file 6. Primer sequences used for quantitative real-time PCR (qPCR).
DOI: 10.6084/m9.figshare.11308085.v1
title: MOESM6 of Microarray and metabolome analysis of hepatic response to fasting and subsequent refeeding in zebrafish (Danio rerio)

description: Additional file 6. Primer sequences used for quantitative real-time PCR (qPCR).
DOI: 10.6084/m9.figshare.11308088
title: MOESM2 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

description: Additional file 2. Core microbiomes in different compartments of C. panzhihuaensis revealed by 16S rRNA gene and ITS sequences, and their significant levels.
DOI: 10.6084/m9.figshare.11308088.v1
title: MOESM2 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

description: Additional file 2. Core microbiomes in different compartments of C. panzhihuaensis revealed by 16S rRNA gene and ITS sequences, and their significant levels.
DOI: 10.6084/m9.figshare.9735239
title: Electrical and thermal analyses of catheter-based irreversible electroporation of digestive tract

description: <b>Introduction:</b> Irreversible electroporation (IRE) combined with a catheter-based electrode during endoscopy is a potential alternative treatment method for digestive tract tumors. The aim of this study was to investigate the electrical injury (EI) and thermal injury (TI) to the digestive tract via numerical analyses and to evaluate the role and impact of electrode configurations and pulse settings on the efficacy and outcomes of IRE. <b>Materials and methods:</b> A finite element method was used to solve the numerical model. A digestive tract model having 4-mm-thick walls and two catheter-based electrode configuration models were constructed. The distributions of electric fields, temperature, electrical conductivity, tissue injury and limitation on the pulse number required for IRE were calculated and compared. <b>Results:</b> Electrode length is an important geometric parameter for electrodes in the monopolar model (MPM), while electrode spacing affects the outcomes in the bipolar model (BPM). Increasing the pulse voltage reduces the pulse number required for tissue ablation, while increasing the risk of TI. In total, there were 6 NT-IRE protocols, 12 thermal-IRE protocols and 30 TI protocols. All of the NT-IRE protocols were set in BPMs with a voltage of 0.50 kV. With increasing electrode spacing, the minimum pulse number decreased. However, thermal effects were inevitable in the MPM. <b>Conclusions:</b> The electrode configuration and pulse settings are adjusted to achieve NT-IRE synergistically. The BPM is more reliable for achieving NT-IRE in 4-mm-thick digestive wall. Future <i>in vitro</i> and <i>in vivo</i> studies are needed to support and validate this conclusion.
DOI: 10.6084/m9.figshare.9735239.v1
title: Electrical and thermal analyses of catheter-based irreversible electroporation of digestive tract

description: <b>Introduction:</b> Irreversible electroporation (IRE) combined with a catheter-based electrode during endoscopy is a potential alternative treatment method for digestive tract tumors. The aim of this study was to investigate the electrical injury (EI) and thermal injury (TI) to the digestive tract via numerical analyses and to evaluate the role and impact of electrode configurations and pulse settings on the efficacy and outcomes of IRE. <b>Materials and methods:</b> A finite element method was used to solve the numerical model. A digestive tract model having 4-mm-thick walls and two catheter-based electrode configuration models were constructed. The distributions of electric fields, temperature, electrical conductivity, tissue injury and limitation on the pulse number required for IRE were calculated and compared. <b>Results:</b> Electrode length is an important geometric parameter for electrodes in the monopolar model (MPM), while electrode spacing affects the outcomes in the bipolar model (BPM). Increasing the pulse voltage reduces the pulse number required for tissue ablation, while increasing the risk of TI. In total, there were 6 NT-IRE protocols, 12 thermal-IRE protocols and 30 TI protocols. All of the NT-IRE protocols were set in BPMs with a voltage of 0.50 kV. With increasing electrode spacing, the minimum pulse number decreased. However, thermal effects were inevitable in the MPM. <b>Conclusions:</b> The electrode configuration and pulse settings are adjusted to achieve NT-IRE synergistically. The BPM is more reliable for achieving NT-IRE in 4-mm-thick digestive wall. Future <i>in vitro</i> and <i>in vivo</i> studies are needed to support and validate this conclusion.
DOI: 10.6084/m9.figshare.20745245.v1
title: Additional file 1 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

description: Additional file 1: Table S1. ICD codes of PAD and T2D. Table S2. MR results between T2D and PAD in Europeans. Table S3. MR results between T2D and PAD in Europeans (without excluding potential pleiotropy SNPs). Table S4. MVMR results between T2D and PAD adjusted by potential risk factors in Europeans. Table S5. Summary of PRS regression of PRS for T2D on PAD status in Europeans. Table S6. Summary of PRS regression of PRS for PAD on T2D status in Europeans. Table S7. Novel SNPs underlying the shared genetics of T2D and PAD in Europeans detected by MTAG. Table S8. Candidate genes associated with comorbid T2D and PAD in Europeans detected by MAGMA. Table S9. Significant SMR associations of gene expression (from Table S8) with T2D, PAD, and their cross-trait. Table S10. MR results between T2D and PAD in East Asians. Table S11. MR results between T2D and PAD in East Asians (without excluding potential pleiotropy SNPs). Table S12. MVMR results between T2D and PAD adjusted by potential risk factors in East Asians. Table S13. Summary of PRS regression of PRS for T2D on PAD status in East Asians. Table S14. Summary of PRS regression of PRS for PAD on T2D status in East Asians. Table S15. Candidate genes associated with comorbid T2D and PAD in East Asians detected by MAGMA. Table S16. Significant SMR associations of gene expression (from Table S15) with T2D, PAD, and their cross-trait. (XLS 383 kb)
DOI: 10.6084/m9.figshare.20745245
title: Additional file 1 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

description: Additional file 1: Table S1. ICD codes of PAD and T2D. Table S2. MR results between T2D and PAD in Europeans. Table S3. MR results between T2D and PAD in Europeans (without excluding potential pleiotropy SNPs). Table S4. MVMR results between T2D and PAD adjusted by potential risk factors in Europeans. Table S5. Summary of PRS regression of PRS for T2D on PAD status in Europeans. Table S6. Summary of PRS regression of PRS for PAD on T2D status in Europeans. Table S7. Novel SNPs underlying the shared genetics of T2D and PAD in Europeans detected by MTAG. Table S8. Candidate genes associated with comorbid T2D and PAD in Europeans detected by MAGMA. Table S9. Significant SMR associations of gene expression (from Table S8) with T2D, PAD, and their cross-trait. Table S10. MR results between T2D and PAD in East Asians. Table S11. MR results between T2D and PAD in East Asians (without excluding potential pleiotropy SNPs). Table S12. MVMR results between T2D and PAD adjusted by potential risk factors in East Asians. Table S13. Summary of PRS regression of PRS for T2D on PAD status in East Asians. Table S14. Summary of PRS regression of PRS for PAD on T2D status in East Asians. Table S15. Candidate genes associated with comorbid T2D and PAD in East Asians detected by MAGMA. Table S16. Significant SMR associations of gene expression (from Table S15) with T2D, PAD, and their cross-trait. (XLS 383 kb)
DOI: 10.6084/m9.figshare.20745285
title: Additional file 1 of Hypoxia-induced MIF induces dysregulation of lipid metabolism in Hep2 laryngocarcinoma through the IL-6/JAK-STAT pathway

description: Additional file 1. Primer sequences for qPCR.
DOI: 10.6084/m9.figshare.20745248.v1
title: Additional file 2 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

description: Additional file 2: Figure S1. Estimated powers of European- or East Asian-based MR models for the causality between T2D and PAD. Figure S2. The power of PRS regression regarding SNP p-value thresholds of different discovery GWAS. Figure S3. The protein-protein interaction (PPI) network for candidate genes.
DOI: 10.6084/m9.figshare.20745285.v1
title: Additional file 1 of Hypoxia-induced MIF induces dysregulation of lipid metabolism in Hep2 laryngocarcinoma through the IL-6/JAK-STAT pathway

description: Additional file 1. Primer sequences for qPCR.
DOI: 10.6084/m9.figshare.20745248
title: Additional file 2 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

description: Additional file 2: Figure S1. Estimated powers of European- or East Asian-based MR models for the causality between T2D and PAD. Figure S2. The power of PRS regression regarding SNP p-value thresholds of different discovery GWAS. Figure S3. The protein-protein interaction (PPI) network for candidate genes.
DOI: 10.6084/m9.figshare.11308127
title: MOESM1 of Matrix metalloproteinase 7 promoted Schwann cell migration and myelination after rat sciatic nerve injury

description: Additional file 1: Table S1. List of differentially expressed genes in MMP7-treated Schwann cells. Gene ID, symbol, reads, p-value, FDR, gene description, and involved GO terms and KEGG pathways of differentially expressed genes were listed.
DOI: 10.6084/m9.figshare.11308127.v1
title: MOESM1 of Matrix metalloproteinase 7 promoted Schwann cell migration and myelination after rat sciatic nerve injury

description: Additional file 1: Table S1. List of differentially expressed genes in MMP7-treated Schwann cells. Gene ID, symbol, reads, p-value, FDR, gene description, and involved GO terms and KEGG pathways of differentially expressed genes were listed.
DOI: 10.6084/m9.figshare.10259588
title: Tidal common reeds in the Yellow River Delta responding to salt stress_Salt stress treatment

description: Tidal common reed (T) in Yellow River Delta responding to salt stress. T300:（0mmol/L NaCl treatment）：T7, T15, T18.
DOI: 10.6084/m9.figshare.8162438
title: Segmental resection combined with anoplasty for the treatment of circumferential mixed hemorrhoids

description: Circumferential mixed hemorrhoids are very difficult to treat non-surgically. Therefore, it is important to explore the surgical methods for its complete resolution as well as maintenance of normal anal anatomy and function. The present study was designed to evaluate the effect of segmented and plastic hemorrhoidectomy (SPH) on patients with circumferential mixed hemorrhoids. A total of 300 patients with circumferential mixed hemorrhoids were divided into experimental group (n=150) undergoing SPH and control group (n=150) undergoing Milligan-Morgan hemorrhoidectomy. There were no differences in cure and effectiveness rates between two groups. Compared with the control group, patients in the experimental group had shorter healing time (15.7±1.3 vs 12.5±0.7 days) and recovery to normal activity (18.5±2.7 vs 14.7±1.2 days). In addition, anal function of all patients in the experimental group was normal during short- and long-term follow-up. However, more cases in the control group showed anal dampness and itching, and poor control of intestinal liquid. Compared with the control group, patients in the experimental group had better outcomes in overall anal function and smoothness at 6, 12, and 18 months after operation as well as patient satisfaction. Furthermore, the rating in the visual analogue scale for defecation pain and edema in the experimental group was less than that in the control group. SPH was more effective, had fewer complications, better protection of anal function, and a better cosmetic result.
DOI: 10.6084/m9.figshare.8162438.v1
title: Segmental resection combined with anoplasty for the treatment of circumferential mixed hemorrhoids

description: Circumferential mixed hemorrhoids are very difficult to treat non-surgically. Therefore, it is important to explore the surgical methods for its complete resolution as well as maintenance of normal anal anatomy and function. The present study was designed to evaluate the effect of segmented and plastic hemorrhoidectomy (SPH) on patients with circumferential mixed hemorrhoids. A total of 300 patients with circumferential mixed hemorrhoids were divided into experimental group (n=150) undergoing SPH and control group (n=150) undergoing Milligan-Morgan hemorrhoidectomy. There were no differences in cure and effectiveness rates between two groups. Compared with the control group, patients in the experimental group had shorter healing time (15.7±1.3 vs 12.5±0.7 days) and recovery to normal activity (18.5±2.7 vs 14.7±1.2 days). In addition, anal function of all patients in the experimental group was normal during short- and long-term follow-up. However, more cases in the control group showed anal dampness and itching, and poor control of intestinal liquid. Compared with the control group, patients in the experimental group had better outcomes in overall anal function and smoothness at 6, 12, and 18 months after operation as well as patient satisfaction. Furthermore, the rating in the visual analogue scale for defecation pain and edema in the experimental group was less than that in the control group. SPH was more effective, had fewer complications, better protection of anal function, and a better cosmetic result.
DOI: 10.6084/m9.figshare.8162453
title: Effect of artemisinin-piperaquine treatment on the electrocardiogram of malaria patients

description: Abstract INTRODUCTION: Concern regarding the cardiotoxicity of antimalarials has been renewed because of their potential to cause QT/QTc interval prolongation related to torsade de pointes (TdP). Artemisinin-piperaquine (AP) is considered an effective artemisinin-based combination therapy (ACT) for malaria. METHODS: This study involved a retrospective analysis of clinical data of 93 hospitalized malaria patients who had received AP orally. Electrocardiograms (ECGs) were obtained at specific time points in the original study. RESULTS: Some cases of QT prolongation were observed. However, no TdP was found. CONCLUSIONS: AP may cause QT interval prolongation in some malaria patients but may not lead to TdP.
DOI: 10.6084/m9.figshare.8162453.v1
title: Effect of artemisinin-piperaquine treatment on the electrocardiogram of malaria patients

description: Abstract INTRODUCTION: Concern regarding the cardiotoxicity of antimalarials has been renewed because of their potential to cause QT/QTc interval prolongation related to torsade de pointes (TdP). Artemisinin-piperaquine (AP) is considered an effective artemisinin-based combination therapy (ACT) for malaria. METHODS: This study involved a retrospective analysis of clinical data of 93 hospitalized malaria patients who had received AP orally. Electrocardiograms (ECGs) were obtained at specific time points in the original study. RESULTS: Some cases of QT prolongation were observed. However, no TdP was found. CONCLUSIONS: AP may cause QT interval prolongation in some malaria patients but may not lead to TdP.
DOI: 10.6084/m9.figshare.16551027
title: Additional file 2 of Combined homologous recombination repair deficiency and immune activation analysis for predicting intensified responses of anthracycline, cyclophosphamide and taxane chemotherapy in triple-negative breast cancer

description: Additional file 2: Table S5. The values for HRD score (transcriptional HRD signature) and immune score of TNBC patients.
DOI: 10.6084/m9.figshare.16551027.v1
title: Additional file 2 of Combined homologous recombination repair deficiency and immune activation analysis for predicting intensified responses of anthracycline, cyclophosphamide and taxane chemotherapy in triple-negative breast cancer

description: Additional file 2: Table S5. The values for HRD score (transcriptional HRD signature) and immune score of TNBC patients.
DOI: 10.6084/m9.figshare.14978212
title: Additional file 5 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 5: Supplementary table 1. Ferroptosis-related genes set
DOI: 10.6084/m9.figshare.14978212.v1
title: Additional file 5 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 5: Supplementary table 1. Ferroptosis-related genes set
DOI: 10.6084/m9.figshare.14978215
title: Additional file 6 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 6: Supplementary table 2. Gene list of immune cells and immune-related functions.
DOI: 10.6084/m9.figshare.14978215.v1
title: Additional file 6 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 6: Supplementary table 2. Gene list of immune cells and immune-related functions.
DOI: 10.6084/m9.figshare.14978218
title: Additional file 7 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 7: Supplementary table 3. GO enrichment results of DEGs between high risk group and low risk group.
DOI: 10.6084/m9.figshare.14978218.v1
title: Additional file 7 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 7: Supplementary table 3. GO enrichment results of DEGs between high risk group and low risk group.
DOI: 10.6084/m9.figshare.14978221
title: Additional file 8 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 8: Supplementary table 4. Pathway enrichment results of DEGs between high risk group and low risk group.
DOI: 10.6084/m9.figshare.14978221.v1
title: Additional file 8 of A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma

description: Additional file 8: Supplementary table 4. Pathway enrichment results of DEGs between high risk group and low risk group.