267 Works

Regulation of microRNA miR-197-3p/CDC28 protein kinase regulatory subunit 1B (CKS1B) axis by Circular RNA hsa_circ_0000285 promotes glioma progression

Tao Deng, Yang Liu, Yanlong Yang, Leyong Yuan, Fangfang Liu, Xiaobo Wang, Qiuying Zhang & Mingshui Xie
Circular RNA circ_0000285 is differentially expressed in several malignancies; however, its role in gliomas is under investigation. Reverse transcription quantitative polymerase chain reaction was conducted to evaluate the expression of circ_0000285, miR-197-3p, and CDC28 protein kinase regulatory subunit 1B (CKS1B) in glioma tissues and cells. Cell Counting Kit-8 and Transwell invasion assays coupled with Western blotting analysis using anti-Bax and anti-Bcl-2 antibodies were performed to evaluate cell proliferation, invasion, and apoptosis. Luciferase reporter and AGO2...

Effects of glycerol and glucose on docosahexaenoic acid synthesis in Aurantiochyrium limacinum SFD-1502 by transcriptome analysis

Huaqiu Zhang, Xiangying Zhao, Chen Zhao, Jiaxiang Zhang, Yang Liu, Mingjing Yao & Jianjun Liu
Docosahexaenoic acid (DHA) has numerous functions in adjusting the organic health and pragmatic value in medicine and food field. In this study, we compared glycerol and glucose as the only carbon source for DHA production by Aurantiochytrium. When the glycerol concentration was 120 g/L, the maximum DHA yield was 11.08 g/L, and the DHA yield increased significantly, reaching 47.67% of the total lipid content. When the cells grew in glucose, the DHA proportion was 37.39%....

Bidirectional regulation of structural damage on autophagy in the C. elegans epidermis

Rong Fu, Xiaowan Jiang, Yuyan Yang, Chunxia Wang, Yun Zhang, Yi Zhu & Huimin Zhang
A variety of disturbances such as starvation, organelle damage, heat stress, hypoxia and pathogen infection can influence the autophagic process. However, how the macroautophagy/autophagy machinery is regulated intrinsically by structural damage of the cell remains largely unknown. In this work, we utilized the C. elegans epidermis as the model to address this question. Our results showed that structural damage by mechanical wounding exerted proximal inhibitory effect and distant promotional effect on autophagy within the same...

Risk factors influencing cure of ultrasound-guided microwave ablation for primary hyperparathyroidism

Fangyi Liu, Li Zang, Yang Liu, Xiaoling Yu, Zhigang Cheng, Zhiyu Han, Jie Yu & Ping Liang
To evaluate the potential risk factors influencing cure rate of ultrasound-guided microwave ablation (MWA) for primary hyperparathyroidism (PHPT). Seventy five patients (25 males and 50 females; mean age, 56.80 ± 12.34; age range, 26–85) with PHPT undergoing MWA under ultrasound guidance were enrolled between May 2017 and December 2020. The cure rate and complications were evaluated after treatment. The potential factors influencing cure rate of ultrasound-guided MWA for PHPT were analyzed by univariate and multivariate...

Clinical and molecular characteristics of acute myeloid leukemia with MPL mutation

Yu Chen, Jundan Xie, Zhen Shen, Jie Shi, Suning Chen & Gang Wang
The current study aimed to explore the incidence of MPL mutations and the clinical and molecular characteristics of AML with MPL mutation. In total, 1509 patients with newly diagnosed AML were retrospectively analyzed between January 2017 and December 2020. MPL mutations were detected via next-generation sequencing. During the same period, we also enrolled 30 patients with other myeloid neoplasms (MNs) with MPL mutation, which included myelodysplastic syndrome (n = 15), myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN) (n...

Constructing new acid-activated anticancer peptide by attaching a desirable anionic binding partner peptide

Yun Zhang, Linlin Chang, Hexin Bao, Xiaoyan Wu, Hui Liu, Sanhu Gou, Jingying Zhang & Jingman Ni
Improving the cell selectivity of anticancer peptides (ACPs) is a major hurdle in their clinical utilisation. In this study, a new acid-activated ACP was designed by conjugating a cationic ACP LK to its anionic binding partner peptide (LEH) via a disulphide linker to trigger antitumor activity at acidic pH while masking its killing activity at normal pH. Three anionic binding peptides containing different numbers of glutamic acid (Glu) and histidine were engineered to obtain an...

Additional file 1 of YAP1 protects against septic liver injury via ferroptosis resistance

Jin Wang, Qian Zhu, Rui Li, Jing Zhang, Xujun Ye & Xinyi Li
Additional file 1. Supplementary figures.

Supplementary document for High energy Q-switched Yb-doped fiber laser based on ternary layered structured Ti2AlC saturable absorber - 6077484.pdf

KANG ZHANG, Jinyue Xie, Xu Sang, Guoqing Sun, Ye Tian, Ming Feng, Feng Song & Wei Huang
Fig. S1. The RF spectrum of Q-switched pulses

Additional file 1 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 1: Fig. S1. Phylogenetic depiction of MAG distributions across Caribbean Ircinia species and redundancy in primary metabolic modes. The heatmap immediately to the right of the tree indicates the ln-transformed relative abundances of each MAG by host specimen. Species abbreviations accompanying specimen labels at the bottom of the heatmap are as follows: ICam (I. campana), IcfR (I. cf. reteplana), IRad (I. radix), ILae (I. laeviconulosa), IBoc (I. bocatorensis B), ILow (I. lowi), IVan...

Additional file 2 of Novel trends of genome evolution in highly complex tropical sponge microbiomes

Joseph B. Kelly, David E. Carlson, Jun Siong Low & Robert W. Thacker
Additional file 2: Fig. S2. Plots depicting prevalence of MAGs associated with Caribbean Ircinia by source and region, inferred using the relative abundance matrix produced by CoverM. A. Bar chart depicting the percent of MAGs that are found across multiple host species. B. Bar chart depicting the regional specificity of MAGs. C. PCA of taxonomic community compositions of each host species’ microbiome.

Supplementary document for Broadband behavior of quadratic metalenses with a wide field of view - 6011078.pdf

Yang Liu, Jianhao Zhang, Xavier Le Roux, Eric Cassan, Delphine Marris-Morini, Laurent Vivien, Carlos Alonso Ramos & Daniele Melati
Supplemental document with additional data, simulation results, and figures.

Robust statistical inference for longitudinal data with nonignorable dropouts

Yujing Shao, Wei Ma & Lei Wang
In this paper, we propose robust statistical inference and variable selection method for generalized linear models that accommodate the outliers, nonignorable dropouts and within-subject correlations. The purpose of our study is threefold. First, we construct the robust and bias-corrected generalized estimating equations (GEEs) by combining the Mallows-type weights, Huber's score function and inverse probability weighting approaches to against the influence of outliers and account for nonignorable dropouts. Subsequently, the generalized method of moments is utilized...

Novel hybrid molecules based on disulfides and 1,2,4-triazole as antiproliferative agents

Junjie Li, Yang Liu, Yanle Men, Zijian Li, Yanping Shi, Xuguang Liu & Baoquan Chen
A series of novel hybrid molecules based on disulfides and 1,2,4-triazole were synthesized, and the structures of the resulting compounds (7a–7g, 8a–8g and 9a–9g) were confirmed by their IR, 1H NMR, 13C NMR and HR-ESI-MS spectroscopic data. The in vitro antiproliferative activity of the tested compounds on human cancer cells A549, Hela, SMMC-7721, and normal cells L929 was determined by CCK-8 assay. The obtained data revealed that most of the tested compounds showed some degrees...

Factors influencing magnetic resonance imaging finding of endopelvic fascial edema after ultrasound-guided high-intensity focused ultrasound ablation of uterine fibroids

Yuhang Liu, Yang Liu, Fajin Lv, Yuqing Zhong, Zhibo Xiao & Furong Lv
Investigate the relationships between endopelvic fascial edema and its influencing factors after ultrasound-guided high-intensity focused ultrasound (USgHIFU) ablation of uterine fibroids. This retrospective study included 688 women with uterine fibroids treated by USgHIFU; based on post-treatment MRI, the patients were divided into two groups: endopelvic fascial edema group and nonedema group. The specific location of fascial edema of each patient was also recorded. Fascial edema and fibroid features and treatment parameters were set as the...

Additional file 1 of Development and validation of an extended Cox prognostic model for patients with ER/PR+ and HER2− breast cancer: a retrospective cohort study

Yiqun Xie, Xizhou Li, Ying Wu, Wenting Cui & Yang Liu
Additional file 1: Appendix 1. Clinicopathologic characteristics of 28 deaths.

Additional file 5 of Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal

Shixing Yang, Qingqing Mao, Yan Wang, Jingxian He, Jie Yang, Xu Chen, Yuqing Xiao, Yumin He, Min Zhao, Juan Lu, Zijun Yang, Ziyuan Dai, Qi Liu, Yuxin Yao, Xiang Lu, Hong Li, Rui Zhou, Jian Zeng, Wang Li, Chenglin Zhou, Xiaochun Wang, Quan Shen, Hui Xu, Xutao Deng, Eric Delwart … & Wen Zhang
Additional file 5. Fig. S32: The host assignment of plant-associated viruses by using BLASTx searching the contigs assembled from the NGS data of each plant species (those containing possible non-plant-infecting virus) against the total mitochondrial proteome database that were downloaded from GenBank.

Additional file 3 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 3: Fig. S3. The impacts of somatic copy number alterations in PDAC cohort, related to Fig. 2. A Bar plots showing pathway enrichment of cis/trans-effect between CNA and protein (left) or phosphoprotein (right). B Distribution of IRF6 status between the younger patients’ group (≤ 60) and the older patients’ group (> 60) (left). The boxplot reveals the comparison of the mRNA (middle) and protein (right) abundance of IRF6 between the younger patients (≤...

Additional file 4 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 4: Fig. S4. Characteristics of PDAC patients with KRASG12D mutations. A The volcano plot showing the phosphosites that significantly altered between tumors with KRASG12D and with other types of KRAS mutations. B The heatmap indicating the phosphorylation abundance of RAF1, MAP2K2, MAPK1 across tumors with different KRAS mutations. C Kaplan-Meier curves for overall survival based on the phosphorylation of E2F1 at S364 (left) and based on the TF activity of E2F1 (right). D...

Additional file 5 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 5: Fig. S5. Integrated multi-omics features in tumor tissues compared with NATs of the PDAC, related to Fig. 3. A Principal component analysis (PCA) of RNA-Seq (19,992 genes) in 54 tumors and 51 NATs. Red, tumors; blue, NATs. B PCA of 7,399 phosphoproteins in 113 paired samples. Red, tumors; blue, NATs. C A volcano plot showing the results of a two-tailed Student’s t test comparing tumors and NATs at transcriptome level. D A...

Additional file 7 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 7: Fig. S7. The expression of phosphotyrosine in PDAC cohort, related to Fig. 3. A. The proportion of phosphorylation sites S, T and Y in tumors and NATs, respectively. B. The comparison of the percentage of phosphorylation sites S, T and Y in Fudan cohort and other gastrointestinal tumor cohorts. C. The scatter plot demonstrating the T/NAT ratio of phosphotyrosine (y axis) and T/NAT ratio of their corresponding proteins (x axis). D. Heatmap...

Additional file 8 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 8: Fig. S8. The effects of diabetes on the proteogenomic characteristics of PDAC, related to Fig. 4. A The boxplot representing the comparison of blood glucose concentration between patients with diabetes and without diabetes. B The Kaplan-Meier curves for overall survival based on diabetic patients with or without medical treatment. C The heatmap showing the distribution of 10q25.3 deletion and MTOR mutations across different samples in TCGA cohort. D The bar plot showing...

Additional file 9 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 9: Fig. S9. 8p11.22 amplification is associated with PDAC metastasis, related to Fig. 5. A Western blot assays were conducted for detecting ADAM9 protein in PANC-1 cells after si-ADAM9-1 and si-ADMA9-2 knocked down. B The scatter plot depicting the correlation between ADAM9 expression and expression of ADAM9-interacting proteins (Spearman’s correlation). C The scatter plot depicting the correlation between the abundance of SRC and pathways (GSVA score). D The boxplots indicating the protein expression...

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...

Registration Year

  • 2022
    267

Resource Types

  • Text
    267

Affiliations

  • Stony Brook University
    267
  • Shanghai Jiao Tong University
    220
  • Zhejiang University
    208
  • Fudan University
    207
  • Sun Yat-sen University
    202
  • Capital Medical University
    192
  • Chinese Academy of Medical Sciences & Peking Union Medical College
    186
  • Sun Yat-sen University Cancer Center
    179
  • University of Chinese Academy of Sciences
    179
  • Shandong University
    161