900 Works

Additional file 1 of 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
Additional file 1: Table A1. The meaning and value of covariates. Table A2. Demographic characteristics of scarlet fever in Sichuan Province, 2016–2019. Fig. A1. Time series of scarlet fever counts in 21 cities (/prefectures) of Sichuan province from 2016 to 2019. Figure A2. The fitted values for 21 cities (/prefectures) in Sichuan Province during 2016–2019. Fig. A3. The estimated multiplicative effect of seasonality on the endemic mean. Table A3. Model selection and comparison. Table A4....

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
Abstract Objective Hyperhomocysteinemia (HHcy) is considered to increase the risk of sarcopenia (S) and remains controversial. In this study, we aimed to investigate the prevalence of S among older Chinese adults and explore whether homocysteine (Hcy) was independently associated with S. Methods This cross-sectional study was performed among older adults hospitalized in the Geriatric Hospital of Nanjing Medical University between June 2017 and December 2021. We measured all participants’ serum Hcy levels, hand grip strength,...

Additional file 24 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 24: Table S2. The Impacts of Somatic Copy Number Alterations in PDAC Cohort. Table S2A Matrix of amplification peaks, followed by the genes contained in them, 95% confidence level. Table S2B Matrix of deletion peaks, followed by the genes contained in them, 95% confidence level. Table S2C Matrix of the top 10 mutated genes in PDAC of Fudan cohort. Table S2D Matrix of the 10 mutated genes used in Figure 1C of ICGC,...

Additional file 27 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 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

Additional file 27 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 27: Table S5. 8p11.22 Amplification Associated with PDAC Metastasis. Table S5A The matrix describing mutations in PDAC metastatic patients and non-metastatic patients. Table S5B Matrix of GSVA scores of pathways significantly altered in PDAC metastatic patients and non-metastatic patients, proteome level. Table S5C Matrix of xCell signatures significantly altered in PDAC metastatic patients and non-metastatic patients, transcriptome level. Table S5D Matrix describing the cis-effects of genes located on chromosome 8p11.22. Table S5E Matrix...

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 11 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 11: Fig. S11. Multi-omics subtypes of PDAC patients, related to Fig. 6. A Consensus matrices of identified clusters (k = 2 to 4) of transcriptomic, proteomic, and phosphoproteomic subtypes. B The consensus CDF and delta area (change in CDF area) plots, as well as the silhouette plots, are shown. C Heatmaps showing the comparison between transcriptomic and phosphoproteomic subtypes (columns) with proteomic subtypes (rows). Each row sums to one, with different entries showing...

Additional file 12 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 12: Fig. S12. Multi-omics characteristics of the three proteomic subtypes, related to Fig. 6. A Bar plot showing the number of overexpressed molecules in each proteomic subtypes at both proteome and transcriptome level. B Heatmap of the characteristic molecules of each proteomic subtypes at proteome (left) and transcriptome (right) level. Molecules previously reported to be associated with PDAC are marked in red. C Scatter plot displaying the significance of molecules that highest expressed...

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 2 of LncRNA CEBPA-DT promotes liver cancer metastasis through DDR2/β-catenin activation via interacting with hnRNPC

Yunshi Cai, Tao Lyu, Hui Li, Chang Liu, Kunlin Xie, Lin Xu, Wei Li, Hu Liu, Jiang Zhu, Yinghao Lyu, Xuping Feng, Tian Lan, Jiayin Yang & Hong Wu
Additional file 2: Fig. S1. A Schematic diagram of the genomic locus of CEBPA-DT (www.ncbi.nlm.nih.gov/). B The protein-coding potential of CEBPA-DT predicted by Open reading frame (ORF) Finder software prediction ( https://www.ncbi.nlm.nih.gov/orffinder/ ). C The protein-coding potential of CEBPA-DT predicted by Coding-Potential Assessment Tool ( wlcb.oit.uci.edu/cpat/ ).

Additional file 5 of LncRNA CEBPA-DT promotes liver cancer metastasis through DDR2/β-catenin activation via interacting with hnRNPC

Yunshi Cai, Tao Lyu, Hui Li, Chang Liu, Kunlin Xie, Lin Xu, Wei Li, Hu Liu, Jiang Zhu, Yinghao Lyu, Xuping Feng, Tian Lan, Jiayin Yang & Hong Wu
Additional file 5: Fig. S4. A Clustering heatmap of significant differentially expressed mRNAs in HCCLM9 cells transfected with negative control or CEBPA-DT siRNAs. B Significantly enriched pathways annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. C Significantly enriched pathways annotated by the Gene Ontology (GO) database. D Significantly enriched pathways annotated by the Molecular Signatures Database (MSigDB). E The binding sites of hnRNPC and 3’UTR of DDR2 were predicted by PRIdictor database...

Additional file 6 of LncRNA CEBPA-DT promotes liver cancer metastasis through DDR2/β-catenin activation via interacting with hnRNPC

Yunshi Cai, Tao Lyu, Hui Li, Chang Liu, Kunlin Xie, Lin Xu, Wei Li, Hu Liu, Jiang Zhu, Yinghao Lyu, Xuping Feng, Tian Lan, Jiayin Yang & Hong Wu
Additional file 6: Fig. S5. A-B The expression levels of DDR2 were measured by western blot and RT-qPCR in indicated HCCLM9 and SNU-449 cells transfected with negative control siRNA or siRNAs targeting DDR2. C-D Cell migration capacity of indicated HCCLM9 and SNU-449 cells were measured by scratch wound-healing assays. Scale bar, 100μm. E-F Cell migration and invasion capacity of indicated HCCLM9 and SNU-449 cells were measured by transwell migration and matrigel invasion assays. Scale bar,...

Integrated physiological and transcriptional dissection reveals the core genes involving nutrient transport and osmoregulatory substance biosynthesis in allohexaploid wheat seedlings under salt stress

Jun-fan Chen, Ying Liu, Tian-yu Zhang, Zheng-fu Zhou, Jin-yong Huang, Ting Zhou & Ying-peng Hua
Abstract Background Soil salinization has become a global problem restricting the seed yield and quality of crops, including wheat (Triticum aestivum L.). Salinity significantly alters plant morphology and severely disrupts physiological homeostasis. Salt tolerance of wheat has been widely studied whereas core ion transporters responsive to salt stress remain elusive. Results In this study, the wheat seedlings were subjected to salinity toxicity for morpho-physiological and transcriptomic analysis of wheat salt tolerance. There was a inversely...

Additional file 17 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 17: Table S10: Acetylation and succinylation modification of Histone proteins in bermudagrass stolon.

Additional file 1 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 1: Figure S1: Western blot detection of holistic protein acetylation and succinylation levels in the stolons of bermudagrass plants under sodium butyrate and sodium malonate treatments. Protein (A) acetylation and (B) succinylation levels were decreased as the treatment concentrations of sodium butyrate and sodium malonate increase. C 20 μg of protein samples were run in SDSPAGE as a loading control for western blotting.

Additional file 2 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 2: Figure S2: Statistics of the matched spectra in acetylome and succinylome profiling data. Distribution of identified peptides according to the peptide length (A, B), precursor ion tolerance (C, D), unique peptide number (E, F) and protein coverage (G, H) in the acetylome (red color) and succinylome (green color) profiling experiments.

Additional file 4 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 4: Figure S4: Acetylation of ribosome subunit proteins in bermudagrass stolons. Proteins with/without PTMs were shown in red/black colors. The numbers of acetylation modification on each protein were marked as indicated.

Additional file 5 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 5: Figure S5: COG functional classification of the acetylated and succinylated proteins with conserved acetylation and succinylation site.

Additional file 5 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 5: Figure S5: COG functional classification of the acetylated and succinylated proteins with conserved acetylation and succinylation site.

Additional file 7 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 7: Figure S7: Raw SDS-PAGE gel image showing the protein purification results. The cropped gels shown as figure 7C and D were extracted from this raw gel.

Additional file 8 of Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Additional file 8: Table S1: Statistics of peptide spectra obtained in this study.

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Bing Zhang, Zhuoting Chen, Qixue Sun & Jianxiu Liu
Abstract Background Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for the fast propagation of bermudagrass plants through asexual clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level. Results In this study, we comprehensively analyzed the acetylation and succinylation modifications of proteins in fast-growing stolons of the bermudagrass cultivar Yangjiang. A total of 4657 lysine acetylation sites...

Typologies of Intergenerational Relations in Urban and Rural China: A Latent Class Analysis

Ning Wang, Maria Evandrou, Jane Falkingham & Maodi Xu
Understanding intergenerational relations in China has become increasingly important against a backdrop of rapid social and demographic transitions and an ongoing urban-rural divide. From the parental perspective, this research investigates patterns and determinants of intergenerational relations between middle-aged and older parents and their non-coresident children in urban and rural China using data from the China Health and Retirement Longitudinal Study (2018) (N = 14,616). Latent class analysis revealed three typologies of intergenerational relations found across...

CIED-Stack gas concentrations, 2015-2018

Ling Tang, Min Jia, Junai Yang, Ling Li, Xin Bo & Zhifu Mi
The Chinese Industrial Emissions Database (CIED) provides inventory of particulate matter (PM), SO2 and NOX from Chinese industries from 2015 to 2018, based on direct measurements from China’s continuous emission monitoring systems (CEMS) network. This document provides stack gas concentrations for China’s different industrial emission sources.

Additional file 4 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 4: Table S3. CBL protein sequences used to build phylogenetic tree.

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