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Cai L, Zhu CX, Zhang XL, Fang Y, Yang HY, Guo LW. [Interpretation of global lung cancer statistics]. Zhonghua Liu Xing Bing Xue Za Zhi 2024; 45:585-590. [PMID: 38678357 DOI: 10.3760/cma.j.cn112338-20230920-00172] [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: 04/29/2024]
Abstract
Lung cancer remains one of the leading cause of global cancer-related mortality, posing a significant burden of disease. Tobacco exposure stands as the foremost risk factor for lung cancer. Since the 1960, global efforts have gradually been implemented to control tobacco exposure, consequently reducing tobacco exposure levels within populations. This shift in exposure levels may have altered the epidemiological characteristics of lung cancer globally. This study aims to describe global lung cancer incidence data across five dimensions: age, gender, region, stage at diagnosis, and survival status, using global cancer registry data and relevant research findings. The objective is to elucidate the current epidemiological features of lung cancer worldwide, providing a scientific basis for lung cancer prevention and control. Furthermore, this study offers corresponding measures and recommendations for lung cancer prevention and control, aligning with the three-tiered cancer prevention strategy. Findings indicate that the incidence and mortality burden of lung cancer is significantly higher among the elderly population (aged 65 years and above) compared to the working-age population (aged 15-64 years). The aged-standardized incidence rate of lung cancer remains higher in males than in females, but the overall aged-standardized incidence rate of lung cancer in males shows a declining trend, while that in females shows an increasing trend. Regions with high and very high human development index (HDI) exhibit a substantially higher incidence and mortality burden of lung cancer compared to regions with low and very low HDI. Japan ranks highest in the diagnosis of stage Ⅰ lung cancer, with a diagnosis rate of 38.6%. Its age-standardized 5-year net survival rate is relatively high at 32.9%. Despite improvements in the survival status of lung cancer in certain countries like China and Japan, the overall prognosis for lung cancer remains pessimistic. Given the current epidemiological characteristics of lung cancer, reinforcing tobacco control measures and reducing female-specific lung cancer risk factors stand as significant goals for primary prevention. Promoting low-dose computed tomography screening for high-risk population, minimizing false-positive rates in lung cancer screening, and promoting medical system reforms and standardized treatment constitute principal measures for secondary and tertiary lung cancer prevention, respectively.
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Affiliation(s)
- L Cai
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Henan Office for Cancer Control and Research, Zhengzhou 450008, China Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - C X Zhu
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Henan Office for Cancer Control and Research, Zhengzhou 450008, China Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - X L Zhang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Henan Office for Cancer Control and Research, Zhengzhou 450008, China Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Y Fang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Henan Office for Cancer Control and Research, Zhengzhou 450008, China Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - H Y Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - L W Guo
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, Henan Office for Cancer Control and Research, Zhengzhou 450008, China Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
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Lv A, BianBaZhuoMa, DeQiong, DaWaZhuoMa, PuBuZhuoMa, Yao D, LangJiQuZhen, Lu Y, Cai L, DaZhen, Tang C, BianBaZhuoMa, Zhang Y, Yin J, Ding T, DaWaCang, Wu M, Chen Y, Li Y. Effect of COVID-19 infection on pregnant women in plateau regions. Public Health 2024; 229:57-62. [PMID: 38401193 DOI: 10.1016/j.puhe.2023.12.029] [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: 08/21/2023] [Revised: 12/04/2023] [Accepted: 12/28/2023] [Indexed: 02/26/2024]
Abstract
OBJECTIVE The present study aims to explore the effect of COVID-19 infection on pregnant women in plateau regions. STUDY DESIGN Data from 381 pregnant women infected with COVID-19 who underwent prenatal examination or treatment at Women and Children's Hospital of Tibet Autonomous Region between January 2020 and December 2022 and 314 pregnant women not infected with COVID-19 were retrospectively collected. METHODS The study participants were divided into an infected and non-infected group according to whether they were infected with COVID-19. Basic information (ethnicity, age, body mass index and gestational age [GA]), vaccination status, intensive care unit (ICU) admission and delivery outcomes were compared. Binary logistic regression was used to analyse the influencing factors of ICU admission. RESULTS The results revealed significant differences in the GA, vaccination rate, blood pressure, partial pressure of oxygen, white blood cell (WBC) count, ICU admission rate, preeclampsia rate, forearm presentation rate, thrombocytopenia rate, syphilis infection rate and placental abruption rate between the two groups (P < 0.05). A univariate analysis showed that COVID-19 infection, hepatitis B virus infection, the WBC count and hypoproteinaemia were risk factors for ICU admission. The results of the multivariate analysis of the ICU admission of pregnant women showed that COVID-19 infection (odds ratio [OR] = 4.271, 95 % confidence interval [CI]: 3.572-5.820, P < 0.05) was a risk factor for ICU admission and the WBC count (OR = 0.935, 95 % CI: 0.874-0.947, P < 0.05) was a protective factor for ICU admission. CONCLUSION Pregnant women are vulnerable to the adverse consequences of COVID-19 infection, and public health measures such as vaccination are needed to protect this population subgroup.
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Affiliation(s)
- A Lv
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO. 1 DaHua Road, Dong Dan, Beijing, 100730, PR China; Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - BianBaZhuoMa
- Lhasa People's Hospital, No. 1, Beijing Middle Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - DeQiong
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaWaZhuoMa
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - PuBuZhuoMa
- Lhasa People's Hospital, No. 1, Beijing Middle Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - D Yao
- Nyingchi People's Hospital, No. 11, Water Garden, Bayi Town, Bayi District, Nyingchi City, Tibet Autonomous Region, 860000, PR China
| | - LangJiQuZhen
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - Y Lu
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - L Cai
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaZhen
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - C Tang
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - BianBaZhuoMa
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - Y Zhang
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - J Yin
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - T Ding
- Women and Children's Hospital of Tibet Autonomous Region, NO. 10 Chagu Avenue, Doilungdêqên District, Liuwu New Area, Lhasa, Tibet Autonomous Region, 851414, PR China
| | - DaWaCang
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - M Wu
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - Y Chen
- Tibet University Medical School, No. 10, Zangda East Road, Chengguan District, Lhasa, Tibet Autonomous Region, 850000, PR China
| | - Y Li
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO. 1 DaHua Road, Dong Dan, Beijing, 100730, PR China.
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Cai L, Li H, Deng J, Zhou R, Zeng Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol 2024; 32:280-291. [PMID: 37722980 DOI: 10.1016/j.tim.2023.08.011] [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: 04/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Junwei Deng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiqian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China; Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
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Cui AL, Xia BC, Zhu Z, Xie ZB, Sun LW, Xu J, Xu J, Li Z, Zhao LQ, Long XR, Yu DS, Zhu B, Zhang F, Mu M, Xie H, Cai L, Zhu Y, Tian XL, Wang B, Gao ZG, Liu XQ, Ren BZ, Han GY, Hu KX, Zhang Y. [Epidemiological characteristics of human respiratory syncytial virus (HRSV) among acute respiratory infection (ARI) cases in 16 provinces of China from 2009 to 2023]. Zhonghua Yu Fang Yi Xue Za Zhi 2024; 58:1-7. [PMID: 38403282 DOI: 10.3760/cma.j.cn112150-20231213-00440] [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: 02/27/2024]
Abstract
Objective: To understand the epidemiological characteristics of human respiratory syncytial virus (HRSV) among acute respiratory infection (ARI) cases in 16 provinces of China from 2009 to 2023. Methods: The data of this study were collected from the ARI surveillance data from 16 provinces in China from 2009 to 2023, with a total of 28 278 ARI cases included in the study. The clinical specimens from ARI cases were screened for HRSV nucleic acid from 2009 to 2023, and differences in virus detection rates among cases of different age groups, regions, and months were analyzed. Results: A total of 28 278 ARI cases were enrolled from January 2009 to September 2023. The age of the cases ranged from<1 month to 112 years, and the age M (Q1, Q3) was 3 years (1 year, 9 years). Among them, 3 062 cases were positive for HRSV nucleic acid, with a total detection rate of 10.83%. From 2009 to 2019, the detection rate of HRSV was 9.33%, and the virus was mainly prevalent in winter and spring. During the Corona Virus Disease 2019 (COVID-19) pandemic, the detection rate of HRSV fluctuated between 6.32% and 18.67%. There was no traditional winter epidemic peak of HRSV from the end of 2022 to the beginning of 2023, and an anti-seasonal epidemic of HRSV occurred from April to May 2023. About 87.95% (2 693/3 062) of positive cases were children under 5 years old, and the difference in the detection rate of HRSV among different age groups was statistically significant (P<0.001), showing a decreasing trend of HRSV detection rate with the increase of age (P<0.001). Among them, the HRSV detection rate (25.69%) was highest in children under 6 months. Compared with 2009-2019, the ranking of HRSV detection rates in different age groups changed from high to low between 2020 and 2023, with the age M (Q1, Q3) of HRSV positive cases increasing from 1 year (6 months, 3 years) to 2 years (11 months, 3 years). Conclusion: Through 15 years of continuous HRSV surveillance analysis, children under 5 years old, especially infants under 6 months old, are the main high-risk population for HRSV infection. During the COVID-19 pandemic, the prevalence and patterns of HRSV in China have changed.
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Affiliation(s)
- A L Cui
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID)/NHC Key Laboratory of Medical Virology and Viral Diseases/National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - B C Xia
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID)/NHC Key Laboratory of Medical Virology and Viral Diseases/National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z Zhu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID)/NHC Key Laboratory of Medical Virology and Viral Diseases/National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Z B Xie
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID)/NHC Key Laboratory of Medical Virology and Viral Diseases/National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - L W Sun
- Precision Medicine Research Center, Children's Hospital of Changchun, Changchun 130061, China
| | - J Xu
- Institute of Expanded Immunization Program, Henan Provincial Center for Disease Control and Prevention, Zhengzhou 450016, China
| | - J Xu
- National institute for viral disease control and prevention, Shaanxi provincial center for disease control and prevention, Xi'an 710054, China
| | - Z Li
- Institute for Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan 250014, China
| | - L Q Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing 100020, China
| | - X R Long
- Department of Infectious Diseases, Children's Hospital Affiliated to Chongqing Medical University, Chongqing 400014, China
| | - D S Yu
- Institute of Pathogen testing, Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China
| | - B Zhu
- Virus Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China
| | - F Zhang
- aboratory of Viral diseases, Qingdao Municipal Centre for Disease Control and Prevention, Qingdao Institute of Prevention Medicine, Qingdao 266000, China
| | - M Mu
- School of Public Health, Anhui University of Science and Technology, Huainan 232001, China
| | - H Xie
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China
| | - L Cai
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
| | - Y Zhu
- Laboratory of Infection and Virology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - X L Tian
- Department of Immunization Program, Neimeng Provincial Center for Disease Control and Prevention, Huhehaote 010000, China
| | - B Wang
- Department of Infectious Diseases, Shenyang Prefecture Center for Disease Control and Prevention, Shenyang 110000, China
| | - Z G Gao
- Institute for infectious disease prevention and treatment, Xinjiang Center for Disease Control and Prevention, Wulumuqi 830002, China
| | - X Q Liu
- Laboratory of Viral Infectious Disease, Key Laboratory of Important and Emerging Viral Infectious Diseases of Jiangxi Health Commission, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China
| | - B Z Ren
- Division of Diseases Detection, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan 030012, China
| | - G Y Han
- Institute for Viral Disease Control and Prevention, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang 050021, China
| | - K X Hu
- Institute of Health Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100123, China
| | - Y Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID)/NHC Key Laboratory of Medical Virology and Viral Diseases/National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Li H, Cai L, Wang L, Wang Y, Xu J, Zhang R. The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea. Microbiol Spectr 2024; 12:e0200223. [PMID: 38193726 PMCID: PMC10846272 DOI: 10.1128/spectrum.02002-23] [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: 05/13/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Liu W, Cai L, Li Y. Application of natural language processing to post-structuring of rectal cancer MRI reports. Clin Radiol 2024; 79:e204-e210. [PMID: 38042740 DOI: 10.1016/j.crad.2023.10.032] [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: 07/27/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 12/04/2023]
Abstract
AIM To evaluate a natural language processing (NLP) system for extracting structured information from the free-form text of rectal cancer magnetic resonance imaging (MRI) reports written in Chinese. MATERIALS AND METHODS A rule-based NLP model that could extract 11 key image features of rectal cancer was constructed using 358 MRI reports of rectal cancer written between 2015 and 2021. Fifty reports written before 2015 and 50 written after 2021 were used as test datasets, and the reference standard was determined by manual extraction of information by two radiologists. The length and reporting rate of image features in pre-2015 and post-2021 datasets, as well as the accuracy, precision, recall, and F1 score of feature extraction by the NLP system, were compared. The time required for the NLP to extract data was compared with that required by the radiologists. RESULTS Reports written after 2021 had longer diagnostic impression sections than reports written before 2015. The reporting rate of key imaging features of rectal cancer was 36.55% before 2015 and 79.82% after 2021. The accuracy, precision, recall, and F1 score of NLP for correct extraction of values from reports were 93.82%, 95.63%, 87.06%, and 91.15%, respectively, for pre-2015 reports, and 92.55%, 98.53%, 94.15%, and 96.29%, respectively, for post-2021 reports. NLP generated all the structured information in <1 second. CONCLUSIONS The NLP system with rule-based pattern matching achieved rapid and accurate structured processing of rectal cancer MRI reports. MRI reports with structured templates are more suitable for NLP-based extraction of information.
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Affiliation(s)
- W Liu
- Department of Radiology, Aerospace Center Hospital, Beijing, 100049, China; Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - L Cai
- School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Y Li
- Department of General Surgery, Aerospace Center Hospital, Beijing, 100049, China.
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Guo LW, Zhang XL, Cai L, Zhu CX, Fang Y, Yang HY, Chen HD. [Current status of global colorectal cancer prevalence, prevention and control]. Zhonghua Zhong Liu Za Zhi 2024; 46:57-65. [PMID: 38246781 DOI: 10.3760/cma.j.cn112152-20231024-00213] [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: 01/23/2024]
Abstract
Objective: This paper provides a brief overview of the epidemiology of colorectal cancer in China and around the world, and discusses how to prevent colorectal cancer to reduce its disease burden. Method: Using the official database of GLOBOCAN 2020, the China Cancer Registry Annual Report compiled by the National Cancer Center, and data from CONCORD-3.Data management was performed by Microsoft Excel 2016 and R 4.2.1 Relevant graphs were generated using the ggplot2 package for result visualization. Result: An estimated 1 931 590 people were diagnosed with colorectal cancer worldwide in 2020 with an age-standardized incidence rate of 19.5 per 100 000. There were about 935 173 deaths caused by colorectal cancer internationally, with an age-standardized mortality rate of 9.0 per 100 000. Overall, colorectal cancer was the fourth most commonly diagnosed cancer and the third leading cause of cancer-related death worldwide in 2020. In China, the age-standardized incidence rate and mortality rate of colorectal cancer was 17.3 per 100 000 and 7.8 per 100 000, respectively. Gender differences in trends were observed, with a decreasing trend in incidence and mortality among females and an increasing trend in incidence and mortality among males. The primary risk factors for colorectal cancer include age, genetic factors, gastrointestinal disorders, dietary habits, and lifestyle et al. Conclusions: Colorectal cancer poses a significant burden globally and in China. The occurrence of colorectal cancer is closely related to physiology, genetics, behavioral habits, lifestyle, and disease factors. To better control the colorectal cancer burden with the lowest cost, specific measures should be taken to reduce exposure to established risk factors. By combining the disease prevention and control strategies of tertiary prevention in China with the characteristic factors of colorectal cancer, the incidence and mortality of colorectal cancer may be effectively controlled.
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Affiliation(s)
- L W Guo
- Henan Office for Cancer Control and Research, Henan Engineering Research Center of Cancer Prevention and Control, Henan International Joint Laboratory of Cancer Prevention, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - X L Zhang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - L Cai
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - C X Zhu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Y Fang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - H Y Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - H D Chen
- Center for Prevention and Early Intervention,National Infrastructures for Translational Medicine,Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
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Wei W, Tian Y, Cai L, Xu Y, Xiao X, Wang Q, Wang H, Dong C, Shao Z, Jiao N, Zhang R. Survival of surface bacteriophages and their hosts in in situ deep-sea environments. Microbiol Spectr 2024; 12:e0453422. [PMID: 38051228 PMCID: PMC10783000 DOI: 10.1128/spectrum.04534-22] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/27/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE The survival of the sinking prokaryotes and viruses in the deep-sea environment is crucial for deep-sea ecosystems and biogeochemical cycles. Through an in situ deep-sea long-term incubation device, our results showed that viral particles and infectivity had still not decayed completely after in situ incubation for 1 year. This suggests that, via infection and lysis, surface viruses with long-term infectious activity in situ deep-sea environments may influence deep-sea microbial populations in terms of activity, function, diversity, and community structure and ultimately affect deep-sea biogeochemical cycles, highlighting the need for additional research in this area.
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Affiliation(s)
- Wei Wei
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xilin Xiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiong Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Haowen Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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9
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Liu Y, Meng X, Zheng H, Cai L, Wei S, He M, He J, Hao Y, Ge C, Liu J, Chen F, Xu Y. A novel long-tailed myovirus represents a new T4-like cyanophage cluster. Front Microbiol 2023; 14:1293846. [PMID: 38029084 PMCID: PMC10665884 DOI: 10.3389/fmicb.2023.1293846] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Cyanophages affect the abundance, diversity, metabolism, and evolution of picocyanobacteria in marine ecosystems. Here we report an estuarine Synechococcus phage, S-CREM2, which represents a novel viral genus and leads to the establishment of a new T4-like cyanophage clade named cluster C. S-CREM2 possesses the longest tail (~418 nm) among isolated cyanomyoviruses and encodes six tail-related proteins that are exclusively homologous to those predicted in the cluster C cyanophages. Furthermore, S-CREM2 may carry three regulatory proteins in the virion, which may play a crucial role in optimizing the host intracellular environment for viral replication at the initial stage of infection. The cluster C cyanophages lack auxiliary metabolic genes (AMGs) that are commonly found in cyanophages of the T4-like clusters A and B and encode unique AMGs like an S-type phycobilin lyase gene. A variation in the composition of tRNA and cis-regulatory RNA genes was observed between the marine and freshwater phage strains in cluster C, reflecting their different modes of coping with hosts and habitats. The cluster C cyanophages are widespread in estuarine and coastal regions and exhibit equivalent or even higher relative abundance compared to those of clusters A and B cyanophages in certain estuarine regions. The isolation of cyanophage S-CREM2 provides new insights into the phage-host interactions mediated by both newly discovered AMGs and virion-associated proteins and emphasizes the ecological significance of cluster C cyanophages in estuarine environments.
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Affiliation(s)
- Yuanfang Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xue Meng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongrui Zheng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Minglu He
- School of Information Science and Engineering, Shandong University, Qingdao, China
| | - Jiale He
- School of Life Science, Shandong University, Qingdao, China
| | - Yue Hao
- School of Life Science, Shandong University, Qingdao, China
| | - Chang Ge
- School of Life Science, Shandong University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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10
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Preedanon S, Suetrong S, Srihom C, Somrithipol S, Kobmoo N, Saengkaewsuk S, Srikitikulchai P, Klaysuban A, Nuankaew S, Chuaseeharonnachai C, Chainuwong B, Muangsong C, Zhang Z, Cai L, Boonyuen N. Eight novel cave fungi in Thailand's Satun Geopark. Fungal Syst Evol 2023; 12:1-30. [PMID: 38455950 PMCID: PMC10915585 DOI: 10.3114/fuse.2023.12.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/12/2023] [Indexed: 03/09/2024] Open
Abstract
Karst caves are unique oligotrophic ecosystems characterised by the scarcity of organic litter, darkness, low to moderate temperatures, and high humidity, supporting diverse fungal communities. Despite their importance, little is known about the fungi in karst caves in Thailand. In 2019, we explored the culturable mycobiota associated with three selected types of substrates (air, soil/sediment and organic litter samples) from two karst caves, the Le Stegodon and Phu Pha Phet Caves, in the Satun UNESCO Global Geopark in southern Thailand. Based on morphological characters and multilocus phylogenetic analyses, eight new species (Actinomortierella caverna, Hypoxylon phuphaphetense, Leptobacillium latisporum, Malbranchea phuphaphetensis, Scedosporium satunense, Sesquicillium cavernum, Thelonectria satunensis and Umbelopsis satunensis) were described, illustrated, and compared to closely related species. These new fungal taxa form independent lineages distinct from other previously described species and classified into eight different families across six orders and two phyla (Ascomycota and Mucoromycota). This paper provides additional evidence that the karst caves located within the Satun UNESCO Global Geopark, situated in the southern region of Thailand, harbour a diverse range of newly discovered species. Citation: Preedanon S, Suetrong S, Srihom C, Somrithipol S, Kobmoo N, Saengkaewsuk S, Srikitikulchai P, Klaysuban A, Nuankaew S, Chuaseeharonnachai C, Chainuwong B, Muangsong C, Zhang ZF, Cai L, Boonyuen N (2023). Eight novel cave fungi in Thailand's Satun Geopark. Fungal Systematics and Evolution 12: 1-30. doi: 10.3114/fuse.2023.12.01.
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Affiliation(s)
- S. Preedanon
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - S. Suetrong
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - C. Srihom
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - S. Somrithipol
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - N. Kobmoo
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - S. Saengkaewsuk
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - P. Srikitikulchai
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - A. Klaysuban
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - S. Nuankaew
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - C. Chuaseeharonnachai
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - B. Chainuwong
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - C. Muangsong
- Innovation for Social and Environmental Management, Mahidol University (MU), Amnatcharoen Campus, Amnatcharoen 37000, Thailand
| | - Z.F. Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 51145, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - N. Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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11
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Cai L, Liu H, Zhang W, Xiao S, Zeng Q, Dang S. Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses. Nat Commun 2023; 14:6438. [PMID: 37833330 PMCID: PMC10575957 DOI: 10.1038/s41467-023-42258-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Hang Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wen Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shiwei Xiao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China.
- Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
- HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, China.
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12
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Xiao Y, Miao Z, Sun J, Xing W, Wei Y, Bai J, Ye H, Si Y, Cai L. Allisartan Isoproxil Promotes Uric Acid Excretion by Interacting with Intestinal Urate Transporters in Hyperuricemic Zebrafish (Danio rerio). Bull Exp Biol Med 2023; 175:638-643. [PMID: 37853267 DOI: 10.1007/s10517-023-05917-9] [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: 08/12/2022] [Indexed: 10/20/2023]
Abstract
To evaluate the urate-lowering effect and potential drug targets of antihypertensive agent allisartan isoproxil (ALI) and its bioactive metabolite EXP3174, we developed an acute hyperuricemic zebrafish model using potassium oxonate and xanthine sodium salt. Losartan potassium served as the positive control (reference drug). In this model, ALI and losartan potassium exerted a greater urate-lowering effect than EXP3174 indicating that the latter is not the critical substance for elimination of uric acid. The quantitative real-time PCR showed that ALI upregulates the expression of intestinal urate transporters genes ABCG2, PDZK1, and SLC2A9 (p<0.01). Thus, we can suggest that this substance promotes uric acid excretion mainly by interacting with intestinal urate transporters.
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Affiliation(s)
- Y Xiao
- Shenzhen Salubris Pharmaceutical Co., Ltd, Shenzhen, Guangdong, China
| | - Z Miao
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China
| | - J Sun
- Shenzhen Salubris Pharmaceutical Co., Ltd, Shenzhen, Guangdong, China
| | - W Xing
- Shenzhen Salubris Pharmaceutical Co., Ltd, Shenzhen, Guangdong, China
| | - Y Wei
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China
| | - J Bai
- Shenzhen Salubris Pharmaceutical Co., Ltd, Shenzhen, Guangdong, China
| | - H Ye
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China
| | - Y Si
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - L Cai
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China.
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13
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Han S, Wang M, Ma Z, Raza M, Zhao P, Liang J, Gao M, Li Y, Wang J, Hu D, Cai L. Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Stud Mycol 2023; 104:87-148. [PMID: 37351543 PMCID: PMC10282163 DOI: 10.3114/sim.2022.104.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/14/2022] [Accepted: 01/17/2023] [Indexed: 11/26/2023] Open
Abstract
Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.
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Affiliation(s)
- S.L. Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - M.M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - Z.Y. Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - M. Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - J.M. Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - M. Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - Y.J. Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - J.W. Wang
- Institute of Biology Co., Ltd., Henan Academy of Science, Zheng Zhou 450008, Henan, P. R. China;
| | - D.M. Hu
- College of Bioscience & Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
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14
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Huang Y, Sun H, Wei S, Cai L, Liu L, Jiang Y, Xin J, Chen Z, Que Y, Kong Z, Li T, Yu H, Zhang J, Gu Y, Zheng Q, Li S, Zhang R, Xia N. Structure and proposed DNA delivery mechanism of a marine roseophage. Nat Commun 2023; 14:3609. [PMID: 37330604 PMCID: PMC10276861 DOI: 10.1038/s41467-023-39220-y] [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: 09/12/2022] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
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Affiliation(s)
- Yang Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hui Sun
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Liqin Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yanan Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jiabao Xin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhenqin Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Yuqiong Que
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Zhibo Kong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Tingting Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Hai Yu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China
| | - Qingbing Zheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, 361102, China.
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Cai L, Tian Y, Li Z, Yang Y, Ai C, Zhang R. A broad-host-range lytic phage vB_VhaS-R18L as a candidate against vibriosis. Front Microbiol 2023; 14:1191157. [PMID: 37333633 PMCID: PMC10272388 DOI: 10.3389/fmicb.2023.1191157] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
Vibriosis is one of the most common bacterial diseases that cause high rates of mortality and considerable economic losses in aquaculture. Phage therapy has been considered as a promising alternative method to antibiotics in the biocontrol of infectious diseases. Genome sequencing and characterization of the phage candidates are prerequisites before field applications to ensure environmental safety. In this study, a lytic phage, named vB_VhaS-R18L (R18L), was isolated from the coastal seawater of Dongshan Island, China. The phage was characterized in terms of morphology, genetic content, infection kinetics, lytic profile, and virion stability. Transmission electronic microscopy indicated that R18L is siphovirus-like, comprising an icosahedral head (diameter 88.6 ± 2.2 nm) and a long noncontractile tail (225 × 11 nm). Genome analysis indicated R18L to be a double-stranded DNA virus with a genome size of 80,965 bp and a G + C content of 44.96%. No genes that encode known toxins or genes implicated in lysogeny control were found in R18L. A one-step growth experiment showed that R18L had a latent period of approximately 40 min and a burst size of 54 phage particles per infected cell. R18L showed lytic activity against a wide range of at least five Vibrio species (V. alginolyticus, V. cholerae, V. harveyi, V. parahemolyticus, and V. proteolyticus). R18L was relatively stable at pH 6-11 and at temperatures ranging from 4°C to 50°C. The broad lytic activity across Vibrio species and the stability in the environment make R18L a potential candidate for phage therapy in controlling vibriosis in aquaculture systems.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yuan Tian
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ziqiang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chunxiang Ai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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16
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Chen ZQ, Zhang D, Wang Z, Song N, Ma AL, Zhang SR, Cai L. [The value of DISCO and MUSE-DWI combined with prostate specific antigen density in the diagnosis and risk stratification of prostate cancer]. Zhonghua Yi Xue Za Zhi 2023; 103:1461-1468. [PMID: 37198108 DOI: 10.3760/cma.j.cn112137-20221018-02176] [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
Objective: To explore the value of differential subsampling with cartesian ordering (DISCO) and multiplexed sensitivity-encoding diffusion weighted-imaging (MUSE-DWI) combined with prostate specific antigen density (PSAD) in the diagnosis and risk stratification of prostate cancer (PCa). Methods: The data of 183 patients [aged from 48 to 86 (68±8) years] with prostate diseases in the General Hospital of Ningxia Medical University from July 2020 to August 2021 were retrospectively collected. Those patients were divided into non-PCa group (n=115) and PCa group (n=68) based on the disease condition. According to the risk degree, PCa group was subdivided into low risk PCa group (n=14) and medium-to-high risk PCa group (n=54). The differences of volume transfer constant (Ktrans), rate constant (Kep), extracellular volume fraction (Ve), apparent diffusion coefficient (ADC) and PSAD between groups were analyzed. Receiver operating characteristic (ROC) curves analysis were conducted for evaluating the diagnostic efficacy of quantitative parameters and PSAD in distinguishing non-PCa and PCa, low-risk PCa and medium-high risk PCa. Multivariate logistic regression model was used for screening out the predictors, which was statistically significant differences between non-PCa group and PCa group, for PCa prediction. Results: Ktrans, Kep, Ve and PSAD of PCa group all were higher than those of non-PCa group, and ADC value was lower than that of non-PCa group, and the differences all were statistically significant (all P<0.001). Ktrans, Kep and PSAD of medium-to-high risk PCa group all were higher than those of low risk PCa group, and ADC value was lower than that of low risk PCa group, and the differences were all statistically significant (all P<0.001). When distinguishing non-PCa from PCa, the area under ROC curve (AUC) of the combined model (Ktrans+Kep+Ve+ADC+PSAD) was higher than that of any single index [0.958 (95%CI: 0.918-0.982) vs 0.881 (95%CI: 0.825-0.924), 0.836 (95%CI: 0.775-0.887), 0.672 (95%CI: 0.599-0.740), 0.940(95%CI: 0.895-0.969), 0.816(95%CI:0.752-0.869), all P<0.05]. When distinguishing low-risk PCa and medium-to-high risk PCa, the AUC of the combined model (Ktrans+Kep+ADC+PSAD) were higher than those of Ktrans, Kep and PSAD[0.933 (95%CI: 0.845-0.979) vs 0.846 (95%CI:0.738-0.922), 0.782 (95%CI:0.665-0.873), 0.84 8(95%CI: 0.740-0.923), all P<0.05]. The multivariate logistic regression analysis showed that Ktrans (OR=1.005, 95%CI:1.001-1.010) and ADC values (OR=0.992, 95%CI:0.989-0.995) were predictors of PCa (P<0.05). Conclusions: DISCO and MUSE-DWI combined with PSAD can distinguish benign and malignant prostate lesions. Ktrans and ADC values were predictors of PCa; Ktrans, Kep, ADC values and PSAD are helpful in predicting the biological behavior of PCa.
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Affiliation(s)
- Z Q Chen
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - D Zhang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - Z Wang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - N Song
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - A L Ma
- Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - S R Zhang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - L Cai
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
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17
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Song XX, Cai L, Liu W, Cui WL, Peng X, Li QF, Dong Y, Yang MD, Wu BQ, Yue TK, Fan JH, Li YY, Li Y. [Development and application syndromic surveillance and early warning system in border area in Yunnan Province]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:845-850. [PMID: 37221077 DOI: 10.3760/cma.j.cn112338-20221013-00882] [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: 05/25/2023]
Abstract
Objective: To establish a dynamic syndromic surveillance system in the border areas of Yunnan Province based on information technology, evaluate its effectiveness and timeliness in the response to common communicable disease epidemics and improve the communicable disease prevention and control in border areas. Methods: Three border counties were selected for full coverage as study areas, and dynamic surveillance for 14 symptoms and 6 syndromes were conducted in medical institutions, the daily collection of information about students' school absence in primary schools and febrile illness in inbound people at border ports were conducted in these counties from January 2016 to February 2018 to establish an early warning system based on mobile phone and computer platform for a field experimental study. Results: With syndromes of rash, influenza-like illness and the numbers of primary school absence, the most common communicable disease events, such as hand foot and mouth disease, influenza and chickenpox, can be identified 1-5 days in advance by using EARS-3C and Kulldorff time-space scanning models with high sensitivity and specificity. The system is easy to use with strong security and feasibility. All the information and the warning alerts are released in the form of interactive charts and visual maps, which can facilitate the timely response. Conclusions: This system is highly effective and easy to operate in the detection of possible outbreaks of common communicable diseases in border areas in real time, so the timely and effective intervention can be conducted to reduce the risk of local and cross-border communicable disease outbreaks. It has practical application value.
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Affiliation(s)
- X X Song
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - L Cai
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - W Liu
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - W L Cui
- School of Public Health, Kunming Medical University, Kunming 650500, China
| | - X Peng
- Yunnan Provincial Center for Disease Control and Prevention, Kunming 650022, China
| | - Q F Li
- Yunnan Provincial Center for Disease Control and Prevention, Kunming 650022, China
| | - Y Dong
- Yunnan Provincial Institute for Endemic Diseases Control and Prevention, Dali 671000, China
| | - M D Yang
- Yunnan Provincial Institute of Parasitic Diseases, Pu'er 665000, China
| | - B Q Wu
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Yunnan Province, Mangshi 678400, China
| | - T K Yue
- Dehong Dai and Jingpo Autonomous Prefecture Center for Disease Control and Prevention, Yunnan Province, Mangshi 678400, China
| | - J H Fan
- Xishuangbanna Dai Autonomous Prefectural Center for Disease Control and Prevention, Yunnan Province, Jinghong 666100, China
| | - Y Y Li
- Xishuangbanna Dai Autonomous Prefectural Center for Disease Control and Prevention, Yunnan Province, Jinghong 666100, China
| | - Y Li
- School of Public Health, Kunming Medical University, Kunming 650500, China
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Cai L, Weinbauer MG, Xie L, Zhang R. The smallest in the deepest: the enigmatic role of viruses in the deep biosphere. Natl Sci Rev 2023; 10:nwad009. [PMID: 36960220 PMCID: PMC10029852 DOI: 10.1093/nsr/nwad009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 08/22/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning and nutrient cycling in a wide range of ecosystems. Although the deep biosphere has been estimated to be the largest reservoir for viruses and their prokaryotic hosts, the biology and ecology of viruses therein remain poorly understood. The deep virosphere is an enigmatic field of study in which many critical questions are still to be answered. Is the deep virosphere simply a repository for deeply preserved, non-functioning virus particles? Or are deep viruses infectious agents that can readily infect suitable hosts and subsequently shape microbial populations and nutrient cycling? Can the cellular content released by viral lysis, and even the organic structures of virions themselves, serve as the source of bioavailable nutrients for microbial activity in the deep biosphere as in other ecosystems? In this review, we synthesize our current knowledge of viruses in the deep biosphere and seek to identify topics with the potential for substantial discoveries in the future.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Markus G Weinbauer
- Sorbonne Universités, UPMC, Université Paris 06, CNRS, Laboratoire d’Océanographie de Villefranche (LOV), Villefranche BP28, France
| | - Le Xie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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19
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Chiang A, Salomonsen RB, Wang A, Holland R, Cai L, Xiao Y, Sadow S, Davey K, Iyengar P. 168P Demographics, clinical characteristics, treatment (tx) patterns and clinical outcomes for patients (pts) with limited-stage SCLC (LS-SCLC). J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00422-7] [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: 04/04/2023]
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20
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Whitaker R, Cai L, Wang A, Qiao Y, Chander P, Mooradian M. 12AP SPOTLIGHT real-world study: Outcomes with or without consolidation durvalumab (D) after chemoradiotherapy (CRT) in patients with unresectable stage III NSCLC. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00379-9] [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: 04/03/2023]
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21
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Cai L, Xu B, Li H, Xu Y, Wei W, Zhang R. Spatiotemporal Shift of T4-Like Phage Community Structure in the Three Largest Estuaries of China. Microbiol Spectr 2023; 11:e0520322. [PMID: 36877016 PMCID: PMC10101079 DOI: 10.1128/spectrum.05203-22] [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: 12/17/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Estuaries are one of the most highly productive and economically important ecosystems at the continent-ocean interface. Estuary productivity is largely determined by the microbial community structure and activity. Viruses are major agents of microbial mortality and are key drivers of global geochemical cycles. However, the taxonomic diversity of viral communities and their spatial-temporal distribution in estuarine ecosystems have been poorly studied. In this study, we investigated the T4-like viral community composition at three major Chinese estuaries in winter and in summer. Diverse T4-like viruses, which were divided into three main clusters (Clusters I to III), were revealed. The Marine Group of Cluster III, with seven identified subgroups, was the most dominant (averaging 76.5% of the total sequences) in the Chinese estuarine ecosystems. Significant variations of T4-like viral community composition were observed among estuaries and seasons, with higher diversity occurring in winter. Among various environmental variables, temperature was a main driver of the viral communities. This study demonstrates viral assemblage diversification and seasonality in Chinese estuarine ecosystems. IMPORTANCE Viruses are ubiquitous but largely uncharacterized members of aquatic environments that cause significant mortality in microbial communities. Recent large-scale oceanic projects have greatly advanced our understanding of viral ecology in marine environments, but those studies mostly focused on oceanic regions. There have yet to be spatiotemporal studies of viral communities in estuarine ecosystems, which are unique habitats that play a significant role in global ecology and biogeochemistry. This work is the first comprehensive study that provides a detailed picture of the spatial and seasonal variation of viral communities (specifically, T4-like viral communities) in three major estuarine ecosystems in China. These findings provide much-needed knowledge regarding estuarine viral ecosystems, which currently lags in oceanic ecosystem research.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Key Laboratory of Coastal Salt Marsh Ecosystems and Resources, Ministry of Natural Resources, Jiangsu Ocean University, Lianyungang, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Shandong, China
| | - Wei Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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22
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Zhang K, Cai L, Gong K. Genotype-phenotype correlations and clinical outcomes of Von Hippel-Lindau disease patients with large deletions. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00394-9] [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: 02/12/2023]
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23
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Zhang X, Zhi K, Yang Y, Cui W, Cai L, Zhao X, Zhang Z, Cao W. Mechanism of Qingre Huoxue Fang treatment on inhibiting angiogenesis of rheumatoid arthritis based on network pharmacology and in vitro experiments. J Physiol Pharmacol 2023; 74. [PMID: 37245233 DOI: 10.26402/jpp.2023.1.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/13/2023]
Abstract
This study aimed to explore the mechanism of Qingre Huoxue Fang (QRHXF) treatment on anti-angiogenesis in rheumatoid arthritis (RA) based on network pharmacology and in vitro experiments. We used the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Therapeutic Target (TTD) database to extract the active components of QRHXF and potential targets for regulating angiogenesis. First, we used Cytoscape bioinformatics software to construct the network of QRHXF-angiogenesis and screened the potential targets. Then, we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the potential core targets. In addition, enzyme-linked immune assay and Western blot were used for in vitro validation and to verify the effects of different concentrations of QRHXF on the expression levels of the vascular endothelial growth factor receptor type 1 (VEGFR-1) and VEGFR-2 cytokines and phosphoinositide 3-kinase (PI3k) and Ak strain transforming (Akt) proteins in human umbilical vein endothelial cells (HUVECs). In results, we screened 179 core QRHXF antiangiogenic targets, including vascular endothelial growth factor (VEGF) cytokines. Enrichment analysis showed that the targets were enriched in 56 core signaling pathways, including PI3k and Akt. In vitro experiments showed that the migration distance and square, adhesion optical density (OD) values, and the number of branch points in tube formation significantly decreased in the QRHXF group compared with the induced group (P<0.01). Notably, the serum levels of VEGFR-1 and VEGFR-2 were lower compared with the induced group (P<0.05 or P<0.01). In addition, the expressions of PI3K and p-Akt proteins were decreased in the middle- and high doses groups (P<0.01). This study's results suggest that the downstream mechanism of QRHXF anti-angiogenesis might inhibit the PI3K-Akt signalling pathway and downregulate VEGF-1 and VEGF-2.
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Affiliation(s)
- X Zhang
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - K Zhi
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Y Yang
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - W Cui
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - L Cai
- School of Chinese Medicine, Southern Medical University, Guangdong, China
| | - X Zhao
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Z Zhang
- Beijing University of Chinese Medicine, Beijing, China
| | - W Cao
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing, China.
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Zhang X, Zhi K, Yang Y, Cui W, Cai L, Zhao X, Zhang Z, Cao W. Mechanism of Qingre Huoxue Fang treatment on inhibiting angiogenesis of rheumatoid arthritis based on network pharmacology and in vitro experiments. J Physiol Pharmacol 2023; 74. [PMID: 37245233 DOI: 10.26402/jpp.2023.10.06] [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] [Received: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 05/30/2023]
Abstract
This study aimed to explore the mechanism of Qingre Huoxue Fang (QRHXF) treatment on anti-angiogenesis in rheumatoid arthritis (RA) based on network pharmacology and in vitro experiments. We used the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Therapeutic Target (TTD) database to extract the active components of QRHXF and potential targets for regulating angiogenesis. First, we used Cytoscape bioinformatics software to construct the network of QRHXF-angiogenesis and screened the potential targets. Then, we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the potential core targets. In addition, enzyme-linked immune assay and Western blot were used for in vitro validation and to verify the effects of different concentrations of QRHXF on the expression levels of the vascular endothelial growth factor receptor type 1 (VEGFR-1) and VEGFR-2 cytokines and phosphoinositide 3-kinase (PI3k) and Ak strain transforming (Akt) proteins in human umbilical vein endothelial cells (HUVECs). In results, we screened 179 core QRHXF antiangiogenic targets, including vascular endothelial growth factor (VEGF) cytokines. Enrichment analysis showed that the targets were enriched in 56 core signaling pathways, including PI3k and Akt. In vitro experiments showed that the migration distance and square, adhesion optical density (OD) values, and the number of branch points in tube formation significantly decreased in the QRHXF group compared with the induced group (P<0.01). Notably, the serum levels of VEGFR-1 and VEGFR-2 were lower compared with the induced group (P<0.05 or P<0.01). In addition, the expressions of PI3K and p-Akt proteins were decreased in the middle- and high doses groups (P<0.01). This study's results suggest that the downstream mechanism of QRHXF anti-angiogenesis might inhibit the PI3K-Akt signalling pathway and downregulate VEGF-1 and VEGF-2.
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Affiliation(s)
- X Zhang
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - K Zhi
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Y Yang
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - W Cui
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - L Cai
- School of Chinese Medicine, Southern Medical University, Guangdong, China
| | - X Zhao
- Department of Rheumatology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Z Zhang
- Beijing University of Chinese Medicine, Beijing, China
| | - W Cao
- Wangjing Hospital of China Academy of Chinese Medical Sciences, Beijing, China.
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Lu Q, Yang X, Cai L. Predicting the MIBC in stalked tumor of VI-RADS 2 using nomogram of MRI characteristics. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)01105-3] [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: 02/12/2023]
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26
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Lu Q, Yang X, Cai L, Zheng B, Chen X, Liang Y, Xin Y, Ma T. Performance of the OncoUrine test on the predictive capacity of non-muscle-invasive bladder cancer patients candidate for repeated transurethral resection. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00650-4] [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: 02/12/2023]
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27
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Liu L, Wu X, Li HF, Zhao Y, Li GH, Cui WL, Rabkin Golden A, Cai L. Trends in the Prevalence of Chronic Non-Communicable Diseases and Multimorbidity across Socioeconomic Gradients in Rural Southwest China. J Nutr Health Aging 2023; 27:457-462. [PMID: 37357330 DOI: 10.1007/s12603-023-1932-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVES This study aimed to determine the changing prevalence of five chronic non-communicable diseases (NCDs)- hypertension, coronary heart disease (CHD), stroke, chronic obstructive pulmonary disease (COPD), and asthma-- and its multimorbidity (refers to the co-existence of two or more chronic diseases in an individual) across socioeconomic spectra in rural southwest China. MEASUREMENTS Two cross-sectional health interviews and examination surveys were conducted among individuals aged ≥35 years in rural China. An individual socioeconomic position (SEP) index was constructed using principal component analysis. Anthropometric measurements, blood pressure, and post-bronchodilator spirometry tests were recorded for each participant. RESULTS The mean age and proportion of men was 56.1 years and 48.4% in 2011, while was 56.6 years and 49.4% in 2021. From 2011 to 2021, the overall prevalence of hypertension, stroke and COPD increased from 26.1%, 1.1%, and 8.7% to 40.4%, 2.4%, and 12.8%, respectively (P < 0.01), while prevalence of CHD (2.1% vs. 2.2%) and asthma (1.4% vs. 1.5%) did not differ between the two study years (P > 0.05). The prevalence of NCDs multimorbidity increased from 2.3% to 9.7%, and was also observed among subgroups categorized by sex, age, ethnicity, level of education, income, and SEP (P < 0.01). In addition, the relative increases in the prevalence of multimorbidity were greater among men, old individuals, ethnic minorities, and those with low level of education and low SEP. Both in 2011 and 2021, ethnic minorities and individuals with lower level of education and low SEP had a higher prevalence of multimorbidity of the five studied chronic NCDs than their counterparts (P <0.01). CONCLUSIONS The prevalence of NCDs multimorbidity increased substantially across all socioeconomic gradients in rural southwest China. Future interventions to further manage NCDs and their multimorbidity must be tailored to address socioeconomic factors.
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Affiliation(s)
- L Liu
- Le CAI, PhD, School of Public Health, Kunming Medical University, 1168 Yu Hua Street Chun Rong Road, Cheng Gong New City, Kunming 650500, China,
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Peters S, Salomonsen RB, Tattersfield R, Wang A, Xiao Y, Cai L, Sadow S, Jassim R, Liu S. 107P Outcomes of patients with metastatic non-small cell lung cancer (mNSCLC) receiving first-line (1L) immunotherapy (IO) with or without chemotherapy (CT): Real-world (RW) evidence vs clinical trial results - CORRELATE. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100211] [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: 12/14/2022]
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29
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Dong XQ, Zhang ZQ, Feng H, Cai L. [A case report of the first and second branchial arch syndrome with torticollis]. Zhonghua Yan Ke Za Zhi 2022; 58:923-924. [PMID: 36348531 DOI: 10.3760/cma.j.cn112142-20220421-00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A 54-month-old female patient presented to the department of ophthalmology with abnormal head posture and facial asymmetry for two years. The patient's facial development was asymmetrical, with the middle 1/3 of the left side shorter than the right side. The left ear is less malformed than the right. There was no obvious abnormality in corneal light reflex and eye movement. Head tilt test ( -). So, paralysis of the superior oblique muscle was excluded. In consultation with the department of maxillofacial surgery, the patient was confirmed as the first and second branchial arch syndrome and torticollis.
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Affiliation(s)
- X Q Dong
- Department of Ophthalmology, Shenzhen University General Hospital, Shenzhen 518000, China
| | - Z Q Zhang
- Department of Ophthalmology, Shenzhen University General Hospital, Shenzhen 518000, China
| | - H Feng
- Department of Ophthalmology, Shenzhen University General Hospital, Shenzhen 518000, China
| | - L Cai
- Department of Ophthalmology, Shenzhen University General Hospital, Shenzhen 518000, China
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Shao Z, Liu Q, Tong Z, Li W, Cai L, Bai Y, Amin K, Deshpande P, Bi Y, Xu B. 21MO Primary results of a China bridging, phase II randomized study of initial endocrine therapy (ET) ± ribociclib (RIB) in pre- & postmenopausal Chinese women with HR+/HER2– ABC. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.030] [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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31
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Shi M, Yin L, Sun Y, Wang C, Cai L, Zhang T, Zhou X, Fawcett JP, Gao X, Gu J. Pharmacokinetic Study of Conjugated Equine Estrogens in Healthy Chinese Postmenopausal Women Using a Parallel Two-Column LC-MS/MS Method. Clin Pharmacokinet 2022; 61:1571-1583. [PMID: 36173592 DOI: 10.1007/s40262-022-01177-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND AND OBJECTIVE: Postmenopausal women often require estrogen supplementation to improve menopausal and postmenopausal vasomotor symptoms and maintain hormonal balance. Conjugated equine estrogens extracted from the urine of pregnant mares are commonly used to provide this estrogen replacement therapy. The complex composition of this mixture of animal sulfated metabolites makes its bioanalysis challenging such that its detailed pharmacokinetics has not been fully characterized. The purpose of this work is to reveal the pharmacokinetic behavior of conjugated equine estrogens in healthy Chinese postmenopausal women by a parallel two-column LC-MS/MS method. METHODS An open-label study was carried out in 35 Chinese healthy postmenopausal women who received a single dose of Premarin® 0.625 mg. A high-throughput column-switching liquid chromatography-tandem mass spectrometry method was developed to determine four conjugated estrogens and two unconjugated estrogens formed by hydrolysis in vivo. The method multiplexes two high-performance liquid chromatography systems into one mass spectrometer and incorporates the positive/negative ion switching acquisition mode of mass spectrometry to significantly increase analysis efficiency. Pharmacokinetics was determined using non-compartmental methods. RESULTS Both conjugated and unconjugated estrogens can be analyzed simultaneously in a single run with an analysis time of 13.0 minutes in the column-switching liquid chromatography-tandem mass spectrometry method as opposed to 23.0 minutes in a single-column liquid chromatography-tandem mass spectrometry system. The exposures (maximum concentration and area under the curve) of estrone and equilin in Chinese women were higher than those in the North American women. CONCLUSIONS The fully validated assay was successfully applied to a pharmacokinetic study in healthy postmenopausal Chinese women after oral administration of a conjugated equine estrogen tablet. This study suggests that Chinese postmenopausal women achieve the same level of unconjugated estrogens in plasma at a lower dose of conjugated equine estrogens than North American women.
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Affiliation(s)
- Meiyun Shi
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China.,School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, People's Republic of China
| | - Lei Yin
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China.,School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, People's Republic of China
| | - Yantong Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun, People's Republic of China
| | - Can Wang
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China
| | - Lanlan Cai
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China
| | - Tinglan Zhang
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China
| | - Xiaotong Zhou
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China
| | - J Paul Fawcett
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China
| | - Xiaoli Gao
- College of Pharmacy, Xinjiang Medical University, Urumqi, 830011, People's Republic of China. .,Xinjiang Key Laboratory of Active Components and Drug Release Technology of Natural Drugs, Urumqi, People's Republic of China. .,Engineering Research Center of Xinjiang and Central Asian Medicine Resources, Ministry of Education, Beijing, People's Republic of China.
| | - Jingkai Gu
- Research Center for Drug Metabolism, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, People's Republic of China.
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Cai L, Feng C, Xie L, Xu B, Wei W, Jiao N, Zhang R. Ecological dynamics and impacts of viruses in Chinese and global estuaries. Water Res 2022; 226:119237. [PMID: 36244143 DOI: 10.1016/j.watres.2022.119237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Estuaries are important ecosystems providing irreplaceable services for humankind and, in turn, are extensively influenced by human activities and climate changes. Microbial processes, which are largely controlled by viruses, are always responsible for the ecological function and environmental problems in estuaries. However, we know little about the ecology and importance of viruses in estuarine systems. Here, we investigated viral ecological dynamics in estuarine systems on local (four largest estuaries in China in different seasons) and global scales. Viral production varied by almost 20-fold in Chinese estuaries with significant seasonality, being responsible for the removal of 1.41%-21.45% of the bacterioplankton standing stock each day, and contributed directly to the organic carbon pool by releasing an average of 3.57 µg of cellular carbon per liter per day. By compiling data from 21 estuaries across the world, we found for the first time that viral population size peaked at mid-latitude and viral production increased towards the equator in estuarine ecosystems. The results indicated the higher viral impact on microbial mortality and dissolved organic matter cycling in tropical estuaries. Our field investigation and global synthesized analysis provide compelling evidence of spatiotemporal variations in estuarine viral dynamics. The global view of viral impacts on estuarine microbial mortality offers important insight for incorporating viruses into ecological models and understanding the environmental implications of the tropicalization of temperate aquatic ecosystems under a scenario of climate warming.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chao Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Le Xie
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China; Department of Ocean Science and Engineering, Southern University of Science and Technology, Guangdong, China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Fujian, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong, China.
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Wang Q, Cai L, Zhang R, Wei S, Li F, Liu Y, Xu Y. A Unique Set of Auxiliary Metabolic Genes Found in an Isolated Cyanophage Sheds New Light on Marine Phage-Host Interactions. Microbiol Spectr 2022; 10:e0236722. [PMID: 36190421 PMCID: PMC9602691 DOI: 10.1128/spectrum.02367-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 06/23/2022] [Accepted: 09/10/2022] [Indexed: 01/04/2023] Open
Abstract
Cyanophages, viruses that infect cyanobacteria, are abundant and widely distributed in aquatic ecosystems, playing important roles in regulating the abundance, activity, diversity, and evolution of cyanobacteria. A T4-like cyanophage, S-SCSM1, infecting Synechococcus and Prochlorococcus strains of different ecotypes, was isolated from the South China Sea in this study. For the first time, a mannose-6-phosphate isomerase (MPI) gene was identified in the cultured cyanophage. At least 11 phylogenetic clusters of cyanophage MPIs were retrieved and identified from the marine metagenomic data sets, indicating that cyanophage MPIs in the marine environment are extremely diverse. The existence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins in the S-SCSM1 genome emphasizes their potential importance and diverse functions in reprogramming host metabolism during phage infection. Novel cell wall synthesis and modification genes found in the S-SCSM1 genome indicate that diverse phenotypic modifications imposed by phages on cyanobacterial hosts remain to be discovered. Two noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome were predicted to be associated with host exopolysaccharide metabolism and photosynthesis. The isolation and genomic characterization of cyanophage S-SCSM1 provide more information on the genetic diversity of cyanophages and phage-host interactions in the marine environment. IMPORTANCE Cyanophages play important ecological roles in aquatic ecosystems. Genomic and proteomic characterizations of the T4-like cyanophage S-SCSM1 indicate that novel and diverse viral genes and phage-host interactions in the marine environment remain unexplored. The first identified mannose-6-phosphate isomerase (MPI) gene from a cultured cyanophage was found in the S-SCSM1 genome, although MPIs were previously found in viral metagenomes at high frequencies similar to those of the cyanophage photosynthetic gene psbA. The presence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins, novel cell wall synthesis and modification genes, a nonbleaching protein A gene, and 2 noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome as well as the presence of a virion-associated regulatory protein indicate the diverse functions that cyanophages have in reprogramming the metabolism and modifying the phenotypes of hosts during infection.
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Affiliation(s)
- Qiong Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People’s Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, People’s Republic of China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, People’s Republic of China
| | - Fang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, People’s Republic of China
| | - Yuanfang Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, People’s Republic of China
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Altorki N, Salomonsen R, Georgoulia N, Diaz Perez I, Wang A, Cai L, Wetherill G, Xiao Y, Fielden C, Gray J. 935P Demographics, clinical characteristics, treatment patterns and clinical outcomes of patients with stages I-III resected NSCLC without known EGFR mutations. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1061] [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: 11/01/2022] Open
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35
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Zhu X, Cai L, Xiao J. [A family with clustered Lynch syndrome: a case report]. Nan Fang Yi Ke Da Xue Xue Bao 2022; 42:1263-1266. [PMID: 36073228 DOI: 10.12122/j.issn.1673-4254.2022.08.21] [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: 11/24/2022]
Abstract
Lynch syndrome (LS) is an autosomal dominant hereditary disease caused by deletion of such DNA mismatch repair (MMR) genes as MLH1, MSH2, MSH6, and PMS2. The functional loss of MMR genes results in instability of the highly repetitive DNA sequence, and may eventually leads to tumor occurrence. Here we report a case of LS- related endometrial cancer in a clustered LS family identified by genetic counseling and genetic testing. For patients with a family history of LSrelated tumors, the diagnosis of LS should be considered, and immunohistochemical testing of MMR and genetic testing for LS should be performed. A definite diagnosis of LS has important clinical significance for individuals and family members, and risk screening and preventive measures can minimize the overall risk of developing LS-related cancers.
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Affiliation(s)
- X Zhu
- Department of Gynecology, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - L Cai
- Department of Gynecology, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - J Xiao
- Department of Gynecology, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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Abbas L, Barber G, Vu H, Cai L, Wang R, Chong B. 673 Metabolomic profiling of cutaneous lupus erythematous. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.684] [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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37
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Wang MM, Crous PW, Sandoval-Denis M, Han SL, Liu F, Liang JM, Duan WJ, Cai L. Fusarium and allied genera from China: species diversity and distribution. Persoonia 2022; 48:1-53. [PMID: 38234691 PMCID: PMC10792286 DOI: 10.3767/persoonia.2023.48.01] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/14/2021] [Indexed: 01/19/2024]
Abstract
The genus Fusarium includes numerous important plant and human pathogens, as well as many industrially and commercially important species. During our investigation of fungal diversity in China, a total of 356 fusarioid isolates were obtained and identified from diverse diseased and healthy plants, or different environmental habitats, i.e., air, carbonatite, compost, faeces, soil and water, representing hitherto one of the most intensive sampling and identification efforts of fusarioid taxa in China. Combining morphology, multi-locus phylogeny and ecological preference, these isolates were identified as 72 species of Fusarium and allied genera, i.e., Bisifusarium (1), Fusarium (60), and Neocosmospora (11). A seven-locus dataset, comprising the 5.8S nuclear ribosomal RNA gene with the two flanking internal transcribed spacer (ITS) regions, the intergenic spacer region of the rDNA (IGS), partial translation elongation factor 1-alpha (tef1), partial calmodulin (cam), partial RNA polymerase largest subunit (rpb1), partial RNA polymerase second largest subunit (rpb2) gene regions, and partial β-tubulin (tub2), were sequenced and employed in phylogenetic analyses. A genus-level phylogenetic tree was constructed using combined tef1, rpb1, and rpb2 sequences, which confirmed the presence of four fusarioid genera among the isolates studied. Further phylogenetic analyses of two allied genera (Bisifusarium and Neocosmospora) and nine species complexes of Fusarium were separately conducted employing different multi-locus datasets, to determine relationships among closely related species. Twelve novel species were identified and described in this paper. The F. babinda species complex is herein renamed as the F. falsibabinda species complex, including descriptions of new species. Sixteen species were reported as new records from China. Citation: Wang MM, Crous PW, Sandoval-Denis M, et al. 2022. Fusarium and allied genera from China: species diversity and distribution. Persoonia 48: 1-53. https://doi.org/10.3767/persoonia.2022.48.01.
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Affiliation(s)
- M M Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- College of Life Science, University of ChineseAcademy of Sciences, Beijing 100049, P. R. China
| | - P W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - S L Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- College of Life Science, University of ChineseAcademy of Sciences, Beijing 100049, P. R. China
| | - F Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - J M Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - W J Duan
- Ningbo Academy of Inspection and Quarantine, Ningbo 315012, P. R. China
- Ningbo Customs, Ningbo 315012, P. R. China
| | - L Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- College of Life Science, University of ChineseAcademy of Sciences, Beijing 100049, P. R. China
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Song N, Wang T, Zhang D, Wang Z, Zhang SR, Yu J, Cai L, Ma AL, Zhang Q, Chen ZQ. [The value of relaxation time quantitative technique from synthetic magnetic resonance imaging in the diagnosis and invasion assessment of prostate cancer]. Zhonghua Yi Xue Za Zhi 2022; 102:1093-1099. [PMID: 35436808 DOI: 10.3760/cma.j.cn112137-20211018-02304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To investigate the application value of relaxation time quantitative technique from synthetic magnetic resonance imaging (MRI) in the diagnosis and invasion assessment of prostate cancer. Methods: A total of 119 patients with prostate diseases [122 regions of interest(ROI)] who underwent routine MRI scan and magnetic resonance image compilation (MAGiC) sequence of prostate from March 2020 to March 2021 in General Hospital of Ningxia Medical University were retrospectively collected, they were divided into prostate cancer group(58 cases, 61 ROI) and non-prostate cancer group(61 cases, 61 ROI) according to the pathological results. In the prostate cancer group, those patients with an age of 48 to 85(69.8±5.9) years, and further divided into two subgroups according to the location of occurrence: peripheral zone cancer group (43 cases, 45 ROI) and transitional zone cancer group (15 cases, 16 ROI). The non-prostate cancer group consisted of patients with benign prostatic hyperplasia or complicated with chronic prostatitis, with an age of 41 to 81(68.6±7.0) years, and they were further divided into two subgroups according to the location of occurrence: non-cancerous peripheral zone group (45 cases, 45 ROI) and transitional zone benign prostatic hyperplasia group(16 cases, 16 ROI). Prostate cancer lesions were classified as low risk (Gleason score ≤6) or intermediate/high risk (Gleason score ≥7). After the post-processing of MAGiC images, T1, T2 and proton density(PD) values of prostate cancer group and non-prostate cancer group were obtained. At the same time, relevant software were used for image post-processing to generate apparent diffusion coefficient (ADC) value, the data between the two groups were analyzed by the Independent sample t-test or Mann-Whitney U-test, and the diagnostic effectiveness of each quantitative parameter in diagnosing prostate cancer and discriminating low risk prostate cancer from intermediate/high risk prostate cancer was analyzed by using receiver operating characteristic curve (ROC) analysis, the correlation between each quantitative parameter and Gleason score were assessed by Spearman correlation analysis. Results: The T1 value and T2 value of the peripheral zone cancer group were lower than those in non-cancerous peripheral zone group [1 201.3 (1 103.5, 1 298.2) ms vs 2 274.0 (1 620.9, 2 776.5) ms; 78.0 (74.0, 83.8) ms vs (160.6±54.9) ms] (all P<0.001), there was no statistically significant in PD value between the two groups (P>0.05). The T1 value and T2 value of the transitional zone cancer group were lower than those in transitional zone benign prostatic hyperplasia group [1 073.3 (1 003.9, 1 164.9) ms vs 1 340.8 (1 208.5, 1 502.8) ms; 76.9 (74.8, 82.8) ms vs 95.1(82.8, 103.4) ms] (all P<0.001), there was no statistically significant in PD value between the two groups (P>0.05). The area under the curve (AUC) of T2 value was similar with the ADC value in discriminating peripheral zone cancer group from non-cancerous peripheral zone group(0.963 vs 0.991, P=0.105), while in discriminating transitional zone cancer group from transitional zone benign prostatic hyperplasia group, the AUC of T2 value、T1 value and ADC value were similar(0.867, 0.930 vs 0.938, all P>0.05). ADC value, T2 value all were negatively correlated with Gleason score (r=-0.747,-0.453, all P<0.001). T2 value and ADC value demonstrated equivalent diagnostic performance in discriminating low risk from intermediate/high risk prostate cancer, and there were no statistically significant (AUC: 0.787 vs 0.943, P=0.069). Conclusions: Quantitative relaxation time T1 and T2 values derived from synthetic MRI can discriminate prostate cancer from other benign pathologies, and T2 value have the equivalent diagnostic performance compared to ADC value. Synthetic MRI has high clinical application value, and T2 value can distinguish low risk prostate cancer from intermediate/high risk prostate cancer.
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Affiliation(s)
- N Song
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - T Wang
- Gansu Provincial Maternity and Child-care Hospital, Lanzhou 730050, China
| | - D Zhang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - Z Wang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - S R Zhang
- Clinical Medicine School of Ningxia Medical University, Yinchuan 750004, China
| | - J Yu
- Department of Genetics, School of Basic Medicine, Ningxia Medical University, Yinchuan 750004, China
| | - L Cai
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - A L Ma
- Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Q Zhang
- Department of Urological Surgery, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Z Q Chen
- Department of Radiology, General Hospital of Ningxia Medical University, Yinchuan 750004, China
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Mooradian M, Allen A, Cai L, Xiao Y, Chander P. 116P Real-world outcomes with durvalumab (durva) after chemoradiotherapy (CRT) in patients with unresectable stage III NSCLC (SPOTLIGHT). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.02.143] [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: 11/01/2022] Open
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Liu F, Ma Z, Hou L, Diao Y, Wu W, Damm U, Song S, Cai L. Updating species diversity of Colletotrichum, with a phylogenomic overview. Stud Mycol 2022; 101:1-56. [PMID: 36059896 PMCID: PMC9365046 DOI: 10.3114/sim.2022.101.01] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/11/2021] [Indexed: 11/07/2022] Open
Abstract
The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 Colletotrichum species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 Colletotrichum species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus.
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Affiliation(s)
- F. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Z.Y. Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - L.W. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Y.Z. Diao
- Novozymes China, No. 14, Xinxi Rd, Shangdi, Beijing, China
| | - W.P. Wu
- Novozymes China, No. 14, Xinxi Rd, Shangdi, Beijing, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - S. Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Chen Q, Bakhshi M, Balci Y, Broders K, Cheewangkoon R, Chen S, Fan X, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenković I, Mostert L, Nakashima N, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies C, Suhaizan L, Suzuki H, Tian C, Tomšovský M, Úrbez-Torres J, Wang W, Wingfield B, Wingfield M, Yang Q, Yang X, Zare R, Zhao P, Groenewald J, Cai L, Crous P. Genera of phytopathogenic fungi: GOPHY 4. Stud Mycol 2022; 101:417-564. [PMID: 36059898 PMCID: PMC9365048 DOI: 10.3114/sim.2022.101.06] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
This paper is the fourth contribution in the Genera of Phytopathogenic Fungi (GOPHY) series. The series provides morphological descriptions and information about the pathology, distribution, hosts and disease symptoms, as well as DNA barcodes for the taxa covered. Moreover, 12 whole-genome sequences for the type or new species in the treated genera are provided. The fourth paper in the GOPHY series covers 19 genera of phytopathogenic fungi and their relatives, including Ascochyta, Cadophora, Celoporthe, Cercospora, Coleophoma, Cytospora, Dendrostoma, Didymella, Endothia, Heterophaeomoniella, Leptosphaerulina, Melampsora, Nigrospora, Pezicula, Phaeomoniella, Pseudocercospora, Pteridopassalora, Zymoseptoria, and one genus of oomycetes, Phytophthora. This study includes two new genera, 30 new species, five new combinations, and 43 typifications of older names. Taxonomic novelties: New genera:Heterophaeomoniella L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pteridopassalora C. Nakash. & Crous; New species:Ascochyta flava Qian Chen & L. Cai, Cadophora domestica L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora rotunda L. Mostert, R. van der Merwe, Halleen & Gramaje, Cadophora vinacea J.R. Úrbez-Torres, D.T. O’Gorman & Gramaje, Cadophora vivarii L. Mostert, Havenga, Halleen & Gramaje, Celoporthe foliorum H. Suzuki, Marinc. & M.J. Wingf., Cercospora alyssopsidis M. Bakhshi, Zare & Crous, Dendrostoma elaeocarpi C.M. Tian & Q. Yang, Didymella chlamydospora Qian Chen & L. Cai, Didymella gei Qian Chen & L. Cai, Didymella ligulariae Qian Chen & L. Cai, Didymella qilianensis Qian Chen & L. Cai, Didymella uniseptata Qian Chen & L. Cai, Endothia cerciana W. Wang. & S.F. Chen, Leptosphaerulina miscanthi Qian Chen & L. Cai, Nigrospora covidalis M. Raza, Qian Chen & L. Cai, Nigrospora globospora M. Raza, Qian Chen & L. Cai, Nigrospora philosophiae-doctoris M. Raza, Qian Chen & L. Cai, Phytophthora transitoria I. Milenković, T. Májek & T. Jung, Phytophthora panamensis T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora variabilis T. Jung, M. Horta Jung & I. Milenković, Pseudocercospora delonicicola C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora farfugii C. Nakash., I. Araki, & Ai Ito, Pseudocercospora hardenbergiae Crous & C. Nakash., Pseudocercospora kenyirana C. Nakash., L. Suhaizan & I. Nurul Faziha, Pseudocercospora perrottetiae Crous, C. Nakash. & C.Y. Chen, Pseudocercospora platyceriicola C. Nakash., Y. Hatt, L. Suhaizan & I. Nurul Faziha, Pseudocercospora stemonicola C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora terengganuensis C. Nakash., Y. Hatt., L. Suhaizan & I. Nurul Faziha, Pseudocercospora xenopunicae Crous & C. Nakash.; New combinations:Heterophaeomoniella pinifoliorum (Hyang B. Lee et al.) L. Mostert, C.F.J. Spies, Halleen & Gramaje, Pseudocercospora pruni-grayanae (Sawada) C. Nakash. & Motohashi., Pseudocercospora togashiana (K. Ito & Tak. Kobay.) C. Nakash. & Tak. Kobay., Pteridopassalora nephrolepidicola (Crous & R.G. Shivas) C. Nakash. & Crous, Pteridopassalora lygodii (Goh & W.H. Hsieh) C. Nakash. & Crous; Typification: Epitypification:Botrytis infestans Mont., Cercospora abeliae Katsuki, Cercospora ceratoniae Pat. & Trab., Cercospora cladrastidis Jacz., Cercospora cryptomeriicola Sawada, Cercospora dalbergiae S.H. Sun, Cercospora ebulicola W. Yamam., Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora ixorana J.M. Yen & Lim, Cercospora liquidambaricola J.M. Yen, Cercospora pancratii Ellis & Everh., Cercospora pini-densiflorae Hori & Nambu, Cercospora profusa Syd. & P. Syd., Cercospora pyracanthae Katsuki, Cercospora horiana Togashi & Katsuki, Cercospora tabernaemontanae Syd. & P. Syd., Cercospora trinidadensis F. Stevens & Solheim, Melampsora laricis-urbanianae Tak. Matsumoto, Melampsora salicis-cupularis Wang, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora angiopteridis Goh & W.H. Hsieh, Pseudocercospora basitruncata Crous, Pseudocercospora boehmeriigena U. Braun, Pseudocercospora coprosmae U. Braun & C.F. Hill, Pseudocercospora cratevicola C. Nakash. & U. Braun, Pseudocercospora cymbidiicola U. Braun & C.F. Hill, Pseudocercospora dodonaeae Boesew., Pseudocercospora euphorbiacearum U. Braun, Pseudocercospora lygodii Goh & W.H. Hsieh, Pseudocercospora metrosideri U. Braun, Pseudocercospora paraexosporioides C. Nakash. & U. Braun, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous, Septogloeum punctatum Wakef.; Neotypification:Cercospora aleuritis I. Miyake; Lectotypification: Cercospora dalbergiae S.H. Sun, Cercospora formosana W. Yamam., Cercospora fukuii W. Yamam., Cercospora glochidionis Sawada, Cercospora profusa Syd. & P. Syd., Melampsora laricis-urbanianae Tak. Matsumoto, Phaeoisariopsis pruni-grayanae Sawada, Pseudocercospora symploci Katsuki & Tak. Kobay. ex U. Braun & Crous. Citation: Chen Q, Bakhshi M, Balci Y, Broders KD, Cheewangkoon R, Chen SF, Fan XL, Gramaje D, Halleen F, Horta Jung M, Jiang N, Jung T, Májek T, Marincowitz S, Milenković T, Mostert L, Nakashima C, Nurul Faziha I, Pan M, Raza M, Scanu B, Spies CFJ, Suhaizan L, Suzuki H, Tian CM, Tomšovský M, Úrbez-Torres JR, Wang W, Wingfield BD, Wingfield MJ, Yang Q, Yang X, Zare R, Zhao P, Groenewald JZ, Cai L, Crous PW (2022). Genera of phytopathogenic fungi: GOPHY 4. Studies in Mycology101: 417–564. doi: 10.3114/sim.2022.101.06.
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Affiliation(s)
- Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - M. Bakhshi
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
| | - R. Cheewangkoon
- Entomology and Plant Pathology Department, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand, 50200
| | - S.F. Chen
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), Zhanjiang 524022, Guangdong Province, China
| | - X.L. Fan
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | | | - F. Halleen
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
- Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenboscvh, 7599, South Africa
| | - M. Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - N. Jiang
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - T. Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - T. Májek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - S. Marincowitz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - I. Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - N. Nakashima
- Graduate school of Bioresources, Mie University, Kurima-machiya 1577, Tsu, Mie, 514-8507, Japan
| | - I. Nurul Faziha
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - M. Pan
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - M. Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - C.F.J. Spies
- ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - L. Suhaizan
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - H. Suzuki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - C.M. Tian
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - M. Tomšovský
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - J.R. Úrbez-Torres
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - W. Wang
- China Eucalypt Research Centre (CERC), Chinese Academy of Forestry (CAF), Zhanjiang 524022, Guangdong Province, China
| | - B.D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - M.J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Q. Yang
- The Key Laboratory for Silviculture and Conservation of the Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - X. Yang
- USDA-ARS, Foreign Disease-Weed Science Research Unit, 1301 Ditto Avenue, Fort Detrick, Maryland, 21702 USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, P.O. Box 117, Oak Ridge, Tennessee, 37831 USA
| | - R. Zare
- Department of Botany, Iranian Research Institute of Plant Protection, P.O. Box 19395-1454, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Zhao P, Liu F, Huang JE, Zhou X, Duan WJ, Cai L. Cronartium rust (Pucciniales, Cronartiaceae): species delineation, diversity and host alternation. MYCOSPHERE 2022. [DOI: 10.5943/mycosphere/13/1/7] [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: 11/06/2022] Open
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43
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Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CHL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat Biotechnol 2022; 40:74-85. [PMID: 34489600 PMCID: PMC8763645 DOI: 10.1038/s41587-021-01006-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
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Affiliation(s)
- T Lohoff
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - S Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - A Missarova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - N Koulena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - N Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - J A Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Genomics Plc, Cambridge, UK
| | - E S Bardot
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C-H L Eng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R C V Tyser
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - R Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - C Guibentif
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - S Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - J Briscoe
- The Francis Crick Institute, London, UK
| | - B D Simons
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - W Reik
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - J Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - L Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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Zang L, Liu Y, Song X, Cai L, Liu K, Luo T, Zhang R. Unique T4-like phages in high-altitude lakes above 4500 m on the Tibetan Plateau. Sci Total Environ 2021; 801:149649. [PMID: 34428653 DOI: 10.1016/j.scitotenv.2021.149649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Viruses are the most abundant biological entities in the biosphere; however, little is known about viral ecology in high altitude lakes. Here, we characterized viruses from 13 lakes, nine of which located ≥4500 m above sea level, on the Tibetan Plateau, the highest plateau on Earth. The abundance of virus-like particle (VLP) in Tibetan lakes ranged from 4.8 ± 0.2 × 105 VLPs mL-1 to 6.0 ± 0.2 × 107 VLPs mL-1 and the virus-to-bacterium ratio was in the lower range of values reported for other lakes. The viral population size was positively correlated with turbidity and negatively correlated with particulate organic carbon concentration. Highly diverse VLP morphologies, including large (~300 nm) morphotypes, were observed. Phylogenetic analysis of T4-like bacteriophages based on major capsid gene (g23) identified a novel viral group, which were detected in abundance in hyposaline and mesosaline Tibetan lakes. Adaptation to lake evolution, water source (glacier-fed or non-glacier-fed) and environmental conditions (e.g., salinity, phosphorus concentration and productivity) are likely responsible for the variation in T4-like myovirus community composition in contrasting Tibetan lakes. This first investigation of viruses in high-altitude alpine lakes above 4500 m could contribute to our understanding of viral ecology in global alpine lakes.
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Affiliation(s)
- Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; University of Chinese Academy of Science, Beijing 100101, China.
| | - Xuanying Song
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.
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Yang WP, Zhou JC, Zhang KN, Xu YW, Cai L, Gong YQ, Gong K. [Identification of the feature of immune cells infiltration in inherited renal carcinoma with von Hippel-Lindau syndrome]. Zhonghua Yi Xue Za Zhi 2021; 101:3789-3793. [PMID: 34895418 DOI: 10.3760/cma.j.cn112137-20210521-01183] [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: 11/05/2022]
Abstract
Objective: To investigate the feature of immune cells infiltration in inherited renal carcinoma with von Hippel-Lindau (VHL) syndrome and their relationship with clinicopathological characteristics and prognosis. Methods: The samples were collected from patients with VHL syndrome renal carcinoma who were diagnosed and treated surgically at the Department of Urology, Peking University First Hospital from 2010 to 2019. RNA-Seq was performed on 6 pairs of VHL syndrome renal carcinoma and adjacent normal tissues. To identify the specific infiltrated immune cells, RNA-Seq data was converted into the infiltration data of 14 types of immune cells using the TIP tool. Immunohistochemical staining was used to verify the expression of the markers of these specific infiltrated immune cells in the paraffin sections of 54 paired VHL syndrome renal carcinoma and adjacent normal tissues, and to analyze their relationship with clinicopathological characteristics and prognosis. Results: Compared with adjacent normal tissues, CD4 Naive infiltration level was significantly down-regulated (0.289±0.009 vs 0.200±0.012,P<0.001) and CD4 Memory infiltration level was significantly up-regulated (0.123±0.014 vs 0.222±0.016,P<0.001) in VHL syndrome renal carcinoma. Immunohistochemical staining results showed that CD45RA (a CD4 Naive cell marker) expression was significantly reduced (50.9±1.9 vs 15.6±0.9,P<0.001) and CD45RO (a CD4 Memory cell marker) expression was significantly increased (22.2±1.1 vs 80.8±4.3,P<0.001) in VHL syndrome renal carcinoma. Besides, lower CD45RA expression and higher CD45RO expression were associated with higher histological grade, advanced tumor stage and shorter disease-free survival (all P<0.01). In addition, CD45RA expression was positively correlated with VHL expression (r=0.693 3, P<0.000 1) and CD45RO expression was negatively correlated with VHL expression (r=-0.609 0, P<0.000 1). Conclusions: This study found that CD4 Naive and CD4 Memory cells may be differentially infiltrated immune cells in VHL syndrome renal carcinoma, and their infiltration levels were associated with the expression of VHL and the prognosis of patients.
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Affiliation(s)
- W P Yang
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - J C Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - K N Zhang
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - Y W Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - L Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - Y Q Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China
| | - K Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China
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Xu YW, Zhou JC, Xie HB, Yang WP, Li L, Zhang KN, Ma KF, Gong YQ, Zhang Z, Cai L, Gong K. [Clinicopathological and prognostic characteristics of clear cell papillary renal cell carcinoma]. Zhonghua Yi Xue Za Zhi 2021; 101:3784-3788. [PMID: 34895417 DOI: 10.3760/cma.j.cn112137-20210701-01482] [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: 11/05/2022]
Abstract
Objective: To analyze the epidemiological, clinicopathological and prognostic characteristics of clear cell papillary renal cell carcinoma (CCPRCC) based on Chinese patient population. Method: Patients with renal cell carcinoma diagnosed at Peking University First Hospital from June 2016 to June 2020 were included in this study based on the inclusion and exclusion criteria. All cases were grouped according to CCPRCC, clear cell renal cell carcinoma (ccRCC), and papillary renal cell carcinoma (pRCC), and the general clinical, postoperative pathological and follow-up data of the patients were retrospectively analyzed. Result: A total of 18 CCPRCC patients were enrolled in this study, accounting for 0.44% (18/4 110) of the postoperative pathologically confirmed renal cell carcinoma cases in our hospital during this time period. The age range of the included patients was 28-86 years old, with a median age of 49.5 years old. There were 11/18 males and 7/18 females. All CCPRCC patients had no family history of renal malignant tumors. Among them, only one patient with CCPRCC had related clinical symptoms, that was intermittent waist and abdomen pain, while the other 17 cases were found by physical examination without any related symptoms. Compared with ccRCC and pRCC, there was no significant difference in their end stage renal disease history(χ2ccRCC=0.291, χ2pRCC=1.161,all P>0.05). The maximum diameter of CCPRCC tumor was smaller than pRCC (χ2=-2.280,P =0.027) but not significantly different from ccRCC (χ2=-0.579,P =0.565). The majority of patients with CCPRCC were in pT1, their pathological stage was earlier than the other two types, and their overall survival was better than ccRCC and pRCC (P<0.05). Conclusion: CCPRCC is a type of renal cell carcinoma with unique epidemiology, clinicopathology and prognostic characteristics. Patients with this subtype have an earlier clinical stage and a better prognosis than ccRCC and pRCC.
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Affiliation(s)
- Y W Xu
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - J C Zhou
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - H B Xie
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - W P Yang
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - L Li
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - K N Zhang
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - K F Ma
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Y Q Gong
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Z Zhang
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - L Cai
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - K Gong
- Department of Urology, Peking University First Hospital, the Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
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Li JL, Zhang M, Cai L, Yue JQ, Wang RF, Guan WB, Wang KZ, Wang LF. [DICER1 and relevant tumor]. Zhonghua Bing Li Xue Za Zhi 2021; 50:1419-1422. [PMID: 34865443 DOI: 10.3760/cma.j.cn112151-20210825-00602] [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: 06/13/2023]
Affiliation(s)
- J L Li
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - M Zhang
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - L Cai
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - J Q Yue
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - R F Wang
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - W B Guan
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - K Z Wang
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - L F Wang
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
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Zhao P, Crous P, Hou L, Duan W, Cai L, Ma Z, Liu F. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 2021; 47:45-105. [PMID: 37693796 PMCID: PMC10486631 DOI: 10.3767/persoonia.2021.47.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 11/25/2022]
Abstract
The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentrospora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens. Citation: Zhao P, Crous PW, Hou LW, et al. 2021. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 47: 45-105. https://doi.org/10.3767/persoonia.2021.47.02.
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Affiliation(s)
- P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - L.W. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - W.J. Duan
- Ningbo Academy of Inspection and Quarantine, Ningbo 315012, China
- Ningbo Customs District P. R. China, Ningbo 315012, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Z.Y. Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - F. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Mooradian M, Allen A, Cai L, Xiao Y, Chander P. 100P SPOTLIGHT real-world study: Patient characteristics and treatment patterns in patients with unresectable stage III NSCLC receiving durvalumab after chemoradiotherapy (CRT). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.10.118] [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: 10/19/2022] Open
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Li L, Shu F, Wang XQ, Wang F, Cai L, Zhao X, Lv HG. Propofol alleviates intestinal ischemia/reperfusion injury in rats through p38 MAPK/NF-κB signaling pathway. Eur Rev Med Pharmacol Sci 2021; 25:1574-1581. [PMID: 33629346 DOI: 10.26355/eurrev_202102_24867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the influences of propofol on intestinal ischemia/reperfusion (I/R) injury in rats through the p38 mitogen-activated protein kinase (MAPK)/nuclear factor-kappa B (NF-κB) signaling pathway. MATERIALS AND METHODS The models of intestinal I/R injury were first successfully established. All rats were randomly divided into 4 groups, namely, S group, I/R group, P group and P + S group. Pathological-morphological changes, injury score and wet-to-dry weight ratio of intestinal tissues as well as oxidative stress indexes in each group of rats were detected. Enzyme-linked immunosorbent assay (ELISA) was applied to measure the levels of inflammatory factors such as creatine kinase-MB (CK-MB), tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) in each group of rats. Furthermore, Western blotting (WB) assay was applied to determine the protein expression levels of p38 MAPK and NF-κB in different groups. RESULTS Intestinal tissue injury was the severest in I/R group, with the infiltration of massive inflammatory cells and oozing of blood (Figure 1A, I/R). Compared with those in I/R group, the infiltration of inflammatory cells and damage to intestinal villi were notably relieved in P group and P + S group, revealing that the intestinal mucosal injury was remarkably repaired in P group and P + S group (Figure 1A, P). Moreover, the intestinal tissue injury score was evidently higher in I/R group, P group and P + S group than that in S group (p<0.05). However, it was markedly lower in P group and P + S group than that in I/R group (p<0.05). I/R group, P group and P + S group exhibited significantly increased wet-to-dry weight ratio of intestinal tissues in comparison with S group (p<0.05). However, P group and P + S group exhibited distinctly lower wet-to-dry weight ratio of intestinal tissues than I/R group (p<0.05). The content of malondialdehyde (MDA) was reduced prominently, while that of superoxide dismutase (SOD) was elevated significantly in P group and P + S group in contrast with those in I/R group (p<0.05). On the contrary, P + S group displayed remarkably lower MDA content and higher SOD content than P group (p<0.05). The levels of CK-MB, TNF-α and IL-6 in the blood rose markedly in I/R group compared with those in S group (p<0.05). However, they declined evidently in P group and P + S group in contrast with those in I/R group (p<0.05). Besides, the protein expression level of phosphorylated p38 MAPK was significantly higher in I/R group, P group and P + S group than that in S group (p<0.05). However, no significant difference was observed in the protein expression of total p38 MAPK among the four groups (p>0.05). However, the protein expression level of phosphorylated p38 MAPK was distinctly down-regulated in P group and P + S group in comparison with that in I/R group (p<0.05). Finally, I/R group, P group and P + S group had a prominently higher protein expression level of NF-κB than S group (p<0.05). However, P group and P + S group exerted a significantly lower protein expression level of NF-κB than I/R group (p<0.05). CONCLUSIONS Propofol decreases the release of inflammatory factors and alleviates intestinal edema by inhibiting the p38 MAPK/NF-κB signaling pathway, thereby mitigating and treating the intestinal I/R injury in rats.
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Affiliation(s)
- L Li
- Department of Anaesthesiology, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China.
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