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Wu Y, Peng Y. Ten computational challenges in human virome studies. Virol Sin 2024:S1995-820X(24)00068-3. [PMID: 38697263 DOI: 10.1016/j.virs.2024.04.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024] Open
Abstract
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the absence of effective methods, particularly in the domain of computational tools. This perspective systematically outlines ten computational challenges spanning various types of virome studies. These challenges arise due to the vast diversity of viromes, the absence of a universal marker gene in viral genomes, the low abundance of virus populations, the remote or minimal homology of viral proteins to known proteins, and the highly dynamic and heterogeneous nature of viromes. For each computational challenge, we discuss the underlying reasons, current research progress, and potential solutions. The resolution of these challenges necessitates ongoing collaboration among computational scientists, virologists, and multidisciplinary experts. In essence, this perspective serves as a comprehensive guide for directing computational efforts in human virome studies.
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Affiliation(s)
- Yifan Wu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
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Lin J, Peng Y, Guo L, Tao S, Li S, Huang W, Yang X, Qiao F, Zong Z. The incidence of surgical site infections in China. J Hosp Infect 2024; 146:206-223. [PMID: 37315807 DOI: 10.1016/j.jhin.2023.06.004] [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: 03/30/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023]
Abstract
Surgical site infections (SSIs) are a common type of healthcare-associated infection. We performed a literature review to demonstrate the incidence of SSIs in mainland China based on studies since 2010. We included 231 eligible studies with ≥30 postoperative patients, comprising 14 providing overall SSI data regardless of surgical sites and 217 reporting SSIs for a specific site. We found that the overall SSI incidence was 2.91% (median; interquartile range: 1.05%, 4.57%) or 3.18% (pooled; 95% confidence interval: 1.85%, 4.51%) and the SSI incidence varied remarkably according to the surgical site between the lowest (median, 1.00%; pooled, 1.69%) in thyroid surgeries and the highest (median, 14.89%; pooled, 12.54%) in colorectal procedures. We uncovered that Enterobacterales and staphylococci were the most common types of micro-organisms associated with SSIs after various abdominal surgeries and cardiac or neurological procedures, respectively. We identified two, nine, and five studies addressing the impact of SSIs on mortality, the length of stay (LOS) in hospital, and additional healthcare-related economic burden, respectively, all of which demonstrated increased mortality, prolonged LOS, and elevated medical costs associated with SSIs among affected patients. Our findings illustrate that SSIs remain a relatively common, serious threat to patient safety in China, requiring more action. To tackle SSIs, we propose to establish a nationwide network for SSI surveillance using unified criteria with the aid of informatic techniques and to tailor and implement countermeasures based on local data and observation. We highlight that the impact of SSIs in China warrants further study.
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Affiliation(s)
- J Lin
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - Y Peng
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - L Guo
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - S Tao
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - S Li
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - W Huang
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - X Yang
- Southern Central Hospital of Yunnan Province, Honghe, China
| | - F Qiao
- Department of Infectious Control, West China Hospital, Sichuan University, Chengdu, China
| | - Z Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
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Wang G, Tang H, Xu S, Zhu H, Peng Y, Wang C. Gastrointestinal: Primary pancreatic epithelioid angiomyolipoma. J Gastroenterol Hepatol 2024; 39:416. [PMID: 37940773 DOI: 10.1111/jgh.16390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Affiliation(s)
- G Wang
- Department of Biliary and Pancreatic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - H Tang
- Department of Biliary and Pancreatic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - S Xu
- Department of Biliary and Pancreatic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - H Zhu
- Department of Biliary and Pancreatic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Y Peng
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - C Wang
- Department of Biliary and Pancreatic Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Meng J, Liu J, Song W, Li H, Wang J, Zhang L, Peng Y, Wu A, Jiang T. PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network. Brief Bioinform 2024; 25:bbae033. [PMID: 38343322 PMCID: PMC10859661 DOI: 10.1093/bib/bbae033] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Vaccination stands as the most effective and economical strategy for prevention and control of influenza. The primary target of neutralizing antibodies is the surface antigen hemagglutinin (HA). However, ongoing mutations in the HA sequence result in antigenic drift. The success of a vaccine is contingent on its antigenic congruence with circulating strains. Thus, predicting antigenic variants and deducing antigenic clusters of influenza viruses are pivotal for recommendation of vaccine strains. The antigenicity of influenza A viruses is determined by the interplay of amino acids in the HA1 sequence. In this study, we exploit the ability of convolutional neural networks (CNNs) to extract spatial feature representations in the convolutional layers, which can discern interactions between amino acid sites. We introduce PREDAC-CNN, a model designed to track antigenic evolution of seasonal influenza A viruses. Accessible at http://predac-cnn.cloudna.cn, PREDAC-CNN formulates a spatially oriented representation of the HA1 sequence, optimized for the convolutional framework. It effectively probes interactions among amino acid sites in the HA1 sequence. Also, PREDAC-CNN focuses exclusively on physicochemical attributes crucial for the antigenicity of influenza viruses, thereby eliminating unnecessary amino acid embeddings. Together, PREDAC-CNN is adept at capturing interactions of amino acid sites within the HA1 sequence and examining the collective impact of point mutations on antigenic variation. Through 5-fold cross-validation and retrospective testing, PREDAC-CNN has shown superior performance in predicting antigenic variants compared to its counterparts. Additionally, PREDAC-CNN has been instrumental in identifying predominant antigenic clusters for A/H3N2 (1968-2023) and A/H1N1 (1977-2023) viruses, significantly aiding in vaccine strain recommendation.
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Affiliation(s)
- Jing Meng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
| | - Jingze Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
| | - Wenkai Song
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Honglei Li
- Beijing Cloudna Technology Company, Limited, Beijing 100029, China
| | | | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha 410082, China
| | - Aiping Wu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
| | - Taijiao Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, Jiangsu, China
- Guangzhou National Laboratory, Guangzhou 510005, China
- State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China
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Xiong J, Peng Y, Li J, Cai S, Wu R. Total iron binding capacity: an independent predictor of prognosis for pulmonary arterial hypertension in systemic lupus erythematosus. Scand J Rheumatol 2024; 53:44-48. [PMID: 37605880 DOI: 10.1080/03009742.2023.2240586] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/21/2023] [Indexed: 08/23/2023]
Abstract
OBJECTIVE To investigate the role of parameters of iron metabolism in systemic lupus erythematosus (SLE) patients with pulmonary arterial hypertension (PAH). METHOD This was a prospective observational study recruiting patients diagnosed with systemic lupus erythematosus-associated pulmonary arterial hypertension (SLE-PAH). Patients with other factors that might lead to PAH were excluded from the study. All patients were assessed for PAH every 1-3 months and were followed up for 6 months. The primary outcome was considered improved if the grade of risk stratification declined at the endpoint; otherwise, it was considered unimproved. RESULTS In total, 29 patients with SLE-PAH were included in this study. The mean of serum ferritin was higher than normal, and total iron binding capacity (TIBC) decreased in 48% of patients. Correlation analyses showed that serum iron (SI) was negatively correlated with World Health Organization functional class (WHO-FC) (r = -0.409, p = 0.028), and positively correlated with Six-Minute Walk Test distance (6MWD) (r = 0.427, p = 0.021) and tricuspid annular plane systolic excursion (TAPSE) (r = 0.388, p = 0.037). Primary outcomes improved in 12 patients at the endpoint, and univariate logistic regression analyses indicated that TIBC was associated with improved primary outcomes in patients with SLE-PAH (odds ratio 12.00, 95% confidence interval 1.90-75.72). CONCLUSION SI was negatively correlated with WHO-FC, and positively correlated with 6MWD and TAPSE. Furthermore, TIBC was associated with improved outcomes of patients with SLE-PAH, which could be an independent predictor of prognosis. Further research is needed to verify the findings.
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Affiliation(s)
- J Xiong
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Y Peng
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - J Li
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - S Cai
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - R Wu
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
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Ye YY, Zhu ZK, Chen M, Peng Y. [Bilateral coronary chimney stenting during transcatheter aortic valve replacement:a case report and literature review]. Zhonghua Xin Xue Guan Bing Za Zhi 2023; 51:1259-1262. [PMID: 38123209 DOI: 10.3760/cma.j.cn112148-20231013-00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Y Y Ye
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Z K Zhu
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - M Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y Peng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
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Fu P, Cai Z, Zhang Z, Meng X, Peng Y. An updated database of virus circular RNAs provides new insights into the biogenesis mechanism of the molecule. Emerg Microbes Infect 2023; 12:2261558. [PMID: 37725485 PMCID: PMC10557547 DOI: 10.1080/22221751.2023.2261558] [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: 06/28/2023] [Accepted: 09/17/2023] [Indexed: 09/21/2023]
Abstract
Virus circular RNAs (circRNA) have been reported to be extensively expressed and play important roles in viral infections. Previously we build the first database of virus circRNAs named VirusCircBase which has been widely used in the field. This study significantly improved the database on both the data quantity and database functionality: the number of virus circRNAs, virus species, host organisms was increased from 46440, 23, 9 to 60859, 43, 22, respectively, and 1902 full-length virus circRNAs were newly added; new functions were added such as visualization of the expression level of virus circRNAs and visualization of virus circRNAs in the Genome Browser. Analysis of the expression of virus circRNAs showed that they had low expression levels in most cells or tissues and showed strong expression heterogeneity. Analysis of the splicing of virus circRNAs showed that they used a much higher proportion of non-canonical back-splicing signals compared to those in animals and plants, and mainly used the A5SS (alternative 5' splice site) in alternative-splicing. Most virus circRNAs have no more than two isoforms. Finally, human genes associated with the virus circRNA production were investigated and more than 1000 human genes exhibited moderate correlations with the expression of virus circRNAs. Most of them showed negative correlations including 42 genes encoding RNA-binding proteins. They were significantly enriched in biological processes related to cell cycle and RNA processing. Overall, the study provides a valuable resource for further studies of virus circRNAs and also provides new insights into the biogenesis mechanisms of virus circRNAs.
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Affiliation(s)
- Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Zhiyuan Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Xiangxian Meng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, People’s Republic of China
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Fu P, Wu Y, Zhang Z, Qiu Y, Wang Y, Peng Y. VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data. Brief Bioinform 2023; 25:bbad444. [PMID: 38048079 PMCID: PMC10753531 DOI: 10.1093/bib/bbad444] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/26/2023] [Accepted: 11/11/2023] [Indexed: 12/05/2023] Open
Abstract
Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn's disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.
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Affiliation(s)
- Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yifan Wu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Zhiyuan Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yirong Wang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
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Zhang Y, Ding N, Li Y, Ouyang M, Fu P, Peng Y, Tan Y. Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles. Autophagy 2023. [PMID: 37974331 DOI: 10.1080/15548627.2023.2284523] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
Extracellular vesicle DNAs (evDNAs) hold significant diagnostic value for various diseases and facilitate transcellular transfer of genetic material. Our study identifies transcription factor FOXM1 as a mediator for directing chromatin genes or DNA fragments (termed FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 binds to MAP1LC3/LC3 in the nucleus, and FOXM1-chDNAs, such as the DUX4 gene and telomere DNA, are designated by FOXM1 binding and translocated to the cytoplasm before being released to EVs through the secretory autophagy during lysosome inhibition (SALI) process involving LC3. Disrupting FOXM1 expression or the SALI process impairs FOXM1-chDNAs incorporation into EVs. FOXM1-chDNAs can be transmitted to recipient cells via EVs and expressed in recipient cells when they carry functional genes. This finding provides an example of how chromatin DNA fragments are specified to EVs by transcription factor FOXM1, revealing its contribution to the formation of evDNAs from nuclear chromatin. It provides a basis for further exploration of the roles of evDNAs in biological processes, such as horizontal gene transfer.
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Affiliation(s)
- Yunsheng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
- The Second Affiliated Hospital, University of South China, Hengyang, Hunan, PR China
| | - Nana Ding
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
| | - Yizhen Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
| | - Min Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
| | - Ping Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
| | - Yousong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
| | - Yongjun Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, PR China
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Lai C, Sun R, Zhang W, Peng Y. Gastrointestinal: A case of IgG4-related disease involving intestinal tract and orbital cavity. J Gastroenterol Hepatol 2023; 38:1865. [PMID: 37340618 DOI: 10.1111/jgh.16254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023]
Affiliation(s)
- C Lai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - R Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - W Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - Y Peng
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha, China
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11
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Zhu Z, You R, Li H, Feng S, Ma H, Tuo C, Meng X, Feng S, Peng Y. Multi-omics data integration reveals the complexity and diversity of host factors associated with influenza virus infection. PeerJ 2023; 11:e16194. [PMID: 37842064 PMCID: PMC10569165 DOI: 10.7717/peerj.16194] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes. Further analysis showed that the dynamic response of human cells to virus infection, cell type and strain specificity contribute significantly to the diversity of DEGs. Additionally, large heterogeneity was also observed in protein-protein interactions between humans and different types or subtypes of influenza viruses. Overall, the study deepens our understanding of the diversity and complexity of interactions between influenza viruses and humans, and provides a valuable resource for further studies on such interactions.
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Affiliation(s)
- Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
- School of Public Health, University of South China, Hengyang, China
| | - Ruina You
- College of Biology, Hunan University, Changsha, China
| | - Huiru Li
- College of Biology, Hunan University, Changsha, China
| | - Shuidong Feng
- School of Public Health, University of South China, Hengyang, China
| | - Huan Ma
- College of Biology, Hunan University, Changsha, China
| | - Chaohao Tuo
- College of Biology, Hunan University, Changsha, China
| | | | - Song Feng
- Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China
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Liu Y, Li H, Peng Y, Gao L, Liu C, Wei B, Luo Z. Impacts of pregnancy and menopause on COVID-19 severity: a systematic review and meta-analysis of 4.6 million women. QJM 2023; 116:755-765. [PMID: 37228103 DOI: 10.1093/qjmed/hcad106] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Corona Virus Disease 2019 (COVID-19) pandemic is still a public health emergency of international concern. However, whether pregnancy and menopause impact the severity of COVID-19 remain unclear. AIM This study is performed to investigate the truth. DESIGN Study appraisal and synthesis follows PRISMA guideline. Meta-analysis is performed in random-effects model. METHODS PubMed, Embase, Cochrane database, Central, CINAHL, ClinicalTrials.gov, WHO COVID-19 database and WHO-ICTRP are searched until 28 March 2023. RESULTS In total, 57 studies (4 640 275 COVID-19 women) were analyzed. Pregnant women were at a lower risk of severe COVID-19, intensive care unit (ICU) admission and disease mortality compared to those nonpregnant women with comparable comorbidities. In contrast, pregnant women with more prepregnancy comorbidities were at a higher risk of severe COVID-19, ICU admission and invasive mechanical ventilation (IMV). In addition, pregnant women with pregnancy complications had a significantly increased risk of severe COVID-19 and ICU admission. Menopause increased COVID-19 severity, IMV requirement and disease mortality. Hormone replacement therapy inhibited COVID-19 severity in postmenopausal women. Premenopausal and postmenopausal women had a lower chance of severe illness than age-matched men. The impact of pregnancy on COVID-19 severity was significant in Americans and Caucasians, whereas the effect of menopause on COVID-19 severity was only significant in Chinese. CONCLUSIONS Pregnancy and menopause are protective and risk factors for severe COVID-19, respectively. The protective role of pregnancy on COVID-19 is minimal and could be counteracted or masked by prepregnancy or pregnancy comorbidities. The administration of estrogen and progesterone may prevent severe COVID-19.
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Affiliation(s)
- Y Liu
- Department of Endocrinology, China Resources and WISCO General Hospital, Wuhan, China
| | - H Li
- Department of Geratology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Y Peng
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - L Gao
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - C Liu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - B Wei
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, China
| | - Z Luo
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
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Peng Y, Xu M, Kong Y, Xing P, Zhang L. Impact of PRaG Therapy on Immune Microenvironment of Bilateral Subcutaneous Tumor Model of Colon Cancer. Int J Radiat Oncol Biol Phys 2023; 117:e270. [PMID: 37785023 DOI: 10.1016/j.ijrobp.2023.06.1235] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Immune microenvironment is closely related to the efficacy of PD-1 inhibitors. The immune microenvironment contains a variety of immune cells, including effector T cells (cytotoxic CD8+T cells and effector CD4+T cells), dendritic cells (DC), and Myeloid-derived suppressor cells (MDSCs). The antitumor effects of PRaG therapy have been confirmed in bilateral subcutaneous transplantation tumor model of colon cancer. But the impact of PRaG therapy on immune microenvironment of such model is unclear. Therefore, the study continued to reveal the changes of immune microenvironment in mice. MATERIALS/METHODS 80 male Balb/c mice aged 6-8 weeks were divided into five groups: control group, PD-1 inhibitor group, radiation group, radiation + PD-1 inhibitor group, and radiation + PD-1 inhibitor +GM-CSF (PRaG therapy) group. Bilateral subcutaneous tumor model of colon cancer in mice was constructed. 3×105 CT26.WT cells were inoculated subcutaneously in the right thigh root, and then the left thigh root 3 days later. Right subcutaneous tumor was selected for radiotherapy of 8 Gy×3. GM-CSF (100ng, i.p.) was given on the 1st day and PD-1 inhibitor (0.25mg/kg, i.p.) was given on the 2nd day after radiotherapy with one cycle every 3 days. On day 15, the spleen, left inguinal lymph node and left subcutaneous tumor of mice were collected. The proportion of immune cells was detected by flow cytometry. RESULTS Compared with other groups, PRaG therapy decreased the proportion of cDC1 in left inguinal lymph node, increased the proportion of cDC2 in left subcutaneous tumor and left inguinal lymph node. Moreover, PRaG therapy increased the proportion of CD8+ effector memory T cells and CD226+CD8+T cells in left inguinal lymph nodes. Finally, PRaG therapy increased the proportion of CD4+, CD8+ central memory T cells and CD69+CD8+T cells and reduced the proportion of M-MDSCs in spleen. CONCLUSION PRaG therapy can improve the immune microenvironment of spleen, unirradiated tumors and inguinal draining lymph nodes of bilateral subcutaneous tumor model of colon cancer in mice.
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Affiliation(s)
- Y Peng
- The Second Affiliated Hospital of Soochow University, Soochow, Jiangsu, China
| | - M Xu
- Department of Radiotherapy& Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Y Kong
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - P Xing
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University Institute of Radiotherapy & Oncology, Soochow University Suzhou Key Laboratory for Radiation Oncology, Suzhou, China
| | - L Zhang
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Kong L, Li Z, Liu Y, Zhang J, Chen M, Zhou Q, Qi X, Deng XW, Peng Y. A Generalized Deep Learning Method for Synthetic CT Generation. Int J Radiat Oncol Biol Phys 2023; 117:e472. [PMID: 37785502 DOI: 10.1016/j.ijrobp.2023.06.1681] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The application of deep learning to generate synthetic CT (sCT) has been widely studied in radiotherapy. Existing methods generally involve data from two different image modalities, such as CBCT-CT or MRI-CT, the quality of sCT is adversely affected by source image quality. We propose a unique method of synthesizing MRI and CBCT into sCT based on single-modal CT for training, and call it SmGAN. MATERIALS/METHODS We used planning CT of a group of 35 head and neck cases to as training data. We then applied two different spatial transformations to the planning CT image to produce the transformed CT1 and CT2. And We used a random style enhancement technique (Shuffle Remap) to modify the image distribution of CT1 which we termed CT1+E. CT1+E was used to simulate the patient's "image of the day" while CT2 to simulate the "planning image". After feeding both CT1+E and CT2 into the generator, we obtained the sCT predicted by the generator. The generator was trained using the Mean Absolute Error (MAE) loss between sCT and CT1. In the actual clinical process, we use the patient's CBCT or MRI instead of CT1+E and the patient's planning CT instead of CT2 as the input of the generator. After processing, we get an sCT that can maintain the spatial position of the image taken on the day, while presenting features similar to the planning CT. The evaluation data we have includes 10 pairs of MRI-Def_CT and 10 pairs of CBCT-Def_CT Head and Neck patients. Def_CT is obtained from the planning CT based on the spatial position deformation of MRI and CBCT. To evaluate the accuracy of sCT based on MRI and CBCT with Def CT, we use a range of metrics, including Hounsfield Unit (HU) difference, peak signal-to-noise ratio (PSNR), structural similarity (SSIM) and gamma pass rate. All results will be benchmarks against the advanced method RegGAN for comparison. RESULTS Compared to RegGAN, the results of SmGAN were significantly better. The mean absolute errors within the body were (44.7±216.2 HU vs. 36.7±131.4 HU) and (64.9±123.7 HU vs. 58.2±152.8 HU) for the CBCT-SCT and MRI-SCT, respectively (Table 1). In addition, experimental results show that SmGAN also outperforms RegGAN in dose calculation accuracy. For example, under the 10% threshold, SmGAN's gamma pass rate of 1mm and 1% is 0.926±0.02, compared with gamma rate of 0.896±0.02 for RegGAN. CONCLUSION We proposed a generalized deep learning model for synthetic CT generation, based on CBCT or MRI images. The proposed algorithm achieved high accuracy of dosimetric metrics, as well as excellent IMRT QA verification results. Compared to other existing synthetic CT generation methods, the proposed SmGAN required a single-modal image for training, which is considered as a major breakthrough in the industry, and is expected to have wide spread of clinical applications.
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Affiliation(s)
- L Kong
- Manteia Technologies Co., Ltd, Xiamen, 361001, People's Republic of China, Xiamen, Fujian, China
| | - Z Li
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Y Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - J Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - M Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Q Zhou
- Manteia Technologies Co., Ltd., Xiamen, China
| | - X Qi
- Dept. of Radiation Oncology, UCLA, Los Angeles, CA
| | - X W Deng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
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Peng Y, Chen S, Liu Y, Zhao L, Liu P, An Q, Zhao C, Deng X, Deraniyagala RL, Stevens CW, Ding X. Mitigation of Dosimetric Uncertainty in MRI-Based Proton Planning Using Spot-Scanning Proton Arc (SPArc) Technique. Int J Radiat Oncol Biol Phys 2023; 117:e614-e615. [PMID: 37785844 DOI: 10.1016/j.ijrobp.2023.06.1992] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) MRI-based synthetic CT (SCT) images created using generative adversarial network (GAN) have been demonstrated to be feasible for intensity-modulated proton therapy (IMPT) planning. However, dose calculation accuracy can be uncertain in some regions within/near the target of head and neck patients due to the local CT number estimation error or sharp dose fall-off. This study investigated the feasibility of using the SPArc technique to mitigate such dosimetric uncertainty. MATERIALS/METHODS A GAN using a 3D U-net as the generator and a 6-layer 3D convolutional neural network as the discriminator was trained with T1-weighted MR-CT image pairs from 162 nasopharyngeal carcinoma patients (14 for validation). The generator was used to generate SCT images from MR images for 7 test patients. For each test patient, the CT image was used to create a SPArc plan and an IMPT plan with the same clinical objectives. The SPArc plans (control point frequency sampling, arc trajectory, etc.) were optimized using a previously developed iterative approach. The dose distributions of both SPArc plans and IMPT plans were re-calculated on the SCT images and compared to the one calculated on the CT images. The dosimetric uncertainty was quantified using the gamma index. RESULTS The 2%/2mm and 3%/3mm passing rates for SPArc plans were (96.9¡À2.7) % and (98.6¡À1.5) %, while the passing rates for IMPT plans were (94.0¡À3.9) % and (96.4+2.9) %. A significant reduction in dosimetric uncertainty was identified for SPArc plans (p ¡Ü0.021). Table 1 shows the passing rates for the 7 test individuals. CONCLUSION SPArc can mitigate the uncertainty of dose calculation in MRI-based proton planning. Further research needs to validate these findings on a larger patient cohort. The study paves the road map for using MRI for SPArc planning.
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Affiliation(s)
- Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - S Chen
- Department of Radiation Oncology, Beaumont Health, Royal Oak, MI
| | - Y Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - L Zhao
- Department of Radiation Oncology, Corewell Health William Beaumont University Hospital, Royal Oak, MI
| | - P Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing, China
| | - Q An
- William Beaumont Hospital, Royal Oak, MI
| | - C Zhao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - X Deng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - R L Deraniyagala
- Department of Radiation Oncology, Beaumont Health, Royal Oak, MI
| | - C W Stevens
- Department of Radiation Oncology, Beaumont Health, Royal Oak, MI
| | - X Ding
- Department of Radiation Oncology, Beaumont Health, Royal Oak, MI
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Jia KY, Chen F, Peng Y, Wei JF, He S, Wei X, Tang H, Meng W, Feng Y, Chen M. Multidetector CT-derived tricuspid annulus measurements predict tricuspid regurgitation reduction after transcatheter aortic valve replacement. Clin Radiol 2023; 78:779-788. [PMID: 37574402 DOI: 10.1016/j.crad.2023.07.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023]
Abstract
AIM To use multidetector row computed tomography (MDCT)-derived tricuspid annulus (TA) measurements to identify predictors for tricuspid regurgitation (TR) reduction after transcatheter aortic valve replacement (TAVR), and to investigate the impact of TR change on prognosis. MATERIALS AND METHODS A retrospective, single-centre study was conducted on consecutive patients who underwent TAVR with concomitant baseline mild or more severe TR from April 2012 to April 2022. TA parameters were measured using MDCT. RESULTS The study comprised 266 patients (mean age 74.2 ± 7.6 years, 147 men) and 45.1% had more than one grade of TR reduction at follow-up. Independent predictors of TR reduction at follow-up were distance between TA centroid and antero-septal commissure (odd ratio [OR] 0.776; 95% confidence interval [CI]: 0.672-0.896, p=0.001), baseline TR of moderate or worse (OR 4.599; 95% CI: 2.193-9.648, p<0.001), systolic pulmonary artery pressure (OR 1.018; 95% CI: 1.002-1.035, p=0.027), age (OR 0.955; 95% CI: 0.920-0.993, p=0.019), and pre-existing atrial fibrillation (OR 0.209; 95% CI: 0.101-0.433, p<0.001). Patients without TR reduction had higher rates of rehospitalisation (hazard ratio [HR] 0.642; 95% CI: 0.413-0.998, p=0.049). CONCLUSIONS The MDCT-derived TA parameter was predictive of TR reduction after TAVR. Persistent TR after TAVR was associated with higher rates of rehospitalisation.
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Affiliation(s)
- K-Y Jia
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - F Chen
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - Y Peng
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - J-F Wei
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - S He
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - X Wei
- Department of Cardiology, Section of Cardiac Ultrasound, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - H Tang
- Department of Cardiology, Section of Cardiac Ultrasound, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China
| | - W Meng
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China.
| | - Y Feng
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China.
| | - M Chen
- Department of Cardiology, West China Hospital, Sichuan University, 37 Guoxue Road, 610041 Chengdu, China.
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Peng Y, Xu M, Kong Y, Xing P, Zhang L. Impact of PRaG Therapy on Peripheral Immune Cells of Subcutaneous Tumor Peritoneal Metastasis Model of Colon Cancer. Int J Radiat Oncol Biol Phys 2023; 117:e255. [PMID: 37784984 DOI: 10.1016/j.ijrobp.2023.06.1201] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Immune cells in peripheral blood may be closely related to the efficacy of immune checkpoint inhibitors. T cells originally present in tumors may have limited antitumor effects, and T cells that respond to immune checkpoint inhibitors may be derived from peripheral blood. Therefore, in this study, subcutaneous tumor peritoneal metastasis model of colon cancer was constructed to reveal the changes of T cells and their subsets (CD4+T cells, CD8+T cells, CD226+T cells), MDSCs and their subsets (G-MDSCs, M-MDSCs) in peripheral blood of mice after PRaG therapy. MATERIALS/METHODS A total of 90 male Balb/c mice aged 6-8 weeks were divided into five groups: control group, PD-1 inhibitor group, radiation group, radiation + PD-1 inhibitor group, and radiation + PD-1 inhibitor +GM-CSF (PRaG therapy) group. The subcutaneous tumor peritoneal metastasis model of colon cancer was constructed. 3×105 CT26.WT cells was inoculated subcutaneously at the right thigh root, and 5 days later, 1×105 CT26.WT cells was inoculated on the left side at the junction of the anterior superior iliac spine and the midabdominal line. The subcutaneous tumor was selected for radiotherapy of 8 Gy×3. GM-CSF (100ng, i.p.) was given on the 1st day and PD-1 inhibitor (0.25mg/kg, i.p.) was given on the 2nd day after radiotherapy with one cycle every 3 days. On day 22, the peripheral blood of mice was collected. The proportion of immune cells was detected by flow cytometry. RESULTS Compared with other groups, PRaG therapy decreased the proportion of CD4+T cells and increased the proportion of CD8+T cells. Moreover, PRaG therapy increased the proportion of CD226+CD4+T cells and CD226+CD8+T cells. Finally, PRaG therapy increased the proportion of M-MDSCs and decreased the proportion of G-MDSCs. CONCLUSION PRaG therapy can improve the immune microenvironment of peripheral blood of subcutaneous tumor peritoneal metastasis model of colon cancer in mice.
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Affiliation(s)
- Y Peng
- The Second Affiliated Hospital of Soochow University, Soochow, Jiangsu, China
| | - M Xu
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Y Kong
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - P Xing
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - L Zhang
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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Huang R, Miao J, Zhang L, Peng Y, Huang S, Han F, Wang L, Deng XW, Zhao C. Radiation-Induced Nasopharyngeal Necrosis in Locally-Recurrent Nasopharyngeal Carcinoma Patients after Re-Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e589-e590. [PMID: 37785783 DOI: 10.1016/j.ijrobp.2023.06.1938] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Re-radiotherapy (re-RT) is the main treatment for locally recurrent nasopharyngeal carcinoma (lrNPC) patients, and commonly led to radiation-induced nasopharyngeal (NP) necrosis, which was lethal but rare study has focused on it. The aim of this study was to evaluate the cause and impact of radiation-induced NP necrosis in lrNPC patients who received re-RT. MATERIALS/METHODS Totally 252 lrNPC patients who received re-RT between January 2013 and December 2020 were retrospectively collected. The inclusion criteria were as follows: (1) no NP necrosis before re-RT; (2) complete medical records, including treatment, clinical and dosimetric information; (3) conventional fractionated radiotherapy. All patients received intensity-modulated radiotherapy ± chemotherapy. Radiation-induced NP necrosis was diagnosed by magnetic resonance imaging and/or electronic nasopharyngoscopy. Dosimetric factors of the planning target volume of primary tumor (PTVp) were extracted from the dose-volume histogram (DVH), which was rescaled to an equivalent dose of 2 Gy per fraction (EQD 2 Gy) using a linear quadratic model. Logistic regression was used to identify the independent prognostic factors for generating the nomogram. RESULTS With a median follow-up of 44.63 months (inter-quartile range [IQR], 27.70 - 69.20 months), 47.6% of patients (120/252) occurred radiation-induced NP necrosis, which mostly happened within 1 year post re-RT (median [IQR], 5.83 [3.37 - 11.57] months). The 3-year overall survival was 83.0% vs 39.7% (P<0.001) in lrNPC patients with or without radiation-induced NP necrosis. Except for the fractionated dose, other dosimetric factors of PTVp were not significantly different between two groups, including D98 (dose to 98% of PTVp), D50, D2 and homogeneity index (Table 1). Furthermore, multivariate analysis showed that continuous variable age (HR [95% CI]: 1.04 [1.02 - 1.07], P = 0.003) and tumor volume (HR [95% CI]: 1.02 [1.01 - 1.03], P<0.001), and fractionated dose > 2.22 Gy (HR [95% CI]: 2.36 [1.32 - 4.21], P = 0.004) were independent factors in predicting radiation-induced NP necrosis, which yielded a C-index of 0.742 (95% CI, 0.682 - 0.803) for OS in the nomogram. CONCLUSION The incidence of radiation-induced NP necrosis was high in lrNPC patients who received re-RT. Patients with older age, larger tumor volume or receiving fractionated dose over 2.22 Gy were more easily to suffer NP necrosis, which need to explore novel treatment strategies to improve patients' survivals.
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Affiliation(s)
- R Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - J Miao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - L Zhang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - S Huang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - F Han
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - L Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - X W Deng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - C Zhao
- Sun Yat-sen University Cancer Center, Guangzhou, China
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Zhang Z, Lu C, Mo B, Bai K, Ge XY, Deng L, Peng Y. Prediction of mammalian virus cross-species transmission based on host proteins. Microbiol Spectr 2023; 11:e0536822. [PMID: 37754753 PMCID: PMC10581197 DOI: 10.1128/spectrum.05368-22] [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: 01/06/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Most emerging viruses are spilled over from mammals. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of newly emerging viruses. This study systematically investigated the host proteins associated with the cross-species transmission of mammalian viruses based on 1,271 pairs of virus-mammal interactions including 382 viruses from 33 viral families and 73 mammal species from 11 orders. Numerous host proteins were found to contribute to the cross-species transmission of mammalian viruses. Host proteins potentially contributing to virus cross-species transmission are specific to viral families, and few overlaps of such host proteins are observed in different viral families. Based on these host proteins, the random-forest (RF) models were built to predict the cross-species transmission potential of mammalian viruses. Moderate performance was obtained when using all viruses together. However, when modeling by viral family, the performance of the RF models varied much among viral families. In 13 viral families such as Flaviviridae, Retroviridae, and Poxviridae, the AUC of the RF model was greater than 0.8. Finally, the contribution of virus receptors to cross-species transmission was evaluated, and the virus receptor was found to have a minor effect in predicting the cross-species transmission of mammalian viruses. The study deepens our understanding of the mechanism of virus cross-species transmission and provides a framework for predicting the cross-species transmission of mammalian viruses. IMPORTANCE Emerging viruses pose serious threats to humans. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of emerging viruses. This study systematically identified host factors associated with cross-species transmission of mammalian viruses and further built machine-learning models for predicting cross-species transmission of the viruses based on host factors including virus receptors. The study not only deepens our understanding of the mechanism of virus cross-species transmission but also provides a framework for predicting the cross-species transmission of mammalian viruses based on host factors.
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Affiliation(s)
- Zheng Zhang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Congyu Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Bocheng Mo
- Hunan Engineering and Technology Research Center for Agricultural Big Data Analysis & Decision-making, College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Kehan Bai
- Hunan Juyoubiotech Co., Ltd, Changsha, Hunan, China
| | - Xing-Yi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
| | - Li Deng
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, Hunan, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, Hunan, China
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Peng Y, Chen J. Ceiling effect of COVID-19 vaccines in China: a retrospective study. Public Health 2023; 222:e19-e20. [PMID: 36517297 PMCID: PMC9647020 DOI: 10.1016/j.puhe.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Y Peng
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
| | - J Chen
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
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Zhao ZG, Li RT, Wei X, Peng Y, Wei JF, He S, Li Q, Li X, Li YJ, Li X, Zhou X, Zheng MX, Chen G, An Q, Chen M, Feng Y. [Preliminary experience of transcatheter pulmonary valve replacement using domestic balloon-expandable valve]. Zhonghua Xin Xue Guan Bing Za Zhi 2023; 51:825-831. [PMID: 37583330 DOI: 10.3760/cma.j.cn112148-20230608-00336] [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] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Objectives: To evaluate the feasibility and preliminary clinical results of transcatheter pulmonary valve replacement (TPVR) with the domestically-produced balloon-expandable Prizvalve system. Methods: This is a prospective single-center observational study. Patients with postoperative right ventricular outflow tract (RVOT) dysfunction, who were admitted to West China Hospital of Sichuan University from September 2021 to March 2023 and deemed anatomically suitable for TPVR with balloon-expandable valve, were included. Clinical, imaging, procedural and follow-up data were analyzed. The immediate procedural results were evaluated by clinical implant success rate, which is defined as successful valve implantation with echocardiography-assessed pulmonary regurgitation
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Affiliation(s)
- Z G Zhao
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - R T Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Wei
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y Peng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - J F Wei
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - S He
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Q Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Li
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y J Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Zhou
- Department of Radiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - M X Zheng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - G Chen
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Q An
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - M Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y Feng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
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22
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Peng Y, Salomoni D, Malinowski G, Zhang W, Hohlfeld J, Buda-Prejbeanu LD, Gorchon J, Vergès M, Lin JX, Lacour D, Sousa RC, Prejbeanu IL, Mangin S, Hehn M. In-plane reorientation induced single laser pulse magnetization reversal. Nat Commun 2023; 14:5000. [PMID: 37591992 PMCID: PMC10435580 DOI: 10.1038/s41467-023-40721-z] [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: 12/07/2022] [Accepted: 08/08/2023] [Indexed: 08/19/2023] Open
Abstract
Single Pulse All Optical Switching represents the ability to reverse the magnetization of a nanostructure using a femtosecond single laser pulse without any applied field. Since the first switching experiments carried out on GdFeCo ferrimagnets, this phenomena has been only recently extended to a few other materials, MnRuGa alloys and Tb/Co multilayers with a very specific range of thickness and composition. Here, we demonstrate that single pulse switching can be obtained for a large range of rare earth-transition metal multilayers, making this phenomenon much more general. Surprisingly, the threshold fluence for switching is observed to be independent of the laser pulse duration. Moreover, at high laser intensities, concentric ring domain structures are induced. These striking features contrast to those observed in Gd based materials pointing towards a different reversal mechanism. Concomitant with the demonstration of an in-plane magnetization reorientation, a precessional reversal mechanism explains all the observed features.
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Affiliation(s)
- Y Peng
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - D Salomoni
- Univ Grenoble Alpes, CEA, CNRS, Grenoble INP, SPINTEC, 38000, Grenoble, France
| | - G Malinowski
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France.
| | - W Zhang
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
- Anhui High Reliability Chips Engineering Laboratory, Hefei Innovation Research Institute, Beihang University, 230013, Hefei, China
- MIIT Key Laboratory of Spintronics, School of Integrated Circuit Science and Engineering, Beihang University, 100191, Beijing, China
| | - J Hohlfeld
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - L D Buda-Prejbeanu
- Univ Grenoble Alpes, CEA, CNRS, Grenoble INP, SPINTEC, 38000, Grenoble, France
| | - J Gorchon
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - M Vergès
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - J X Lin
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - D Lacour
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - R C Sousa
- Univ Grenoble Alpes, CEA, CNRS, Grenoble INP, SPINTEC, 38000, Grenoble, France
| | - I L Prejbeanu
- Univ Grenoble Alpes, CEA, CNRS, Grenoble INP, SPINTEC, 38000, Grenoble, France
| | - S Mangin
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France
| | - M Hehn
- Université de Lorraine, CNRS, IJL, F-54000, Nancy, France.
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23
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Liu M, Liu J, Song W, Peng Y, Ding X, Deng L, Jiang T. Development of PREDAC-H1pdm to model the antigenic evolution of influenza A/(H1N1) pdm09 viruses. Virol Sin 2023; 38:541-548. [PMID: 37211247 PMCID: PMC10436056 DOI: 10.1016/j.virs.2023.05.008] [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: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
The Influenza A (H1N1) pdm09 virus caused a global pandemic in 2009 and has circulated seasonally ever since. As the continual genetic evolution of hemagglutinin in this virus leads to antigenic drift, rapid identification of antigenic variants and characterization of the antigenic evolution are needed. In this study, we developed PREDAC-H1pdm, a model to predict antigenic relationships between H1N1pdm viruses and identify antigenic clusters for post-2009 pandemic H1N1 strains. Our model performed well in predicting antigenic variants, which was helpful in influenza surveillance. By mapping the antigenic clusters for H1N1pdm, we found that substitutions on the Sa epitope were common for H1N1pdm, whereas for the former seasonal H1N1, substitutions on the Sb epitope were more common in antigenic evolution. Additionally, the localized epidemic pattern of H1N1pdm was more obvious than that of the former seasonal H1N1, which could make vaccine recommendation more sophisticated. Overall, the antigenic relationship prediction model we developed provides a rapid determination method for identifying antigenic variants, and the further analysis of evolutionary and epidemic characteristics can facilitate vaccine recommendations and influenza surveillance for H1N1pdm.
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Affiliation(s)
- Mi Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Jingze Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Wenjun Song
- Guangzhou Laboratory, Guangzhou, 510005, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Xiao Ding
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Lizong Deng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Suzhou, 215123, China; Guangzhou Laboratory, Guangzhou, 510005, China; State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China.
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24
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Peng Y, Wang LY, Zhang G, Liu JQ, Zeng W, Li Z, Lu X. [Construction of a dual fluorescent reporter system for tracing horizontal transfer of mcr-1-carrying plasmid]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1063-1067. [PMID: 37400217 DOI: 10.3760/cma.j.cn112150-20230103-00004] [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] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
The green fluorescent reporter gene was inserted into the gene interval of polymyxin resistant mcr-1-carrying plasmid (pSH13G841) by homologous recombination of suicide plasmid. At the same time, E. coli J53 with red fluorescent reporter gene was constructed. Using the ability of spontaneous conjugation of drug resistant plasmid (pSH13G841), pSH13G841-GFP plasmid was transferred into J53 RFP bacteria to construct a double fluorescent labeled donor bacterium. The two light-emitting systems could stably and spontaneously express fluorescence without mutual interference. The dual fluorescence report system constructed can be used for visual tracing horizontal transfer of mcr-1-carrying plasmid, the subsequent model can study the colonization, transfer and prognosis of drug-resistant bacteria/drug-resistant genes mcr-1 by using mouse in vivo imaging technology.
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Affiliation(s)
- Y Peng
- Diarrhea Department, Institute for Communicable Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - L Y Wang
- Diarrhea Department, Institute for Communicable Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - G Zhang
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - J Q Liu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - W Zeng
- School of Public Health, Shandong University, Jinan 250012, China
| | - Z Li
- Diarrhea Department, Institute for Communicable Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - X Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases/Institute for Communicable Disease Prevention and Control, Beijing 102206, China
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25
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He J, Mei Q, Peng Y, Xie J, Li W, Ding C, Jiang C, Chen Q, Wang J, Zhang Y, Ni S, Yu J, Liu T, Yang W, Gong L, Zhang X, Yuan Y, Zhang Z, He L, He H, Sun Y, Wu J, Liu Z, Gao Y. Are the original SARS-CoV-2 novel mutants from in vitro culture able to escape the immune response? J Med Virol 2023; 95:e28931. [PMID: 37448226 DOI: 10.1002/jmv.28931] [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: 02/05/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Monitoring variations in the virus genome to understand the SARS-CoV-2 evolution and spread of the virus is extremely important. Seven early SARS-CoV-2 isolates in China were cultured in vitro and were analyzed for their viral infectivity through viral growth assay, tissue culture infectious dose (TCID50 ) assay, spike protein quantification, and next generation sequencing analysis, and the resultant mutations in spike protein were used to generate the corresponding pseudoviruses for analysis of immune escape from vaccination and postinfection immunity. The results revealed that in vitro cultured SARS-CoV-2 virus had much higher mutation frequency (up to ~20 times) than that in infected patients, suggesting that SARS-CoV-2 diversify under favorable conditions. Monitoring viral mutations is not only helpful for better understanding of virus evolution and virulence change, but also the key to prevent virus transmission and disease progression. Compared with the D614G reference strain, a pseudovirus strain of SARS-CoV-2 was constructed with a high mutation rate site on the spike protein. We found some novel spike mutations during in vitro culture, such as E868Q, conferred further immune escape ability.
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Affiliation(s)
- Jun He
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Qingmin Mei
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yousong Peng
- Hunan Provincial Key Laboratory of Medical Virology, Bioinformatics Center, College of Biology, Hunan University, Changsha, China
| | - Jiajia Xie
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Weiwei Li
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Chengchao Ding
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengcheng Jiang
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingqing Chen
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Jing Wang
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuqing Zhang
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Shuangshuang Ni
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Junling Yu
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Beijing, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Beijing, China
| | - Lei Gong
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Xiangyu Zhang
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yuan Yuan
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Zhuhui Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Lan He
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Hongliang He
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong Sun
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Jiabing Wu
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Zhirong Liu
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Yong Gao
- United Laboratory of The First Affiliated Hospital of USTC and Anhui Provincial Center for Disease Control and Prevention, Hefei, China
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, Anhui, China
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26
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Chen F, Zhao ZG, Yao YJ, Zhu ZK, Li X, Zheng MX, Zhou X, Peng Y, Wei JF, Wei X, Liang YJ, Chen G, Zhu T, Meng W, Feng Y, Chen M. [Feasibility and safety of transseptal transcatheter mitral valve replacement for severe mitral regurgitation]. Zhonghua Yi Xue Za Zhi 2023; 103:1849-1854. [PMID: 37357191 DOI: 10.3760/cma.j.cn112137-20221109-02359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
A prospective, single-center, single-arm, and open-design study was performed to evaluate the feasibility and safety of transseptal transcatheter mitral valve replacement in the treatment of severe mitral regurgitation. Patients with symptomatic moderate-severe or severe mitral regurgitation at high-surgical risk and anatomically appropriate for the HighLife transseptal mitral valve replacement (TSMVR) system in West China Hospital, Sichuan University from December 2021 to August 2022 were enrolled. Four patients (1 male and 3 females) with severe mitral regurgitation were included, with a median age of 68.5 (64.0-77.0) years and a median Society of Thoracic Surgeons (STS) score of 8.1% (6.4%-8.9%). Technical success was achieved in all the patients. There was no residual mitral regurgitation, paravalvular leakage, or left ventricular outflow tract obstruction. Three major cardiovascular and cerebrovascular adverse events occurred within 30 days after the procedure, including ventricular tachycardia, iatrogenic atrial septal defect closure, and heart failure readmission. The current study preliminarily demonstrates that transcatheter mitral valve replacement using the HighLife system via the transseptal approach for severe mitral regurgitation is feasible and relatively safe.
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Affiliation(s)
- F Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Z G Zhao
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y J Yao
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Z K Zhu
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Li
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - M X Zheng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Zhou
- Department of Radiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y Peng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - J F Wei
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - X Wei
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y J Liang
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - G Chen
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - T Zhu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - W Meng
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Y Feng
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - M Chen
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu 610041, China
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27
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Li H, Liu S, Feng Q, Deng R, Wang J, Wang X, Tian R, Xu Y, Chen S, Liu Q, Wang L, Li X, Wan M, Peng Y, Tang S, Xue B, Zhu H. Regulation of PKR-dependent RNA translation inhibition by TRIM21 upon virus infection or other stress. PLoS Pathog 2023; 19:e1011443. [PMID: 37327222 DOI: 10.1371/journal.ppat.1011443] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/25/2023] [Indexed: 06/18/2023] Open
Abstract
The host always employs various ways to defend against viral infection and spread. However, viruses have evolved their own effective strategies, such as inhibition of RNA translation of the antiviral effectors, to destroy the host's defense barriers. Protein synthesis, commonly controlled by the α-subunit of eukaryotic translation initiation factor 2 (eIF2α), is a basic cellular biological process among all species. In response to viral infection, in addition to inducing the transcription of antiviral cytokines by innate immunity, infected cells also inhibit the RNA translation of antiviral factors by activating the protein kinase R (PKR)-eIF2α signaling pathway. Regulation of innate immunity has been well studied; however, regulation of the PKR-eIF2α signaling pathway remains unclear. In this study, we found that the E3 ligase TRIM21 negatively regulates the PKR-eIF2α signaling pathway. Mechanistically, TRIM21 interacts with the PKR phosphatase PP1α and promotes K6-linked polyubiquitination of PP1α. Ubiquitinated PP1α augments its interaction with PKR, causing PKR dephosphorylation and subsequent translational inhibition release. Furthermore, TRIM21 can constitutively restrict viral infection by reversing PKR-dependent translational inhibition of various previously known and unknown antiviral factors. Our study highlights a previously undiscovered role of TRIM21 in regulating translation, which will provide new insights into the host antiviral response and novel targets for the treatment of translation-associated diseases in the clinic.
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Affiliation(s)
- Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Shun Liu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Qing Feng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Rilin Deng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Jingjing Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Xintao Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Renyun Tian
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yan Xu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Shengwen Chen
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Qian Liu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Luoling Wang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Xinran Li
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Mengyu Wan
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yousong Peng
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Songqing Tang
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Binbin Xue
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Pathogen Biology and Immunology, Institute of Pathogen Biology and Immunology, School of Basic Medicine and Life Science, The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The First Affiliated Hospital and The Second Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, Hunan Provincial Key Laboratory of Medical Virology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Pathogen Biology and Immunology, Institute of Pathogen Biology and Immunology, School of Basic Medicine and Life Science, The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The First Affiliated Hospital and The Second Affiliated Hospital of Hainan Medical University, Hainan Medical University, Hainan, China
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28
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Zhao L, Peng Y, Pan ZQ. [Corneal melt after intracorneal ring segment implantations: a case report]. Zhonghua Yan Ke Za Zhi 2023; 59:481-483. [PMID: 37264579 DOI: 10.3760/cma.j.cn112142-20221113-00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A 50-year-old female patient presented to the Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, with complaints of right eye pain, tearing, and difficulty opening the eye for over a month after intrastromal corneal ring segment (ICRS) implantation 18 years prior in both eyes. Slit lamp examination revealed corneal stromal melting around the ICRS at the 3 to 4 o'clock position of the right eye, with fluorescein staining. Optical coherence tomography showed epithelial and superficial stromal layer defects in the area of the lesion. The patient was diagnosed with corneal melting after ICRS implantation in the right eye. Under general anesthesia, the corneal stromal ring was removed, and deep lamellar keratoplasty was performed. The patient had no discomfort and the corneal graft remained transparent after the surgery.
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Affiliation(s)
- L Zhao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing 100730, China
| | - Y Peng
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing 100730, China
| | - Z Q Pan
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology & Visual Sciences, Beijing 100730, China
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29
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Peng Y, Liao X, Zhu L, Zhang Y. [Prevalence of parasitic infections in human stool samples from a hospital in Chenzhou City of Hunan Province]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2023; 35:291-293. [PMID: 37455102 DOI: 10.16250/j.32.1374.2022211] [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] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
OBJECTIVE To investigate the prevalence of parasitic infections in human stool samples from a hospital in Chenzhou City, Hunan Province, so as to provide insights into the management of intestinal parasitic diseases. METHODS Stool samples were collected from patients admitted to a hospital in Chenzhou City from September 2020 to March 2021, subjected to physiological saline smearing and microscopy for detection of intestinal parasites. The prevalence of parasitic infections and the species of parasites were descriptively analyzed. RESULTS The overall prevalence of intestinal parasitic infections was 1.61% in the 10 728 stool samples, and there were 3 samples with mixed infections of two parasite species. A total of seven parasite species were identified, including Blastocystis hominis (162 cases, 1.55%), Giardia lamblia (5 cases, 0.05%), Dientamoeba fragilis (5 cases, 0.05%), Endolimax nana (one case, 0.01%), Iodamoeba bütschlii (one case, 0.01%), Strongyloides stercoralis (one case, 0.01%) and Trichomonas hominis (one case, 0.01%). The prevalence of intestinal parasitic infection was significantly higher among women than in men (2.14% vs. 1.25%; χ2 = 13.01, P < 0.01), and a high prevalence rate was seen among patients at ages of 20 to 30 years (2.99%) and 80 years and older (2.86%); however, no age-specific prevalence of intestinal parasitic infection was detected (χ2 = 12.45, P > 0.05). CONCLUSIONS The overall prevalence of intestinal parasitic infection was low among patients admitted to a hospital in Chenzhou City, and gender-specific prevalence was found. Food-borne and opportunistic parasites were predominant intestinal parasites, including B. hominis, G. lamblia and D. fragilis.
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Affiliation(s)
- Y Peng
- Chenzhou First People's Hospital, Chenzhou, Hunan 423000, China
| | - X Liao
- Chenzhou First People's Hospital, Chenzhou, Hunan 423000, China
| | - L Zhu
- Chenzhou First People's Hospital, Chenzhou, Hunan 423000, China
| | - Y Zhang
- Chenzhou First People's Hospital, Chenzhou, Hunan 423000, China
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Lin S, He L, Ji L, Peng Y, Liu K, Lyu Q, Wang J, Li YM, Zhang L, Xie MX, Yang YL. [Analysis on missed diagnosis or misdiagnosis of anomalous origin of left coronary artery from pulmonary artery by echocardiography from one single medical center]. Zhonghua Xin Xue Guan Bing Za Zhi 2023; 51:481-489. [PMID: 37198119 DOI: 10.3760/cma.j.cn112148-20220712-00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Objectives: To analyze the reasons of missed diagnosis or misdiagnosis on anomalous origin of left coronary artery from pulmonary artery (ALCAPA) by echocardiography. Methods: This is a retrospective study. Patients with ALCAPA who underwent surgical treatment in Union Hospital, Tongji Medical College, Huazhong University of Science and Technology from August 2008 to December 2021 were included. According to the results of preoperative echocardiography and surgical diagnosis, the patients were divided into confirmed group or missed diagnosis/misdiagnosis group. The results of preoperative echocardiography were collected, and the specific echocardiographic signs were analyzed. According to the experience of the doctors, the echocardiographic signs were divided into four types, namely clear displayed, vague/doubtful displayed, no display and no notice, and the display rate of each sign was calculated (display rate=number of clearly displayed cases/total number of cases×100%). By referring the surgical data, we analyzed and recorded the pathological anatomy and pathophysiological characteristics of the patients, and the rate of missed diagnosis/misdiagnosis of echocardiography in patients with different characteristics was compared. Results: A total of 21 patients were enrolled, including 11 males, aged 1.8 (0.8, 12.3) years (range 1 month to 47 years). Except for one patient with anomalous origin of left anterior descending artery, the others were all originated from the main left coronary artery (LCA). There were 13 cases of ALCAPA in infant and children, and 8 cases of adult ALCAPA. There were 15 cases in the confirmed group (diagnostic accuracy was 71.4% (15/21)), and 6 cases in the missed diagnosis/misdiagnosis group (three cases were misdiagnosed as primary endocardial fibroelastosis, two cases were misdiagnosed as coronary-pulmonary artery fistula; and one case was missed diagnosis). The working years of the physicians in the confirmed group were longer than those in the missed diagnosis/misdiagnosed group ((12.8±5.6) years vs. (8.3±4.7) years, P=0.045). In infants with ALCAPA, the detection rate of LCA-pulmonary shunt (8/10 vs. 0, P=0.035) and coronary collateral circulation (7/10 vs. 0, P=0.042) in confirmed group was higher than that in missed diagnosis/misdiagnosed group. In adult ALCAPA patients, the detection rate of LCA-pulmonary artery shunt was higher in confirmed group than that in missed diagnosis/misdiagnosed group (4/5 vs. 0, P=0.021). The missed diagnosis/misdiagnosis rate of adult type was higher than that of infant type (3/8 vs. 3/13, P=0.410). The rate of missed diagnosis/misdiagnosis was higher in patients with abnormal origin of branches than that of abnormal origin of main trunk (1/1 vs. 5/21, P=0.028). The rate of missed diagnosis/misdiagnosis in patients with LCA running between the main and pulmonary arteries was higher than that distant from the main pulmonary artery septum (4/7 vs. 2/14, P=0.064). The rate of missed diagnosis/misdiagnosis in patients with severe pulmonary hypertension was higher than that in patients without severe pulmonary hypertension (2/3 vs. 4/18, P=0.184). The reasons with an echocardiography missed diagnosis/misdiagnosis rate of≥50% included that (1) the proximal segment of LCA ran between the main and pulmonary arteries; (2) abnormal opening of LCA at the right posterior part of the pulmonary artery; (3) abnormal origin of LCA branches; (4) complicated with severe pulmonary hypertension. Conclusions: Echocardiography physicians' knowledge of ALCAPA and diagnostic vigilance are critical to the accuracy of diagnosis. Attention should be paid to the pediatric cases with no obvious precipitating factors of left ventricular enlargement, regardless of whether the left ventricular function is normal or not, the origin of coronary artery should be routinely explored.
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Affiliation(s)
- S Lin
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - L He
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - L Ji
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Y Peng
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - K Liu
- Department of Ultrasound, Hubei No.3 People's Hospital of Jianghan University, Wuhan 430030, China
| | - Q Lyu
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - J Wang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Y M Li
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - L Zhang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - M X Xie
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
| | - Y L Yang
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Province Clinical Research Center for Medical Imaging, Hubei Province Key Laboratory of Molecular Imaging, Wuhan 430022, China
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Peng Y, Li Z, Song DJ. [Different forms of free radial collateral artery perforator flaps for reconstruction after removal of oral tumors]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2023; 58:358-362. [PMID: 37026157 DOI: 10.3760/cma.j.cn115330-20221004-00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Objective: To investigate the efficacies of different forms of free radial collateral artery perforator flaps in repairing the defects after oral tumor surgeries. Methods: From May 2016 to March 2021, 28 patients (22 males, 6 females, aged 35-62 years) with oral tumors admitted by Hunan Cancer Hospital received the reconstructive surgeries with the free radial collateral artery perforator flaps after removal of oral tumors, including 24 cases of tongue cancer (11 cases of tongue marginal cancer, 9 cases of tongue belly cancer and 4 cases of tongue cancer involved in the floor of the mouth) and 4 cases of buccal and oral cancer. Four forms of radial collateral artery perforator flaps were used: single perforator flaps for 6 cases, double perforators flaps for 7 cases, flaps without perforator visualization for 10 cases and chimeric perforator myocutaneous flaps for 5 cases. The recipient vessels were the superior thyroid artery and superior thyroid vein, and if second concomitant vein available, it was anastomosed with internal jugular vein in end-to-side fashion. SPSS 20.0 statistical software was used to analyze the data. Results: The mean length of flaps was (9.7±0.4) cm, mean width (4.4±0.3) cm and mean thickness (1.1±0.4) cm. The mean length of the vascular pedicles was (7.1±0.6)cm (6.0-8.0 cm), the mean diameter of the radial accessory arteries was (1.1±0.3)mm (0.8-1.3 mm). Eleven cases(39.3%) had respectively one accompanying vein and 17 cases(60.7%) had respectively two accompanying veins, with the mean diameter of (1.1±0.3) mm (0.8-1.3 mm). All the 28 flaps survived, the donor and recipient wounds healed in one stage, the appearances of the flaps were satisfactory, only linear scars remained in the donor sites, and the upper arm functions were not significantly affected. Follow up for 12-43 months showed that the flaps were soft with partially mucosalization, the reconstructed tongue and buccal cavity were in good shape, and the swallowing and language functions were satisfactory. The swallowing and language functions were retained to the greatest extent in 3 cases with near total tongue resection, although the functions were still significantly affected. There was no local recurrence of the tumor during follow-up. One case had regional lymph node metastasis, and further lymph node dissection and comprehensive treatment were performed, with satisfactory outcomes. Conclusions: The vascular pedicle of the radial collateral artery perforator flap has a constant anatomy, which can be prepared in different forms to improve the safety of the operation and minimize the donor site damage. It is an ideal choice for the repair of small and medium-sized defects after oral tumor surgery.
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Affiliation(s)
- Y Peng
- Department of Otolaryngology, Changsha Fourth Hospital, Changsha 410008, China
| | - Z Li
- Department of Oncology Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - D J Song
- Department of Oncology Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
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Deng L, Ding L, Duan X, Peng Y. Shared molecular signatures between coronavirus infection and neurodegenerative diseases provide targets for broad-spectrum drug development. Sci Rep 2023; 13:5457. [PMID: 37015947 PMCID: PMC10071237 DOI: 10.1038/s41598-023-29778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/10/2023] [Indexed: 04/06/2023] Open
Abstract
Growing evidences have suggested the association between coronavirus infection and neurodegenerative diseases. However, the molecular mechanism behind the association is complex and remains to be clarified. This study integrated human genes involved in infections of three coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV from multi-omics data, and investigated the shared genes and molecular functions between coronavirus infection and two neurodegenerative diseases, namely Alzheimer's Disease (AD) and Parkinson's Disease (PD). Seven genes including HSP90AA1, ALDH2, CAV1, COMT, MTOR, IGF2R and HSPA1A, and several inflammation and stress response-related molecular functions such as MAPK signaling pathway, NF-kappa B signaling pathway, responses to oxidative or chemical stress were common to both coronavirus infection and neurodegenerative diseases. These genes were further found to interact with more than 20 other viruses. Finally, drugs targeting these genes were identified. The study would not only help clarify the molecular mechanism behind the association between coronavirus infection and neurodegenerative diseases, but also provide novel targets for the development of broad-spectrum drugs against both coronaviruses and neurodegenerative diseases.
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Affiliation(s)
- Li Deng
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Ling Ding
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Xianlai Duan
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China.
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China.
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Peng Y, Meng H, Li PX, Jiang YF, Fu XB. [Research advances of stem cell-based tissue engineering repair materials in promoting the healing of chronic refractory wounds on the body surface]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2023; 39:290-295. [PMID: 37805728 DOI: 10.3760/cma.j.cn501225-20220407-00126] [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] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Repairing chronic refractory wounds on the body surface is a complex medical problem involving all stages of wound healing. In recent years, stem cells (SCs) and tissue engineering (TE) have brought hope for repairing chronic refractory wounds. SCs have excellent regenerative and paracrine effects; various TE strategies have the potential to repair chronic refractory wounds on the body surface and also improve the delivery efficiency of SCs. This article reviews the pathological characteristics of chronic refractory wounds, SCs used to repair chronic refractory wounds, and SC-based TE wound repair strategies.
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Affiliation(s)
- Y Peng
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, the PLA General Hospital, Beijing 100048, China
| | - H Meng
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, the PLA General Hospital, Beijing 100048, China
| | - P X Li
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Y F Jiang
- Department for Wound Repair and Plastic Surgery, PLA Strategic Support Force Characteristic Medical Center, Beijing 100005, China
| | - X B Fu
- Research Center for Wound Repair and Tissue Regeneration, Medical Innovation Research Department, the PLA General Hospital, Beijing 100048, China School of Medicine, Nankai University, Tianjin 300071, China
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Zhao Q, Sun X, Liu K, Peng Y, Jin D, Shen W, Wang R. Correlation between capsule endoscopy classification and CT lymphangiography of primary intestinal lymphangiectasia. Clin Radiol 2023; 78:219-226. [PMID: 36509551 DOI: 10.1016/j.crad.2022.10.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/21/2022] [Accepted: 10/05/2022] [Indexed: 12/13/2022]
Abstract
AIM To investigate the correlation between capsule endoscopy (CE) classification of primary intestinal lymphangiectasia (PIL) and computed tomography (CT) lymphangiography (CTL). MATERIALS AND METHODS A total of 52 patients with diagnosed PIL were enrolled. All patients were examined using CTL and small intestinal CE before surgery. CE assessments included the morphology, scope, colour, and size of lesions. CTL assessments included intestinal wall, lymphatic vessel dilatation, lymph fluid reflux, and lymphatic fistula. Patients were divided into three groups according to type diagnosed by CE, and the CTL characteristics were analysed among the groups. RESULTS CE showed 15 patients with type I, 27 with II, and 10 with type III. Intestinal wall thickening was observed in 15 type I, 21 type II, and seven type III. Pericardial effusion was observed in only three type I patients; the difference among types was statistically significant (p=0.02). Abnormal contrast agent distribution in the intestinal wall and mesentery was observed in 15 type II patients, and the difference was significantly greater than that of types I and III (p=0.02). Abnormal contrast agent distribution in the abdominal cavity was observed in 12 type II, and the difference was statistically significant (p=0.03). CONCLUSION The CE PIL classification reflects the extent and scope of intestinal mucosa lesions; CTL more systematically demonstrates abnormal lymphatic vessels or reflux, and its manifestations of PIL are related to the CE classification. The combination of CTL with CE is useful for accurately evaluating PIL, and provides guidance for preoperative assessment and treatment management of PIL patients.
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Affiliation(s)
- Q Zhao
- Department of Radiology, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - X Sun
- Department of Radiology, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - K Liu
- Department of Gastroenterology, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Y Peng
- Beijing Jiaotong University, China
| | - D Jin
- Peking University Third Hospital, China
| | - W Shen
- Department of Lymph Surgery, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - R Wang
- Department of Radiology, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
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Cai Z, Fu P, Xu L, Deng L, Peng Y. Systematic identification and characterization of viral small RNAs from small RNA-Seq data. J Med Virol 2023; 95:e28617. [PMID: 36840404 DOI: 10.1002/jmv.28617] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/03/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Virus-encoded small RNAs (vsRNAs) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of 19,734 high-confidence vsRNAs including 2,746 miRNAs in 64 viral species from more than 800 samples of public small RNA-Seq data. The number of vsRNAs identified in viruses varied from 1 to 2,489 with a median of 170. The length distribution of vsRNAs peaked at 21 and 22 nt. Plant viruses were found to express larger number and higher levels of vsRNAs than those of animal viruses. Besides, the number of vsRNAs identified increased as the viral infection persisted. Interestingly, the vsRNA showed strong expression specificity as little overlap was observed among vsRNAs identified in different strains of a virus, or in different hosts, cells, or tissues infected by the same virus. Little conservation was observed among vsRNAs of different viruses. The viral miRNAs were found to interact with host genes involved in multiple biological processes related to organization, development, action potential, polarity establishment, methylation, immune response, gene regulation, localization, and so on. To facilitate the usage of vsRNAs, a database named vsRNAdb was built to organize and store vsRNAs which is available at http://www.computationalbiology.cn/vsRNAdb/#/. Overall, the study deepens our understanding about the diversity and complexity of vsRNAs and provides a rich resource for further studies of vsRNAs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Lihua Xu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Li Deng
- Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, 410015, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
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Li Y, Luo B, Tong B, Xie Z, Cao J, Bai X, Peng Y, Wu Y, Wang W, Qi X. The role and molecular mechanism of gut microbiota in Graves' orbitopathy. J Endocrinol Invest 2023; 46:305-317. [PMID: 35986869 DOI: 10.1007/s40618-022-01902-7] [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: 05/05/2022] [Accepted: 08/10/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Graves' orbitopathy (GO) is an autoimmune orbital disorder. Gut microbiota dysfunction plays a vital role in autoimmune diseases, including Graves' disease (GD) and GO. In the present study, we aimed to investigate the change of gut microbiota in GD/GO using mouse model. METHODS The murine model of GD/GO was established by the challenge of adenovirus expressing thyroid-stimulating hormone (TSH) receptor (TSHR) (Ad-TSHR). The histological changes of orbital and thyroid tissues were analyzed by hematoxylin and eosin (H&E), Masson staining, and immunohistochemistry (IHC) staining. The fecal samples were collected for 16S rRNA gene sequencing and bioinformatics analysis. RESULTS The GD/GO model was established successfully, as manifested as the broadened eyelid, exophthalmia and conjunctive redness, severe inflammatory infiltration among thyroid glands and between extraocular muscle space, hypertrophic extraocular muscles, elevated thyroxine (T4) and decreased TSH, and positive CD34, CD40, collagen I, and α-SMA staining. A total of 222 operational taxonomic units (OUTs) were overlapped between mice in the Ad-NC and Ad-TSHR groups. The microbial composition of the samples in the two groups was mainly Bacteroidia and Clostridia, and the Ad-NC group had a significantly lower content of Bacteroidia and higher content of Clostridia. KEGG orthology analysis results revealed differences in dehydrogenase, aspartic acid, bile acid, chalcone synthase, acetyltransferase, glutamylcyclotransferase, glycogenin, and 1-phosphatidylinositol-4-phosphate 5-kinase between two groups; enzyme commission (EC) analysis results revealed differences in several dehydrogenase, oxidase, thioxy/reductase between two groups; MetaCyc pathways analysis results revealed differences in isoleucine degradation, oxidation of C1 compounds, tricarboxylic acid (TCA) cycle IV, taurine degradation, and biosynthesis of paromamine, heme, colonic acid building blocks, butanediol, lysine/threonine/methionine, and histidine/purine/pyrimidine between two groups. CONCLUSION This study induced a mouse model of GD/GO by Ad-TSHR challenge, and gut microbiota characteristics were identified in the GD/GO mice. The Bacteroidia and Clostridia abundance was changed in the GD/GO mice. These findings may lay a solid experimental foundation for developing personalized treatment regimens for GD patients according to the individual gut microbiota. Given the potential impact of regional differences on intestinal microbiota, this study in China may provide a reference for the global overview of the gut-thyroid axis hypothesis.
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Affiliation(s)
- Y Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - B Luo
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - B Tong
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Z Xie
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - J Cao
- Department of Ophthalmology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, China
| | - X Bai
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Y Peng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Y Wu
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China
| | - W Wang
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, 410000, Hunan, China
| | - X Qi
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, No. 139, Renmin Middle Road, Changsha, 410011, Hunan, China.
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Zhong QY, Zhang XY, Luo HH, Jiang X, Zeng XY, Jiang J, Xia HF, Peng Y, Lyu MH, Tang XW. [Analysis of the characteristics of retracted scientific papers in the field of global liver diseases published by Chinese scholars]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:96-100. [PMID: 36948856 DOI: 10.3760/cma.j.cn501113-20210324-00138] [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] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Objective: To analyze the characteristics of scientific papers in the field of global liver diseases published by Chinese scholars that were retracted for diverse reasons from the Retraction Watch database, so as to provide a reference to publishing-related papers. Methods: The Retraction Watch database was retrieved for retracted papers in the field of global liver disease published by Chinese scholars from March 1, 2008 to January 28, 2021. The regional distribution, source journals, reasons for retraction, publication and retraction times, and others were analyzed. Results: A total of 101 retracted papers that were distributed across 21 provinces/cities were retrieved. Zhejiang area (n = 17) had the most retracted papers, followed by Shanghai (n = 14), and Beijing (n = 11). The vast majority were research papers (n = 95). The journal PLoS One had the highest number of retracted papers. In terms of time distribution, 2019 (n = 36) had the most retracted papers. 23 papers, accounting for 8.3% of all retractions, were retracted owing to journal or publisher concerns. Liver cancer (34%), liver transplantation (16%), hepatitis (14%), and others were the main areas of retracted papers. Conclusion: Chinese scholars have a large number of retracted articles in the field of global liver diseases. A journal or publisher chooses to retract a manuscript after investigating and discovering more flawed problems, which, however, require further support, revision, and supervision from the editorial and academic circles.
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Affiliation(s)
- Q Y Zhong
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China Clinical College of South West Medical University, Luzhou 646000, China
| | - X Y Zhang
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China Clinical College of South West Medical University, Luzhou 646000, China
| | - H H Luo
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China Clinical College of South West Medical University, Luzhou 646000, China
| | - X Jiang
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - X Y Zeng
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - J Jiang
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - H F Xia
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - Y Peng
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - M H Lyu
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
| | - X W Tang
- Department of Gastenterology, The Affiliated Hospital of South West Medical University, Luzhou 646000, China
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Peng Y, Yuan F, Xie F, Yang H, Wang S, Wang C, Yang Y, Du W, Liu M, Wang S. Comparison of automated breast volume scanning with conventional ultrasonography, mammography, and MRI to assess residual breast cancer after neoadjuvant therapy by molecular type. Clin Radiol 2023; 78:e393-e400. [PMID: 36822980 DOI: 10.1016/j.crad.2022.12.002] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/28/2022] [Accepted: 12/04/2022] [Indexed: 01/15/2023]
Abstract
AIM To compare the accuracy of hand-held ultrasonography (US), mammography (MG), magnetic resonance imaging (MRI), and automated breast volume scanning (ABVS) in defining residual breast cancer tumour size after neoadjuvant therapy (NAT). MATERIALS AND METHODS Patients diagnosed breast cancer and who received NAT at the Breast Center, Peking University People's Hospital, were enrolled prospectively. Imaging was performed after the last cycle of NAT. The residual tumour size, intraclass correlation coefficients (ICCs), and receiver operating characteristic (ROC) to predict pathological complete response (pCR) were analysed. RESULTS A total of 156 patients with 159 tumours were analysed. ABVS had a moderate correlation with histopathology residual tumour size (ICC = 0.666), and showed high agreement among triple-positive tumours (ICC = 0.797). With 5 mm as the threshold, the coincidence rate reached 64.7% between ABVS and pathological size, which was significantly higher than that between US, MG, MRI, and pathological size (50%, 45.1%, 41.4%; p=0.009, p=0.001, p<0.001, respectively). For ROC analysis, ABVS demonstrated a higher area under the ROC curve, but with no statistical difference, except for MG (0.855, 0.816, 0.819, and 0.788, respectively; p=0.183 for US, p=0.044 for MG, and p=0.397 for MRI, with ABVS as the reference). CONCLUSIONS The longest tumour diameter on ABVS had a moderate correlation with pathological residual invasive tumour size. ABVS was shown to have good ability to predict pCR and would appear to be a potential useful tool for the assessment after NAT for breast cancer.
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Affiliation(s)
- Y Peng
- Breast Center, Peking University People's Hospital, Beijing, China
| | - F Yuan
- Department of Radiology, Breast Center, Peking University People's Hospital, Beijing, China
| | - F Xie
- Breast Center, Peking University People's Hospital, Beijing, China
| | - H Yang
- Breast Center, Peking University People's Hospital, Beijing, China
| | - S Wang
- Breast Center, Peking University People's Hospital, Beijing, China
| | - C Wang
- Breast Center, Peking University People's Hospital, Beijing, China
| | - Y Yang
- Breast Center, Peking University People's Hospital, Beijing, China
| | - W Du
- Breast Center, Peking University People's Hospital, Beijing, China
| | - M Liu
- Breast Center, Peking University People's Hospital, Beijing, China.
| | - S Wang
- Breast Center, Peking University People's Hospital, Beijing, China.
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Peng Y, Li Z, Song DJ. [Anatomical classification of adductor magnus perforator flap and its application in head and neck reconstruction]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2023; 58:37-41. [PMID: 36603864 DOI: 10.3760/cma.j.cn115330-20220530-00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Objective: To investigate the anatomical classification of adductor magnus perforator flap and its application in head and neck reconstruction. Methods: From January 2017 to January 2020, Hunan Cancer Hospital treated 27 cases of oral tumor patients (15 cases of tongue cancer, 9 cases of gingival cancer and 3 cases of buccal cancer), including 24 males and 3 females, aged 31-56 years old. The course of disease was 1-12 months. Secondary soft tissue defects with the sizes of 5.0 cm × 3.5 cm to 11.0 cm × 8.0 cm were left after radical resection of the tumors, and were repaired with free adductor magnus perforator flaps. The flaps based on the origing locations of perforator vessels were divided into three categories: ① intramuscular perforator: vessel originated between the gracilis muscle and the adductor magnus or passed through a few adductor magnus muscles; ② adductor magnus middle layer perforator: vessel run between the deep and superficial layers of adductor magnus; ③ adductor magnus deep layer perforator: vessel run between the deep layer of adductor magnus and the semimembranous muscle. Descriptive analysis was used in this research. Results: Perforator vessels of adductor magnus were found in all cases, with a total of 62 perforator branches of adductor magnus. The anatomical classification of the perforator vessels was as follows: 12 branches for class ①, 31 branches for class ② and 19 branches for class ③. The vascular pedicles of the free adductor major perforator flaps included type ① for 3 cases, type ② for 16 cases and type ③ for 8 cases. All 27 flaps survived and the donor sites were closed directly. In 18 cases, the perforator arteries and the venae comitan were respectively anastomosed with the superior thyroid arteries and veins. In 9 cases, the pedicle arteries and the venae comitan were respectively anastomosed with the facial arteries and veins. Follow up for 12-40 months showed that the appearances of the flaps and the swallowing and language functions of patients were satisfactory, apart from linear scars were left in the donor sites with no significant affect on the functions of thigh. Local recurrence occurred in 3 cases and radical surgeries were performed again followed by repairs with pedicled pectoralis major myocutaneous flaps. Cervical lymph node metastasis occurred in 2 cases and cervical lymph node dissection was performed again. Conclusions: The adductor magnus perforator flap has soft texture, constant perforator vessel anatomy, flexible donor location and harvesting forms, and less damage to the donor site. It is an ideal choice for postoperative reconstruction in head and neck tumors.
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Affiliation(s)
- Y Peng
- Department of Otolaryngology, Changsha Fourth Hospital, Changsha 410008, China
| | - Z Li
- Department of Oncology Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
| | - D J Song
- Department of Oncology Plastic Surgery, Hunan Cancer Hospital, Changsha 410008, China
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Deng L, Fu P, Ding L, Duan X, Feng S, Peng Y. Virome analysis provides new insights into the association between viruses and Parkinson's disease. J Med Virol 2023; 95:e28111. [PMID: 36042689 DOI: 10.1002/jmv.28111] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
Parkinson's disease (PD) is a kind of neurodegenerative disease that causes a huge burden to society. Previous studies have suggested the association between PD and multiple viruses. However, there is still a lack of a virome study about PD. This study systematically identified viruses from the public RNA-sequencing data of more than 700 samples from both PD patients and the control group (most were healthy people). Only nine viruses such as human betaherpesvirus 5 and Merkel cell polyomavirus have been detected in several human brain tissues of the central nervous system, the appendix, and blood of PD patients, and all of these viruses were also detected in the control group. Most viruses were observed to have low abundance in no more than three tissues. No statistically significant differences were observed between the virus abundance in the PD patients and the control group for all viruses. The positive rates of most viruses in PD patients were higher or similar to that in the control group, although those were less than 5% for most viruses. Overall, this is the first study to systematically investigate the virome in PD patients, and provides new insights into the association between viruses and PD.
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Affiliation(s)
- Li Deng
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Ping Fu
- Bioinformatics Center, Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha, China
| | - Ling Ding
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Xianlai Duan
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Song Feng
- Network Information Center, Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- Bioinformatics Center, Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha, China
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Huo YP, Liu F, Wu JP, Zhang YK, Feng CM, Peng Y. Platinum Immobilized in Imidazolyl Schiff Base-Containing Nitrogen-Rich Covalent Organic Polymer as a Catalyst for Hydrosilylation. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010176] [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: 03/11/2023]
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Peng Y, Li Z, Hu J, Wu T. Palladium-Catalyzed Denitrative Mizoroki–Heck Reactions of Aryl or Alkyl Olefins with Nitrobenzenes. Russ J Org Chem 2022. [DOI: 10.1134/s1070428022120168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Afridi MI, Zheng Z, Liu J, Liu L, Zhang S, Zhu Z, Peng Y, Zhou D, Tu H. The bZIP Transcription Factor BATF3/ZIP-10 Suppresses Innate Immunity by Attenuating PMK-1/p38 Signaling. Int Immunol 2022; 35:181-196. [PMID: 36409527 DOI: 10.1093/intimm/dxac053] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Abstract
Innate immunity is the first line of host defense against pathogenic invasion in metazoans. The transcription factor BATF3 plays a crucial role in the development of conventional dendritic cells and the program of CD8 + T cell survival and memory, but the role of BATF3 in innate immunity response remains unclear. Here, we show an evolutionarily conserved basic-region leucine zipper (bZIP) transcription factor BATF3/ZIP-10 suppresses innate immune response through repressing p38/PMK-1 MAPK pathway in vitro and in vivo. The worm mutant lacking C. elegans homolog BATF3, ZIP-10, exhibited enhanced resistance to PA14 infection, which was completely rescued by transgenic expression of either endogenous zip-10 or mouse or human Batf3 cDNA driven by worm zip-10 promoter. ZIP-10 expression was inhibited by a microRNA miR-60 that was downregulated upon PA14 infection. Moreover, the level of phosphorylated but not total PMK-1/p38 was attenuated by ZIP-10 and stimulated by miR-60. The human HEK293 cells with Batf3 overexpression or RNAi knockdown exhibited the reduction or increase of the cell viability upon P. aeruginosa PA14 infection, respectively. The overexpression of either worm ZIP-10 or human BATF3 abolished the activation of p38 and inhibited the expression of the antimicrobial peptide and cytokine genes in HEK293 cells. Our findings indicate that the genetic transcriptional program of the evolutionally conserved bZIP transcription factor BATF3/ZIP-10 suppresses the innate immunity by attenuating the p38 MAPK signaling activity, which expands our understanding of the pathological mechanisms underlying relevant infectious diseases.
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Affiliation(s)
- Muhammad Irfan Afridi
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Zhongfan Zheng
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Junqiang Liu
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Lijuan Liu
- Department of Neurology, First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha , Hunan, 410007, China
| | - Shan Zhang
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Zhaozhong Zhu
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Yousong Peng
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
| | - Desheng Zhou
- Department of Neurology, First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha , Hunan, 410007, China
| | - Haijun Tu
- Institute of Neuroscience, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology , Hunan University, Changsha 410082, Hunan, China
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Cai Z, Fu P, Qiu Y, Wu A, Zhang G, Wang Y, Jiang T, Ge XY, Zhu H, Peng Y. vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data. Brief Bioinform 2022; 23:6827719. [PMID: 36377755 DOI: 10.1093/bib/bbac496] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.
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Affiliation(s)
- Zena Cai
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ping Fu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Ye Qiu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, China
| | - Gaihua Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yirong Wang
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | | | - Xing-Yi Ge
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Haizhen Zhu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
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Liu T, Peng Y, Wu J, Lu S, He Y, Li X, Sun L, Song S, Zhang S, Li Z, Wang X, Zhang S, Liu M, Kou Z. Surveillance of avian influenza viruses in live bird markets of Shandong province from 2013 to 2019. Front Microbiol 2022; 13:1030545. [PMID: 36406436 PMCID: PMC9670132 DOI: 10.3389/fmicb.2022.1030545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Avian influenza viruses (AIVs) seriously affect the poultry industry and pose a great threat to humans. Timely surveillance of AIVs is the basis for preparedness of the virus. This study reported the long-term surveillance of AIVs in the live bird market (LBM) of 16 cities in Shandong province from 2013 to 2019. A total of 29,895 samples were obtained and the overall positive rate of AIVs was 9.7%. The H9 was found to be the most predominant subtype in most of the time and contributed most to the monthly positve rate of AIVs as supported by the univariate and multivariate analysis, while H5 and H7 only circulated in some short periods. Then, the whole-genome sequences of 62 representative H9N2 viruses including one human isolate from a 7-year-old boy in were determined and they were genetically similar to each other with the median pairwise sequence identities ranging from 0.96 to 0.98 for all segments. The newly sequenced viruses were most similar to viruses isolated in chickens in mainland China, especially the provinces in Eastern China. Phylogenetic analysis showed that these newly sequenced H9N2 viruses belonged to the same clade for all segments except PB1. Nearly all of these viruses belonged to the G57 genotype which has dominated in China since 2010. Finally, several molecular markers associated with human adaptation, mammalian virulence, and drug resistance were identified in the newly sequenced H9N2 viruses. Overall, the study deepens our understanding of the epidemic and evolution of AIVs and provides a basis for effective control of AIVs in China.
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Affiliation(s)
- Ti Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Julong Wu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shangwen Lu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Yujie He
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Xiyan Li
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lin Sun
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shaoxia Song
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shengyang Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Zhong Li
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Xianjun Wang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Shu Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
| | - Mi Liu
- Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Mi Liu,
| | - Zengqiang Kou
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, China
- *Correspondence: Zengqiang Kou,
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Zhang W, Li Z, Peng Y, Yin Y, Zhou Q. Patient-Specific Daily Updated Deep Learning Auto-Segmentation for MRI-Guided Adaptive Radiotherapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.911] [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: 11/27/2022]
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Zhu H, Xie D, Yang Y, Wang Y, Huang R, Chen X, Wang B, Peng Y, Wang J, Xiao D, Wu D, Qian C, Deng X. The Immune Response and Intestinal Injury after X-Ray FLASH Irradiation in Murine Breast Cancer Transplanted Models. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.457] [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: 11/30/2022]
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Kato K, Yoon H, Raymond E, Hubner R, Shu Y, Pan Y, Park S, Ping L, Jiang Y, Zhang J, Wu X, Yao Y, Shen L, Kojima T, Lin CY, Wang L, Tao A, Peng Y, Li L, Xu J. 70O Randomized, global, phase III study of tislelizumab (TIS) + chemotherapy (chemo) vs chemo as first-line (1L) therapy for advanced or metastatic esophageal squamous cell carcinoma (ESCC) (RATIONALE-306): Asia subgroup. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.106] [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: 12/07/2022] Open
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Wu F, Liu J, Hu C, Liu J, Zhao W, Wu Y, Xu Y, Hu J, Xiao L, Liu X, Pan Y, Zeng Y, Shi S, Peng Y, Jiang Y. EP01.07-005 Combined Diffusion-Weighted Imaging and Dynamic Contrast-Enhanced MRI for Diagnosing Indeterminate Pulmonary Nodules. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.326] [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: 10/14/2022]
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Du R, Ming J, Geng J, Sui X, Li S, Liu Z, Zhu X, Cai Y, Wang Z, L. Tang, Zhang X, Peng Z, Yan Y, Li Z, Peng Y, Wu A, Li Y, Li Z, Wang W, Ji J. 1215P Neoadjuvant concurrent chemoradiotherapy combined with immunotherapy in the treatment of adenocarcinoma of the oesophagogastric junction: A phase II study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1333] [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: 11/29/2022] Open
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