1.Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing
Li Ya ZHANG ; Zhe Wen SU ; Chen Rui WANG ; Yan LI ; Feng Jun ZHANG ; Hui Sheng LIU ; He Dan HU ; Xiao Chong XU ; Yu Jia YIN ; Kai Qi YIN ; Ying HE ; Fan LI ; Hong Shi FU ; Kai NIE ; Dong Guo LIANG ; Yong TAO ; Tao Song XU ; Feng Chao MA ; Yu Huan WANG
Biomedical and Environmental Sciences 2024;37(3):294-302
Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing. Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing. Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing. Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
2.The impact of short-course total neoadjuvant therapy, long-course chemoradiotherapy, and upfront surgery on the technical difficulty of total mesorectal excision: an observational study with an intraoperative perspective
Cheryl Xi-Zi CHONG ; Frederick H. KOH ; Hui-Lin TAN ; Sharmini Su SIVARAJAH ; Jia-Lin NG ; Leonard Ming-Li HO ; Darius Kang-Lie AW ; Wen-Hsin KOO ; Shuting HAN ; Si-Lin KOO ; Connie Siew-Poh YIP ; Fu-Qiang WANG ; Fung-Joon FOO ; Winson Jianhong TAN
Annals of Coloproctology 2024;40(5):451-458
Purpose:
Total neoadjuvant therapy (TNT) is becoming the standard of care for locally advanced rectal cancer. However, surgery is deferred for months after completion, which may lead to fibrosis and increased surgical difficulty. The aim of this study was to assess whether TNT (TNT-RAPIDO) is associated with increased difficulty of total mesorectal excision (TME) compared with long-course chemoradiotherapy (LCRT) and upfront surgery.
Methods:
Twelve laparoscopic videos of low anterior resection with TME for rectal cancer were prospectively collected from January 2020 to October 2021, with 4 videos in each arm. Seven colorectal surgeons assessed the videos independently, graded the difficulty of TME using a visual analog scale and attempted to identify which category the videos belonged to.
Results:
The median age was 67 years, and 10 patients were male. The median interval to surgery from radiotherapy was 13 weeks in the LCRT group and 24 weeks in the TNT-RAPIDO group. There was no significant difference in the visual analog scale for difficulty in TME between the 3 groups (LCRT, 3.2; TNT-RAPIDO, 4.6; upfront, 4.1; P=0.12). A subgroup analysis showed similar difficulty between groups (LCRT 3.2 vs. TNT-RAPIDO 4.6, P=0.05; TNT-RAPIDO 4.6 vs. upfront 4.1, P=0.54). During video assessments, surgeons correctly identified the prior treatment modality in 42% of the cases. TNT-RAPIDO videos had the highest recognition rate (71%), significantly outperforming both LCRT (29%) and upfront surgery (25%, P=0.01).
Conclusion
TNT does not appear to increase the surgical difficulty of TME.
3.Artificial intelligence predicts direct-acting antivirals failure among hepatitis C virus patients: A nationwide hepatitis C virus registry program
Ming-Ying LU ; Chung-Feng HUANG ; Chao-Hung HUNG ; Chi‐Ming TAI ; Lein-Ray MO ; Hsing-Tao KUO ; Kuo-Chih TSENG ; Ching-Chu LO ; Ming-Jong BAIR ; Szu-Jen WANG ; Jee-Fu HUANG ; Ming-Lun YEH ; Chun-Ting CHEN ; Ming-Chang TSAI ; Chien-Wei HUANG ; Pei-Lun LEE ; Tzeng-Hue YANG ; Yi-Hsiang HUANG ; Lee-Won CHONG ; Chien-Lin CHEN ; Chi-Chieh YANG ; Sheng‐Shun YANG ; Pin-Nan CHENG ; Tsai-Yuan HSIEH ; Jui-Ting HU ; Wen-Chih WU ; Chien-Yu CHENG ; Guei-Ying CHEN ; Guo-Xiong ZHOU ; Wei-Lun TSAI ; Chien-Neng KAO ; Chih-Lang LIN ; Chia-Chi WANG ; Ta-Ya LIN ; Chih‐Lin LIN ; Wei-Wen SU ; Tzong-Hsi LEE ; Te-Sheng CHANG ; Chun-Jen LIU ; Chia-Yen DAI ; Jia-Horng KAO ; Han-Chieh LIN ; Wan-Long CHUANG ; Cheng-Yuan PENG ; Chun-Wei- TSAI ; Chi-Yi CHEN ; Ming-Lung YU ;
Clinical and Molecular Hepatology 2024;30(1):64-79
Background/Aims:
Despite the high efficacy of direct-acting antivirals (DAAs), approximately 1–3% of hepatitis C virus (HCV) patients fail to achieve a sustained virological response. We conducted a nationwide study to investigate risk factors associated with DAA treatment failure. Machine-learning algorithms have been applied to discriminate subjects who may fail to respond to DAA therapy.
Methods:
We analyzed the Taiwan HCV Registry Program database to explore predictors of DAA failure in HCV patients. Fifty-five host and virological features were assessed using multivariate logistic regression, decision tree, random forest, eXtreme Gradient Boosting (XGBoost), and artificial neural network. The primary outcome was undetectable HCV RNA at 12 weeks after the end of treatment.
Results:
The training (n=23,955) and validation (n=10,346) datasets had similar baseline demographics, with an overall DAA failure rate of 1.6% (n=538). Multivariate logistic regression analysis revealed that liver cirrhosis, hepatocellular carcinoma, poor DAA adherence, and higher hemoglobin A1c were significantly associated with virological failure. XGBoost outperformed the other algorithms and logistic regression models, with an area under the receiver operating characteristic curve of 1.000 in the training dataset and 0.803 in the validation dataset. The top five predictors of treatment failure were HCV RNA, body mass index, α-fetoprotein, platelets, and FIB-4 index. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the XGBoost model (cutoff value=0.5) were 99.5%, 69.7%, 99.9%, 97.4%, and 99.5%, respectively, for the entire dataset.
Conclusions
Machine learning algorithms effectively provide risk stratification for DAA failure and additional information on the factors associated with DAA failure.
5.Epidemiological characteristics and antimicrobial resistance of 151 cases of melioidosis in Hainan Province
ZENG Zeng ; LUO Xiao-man ; FU Rui-jia ; ZHANG Nan ; CHEN Lin ; CHEN Shao-wen ; LIN Chong ; FU Sheng-miao
China Tropical Medicine 2023;23(6):568-
Abstract: Objective To analyze the epidemiological characteristics of 151 cases of melioidosis and the drug resistance of Burkholderia pseudomallei (BP), in order to provide the basis for diagnosis, treatment and reasonable prevention of melioidosis. Methods A total of 151 inpatients and outpatients from the Second Affiliated Hospital of Hainan Medical University from January 1, 2013 to August 31, 2022 were collected, and clinical specimens were submitted for examination to isolate and identify BP strains. The clinical data of 151cases of melioidosis and the drug resistance characteristics of pathogenic bacteria were retrospectively analyzed, and using SPSS26.0 software for statistical analysis. Results Among 151 cases with BP infection, there were 138 males (91.4%) and 13 females (8.6%); the most patients were aged from 45-<60 years old, accounting for 74 cases (49.0%); melioidosis incidence was concentrated in October (19.2%), November (19.2%), August (9.9%) and July (8.6%), and; the number of confirmed cases showed an increasing trend and the time for confirmation was <10 d; Internal medicine system (31.1%), surgery system (26.5%) and intensive care department (20.5%) were the common departments for treating melioidosis; blood (49.0%), sputum (9.9%) and wound secretion (8.6%) were the main clinical specimens for detecting BP; pulmonary infection (68.2%), sepsis (35.1%) and local suppurative infection (23.8%) were the top clinical manifestations in patients with BP infection; the effective rate of treating melioidosis was 74.8%; abnormal liver function was a risk factor for the curative effect of melioidosis (χ2=5.010, P<0.05); the sensitivity rates of BP strains to sulfamethoxazole-trimethoprim (SXT), doxycycline (DOX), imipenem(IPM), ceftazidime (CAZ), amoxicillin/clavulanate (AMC) and tetracycline (TCY) were generally more than 90%, with sensitivities of 98.7%, 97.2%, 96.7%, 94.0%, 93.2% and 90.7%, respectively. Conclusions It can be concluded that misdiagnosis or missed diagnosis of melioidosis is easy to occur, and the understanding of the epidemiological characteristics and risk factors in this area should be strengthened. The sensitivity of BP to commonly used antibiotics has shown a certain downward trend, clinical use should be standardized, and drug resistance monitoring should be strengthened to improve the efficacy of melioidosis treatment.
6.Antibody levels of measles, rubella and mumps viruses in healthy population in Shanghai from 2010 to 2020.
Yu Ying YANG ; Su Wen TANG ; Wei TANG ; Jia Lei FAN ; Zhi LI ; Jia Wei YANG ; Jia REN ; Chong Shan LI
Chinese Journal of Preventive Medicine 2022;56(8):1095-1100
Objective: To determine IgG antibody levels of measles, rubella, mumps in healthy population in Shanghai from 2010 to 2020 and analyze the trend of antibody changes in different age groups. Methods: 10 828 healthy people without measles, rubella and mumps in Shanghai were included in the study from 2010 to 2020. Serum samples were collected from 12 age groups, and the serum IgG antibody of measles, rubella and mumps were detected by ELISA. The difference of antibody positive rates and antibody levels were analyzed. Results: The median age M (Q1, Q3) of 10 828 objects were 8 years old (9 months old, 20 years old). Males accounted for 48.34% (5 234/10 828) and females accounted for 50.92% (5 514/10 828). Unknown gender information accounted for 0.74% (80/10 828), and 27.03% (2 927/10 828) of participants had unknown MMR immunization history. The total positive rates of measles, rubella and mumps IgG antibody were 76.78%, 64.46% and 64.29% and their GMCs were 541.45 mIU/ml, 31.76 IU/ml and 133.73 U/ml respectively. There were significant differences in serum IgG antibody GMC of measles, rubella and mumps in each year (Fmeasles=180.74, P<0.001; Frubella=189.95, P<0.001; Fmumps=122.40, P<0.001). The positive rate of measles antibody was higher than that of rubella and mumps, and the difference was statistically significant (χ²=518.09, P<0.001). Conclusion: The level of measles IgG antibody in healthy people in Shanghai is higher, while the level of rubella and mumps IgG antibody is slightly lower.
Adult
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Antibodies, Viral
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Child
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China/epidemiology*
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Female
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Humans
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Immunoglobulin G
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Infant
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Male
;
Measles/prevention & control*
;
Measles-Mumps-Rubella Vaccine
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Mumps/prevention & control*
;
Mumps virus
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Rubella/prevention & control*
;
Young Adult
7.EPOSTER • DRUG DISCOVERY AND DEVELOPMENT
Marwan Ibrahim ; Olivier D LaFlamme ; Turgay Akay ; Julia Barczuk ; Wioletta Rozpedek-Kaminska ; Grzegorz Galita ; Natalia Siwecka ; Ireneusz Majsterek ; Sharmni Vishnu K. ; Thin Thin Wi ; Saint Nway Aye ; Arun Kumar ; Grace Devadason ; Fatin Aqilah Binti Ishak ; Goh Jia Shen ; Dhaniya A/P Subramaniam ; Hiew Ke Wei ; Hong Yan Ren ; Sivalingam Nalliah ; Nikitha Lalindri Mareena Senaratne ; Chong Chun Wie ; Divya Gopinath ; Pang Yi Xuan ; Mohamed Ismath Fathima Fahumida ; Muhammad Imran Bin Al Nazir Hussain ; Nethmi Thathsarani Jayathilake ; Sujata Khobragade ; Htoo Htoo Kyaw Soe ; Soe Moe ; Mila Nu Nu Htay ; Rosamund Koo ; Tan Wai Yee ; Wong Zi Qin ; Lau Kai Yee ; Ali Haider Mohammed ; Ali Blebil ; Juman Dujaili ; Alicia Yu Tian Tan ; Cheryl Yan Yen Ng ; Ching Xin Ni ; Michelle Ng Yeen Tan ; Kokila A/P Thiagarajah ; Justin Jing Cherg Chong ; Yong Khai Pang ; Pei Wern Hue ; Raksaini Sivasubramaniam ; Fathimath Hadhima ; Jun Jean Ong ; Matthew Joseph Manavalan ; Reyna Rehan ; Tularama Naidu ; Hansi Amarasinghe ; Minosh Kumar ; Sdney Jia Eer Tew ; Yee Sin Chong ; Yi Ting Sim ; Qi Xuan Ng ; Wei Jin Wong ; Shaun Wen Huey Lee ; Ronald Fook Seng Lee ; Wei Ni Tay ; Yi Tan ; Wai Yew Yang ; Shu Hwa Ong ; Yee Siew Lim ; Siddique Abu Nowajish ; Zobaidul Amin ; Umajeyam Anbarasan ; Lim Kean Ghee ; John Pinto ; Quek Jia Hui ; Ching Xiu Wei ; Dominic Lim Tao Ran ; Philip George ; Chandramani Thuraisingham ; Tan Kok Joon ; Wong Zhi Hang ; Freya Tang Sin Wei ; Ho Ket Li ; Shu Shuen Yee ; Goon Month Lim ; Wen Tien Tan ; Sin Wei Tang
International e-Journal of Science, Medicine and Education 2022;16(Suppl1):21-37
8.SingHealth Radiology Archives pictorial essay Part 2: gastroenterology, musculoskeletal, and obstetrics and gynaecology cases.
Mark Bangwei TAN ; Kim Ping TAN ; Joey Chan Yiing BEH ; Eugenie Yi Kar CHAN ; Kenneth Fu Wen CHIN ; Zong Yi CHIN ; Wei Ming CHUA ; Aaron Wei-Loong CHONG ; Gary Tianyu GU ; Wenlu HOU ; Anna Chooi Yan LAI ; Rebekah Zhuyi LEE ; Perry Jia Ren LIEW ; May Yi Shan LIM ; Joshua Li Liang LIM ; Zehao TAN ; Eelin TAN ; Grace Siew Lim TAN ; Timothy Shao Ern TAN ; Eu Jin TAN ; Alexander Sheng Ming TAN ; Yet Yen YAN ; Winston Eng Hoe LIM
Singapore medical journal 2021;62(1):8-15
The Singapore Health Services cluster (SingHealth) radiology film archives are a valuable repository of local radiological cases dating back to the 1950s. Some of the cases in the archives are of historical medical interest, i.e. cerebral angiography in the workup of patients with hemiplegia. Other cases are of historical social interest, being conditions seen during earlier stages of Singapore's development, i.e. bound feet. The archives form a unique portal into the development of local radiology as well as the national development of Singapore. A selection from the archives is published in commemoration of the International Day of Radiology in 2020, as well as the 200th anniversary of the Singapore General Hospital in 2021. This pictorial essay comprises gastroenterology, musculoskeletal and obstetrics and gynaecology cases from the archives.
9.Effect of Fangji Huangqitang on DBA/1 Mice Collagen Induced Arthritis and Synovial Angiogenesis
Lian-hua HE ; Hui-jie LUAN ; Hong-ying SHAN ; Bo YANG ; Juan HE ; Yi-ping HU ; Jia-jing DAI ; Hui-juan WAN ; Chong-zhou FANG ; Qing-wen WANG
Chinese Journal of Experimental Traditional Medical Formulae 2021;27(17):16-23
Objective:To observe the effect of Fangji Huangqitang (FJHQT) on collagen induced arthritis (CIA) and synovial angiogenesis in DBA/1 mice. Method:DBA/1 mice were randomly divided into normal group, CIA group and FJHQT group. DBA/1 mice in CIA group and FJHQT group were immunized with bovine type Ⅱ collagen and complete Freund's adjuvant on the first day, and DBA/1 mice were immunized with bovine type Ⅱ collagen and incomplete Freund's adjuvant on the 21st day to establish CIA model. On the day of the second immunization, the drug was given by gavage once a day for 28 days. On the 22nd day, the arthritis score and other symptoms of CIA mice were observed. On the 49th day, Hematoxylin eosin (HE) staining was carried out to observe the angiogenesis in the synovium of CIA mice, the expression of vascular endothelial cell marker platelet endothelial cell adhesion molecule-1 (CD31) and vascular endothelial growth factor (VEGF) in the synovium of CIA mice were detected. Immunofluorescence double staining was used to detect the mature and immature vessels in the synovium of CIA mice. And the microvascular growth of the rat thoracic aortic ring was induced by VEGF (20 μg·L-1). The effects of FJHQT (0.25, 0.5, 1 g·L-1) at different concentrations were observed under microscope. Result:Compared with the normal group, the inflammation, joints, red and swelling of the inflammatory joints of the CIA group were significantly increased (
10.A rapid identification of authenticity and specifications of Chinese medicine Fritillariae Cirrhosae Bulbus based on E-eye technology.
Rui-Xin LIU ; Xiao-Jia HAO ; Hui-Jie ZHANG ; Lu ZHANG ; Xin-Jing GUI ; Zhao-Zhou LIN ; Chong-Nian LUO ; Liang-Yu TIAN ; Yan-Li WANG ; Wen-Hao FENG ; Jing YAO ; Xue-Lin LI
China Journal of Chinese Materia Medica 2020;45(14):3441-3451
The quality of traditional Chinese medicine tablets is correlated with clinical efficacy and drug safety, and plays a great role in promoting the development of traditional Chinese medicine. However, the existing traditional artificial identification and modern instrument detection in terms of accuracy and timeliness have both advantages and disadvantages. Therefore, how to quickly and accurately identify the quality of traditional Chinese medicine tablets has become a high-profile issue. The purpose of this paper is to explore the feasibility of the application of electronic eye technology in the study of rapid identification of traditional Chinese medicine quality. A total of 80 batches of samples were collected and tested by Fritillariae Cirrhosae Bulbus for traditional empirical identification(M_1) and modern pharmacopeia(M_2). The optical data was collected from electronic eyes, and the chemical metrology was used to establish suitable discrimination models(M_3). Four authenticity and commodity specification models, namely identification analysis(DA), minimum bidirectional support vector machine(LS-SVM), partial minimum two-multiplier analysis(PLS-DA), main component analysis identification analysis(PCA-DA), were established, respectively. The accuracies of the authenticity identification models were 82.5%, 90.0%, 96.2% and 93.8%, while the accuracies of the commodity specification identification models were 89.3%, 96.0%, 90.7% and 97.3%, respectively. The models were well judged, the authenticity identification was based on the final identification model of PLS-DA, and the commodity specification was based on the final identification model of PCA-DA. There was no significant difference between its accuracy and M_1, and the time of determination was much shorter than M_2(P<0.01). Therefore, electronic-eye technology could be used for the rapid identification of the quality of Fritillariae Cirrhosae Bulbus.
Drugs, Chinese Herbal
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Fritillaria
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Medicine, Chinese Traditional
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Plant Roots
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Technology


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