876 Works

Additional file 3 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 3: Table S1 Analysis of variance for LL, LW and LA in an F1 population using mixed model for two years in two locations (CP and LF)

Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor prognosis. Proteogenomic characterization and integrative proteomic analysis provide a functional context to annotate genomic abnormalities with prognostic value. Methods We performed an integrated multi-omics analysis, including whole-exome sequencing, RNA-seq, proteomic, and phosphoproteomic analysis of 217 PDAC tumors with paired non-tumor adjacent tissues. In vivo functional experiments were performed to further illustrate the biological events related to PDAC tumorigenesis and progression. Results A comprehensive...

Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with poor prognosis. Proteogenomic characterization and integrative proteomic analysis provide a functional context to annotate genomic abnormalities with prognostic value. Methods We performed an integrated multi-omics analysis, including whole-exome sequencing, RNA-seq, proteomic, and phosphoproteomic analysis of 217 PDAC tumors with paired non-tumor adjacent tissues. In vivo functional experiments were performed to further illustrate the biological events related to PDAC tumorigenesis and progression. Results A comprehensive...

Effects of Two Common Binders on Decomposition Mechanism of HMX Molecule Under Linear Temperature Rise

Wanxiao Guo, Yaning Li, Chunyu Pan, Ning Wang, Zhiwei Han, Boliang Wang & Han Ma
The effects of two common binders (BR and F binder) on the thermal decomposition of HMX molecules during linear heating were studied by molecular dynamics simulation. It was found that both binders can induce the decomposition reaction of HMX molecules earlier, promote the conversion of intermediate products to stable products, and reduce the activation energy and potential energy barrier of the system. The induction of the binder in the composite system makes the initial decomposition...

Additional file 20 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 20: Fig. S20. HOGA1 regulated LARP7 expression, related to Fig. 8. A The association of the mRNA expression of HOGA1with prognosis (log-rank test). B Boxplot showing the differential expression of HOGA1 between tumors and NATs in CPTAC cohort (Student’s t test). C Expression of HOGA1, LARP7, CDK1, CCNB1, and CCNB2, in tumor tissues were detected by western blot analysis. N = non-tumor adjacent tissue, T = tumor tissue. D The impacts of HOGA1...

Additional file 26 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 26: Table S4. The Effects of Diabetes on the Proteogenomic Characteristics of PDAC. Table S4A Mutations and arm events information in PDAC patients with or without diabetes history. Table S4B Matrix of differential pathway enrichment in patients with or without diabetes history at mRNA level. Table S4C Matrix of differential pathway enrichment in patients with or without diabetes history at protein level.

Additional file 2 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 2: Fig. S2. Phosphoproteomic characterization, related to Fig. 1. A. MS2 spectrums of the YAP1 at S109 and RB1 at S807. B. IHC staining of YAP1 at S109 and RB1 at S807 in PDAC tumor tissues and NATs. C. Boxplot indicting the phosphosite expression of YAP1_pS109 and RB1_pS807 between tumors and NATs.

Spatiotemporal dynamics and potential ecological drivers of acute respiratory infectious diseases: an example of scarlet fever in Sichuan Province

Cheng Li, Rujun Liao, Wenhui Zhu, Guiyu Jiang, Yumeng Wang, Ling Li, Tao Zhang & Qiang Lv
Abstract Object Scarlet fever is an acute respiratory infectious disease that endangers public health and imposes a huge economic burden. In this paper, we systematically studied its spatial and temporal evolution and explore its potential ecological drivers. The goal of this research is to provide a reference for analysis based on surveillance data of scarlet fever and other acute respiratory infectious illnesses, and offer suggestions for prevention and control. Method This research is based on...

Additional file 10 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 10: Fig. S10. Protein expression changes in PANC-1 cell lines after ADAM9 knocked down and the co-expressed proteins of ADAM9, related to Fig. 5. A The schematic work flow of validation experiments for the protein expression changes after ADAM9 knocked down. B The volcano plot showed the proteins that significantly altered between PANC-1 cells with ADAM9 KD and Scrambled siRNA. The GO processes enriched by proteins downregulated in ADAM9 KD cell lines are...

Additional file 2 of Association between serum homocysteine and sarcopenia among hospitalized older Chinese adults: a cross-sectional study

Bing Lu, Lingyu Shen, Haiqiong Zhu, Ling Xi, Wei Wang & Xiaojun Ouyang
Additional file 2: Fig. S1. Multicollinearity analysis for Hb, ALT and ALB.

Additional file 3 of Prognostic value of creatinine-to-cystatin c ratio in patients with type 2 diabetes mellitus: a cohort study

Wen Wei, Shanggang Li, Jin Liu, Yong Liu, Kaihong Chen, Shiqun Chen, Mei Tu & Hong Chen
Additional file 3: Figure S1. Time-dependent ROC analysis for 5-year Mortality. A The cut-off value is 1.0 for men; B. The cut-off value is 0.8 for women.

Additional file 3 of Prognostic value of creatinine-to-cystatin c ratio in patients with type 2 diabetes mellitus: a cohort study

Wen Wei, Shanggang Li, Jin Liu, Yong Liu, Kaihong Chen, Shiqun Chen, Mei Tu & Hong Chen
Additional file 3: Figure S1. Time-dependent ROC analysis for 5-year Mortality. A The cut-off value is 1.0 for men; B. The cut-off value is 0.8 for women.

Additional file 1 of Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress

Xiao-Xia Zhang, Xiao-Long Ren, Xiao-Tong Qi, Zhi-Min Yang, Xiao-Lei Feng, Tian Zhang, Hui-Jie Wang, Peng Liang, Qi-Ying Jiang, Wen-Jun Yang, Yuan Fu, Min Chen, Zhi-Xi Fu & Bo Xu
Additional file 1: Table S1. Summary of CBL gene characteristics in Medicago and C. arietinum.

Additional file 2 of Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress

Xiao-Xia Zhang, Xiao-Long Ren, Xiao-Tong Qi, Zhi-Min Yang, Xiao-Lei Feng, Tian Zhang, Hui-Jie Wang, Peng Liang, Qi-Ying Jiang, Wen-Jun Yang, Yuan Fu, Min Chen, Zhi-Xi Fu & Bo Xu
Additional file 2: Table S2. Summary of CIPK gene characteristics in Medicago and C. arietinum.

Additional file 6 of Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress

Xiao-Xia Zhang, Xiao-Long Ren, Xiao-Tong Qi, Zhi-Min Yang, Xiao-Lei Feng, Tian Zhang, Hui-Jie Wang, Peng Liang, Qi-Ying Jiang, Wen-Jun Yang, Yuan Fu, Min Chen, Zhi-Xi Fu & Bo Xu
Additional file 6: Table S4. CIPK protein sequences used to build phylogenetic tree.

Additional file 8 of Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress

Xiao-Xia Zhang, Xiao-Long Ren, Xiao-Tong Qi, Zhi-Min Yang, Xiao-Lei Feng, Tian Zhang, Hui-Jie Wang, Peng Liang, Qi-Ying Jiang, Wen-Jun Yang, Yuan Fu, Min Chen, Zhi-Xi Fu & Bo Xu
Additional file 8: Figure S3. Synteny analysis of CBL and CIPK genes among four allelic chromosomes in M. sativa spp. sativa. CBL genes are in red, and CIPK genes are in gray. Red lines represent the collinearity of duplicated CBL genes, and gray lines indicate the collinearity of duplicated CIPK genes. Four sets of chromosomes in chromosome circles are represented by four different colors, light green for the first set of chromosomes (MsaX.1), light blue...

Prognostic value of creatinine-to-cystatin c ratio in patients with type 2 diabetes mellitus: a cohort study

Wen Wei, Shanggang Li, Jin Liu, Yong Liu, Kaihong Chen, Shiqun Chen, Mei Tu & Hong Chen
Abstract Background The serum creatinine-to-cystatin C ratio (Scr/Scys) has been suggested as a surrogate marker of muscle mass and a predictor of adverse outcomes in many diseases. However, the prognostic value of Scr/Scys in patients with type 2 diabetes mellitus (T2DM) is unknown. The aim of this study is to assess the prognostic value of Scr/Scys in patients with T2DM. Methods In this retrospective observational study, we enrolled 3668 T2DM patients undergoing coronary angiography (CAG)....

Self-assembly of DNA nanostructure containing cell-specific aptamer as a precise drug delivery system for cancer therapy in non-small cell lung cancer

Ning Wang, Chang Yu, Tingting Xu, Dan Yao, Lingye Zhu, Zhifa Shen & Xiaoying Huang
Abstract Background As the most common subtype in lung cancer, the precise and efficient treatment for non-small cell lung cancer (NSCLC) remains an outstanding challenge owing to early metastasis and poor prognosis. Chemotherapy, the most commonly used treatment modality, is a difficult choice for many cancer patients due to insufficient drug accumulation in tumor sites and severe systemic side-effects. In this study, we constructed a cell-specific aptamer-modified DNA nanostructure (Apt-NS) as a targeting drug delivery...

Additional file 2 of STEAP3 can predict the prognosis and shape the tumor microenvironment of clear cell renal cell carcinoma

Jiyue Wu, Qing Bi, Xiang Zheng, Huawei Cao, Changzhen Hao, Zejia Sun & Wei Wang
Additional file 2: Table S2: Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis of the STEAP3-related genes.

Additional file 1 of Self-assembly of DNA nanostructure containing cell-specific aptamer as a precise drug delivery system for cancer therapy in non-small cell lung cancer

Ning Wang, Chang Yu, Tingting Xu, Dan Yao, Lingye Zhu, Zhifa Shen & Xiaoying Huang
Additional file 1: Scheme S1. The self-assembly process from single-strand DNA to a structural unit. The detail base sequences of three single-strand DNA, including S6 (aptamer), PP (palindrome probe), and Linker, are displayed in the pattern diagram. Figure S1. 8% PAGE image showing the influence of palindrome sequences on the synthesis of DNA nanostructure. CP (common probe) was instead of PP (palindrome probe). C-NS represented the synthetic products from self-assembly system in the absence of...

Additional file 2 of Interaction of miR-200a-3p with YAP regulates cell proliferation and metastasis differentially in HPV-positive and HPV-negative cervical cancer cells

Hong Chen, Lingling Gu, Min Zhang, Huifen Chen, Hong Liao, Xueping Cao, Lu Yu & Jun Zhang
Additional file 2: Fig. 2H. Full-length blots in Figure 2H C33A (left) and Siha (right) cells. The red solid lines are the figures in the manuscript. Fig. 2J. Full-length blots in Figure 2J C33A (left) and Siha (right) cells. The red solid lines are the figures in the manuscript. Supplementary Fig. S2. Full-length blots in Supplementary Fig S2. The red solid lines are the figures in the manuscript.

Additional file 5 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 5: Table S3. List of 2,061 up-regulated genes (‘sativa’ Vs ‘falcata’).

Additional file 6 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 6: Table S4. List of 1,709 down-regulated genes (‘sativa’ Vs ‘falcata’).

Additional file 6 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 6: Table S4. List of 1,709 down-regulated genes (‘sativa’ Vs ‘falcata’).

Additional file 7 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

Xueqian Jiang, Xijiang Yang, Fan Zhang, Tianhui Yang, Changfu Yang, Fei He, Ting Gao, Chuan Wang, Qingchuan Yang, Zhen Wang & Junmei Kang
Additional file 7: Table S5. The information of the seven candidates.

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