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Liu X, Tao Y, Cai Z, Bao P, Ma H, Li K, Li M, Zhu Y, Lu ZJ. Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data. Bioinformatics 2024:btae316. [PMID: 38741230 DOI: 10.1093/bioinformatics/btae316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/29/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
MOTIVATION Multi-omics data provide a comprehensive view of gene regulation at multiple levels, which is helpful in achieving accurate diagnosis of complex diseases like cancer. However, conventional integration methods rarely utilize prior biological knowledge and lack interpretability. RESULTS To integrate various multi-omics data of tissue and liquid biopsies for disease diagnosis and prognosis, we developed a biological pathway informed Transformer, Pathformer. It embeds multi-omics input with a compacted multi-modal vector and a pathway-based sparse neural network. Pathformer also leverages criss-cross attention mechanism to capture the crosstalk between different pathways and modalities. We first benchmarked Pathformer with 18 comparable methods on multiple cancer datasets, where Pathformer outperformed all the other methods, with an average improvement of 6.3%-14.7% in F1 score for cancer survival prediction, 5.1%-12% for cancer stage prediction, and 8.1%-13.6% for cancer drug response prediction. Subsequently, for cancer prognosis prediction based on tissue multi-omics data, we used a case study to demonstrate the biological interpretability of Pathformer by identifying key pathways and their biological crosstalk. Then, for cancer early diagnosis based on liquid biopsy data, we used plasma and platelet datasets to demonstrate Pathformer's potential of clinical applications in cancer screening. Moreover, we revealed deregulation of interesting pathways (e.g., scavenger receptor pathway) and their crosstalk in cancer patients' blood, providing potential candidate targets for cancer microenvironment study. AVAILABILITY Pathformer is implemented and freely available at https://github.com/lulab/Pathformer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
| | - Zilin Cai
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
| | - Hongli Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
| | - Kexing Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology, Beijing, 100730, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Changping District, Beijing, 102206, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing, 100084, China
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Wang Y, Wang B, Chen J, Sun L, Hou Y, Wang Y, Wang J, Gan J, Barmukh R, Li S, Fan Z, Bao P, Cao B, Cai C, Jing X, Singh BK, Varshney RK, Zhao H. Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo. J Environ Manage 2024; 351:119977. [PMID: 38160549 DOI: 10.1016/j.jenvman.2023.119977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/10/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH4+) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability.
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Affiliation(s)
- Yu Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | | | - Jianwei Chen
- BGI Research, Qingdao 266555, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lei Sun
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Yinguang Hou
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | | | - Jiongliang Wang
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Huangpu District, Guangzhou 510530, China
| | - Junwei Gan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Shanying Li
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Zeyu Fan
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Pengfei Bao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Bingchen Cao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Chunju Cai
- Changning Bamboo Forest Ecosystem National Research Station, Yibin, Sichuan 644300, China
| | - Xiong Jing
- National Agricultural Exhibition Center/China Agricultural Museum, Beijing 100125, China
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Hawkesbury Institute for the Environment Western Sydney University, Penrith, NSW 2751, Australia
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia.
| | - Hansheng Zhao
- Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing 100102, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China.
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Li M, Zhou T, Han M, Wang H, Bao P, Tao Y, Chen X, Wu G, Liu T, Wang X, Lu Q, Zhu Y, Lu ZJ. cfOmics: a cell-free multi-Omics database for diseases. Nucleic Acids Res 2024; 52:D607-D621. [PMID: 37757861 PMCID: PMC10767897 DOI: 10.1093/nar/gkad777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Liquid biopsy has emerged as a promising non-invasive approach for detecting, monitoring diseases, and predicting their recurrence. However, the effective utilization of liquid biopsy data to identify reliable biomarkers for various cancers and other diseases requires further exploration. Here, we present cfOmics, a web-accessible database (https://cfomics.ncRNAlab.org/) that integrates comprehensive multi-omics liquid biopsy data, including cfDNA, cfRNA based on next-generation sequencing, and proteome, metabolome based on mass-spectrometry data. As the first multi-omics database in the field, cfOmics encompasses a total of 17 distinct data types and 13 specimen variations across 69 disease conditions, with a collection of 11345 samples. Moreover, cfOmics includes reported potential biomarkers for reference. To facilitate effective analysis and visualization of multi-omics data, cfOmics offers powerful functionalities to its users. These functionalities include browsing, profile visualization, the Integrative Genomic Viewer, and correlation analysis, all centered around genes, microbes, or end-motifs. The primary objective of cfOmics is to assist researchers in the field of liquid biopsy by providing comprehensive multi-omics data. This enables them to explore cell-free data and extract profound insights that can significantly impact disease diagnosis, treatment monitoring, and management.
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Affiliation(s)
- Mingyang Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Tianxiu Zhou
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Mingfei Han
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaoqing Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Guansheng Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianyou Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojuan Wang
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Qian Lu
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
- Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, 38 Life Science Park, Changping District, Beijing 102206, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
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4
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Tao Y, Xing S, Zuo S, Bao P, Jin Y, Li Y, Li M, Wu Y, Chen S, Wang X, Zhu Y, Feng Y, Zhang X, Wang X, Xi Q, Lu Q, Wang P, Lu ZJ. Cell-free multi-omics analysis reveals potential biomarkers in gastrointestinal cancer patients' blood. Cell Rep Med 2023; 4:101281. [PMID: 37992683 PMCID: PMC10694666 DOI: 10.1016/j.xcrm.2023.101281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
During cancer progression, tumorigenic and immune signals are spread through circulating molecules, such as cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in the blood. So far, they have not been comprehensively investigated in gastrointestinal cancers. Here, we profile 4 categories of cell-free omics data from patients with colorectal cancer and patients with stomach adenocarcinoma and then assay 15 types of genomic, epigenomic, and transcriptomic variations. We find that multi-omics data are more appropriate for detection of cancer genes compared with single-omics data. In particular, cfRNAs are more sensitive and informative than cfDNAs in terms of detection rate, enriched functional pathways, etc. Moreover, we identify several peripheral immune signatures that are suppressed in patients with cancer. Specifically, we establish a γδ-T cell score and a cancer-associated-fibroblast (CAF) score, providing insights into clinical statuses like cancer stage and survival. Overall, we reveal a cell-free multi-molecular landscape that is useful for blood monitoring in personalized cancer treatment.
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Affiliation(s)
- Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Shuai Zuo
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Mingyang Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yingchao Wu
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Shanwen Chen
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China
| | - Xiaojuan Wang
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China
| | - Yumin Zhu
- Medical school, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Ying Feng
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xiaohua Zhang
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xianbo Wang
- Department of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qian Lu
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China; Hepatopancreatobiliary Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, No. 168, Litang Road, Changping District, Beijing 102218, China.
| | - Pengyuan Wang
- Gastro-Intestinal Surgery, Peking University First Hospital, Beijing 100034, China.
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Precision Medicine, Tsinghua University, Beijing 100084, China.
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Meng Z, Yuan B, Yang S, Fu X, Zhang B, Xu K, Bao P, Huang Y. Identification of potential biomarkers and candidate therapeutic drugs for clear cell renal cell carcinoma by bioinformatic analysis and reverse network pharmacology. Medicine (Baltimore) 2023; 102:e34929. [PMID: 37657024 PMCID: PMC10476848 DOI: 10.1097/md.0000000000034929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023] Open
Abstract
This study aims to analyze the potential biomarkers using bioinformatics technology, explore the pathogenesis, and investigate potential Chinese herbal ingredients for the Clear cell renal cell carcinoma (ccRCC), which could provide theoretical basis for early diagnosis and effective treatment of ccRCC. The gene expression datasets GSE6344 and GSE53757 were obtained from the Gene Expression Omnibus database to screen differentially expressed genes (DEGs) involved in ccRCC carcinogenesis and disease progression. Enrichment analyses, protein-protein interaction networks construction, survival analysis and herbal medicines screening were performed with related software and online analysis platforms. Moreover, network pharmacology analysis has also been performed to screen potential target drugs of ccRCC and molecular docking analysis has been used to validate their effects. Total 274 common DEGs were extracted through above process, including 194 up-regulated genes and 80 down-regulated genes. The enrichment analysis revealed that DEGs were significantly focused on multiple amino acid metabolism and HIF signaling pathway. Ten hub genes, including FLT1, BDNF, LCP2, AGXT2, PLG, SLC13A3, SLC47A2, SLC22A8, SLC22A7, and SLC13A3, were screened. Survival analysis showed that FLT1, BDNF, AGXT2, PLG, SLC47A2, SLC22A8, and SLC12A3 were closely correlated with the overall survival of ccRCC, and AGXT2, SLC47A2, SLC22A8, and SLC22A7 were closely associated with DFS. The potential therapeutic herbs that have been screened were Danshen, Baiguo, Yinxing, Huangqin and Chuanshanlong. The active compounds which may be effective in ccRCC treatment were kaempferol, Scillaren A and (-)-epigallocatechin-3-gallate.
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Affiliation(s)
- Zhuo Meng
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Bo Yuan
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Shuang Yang
- Institute of Medical Information, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaotong Fu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Baoyue Zhang
- Institute of Epidemiology and Health Care, University College London, London, UK
| | - Kun Xu
- Peking University Medical library, Beijing, China
| | - Pengfei Bao
- School of Economics and Management, Beijing Jiaotong University, Beijing, China
| | - Youliang Huang
- School of Management, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Chinese Medicine Development and Strategy, Beijing University of Chinese Medicine, Beijing, China
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Ji A, Bao P, Ma A, Wei X. An Efficient Prephenate Dehydrogenase Gene for the Biosynthesis of L-tyrosine: Gene Mining, Sequence Analysis, and Expression Optimization. Foods 2023; 12:3084. [PMID: 37628083 PMCID: PMC10453860 DOI: 10.3390/foods12163084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
L-tyrosine is a key precursor for synthesis of various functional substances, but the microbial production of L-tyrosine faces huge challenges. The development of new microbial chassis cell and gene resource is especially important for the biosynthesis of L-tyrosine. In this study, the optimal host strain Bacillus amyloliquefaciens HZ-12 was firstly selected by detecting the production capacity of L-tyrosine. Subsequently, the recombinant expression of 15 prephenate dehydrogenase genes led to the discovery of the best gene, Bao-tyrA from B. amyloliquefaciens HZ-12. After the overexpression of Bao-tyrA, the L-tyrosine yield of the recombinant strain HZ/P43-Bao-tyrA reach 411 mg/L, increased by 42% compared with the control strain (HZ/pHY300PLK). Moreover, the nucleic acid sequence and deduced amino acid sequence of the gene Bao-tyrA were analyzed, and their conservative sites and catalytic mechanisms were proposed. Finally, the expression of Bao-tyrA was regulated through a promoter and 5'-UTR sequence to obtain the optimal expression elements. Thereby, the maximum L-tyrosine yield of 475 mg/L was obtained from HZ/P43-UTR3-Bao-tyrA. B. amyloliquefaciens was applied for the first time to produce L-tyrosine, and the optimal prephenate dehydrogenase gene Bao-tyrA and corresponding expression elements were obtained. This study provides new microbial host and gene resource for the construction of efficient L-tyrosine chassis cells, and also lays a solid foundation for the production of various functional tyrosine derivatives.
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Affiliation(s)
- Anying Ji
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.J.); (P.B.); (A.M.)
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Pengfei Bao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.J.); (P.B.); (A.M.)
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Aimin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.J.); (P.B.); (A.M.)
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xuetuan Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (A.J.); (P.B.); (A.M.)
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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7
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Ning C, Cai P, Liu X, Li G, Bao P, Yan L, Ning M, Tang K, Luo Y, Guo H, Wang Y, Wang Z, Chen L, Lu ZJ, Yin J. A comprehensive evaluation of full-spectrum cell-free RNAs highlights cell-free RNA fragments for early-stage hepatocellular carcinoma detection. EBioMedicine 2023; 93:104645. [PMID: 37315449 PMCID: PMC10363443 DOI: 10.1016/j.ebiom.2023.104645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Various studies have reported cell-free RNAs (cfRNAs) as noninvasive biomarkers for detecting hepatocellular carcinoma (HCC). However, they have not been independently validated, and some results are contradictory. We provided a comprehensive evaluation of various types of cfRNA biomarkers and a full mining of the biomarker potential of new features of cfRNA. METHODS We first systematically reviewed reported cfRNA biomarkers and calculated dysregulated post-transcriptional events and cfRNA fragments. In 3 independent multicentre cohorts, we further selected 6 cfRNAs using RT-qPCR, built a panel called HCCMDP with AFP using machine learning, and internally and externally validated HCCMDP's performance. FINDINGS We identified 23 cfRNA biomarker candidates from a systematic review and analysis of 5 cfRNA-seq datasets. Notably, we defined the cfRNA domain to describe cfRNA fragments systematically. In the verification cohort (n = 183), cfRNA fragments were more likely to be verified, while circRNA and chimeric RNA candidates were neither abundant nor stable as qPCR-based biomarkers. In the algorithm development cohort (n = 287), we build and test the panel HCCMDP with 6 cfRNA markers and AFP. In the independent validation cohort (n = 171), HCCMDP can distinguish HCC patients from control groups (all: AUC = 0.925; CHB: AUC = 0.909; LC: AUC = 0.916), and performs well in distinguishing early-stage HCC patients (all: AUC = 0.936; CHB: AUC = 0.917; LC: AUC = 0.928). INTERPRETATION This study comprehensively evaluated full-spectrum cfRNA biomarker types for HCC detection, highlighted the cfRNA fragment as a promising biomarker type in HCC detection, and provided a panel HCCMDP. FUNDING National Natural Science Foundation of China, and The National Key Basic Research Program (973 program).
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Affiliation(s)
- Chun Ning
- Chinese Academy of Medical Sciences & Peking Union Medical College, No. 9 Dongdansantiao, Beijing, 100730, China; MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Peng Cai
- Department of Epidemiology, Naval Medical University, Key Laboratory of Biosafety Defense, Ministry of Education, Shanghai, 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guangtao Li
- Department of Hepatobiliary Cancer, Liver Cancer Research Centre, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin, 300060, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lu Yan
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Ning
- Tianjin Third Central Hospital, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Kaichen Tang
- Chinese Academy of Medical Sciences & Peking Union Medical College, No. 9 Dongdansantiao, Beijing, 100730, China; MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yi Luo
- Department of Hepatobiliary Cancer, Liver Cancer Research Centre, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin, 300060, China
| | - Hua Guo
- Department of Hepatobiliary Cancer, Liver Cancer Research Centre, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin, 300060, China
| | - Yunjiu Wang
- Department of Clinical Laboratory, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 200433, China
| | - Zhuoran Wang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, 200433, China
| | - Lu Chen
- Department of Hepatobiliary Cancer, Liver Cancer Research Centre, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin, 300060, China.
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Centre for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jianhua Yin
- Department of Epidemiology, Naval Medical University, Key Laboratory of Biosafety Defense, Ministry of Education, Shanghai, 200433, China.
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Bao P, Li P, Zhou X, Zhang H, You S, Xu Z, Wu Q. SMAR1 inhibits proliferation, EMT and Warburg effect of bladder cancer cells by suppressing the activity of the Wnt/β-catenin signaling pathway. Cell Cycle 2023; 22:229-241. [PMID: 35980125 PMCID: PMC9817122 DOI: 10.1080/15384101.2022.2112006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 07/01/2022] [Accepted: 08/08/2022] [Indexed: 01/11/2023] Open
Abstract
This study aimed to investigate the effects of scaffold matrix attachment region binding protein 1 (SMAR1) on the development of bladder cancer (BCa). SMAR1 expression in paired tumor and corresponding adjacent normal tissues from 55 BCa patients was detected by quantitative reverse transcription-polymerase chain reaction. BCa cells were transfected to regulate SMAR1 expression. BCa cells were treated with XAV-939, LiCl and 2-deoxyglucose. The effect of SMAR1 on the viability, proliferation, migration, invasion and Warburg effect of BCa cells was researched by counting kit-8, colony formation assay, Transwell and aerobic glycolysis assays. Western blot was performed to detect protein expression. BCa cell growth in vivo was recorded in nude mice. Immunohistochemical staining was performed for clinical and xenografted tumor tissue specimens. SMAR1 expression was down-regulated in BCa patients, associating with worse prognoses. SMAR1 knockdown enhanced the viability, proliferation, migration, invasion, EMT and Warburg effect of BCa cells. The opposite effect was found in the SMAR1 overexpression BCa cells. XAV-939 treatment reversed the elevation of β-catenin, c-Myc and Cyclin D1 proteins expression and Warburg effect in Bca cells post-SMAR1 knockdown. LiCl treatment abrogated the inhibition of β-catenin, c-Myc and Cyclin D1 proteins expression and Warburg effect proteins due to SMAR1 overexpression in BCa cells. SMAR1 overexpression inhibited the growth of BCa cells in vivo. SMAR1 might suppress the Wnt/β-catenin signaling pathway activity to inhibit the progression of BCa. It might be an effective treatment target for BCa.
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Affiliation(s)
- Pengfei Bao
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Peng Li
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Xiaoqing Zhou
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Huijiang Zhang
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Shengjie You
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Zhaoyu Xu
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
| | - Qi Wu
- Department of Urology, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, P. R. China
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9
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Zhang B, Ao B, Lu X, Yang S, Bao P, Wang H, Li R, Huang Y. Global research trends on precision oncology: A systematic review, bibliometrics, and visualized study. Medicine (Baltimore) 2022; 101:e31380. [PMID: 36316889 PMCID: PMC9622693 DOI: 10.1097/md.0000000000031380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Advances in next-generation sequencing technologies are changing the ways cancer diagnosis and treatment, which leads to a new branch of precision medicine: "Precision Oncology". This study aims to deliver a structured overview to carry out a bibliometric analysis of precision oncology research over the past 10 years retrospectively. METHODS Bibliometric methods including clustering analysis and co-occurrence visualized study were conducted based on publications of academic databases Web of Science Main Collection from 1st January 2012, to 31st December 2021. This study analyzed the information about related research outputs, countries, institutions, authors, cited papers, and hot topics. RESULTS 7163 papers related to precision oncology were identified. Since 2014, the number of articles has proliferated, and oncology precision has attracted significant attention from scholars worldwide in recent years. The USA leads the research in this field, and the League of European Research Universities is the primary research institution. Research institutions from Asia paid more attention to this field through high-level international cooperation. Besides, there are still many issues expected to be explored and evaluated correctly. Such as the considerable uncertainty that pharmacogenomic methods have no significant influence on patient outcomes. CONCLUSIONS Precision oncology serves as an essential method in clinical treatment, and is closely related to biological study, including biochemistry, molecular and genetics, advanced technology, and pharmacology discovery. The future research prospect would be the broad involvement of social participation and global cooperation in oncology precision research to acquire better results via the balance of technology and public health policy.
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Affiliation(s)
- Baoyue Zhang
- Institute of Epidemiology and Health Care, University College London, London, UK
| | - Bo Ao
- Department of Pediatrics, China-Japan Friendship Hospital, Beijing, China
| | - Xinyue Lu
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Shuang Yang
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Pengfei Bao
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Hongyun Wang
- School of Management, Beijing University of Chinese Medicine, Beijing, China
| | - Ruifeng Li
- School of Management, Beijing University of Chinese Medicine, Beijing, China
- *Correspondences: Youliang Huang, School of Management, Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong lu, Beijing 100029, China (e-mail: ), China (e-mail: )
| | - Youliang Huang
- School of Management, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Chinese Medicine Development and Strategy, Beijing University of Chinese Medicine, Beijing, China
- *Correspondences: Youliang Huang, School of Management, Beijing University of Chinese Medicine, No. 11 Bei San Huan Dong lu, Beijing 100029, China (e-mail: ), China (e-mail: )
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Krueger J, Eyerich K, Greving C, Sachen K, Hammaker D, Bao P, Lacy E, Elloso M, Orlovsky Y, McInnes I, Fourie A. LB989 Differentiation of therapeutic antibodies targeting IL-23. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.1013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Zhao W, Zhang S, Zhu Y, Xi X, Bao P, Ma Z, Kapral T, Chen S, Zagrovic B, Yang Y, Lu Z. POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res 2022; 50:D287-D294. [PMID: 34403477 PMCID: PMC8728292 DOI: 10.1093/nar/gkab702] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/08/2021] [Accepted: 08/14/2021] [Indexed: 02/02/2023] Open
Abstract
RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.
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Affiliation(s)
- Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shang Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ziyuan Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Thomas H Kapral
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Shuyuan Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Faculty of Science, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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12
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Xu Z, Ye J, Bao P, Wu Q, Xie F, Li P. Long non-coding RNA SNHG3 promotes the progression of clear cell renal cell carcinoma via regulating BIRC5 expression. Transl Cancer Res 2021; 10:4502-4513. [PMID: 35116306 PMCID: PMC8798718 DOI: 10.21037/tcr-21-1802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023]
Abstract
Background Research has shown that the progression of clear cell renal cell carcinoma (ccRCC) is modulated by long non-coding RNAs (lncRNAs). However, the roles of specific lncRNAs in the malignancy of ccRCC are still unknown. Methods TCGA and GSE66272 datasets were used to predict differentially expressed genes (DEGs) in ccRCC. ENCORI database was employed to display BIRC5 miRNA network and potential lncRNA interactions for miRNAs. KM plotter and correlation analyses were performed to identify the overall survival (OS)- and BIRC5-related miRNAs. Quantitative real-time PCR (qRT-PCR) was used to verify the BIRC5 mRNA in the seventy paired clinical samples of ccRCC tissues. The ccRCC A498 and 786-O were individually transfected with lncRNA SNHG3 and LINC00997 and then western blotting was used to detect the BIRC5 protein expression. The Dual-luciferase reporter assay was used to examine the regulatory interaction between lncRNA SNHG3 and microRNA (miRNA/miR)-10b-5p. Results BICR5 is associated with the progression of ccRCC. The two novel lncRNAs (LINC00997, SNHG3) were up-regulated in ccRCC tissues and positively with the BICR5 protein expression. However, Suppressing SNHG3 expression reduced BIRC5 protein expression compared with the LINC00997, most importantly, Suppressing SNHG3 expression suppressed tumor progression in vitro. In addition, SNHG3 promotes the expression of BIRC5 protein by sponging microRNA-10b-5p. Conclusions Our findings suggest that SNHG3 plays a vital role in promoting ccRCC via the microRNA-10b-5p/BIRC5 axis and may serve as a novel therapeutic target for the treatment of patients with ccRCC.
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Affiliation(s)
- Zhaoyu Xu
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Junjie Ye
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Pengfei Bao
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Qi Wu
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Fuchen Xie
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Peng Li
- Department of Urology, Lishui People's Hospital, Lishui, China
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13
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Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, Cai P, Xing S, Bao P, Jin Y, Zhao W, Chen Y, Zhao H, Jia X, Lu S, Lu Y, Chen L, Yin J, Lu ZJ. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 2021; 11:181-193. [PMID: 33391469 PMCID: PMC7681086 DOI: 10.7150/thno.48206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. Methods: We investigated different variations (i.e. differential expression, alternative splicing, alternative polyadenylation, and differential editing) in diverse long exRNA species (e.g. long noncoding RNAs and circular RNAs) using 79 plasma exosomal RNA-seq (exoRNA-seq) datasets of multiple cancer types. We then integrated 53 exoRNA-seq datasets and 65 self-profiled cell-free RNA-seq (cfRNA-seq) datasets to identify recurrent variations in liver cancer patients. We further combined TCGA tissue RNA-seq datasets and validated biomarker candidates by RT-qPCR in an individual cohort of more than 100 plasma samples. Finally, we used machine learning models to identify a signature of 3 noncoding RNAs for the detection of liver cancer. Results: We found that different types of RNA variations identified from exoRNA-seq data were enriched in pathways related to tumorigenesis and metastasis, immune, and metabolism, suggesting that cancer signals can be detected from long exRNAs. Subsequently, we identified more than 100 recurrent variations in plasma from liver cancer patients by integrating exoRNA-seq and cfRNA-seq datasets. From these datasets, 5 significantly up-regulated long exRNAs were confirmed by TCGA data and validated by RT-qPCR in an independent cohort. When using machine learning models to combine two of these validated circular and structured RNAs (SNORD3B-1, circ-0080695) with a miRNA (miR-122) as a panel to classify liver cancer patients from healthy donors, the average AUROC of the cross-validation was 89.4%. The selected 3-RNA panel successfully detected 79.2% AFP-negative samples and 77.1% early-stage liver cancer samples in the testing and validation sets. Conclusions: Our study revealed that different types of RNA variations related to cancer can be detected in plasma and identified a 3-RNA detection panel for liver cancer, especially for AFP-negative and early-stage patients.
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Affiliation(s)
- Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weina Tang
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghui Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Shanshan Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Yinying Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 201805, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Wang Y, Ma Z, Zheng Y, Liu B, Bao P, Wu X, Yu C, Wen Z, Ma T, Liu J, Liu C, Ma D, Wu H, Li J, Yuan Y, Lu N, Zhao H, Li Y, Yang S, Zhang R, Dai J, Hu M. Establishment of an osteoporosis model in tree shrews by bilateral ovariectomy and comprehensive evaluation. Exp Ther Med 2019; 17:3644-3654. [PMID: 30988748 PMCID: PMC6447825 DOI: 10.3892/etm.2019.7339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/14/2019] [Indexed: 12/31/2022] Open
Abstract
Osteoporosis (OP) treatment has always been challenging for elderly menopausal females. An animal model with a closer genetic association to human OP is essential for treatment research. Given its close genetic association to primates, the tree shrew is a suitable candidate for meeting the requirements for such an animal model. In the present study, a tree shrew OP model induced by ovariectomy (OVX), was established. Evaluation by multiple analysis methods, including blood biochemical indicators, uterus coefficients, micro-computed tomography analysis, histochemical analysis and scanning electron microscopic observation indicated that OVX was an appropriate method to establish the OP model in tree shrews. In addition, the biomolecular characteristics of OVX-induced osteoporosis were also assessed by transcriptome sequencing and bioinformatics analysis. The present study provides the methods used to confirm the successful establishment of the OP model in tree shrew, and suggests that the OP model is appropriate for human OP research.
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Affiliation(s)
- Yaolong Wang
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Zhaoxia Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Yuanyuan Zheng
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Baoling Liu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Pengfei Bao
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Xingfei Wu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Congtao Yu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Zhengqi Wen
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Tiekun Ma
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jinxue Liu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Change Liu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Daiping Ma
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Haiying Wu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Yong Yuan
- Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Ning Lu
- Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Hongbin Zhao
- Department of Orthopaedics, First People's Hospital of Yunnan Province, Kunming, Yunnan 650011, P.R. China
| | - Yanjiao Li
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
| | - Suping Yang
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China.,Department of Orthopaedics, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
| | - Rongping Zhang
- Department of Pharmacy, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, P.R. China
| | - Min Hu
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases and Yunnan Stem Cell Translational Research Center, Kunming University, Kunming, Yunnan 650214, P.R. China
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15
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Yu C, Dai L, Ma Z, Zhao H, Yuan Y, Zhang Y, Bao P, Su Y, Ma D, Liu C, Wu X, Liu J, Li Y, Wang B, Hu M. Effect of Osteoking on the osteogenic and adipogenic differentiation potential of rat bone marrow mesenchymal stem cells in vitro. Altern Ther Health Med 2019; 19:36. [PMID: 30704468 PMCID: PMC6357478 DOI: 10.1186/s12906-019-2435-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
Abstract
Background Bone damage is a condition that affects the quality of life of patients. Mesenchymal stem cells (MSCs) are important for bone repair. Osteoking is a natural compound in traditional Chinese Medicine used to treat bone diseases; however, the effect of Osteoking on the differentiation of MSCs has not been reported. In this study, we aimed to investigate the effect of Osteoking on the osteogenic and adipogenic differentiation potential of rat bone marrow mesenchymal stem cells (rbMSCs). Methods The effects of Osteoking on the proliferation and differentiation of rbMSCs were investigated. Different concentrations of Osteoking were prepared, and its cytotoxicity was evaluated by CCK-8 assay. The expression of osteogenic and adipogenic genes were determined, and several staining methods were used to reveal the osteogenic and adipogenic differentiation potential of rbMSCs. Results Our results show that appropriate concentrations of Osteoking can enhance osteogenic differentiation of rbMSCs and reduce adipogenic differentiation without any effect on proliferation. This may be related to the changes in related gene expression. Conclusion Osteoking enhances osteogenic differentiation and inhibits adipogenic differentiation of rbMSCs. Therefore, Osteoking may have a therapeutic potential for treating bone disease caused by changes in differentiation function of MSCs.
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16
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Hu X, Tang J, Hu X, Bao P, Pan J, Ou Y, Deng W, Liang Y. Imatinib inhibits CSF1R that stimulates proliferation of rheumatoid arthritis fibroblast-like synoviocytes. Clin Exp Immunol 2018; 195:237-250. [PMID: 30281780 DOI: 10.1111/cei.13220] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
In this study, we aimed to explore the effects of imatinib on the proliferation of rheumatoid arthritis synovial cell (RA-FLS) and inflammatory responses by regulating CSF1R. Differential genes were screened via microarray analysis, followed by being analysed through the weighted co-expression network (WGCNA) network, that included module and cluster analysis. The relationship between imatinib and genes was visualized using the Search Tool for the Retrieval of Interacting Genes (STITCH) database. Expressions of mRNA and protein were determined by reverse transcription-polymerase chain reaction (RT-PCR) and Western blot, respectively. Cell viability was examined via clone formation assay, while cell cycle and apoptosis were analysed through flow cytometry analysis. The hub gene CSF1R was ultimately determined by microarray analysis and WGCNA analysis. Colony-stimulating-factor receptor-1 (SF1R) was highly expressed in rheumatoid arthritis tissues and cells, and CSF1R over-expression could promote inflammatory responses. Moreover, CSF1R could promote RA-FLS proliferation, inhibit apoptosis and accelerate the cell cycle. The targeting relationship between imatinib and CSF1R was also validated in this study. Imatinib attenuated RA-FLS inflammation in a concentration-dependent manner. Meanwhile, imatinib could inhibit RA-FLS proliferation and promote apoptosis, ultimately reducing the damage of RA-FLS. Over-expression of CSF1R accelerated the cell cycle and proliferation of RA-FLS, while inhibiting cell apoptosis. Conversely, imatinib could significantly restrain the cell cycle and viability of RA-FLS and accelerated apoptosis via suppression of CSF1R expression. Further, histological and serological assay investigated and proved the proinflammatory effects of CSF1R in RA rabbits.
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Affiliation(s)
- X Hu
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong, China
| | - J Tang
- Department of Orthopedics, The People's Hospital of Gaozhou, Guangdong, China
| | - X Hu
- Center for Medical Genetics, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - P Bao
- Department of Medical, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong, China
| | - J Pan
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong, China
| | - Y Ou
- Department of Trauma and Joint Surgery, Shunde Hospital of Southern Medical University, Guangdong, China
| | - W Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong, China
| | - Y Liang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangdong, China
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17
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Xie X, Yang Y, Ren Q, Ding X, Bao P, Yan B, Yan X, Han J, Yan P, Qiu Q. Accumulation of deleterious mutations in the domestic yak genome. Anim Genet 2018; 49:384-392. [DOI: 10.1111/age.12703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2018] [Indexed: 12/19/2022]
Affiliation(s)
- X. Xie
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Y. Yang
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Q. Ren
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Ding
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - P. Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - B. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - X. Yan
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - J. Han
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - P. Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province; Lanzhou Institute of Husbandry and Pharmaceutical Sciences; Chinese Academy of Agricultural Science; Lanzhou 730050 China
| | - Q. Qiu
- State Key Laboratory of Grassland Agro-Ecosystem; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
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18
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Bao P, Cartron ML, Sheikh KH, Johnson BRG, Hunter CN, Evans SD. Controlling transmembrane protein concentration and orientation in supported lipid bilayers. Chem Commun (Camb) 2018; 53:4250-4253. [PMID: 28361139 DOI: 10.1039/c7cc01023k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trans-membrane protein - proteorhodopsin (pR) has been incorporated into supported lipid bilayers (SLB). In-plane electric fields have been used to manipulate the orientation and concentration of these proteins, within the SLB, through electrophoresis leading to a 25-fold increase concentration of pR.
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Affiliation(s)
- P Bao
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
| | - M L Cartron
- Department of Molecular Biology & Biotechnology, University of Sheffield, S10 2TH, UK
| | - K H Sheikh
- School of Biomedical Science, University of Leeds, LS2 9JT, UK
| | - B R G Johnson
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
| | - C N Hunter
- Department of Molecular Biology & Biotechnology, University of Sheffield, S10 2TH, UK
| | - S D Evans
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
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19
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Wang D, Lin C, Jia H, Ma N, Sun L, Xu X, Yang L, Yang F, Zhang H, Bao P. Near-barrier Fusion Evaporation and Fission of 28Si+ 174Yb and 32S+ 170Er. EPJ Web Conf 2017. [DOI: 10.1051/epjconf/201716300063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Cocho D, Sagales M, Cobo M, Homs I, Serra J, Pou M, Perez G, Pujol G, Tantinya S, Bao P, Aloy A, Sabater R, Gendre J, Otermin P. Reducción de la tasa de broncoaspiración con el test 2 volúmenes/3 texturas con pulsioximetría en una unidad de ictus. Neurologia 2017; 32:22-28. [DOI: 10.1016/j.nrl.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/15/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022] Open
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21
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Saadaoui H, Luo X, Salman Z, Cui XY, Bao NN, Bao P, Zheng RK, Tseng LT, Du YH, Prokscha T, Suter A, Liu T, Wang YR, Li S, Ding J, Ringer SP, Morenzoni E, Yi JB. Intrinsic Ferromagnetism in the Diluted Magnetic Semiconductor Co:TiO_{2}. Phys Rev Lett 2016; 117:227202. [PMID: 27925730 DOI: 10.1103/physrevlett.117.227202] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Indexed: 06/06/2023]
Abstract
Here we present a study of magnetism in Co_{0.05}Ti_{0.95}O_{2-δ} anatase films grown by pulsed laser deposition under a variety of oxygen partial pressures and deposition rates. Energy-dispersive spectrometry and transmission electron microscopy analyses indicate that a high deposition rate leads to a homogeneous microstructure, while a very low rate or postannealing results in cobalt clustering. Depth resolved low-energy muon spin rotation experiments show that films grown at a low oxygen partial pressure (≈10^{-6} torr) with a uniform structure are fully magnetic, indicating intrinsic ferromagnetism. First principles calculations identify the beneficial role of low oxygen partial pressure in the realization of uniform carrier-mediated ferromagnetism. This work demonstrates that Co:TiO_{2} is an intrinsic diluted magnetic semiconductor.
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Affiliation(s)
- H Saadaoui
- Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - X Luo
- School of Materials Science and Engineering, UNSW, Sydney, New South Wales 2052, Australia
| | - Z Salman
- Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - X Y Cui
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - N N Bao
- Department of Materials Science and Engineering, National University of Singapore, 119260, Singapore
| | - P Bao
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - R K Zheng
- School of Physics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - L T Tseng
- School of Materials Science and Engineering, UNSW, Sydney, New South Wales 2052, Australia
| | - Y H Du
- Institute of Chemical and Engineering Science, Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, 627833, Singapore
| | - T Prokscha
- Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - A Suter
- Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - T Liu
- ANKA, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Y R Wang
- School of Materials Science and Engineering, UNSW, Sydney, New South Wales 2052, Australia
| | - S Li
- School of Materials Science and Engineering, UNSW, Sydney, New South Wales 2052, Australia
| | - J Ding
- Department of Materials Science and Engineering, National University of Singapore, 119260, Singapore
| | - S P Ringer
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
- The Australian Institute for Nanoscale Science and Technology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - E Morenzoni
- Laboratory for Muon Spin Spectroscopy, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - J B Yi
- School of Materials Science and Engineering, UNSW, Sydney, New South Wales 2052, Australia
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22
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Huang Z, Wen W, Zheng Y, Gao YT, Wu C, Bao P, Wang C, Gu K, Peng P, Gong Y, Zhang M, Xiang Y, Zhong W, Jin F, Xiang YB, Shu XO, Beeghly-Fadiel A. Breast cancer incidence and mortality: trends over 40 years among women in Shanghai, China. Ann Oncol 2016; 27:1129-1134. [PMID: 27013394 PMCID: PMC4880061 DOI: 10.1093/annonc/mdw069] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/02/2015] [Accepted: 02/07/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Breast cancer incidence rates are increasing among Asian women, likely due to the changes in risk factors caused by globalization. Trends in breast cancer rates among Chinese women may differ from other Asian regions due to the implementation of a nationwide family planning program and resulting changes in women's reproductive practices. Appraisal of cancer trends can direct cancer control and public health planning, but relevant studies in China are scarce due to a lack of long-term data. We sought to evaluate secular time trends in breast cancer incidence and mortality using 40 years of cancer registry data for women in urban Shanghai. MATERIALS AND METHODS Data on invasive breast cancer incidence and mortality were collected by the Shanghai Cancer Registry. Age-standardized rates (ASRs) for incidence and mortality were calculated using the Segi/Doll 1960 world standard population. Age, period, and birth cohort effects were evaluated using age-period-cohort (APC) Poisson regression models. Overall linear trends, interpreted as the estimated annual percentage change (EAPC), were derived from the net drift in age-drift models. RESULTS A total of 53 885 breast cancer cases and 17 235 breast cancer-specific deaths were documented among women in urban Shanghai between 1 January 1973 and 31 December 2012. Breast cancer incidence and mortality ASRs increased by 141.2% and 26.6%, respectively. Significant age, cohort, and period effects were identified in both incidence and mortality APC models; cohort effects were pronounced. Overall, a substantial increase in breast cancer incidence (EAPC = 2.96%/year) and a moderate increase in breast cancer mortality (EAPC = 0.87%/year) was observed. A notable downward trend in mortality was identified among younger women born after 1960. CONCLUSIONS Forty years of cancer registry data document a tremendous increase in incidence and a slight increase in mortality for breast cancer among women in Shanghai. Effective, appropriate, and affordable breast cancer prevention and control strategies are urgently needed in China.
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Affiliation(s)
- Z Huang
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - W Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - Y Zheng
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China.
| | - Y T Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai
| | - C Wu
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - P Bao
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - C Wang
- Department of Vital Statistics, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - K Gu
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - P Peng
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Y Gong
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - M Zhang
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Y Xiang
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - W Zhong
- Department of Cancer Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - F Jin
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai
| | - Y B Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai
| | - X O Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
| | - A Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
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23
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Chen B, Yu Q, Yang Q, Bao P, Zhang W, Lou L, Zhu W, Wang G. Large-area high quality MoS2monolayers grown by sulfur vapor counter flow diffusion. RSC Adv 2016. [DOI: 10.1039/c6ra03641d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sulfur vapor counter flow diffusion moderates MoO3sulfurization and benefits monolayer MoS2growth.
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Affiliation(s)
- Bo Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Qingxuan Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Qiuyun Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Pengfei Bao
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Wenlong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Liren Lou
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Wei Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Guanzhong Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics
- University of Science and Technology of China
- Hefei
- People's Republic of China
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24
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Cheng N, Bao P, Evans SD, Leggett GJ, Armes SP. Facile Formation of Highly Mobile Supported Lipid Bilayers on Surface-Quaternized pH-Responsive Polymer Brushes. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- N. Cheng
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - P. Bao
- Molecular and Nanoscale Physics Group,
School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - S. D. Evans
- Molecular and Nanoscale Physics Group,
School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - G. J. Leggett
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - S. P. Armes
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
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25
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Onal S, Lai-Yuen S, Bao P, Weitzenfeld A, Hogue D, Hart S. Quantitative assessment of new MRI-based measurements to differentiate low and high stages of pelvic organ prolapse using support vector machines. Int Urogynecol J 2014; 26:707-13. [PMID: 25429825 DOI: 10.1007/s00192-014-2582-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 11/10/2014] [Indexed: 11/26/2022]
Abstract
INTRODUCTION AND HYPOTHESIS The objective of this study was to quantitatively assess the ability of new MRI-based measurements to differentiate low and high stages of pelvic organ prolapse. New measurements representing pelvic structural characteristics are proposed and analyzed using support vector machines (SVM). METHODS This retrospective study used data from 207 women with different types and stages of prolapse. Their demographic information, clinical history, and dynamic MRI data were obtained from the database. New MRI measurements were extracted and analyzed based on these reference lines: pubococcygeal line (PCL), mid-pubic line (MPL), true conjugate line (TCL), obstetric conjugate line (OCL), and diagonal conjugate line (DCL). A classification model using SVM was designed to assess the impact of the features (variables) in classifying prolapse into low or high stage. RESULTS The classification model using SVM can accurately identified anterior prolapse with very high accuracy (>0.90), and apical and posterior prolapse with good accuracy (0.80 - 0.90). Two newly proposed MRI-based features were found to be significant in the identification of anterior and posterior prolapse: the angle between TCL and MPL for anterior prolapse, and the angle between DCL and PCL for posterior prolapse. The overall accuracy of posterior prolapse identification increased from 47% to 80% when the newly proposed MRI-based features were taken into consideration. CONCLUSIONS The proposed MRI-based measurements are effective in differentiating low and high stages of pelvic organ prolapse, particularly for posterior prolapse.
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Affiliation(s)
- S Onal
- Department of Mechanical and Industrial Engineering, Southern Illinois University-Edwardsville, Edwardsville, IL, USA
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26
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Olman CA, Bao P, Engel SA, Grant AN, Purington C, Qiu C, Schallmo MP, Tjan BS. Do hemifield representations co-opt ocular dominance column structure in achiasma? J Vis 2014. [DOI: 10.1167/14.10.377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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27
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Files BT, Baluch F, Bao P, Purington C, Tjan BS. Overlapping but non-interacting neural populations in early visual cortex of a human subject with no optic chiasm. J Vis 2014. [DOI: 10.1167/14.10.685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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28
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Bao P, Purington C, Tjan BS. Separating neuronal suppression from hemodynamic suppression. J Vis 2014. [DOI: 10.1167/14.10.1403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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29
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Yeoh WK, Cui XY, Gault B, De Silva KSB, Xu X, Liu HW, Yen HW, Wong D, Bao P, Larson DJ, Martin I, Li WX, Zheng RK, Wang XL, Dou SX, Ringer SP. On the roles of graphene oxide doping for enhanced supercurrent in MgB2 based superconductors. Nanoscale 2014; 6:6166-6172. [PMID: 24793305 DOI: 10.1039/c4nr00415a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Due to their graphene-like properties after oxygen reduction, incorporation of graphene oxide (GO) sheets into correlated-electron materials offers a new pathway for tailoring their properties. Fabricating GO nanocomposites with polycrystalline MgB2 superconductors leads to an order of magnitude enhancement of the supercurrent at 5 K/8 T and 20 K/4 T. Herein, we introduce a novel experimental approach to overcome the formidable challenge of performing quantitative microscopy and microanalysis of such composites, so as to unveil how GO doping influences the structure and hence the material properties. Atom probe microscopy and electron microscopy were used to directly image the GO within the MgB2, and we combined these data with computational simulations to derive the property-enhancing mechanisms. Our results reveal synergetic effects of GO, namely, via localized atomic (carbon and oxygen) doping as well as texturing of the crystals, which provide both inter- and intra-granular flux pinning. This study opens up new insights into how low-dimensional nanostructures can be integrated into composites to modify the overall properties, using a methodology amenable to a wide range of applications.
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Affiliation(s)
- W K Yeoh
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, New South Wales 2006, Australia.
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30
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Onal S, Lai-Yuen S, Bao P, Weitzenfeld A, Greene K, Kedar R, Hart S. Assessment of a semiautomated pelvic floor measurement model for evaluating pelvic organ prolapse on MRI. Int Urogynecol J 2014; 25:767-73. [PMID: 24429795 DOI: 10.1007/s00192-013-2287-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
Abstract
INTRODUCTION AND HYPOTHESIS The objective of this study was to assess the performance of a semiautomated pelvic floor measurement algorithmic model on dynamic magnetic resonance imaging (MRI) images compared with manual pelvic floor measurements for pelvic organ prolapse (POP) evaluation. METHODS We examined 15 MRIs along the midsagittal view. Five reference points used for pelvic floor measurements were identified both manually and using our semiautomated measurement model. The two processes were compared in terms of accuracy and precision. RESULTS The semiautomated pelvic floor measurement model provided highly consistent and accurate locations for all reference points on MRI. Results also showed that the model can identify the reference points faster than the manual-point identification process. CONCLUSION The semiautomated pelvic floor measurement model can be used to facilitate and improve the process of pelvic floor measurements on MRI. This will enable high throughput analysis of MRI data to improve the correlation analysis with clinical outcomes and potentially improve POP assessment.
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Affiliation(s)
- S Onal
- Department of Industrial & Management Systems Engineering, University of South Florida, 4202 East Fowler Avenue, ENB 118, Tampa, FL, 33620, USA,
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Tjan BS, Bao P. Iso-eccentric correlations in the human visual cortex - fingerprints of feedbacks. J Vis 2013. [DOI: 10.1167/13.15.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Tjan BS, Bao P, Purington C. Identifying the relationship between fMRI BOLD response and neuronal activity with an achiasmatic human subject. J Vis 2013. [DOI: 10.1167/13.9.1263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bao P, Tjan BS. Effects of image content and content-selective attention on the form-evoked BOLD response in the ventral visual areas: a linear sum-of-components model. J Vis 2013. [DOI: 10.1167/13.9.768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bao P, Huang H, Hu ZY, Häggblom M, Zhu YG. Impact of temperature, CO2
fixation and nitrate reduction on selenium reduction, by a paddy soil Clostridium
strain. J Appl Microbiol 2013. [DOI: 10.1111/jam.12084] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- P. Bao
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - H. Huang
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Z.-Y. Hu
- College of Resources and Environment; Graduate University of Chinese Academy of Sciences; Beijing China
| | - M.M. Häggblom
- Rutgers University; Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; New Brunswick NJ USA
| | - Y.-G. Zhu
- State Key Lab of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment, Chinese Academy of Sciences; Xiamen China
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Wang H, Wang G, Bao P, Yang S, Zhu W, Xie X, Zhang WJ. Correction to Controllable Synthesis of Submillimeter Single-Crystal Monolayer Graphene Domains on Copper Foils by Suppressing Nucleation. J Am Chem Soc 2012. [DOI: 10.1021/ja3103023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Tjan BS, Kwon M, Millin R, Bao P. Crowding modulates activity in V1. J Vis 2012. [DOI: 10.1167/12.9.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bao P, Purington C, Tjan BS. Overlap but not interact: fine grain organization of neural populations in the visual cortex of achiasmia revealed with long-term fMRI adaption. J Vis 2012. [DOI: 10.1167/12.9.790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Cunningham SI, Weiland JD, Bao P, Tjan BS. Primary Visual Cortex Activation Responses to Tactile Stimulation in Late-Blind Individuals with Retinitis Pigmentosa. J Vis 2012. [DOI: 10.1167/12.9.1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Wang H, Wang G, Bao P, Yang S, Zhu W, Xie X, Zhang WJ. Controllable Synthesis of Submillimeter Single-Crystal Monolayer Graphene Domains on Copper Foils by Suppressing Nucleation. J Am Chem Soc 2012; 134:3627-30. [DOI: 10.1021/ja2105976] [Citation(s) in RCA: 315] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hong Wang
- Hefei National Laboratory for
Physical Sciences at Microscale, and Department of Physics, University of Science and Technology of China, Hefei,
Anhui, 230026, P. R. China
| | - Guanzhong Wang
- Hefei National Laboratory for
Physical Sciences at Microscale, and Department of Physics, University of Science and Technology of China, Hefei,
Anhui, 230026, P. R. China
| | - Pengfei Bao
- Hefei National Laboratory for
Physical Sciences at Microscale, and Department of Physics, University of Science and Technology of China, Hefei,
Anhui, 230026, P. R. China
| | - Shaolin Yang
- Hefei National Laboratory for
Physical Sciences at Microscale, and Department of Physics, University of Science and Technology of China, Hefei,
Anhui, 230026, P. R. China
| | - Wei Zhu
- Hefei National Laboratory for
Physical Sciences at Microscale, and Department of Physics, University of Science and Technology of China, Hefei,
Anhui, 230026, P. R. China
| | - Xing Xie
- Center of Super-Diamond and
Advanced Films (COSDAF), and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R.
China
| | - Wen-Jun Zhang
- Center of Super-Diamond and
Advanced Films (COSDAF), and Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, P. R.
China
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Wilkinson MN, Jayaraman V, Watkins K, Bao P, Buscaglia JM. Newly developed flexible endoscopic scissors for removal of a nasogastric tube trapped within a gastrojejunal anastomotic staple line. Endoscopy 2011; 43 Suppl 2 UCTN:E234-5. [PMID: 21773962 DOI: 10.1055/s-0030-1256426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- M N Wilkinson
- Department of Medicine, Stony Brook University Medical Center, State University of New York at Stony Brook, Stony Brook, New York 11794, USA.
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Bao P, Pantazis D, Tjan BS. A method to infer the retinotopy with landmark-based cortical surface co-registration. J Vis 2011. [DOI: 10.1167/11.11.878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bao P, Wu C, Gu K, Wang C, Huang Z, Peng P, Gong Y, Xiang Y, Dong W, Lu W, Zheng Y. Mortality trends in female breast cancer from 1973 to 2007 in urban Shanghai. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wu C, Bao P, Zheng Y, Gu K, Wang C, Huang Z, Peng P, Gong Y, Xiang Y, Dong W, Lu W. Survival in gastric cancer: A population-based cancer registry among residents in Shanghai, China. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e12014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Liang C, Yan P, Yao Y, Pei J, Guo X, Zeng Y, Bao P, Chu M. A novel single nucleotide polymorphism (SNP) of the <i>IGF1R</i> gene and the association with growth traits in yak (Brief Report). Arch Anim Breed 2010. [DOI: 10.5194/aab-53-626-2010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The insulin-like growth factor-I (IGF1) is a peptide growth factor that exerts mitogenic and metabolic activities, which are regulators of growth, survival and cell differentiation in a number of cell and tissue types. To elicit its effects, IGF1 must bind its receptors. The insulinlike growth factor 1 receptor (IGF1R) is similar to insulin receptor (INSR) and it mediates the growth-promoting effect of IGF1. The IGF1R gene, therefore, was selected as a biological candidate gene for growth, body composition, metabolic, and skeletal traits in animals (Rothschild et al. 1997). By now, no polymorphism of yak (Bos grunniensL) IGF1R gene is reported. In the present paper, the partial exon 1 region of IGF1R was screened to detect the SNPs in Chinese yak breeds. Associations of SNP of IGF1R with growth traits were analysed.
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Bao P, Tjan BS. Task dependence and level of processing in category-specific regions of the ventral stream. J Vis 2010. [DOI: 10.1167/10.7.980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Li Y, Bao P, Xue W. [Research on information extraction of electronic medical records in Chinese]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2010; 27:757-762. [PMID: 20842840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This is a research to enhance the application of natural language understanding and ontology in the Chinese medical text semantic annotation and content analysis, and so to provide technology support for the computer-readable electronic medical records (EMR). The Chinese EMR information extraction and statistical analysis of related subjects in accordance to the user's demands were performed through building the named entity rules, the classified word list and field ontology by using GATE platform on the basis of EMR text set's construction and pre-processing. The automatic and artificial semantic annotation of EMR text set was implemented. The situation of drugs used in medicinal treatment and the distribution of patients' age and sex were obtained. The ontology-based semantic information extraction can improve the function of computer for text understanding, and the discovery of knowledge in EMR through field ontology is feasible.
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Affiliation(s)
- Yi Li
- Medical Information Institute of Chinese PLA General Hospital, Beijing 100853, China.
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You N, Tao K, Zhao W, Bao P, Li R, You H, Zhang M, Gao Z, Gao Z, Dou K. Diphenhydramine modulates cytokines and induces apoptosis in experimental acute pancreatitis. ACTA ACUST UNITED AC 2010; 32:311-8. [PMID: 20664821 DOI: 10.1358/mf.2010.32.5.1428739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In this study, we investigated the therapeutic potential of diphenhydramine (DPH), a H(1) receptor antagonist, on taurocholate-induced acute pancreatitis and the underlying mechanisms involved. Rats were randomly divided into sham-operated, model, DPH-treated, octreotide-treated and the DPH plus octreotide combination therapy groups (n = 30 per group). Animals were sacrificed 3, 6 and 24 h after modeling and drug administration (n = 10 per time point) and sera, pancreas and lungs were harvested for further studies. DPH and octreotide monotherapy relieved histopathological injuries in multiple organs when compared to the model group. Combination therapy (DPH + octreotide) demonstrated better therapeutic potential than monotherapy. Data indicated that combination therapy had a better ability to reduce average mortality rates in rats, decrease the number of inflammatory cells, attenuate necrosis, upregulate the levels of amylase, TNF-alpha and IL-8 and downregulate the levels of IL-10 in the serum. Moreover, enhanced expression of Bax in the pancreas and lung were recorded suggesting a pro-apoptotic mechanism involved in the therapeutic potential of DPH. Our study demonstrated the therapeutic potential of DPH in acute pancreatitis and suggested a novel strategy for clinical management of this disease.
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Affiliation(s)
- N You
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, P.R. China
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