1.Cloning,Sequence Analysis and Expression in E.coli of the EP0 Gene of Pseudorabies Virus Ea Strain
Liu-Rong, FANG ; Huan-chun, CHEN ; Shao-bo, XIAO ; Xiang-Ru, MA ; Ge-fei, WANG
Virologica Sinica 2001;16(2):183-187
The 1.23 kb DNA fragment encoding the early protein EP0 of pseudorabies virus (PRV) Ea strain was amplified by PCR technique and cloned into pBluescriptII sk+.Three sequencing plasmids containing the partial fragment of the EP0 gene were constructed and the sequences were obtained by Sanger's sequencing technique. Compared with PRV InFh strain, there were multipile site-mutations and a deleted-mutation in the EP0 gene of PRV strain Ea,and the diversity of amino acid residues also existed.Then, the EP0 gene was inserted into an expression vector, pET-28a, fused into the downstream of the 6ΧHis-Tag in frame, to yield the expression plasmid pETEP0. After induction by IPTG, a high expression of fusion protein was obtained, SDS-PAGE analysis and Western blotting showed that the fusion protein was 62kD and the protein was specific to antisera against PRV Ea strain. This indicated that the EP0 gene be expressed in BL21(DE3) and the expression products have immuno-genicity.
2.The relationship between perfusion defects on myocardial SPECT and stenotic severity on CT coronary angiography
Jian-ming, LI ; Rong-fang, SHI ; Ting, LI ; Xiao-bin, ZHAO ; Ru-ming, LU ; Yu, LIANG
Chinese Journal of Nuclear Medicine 2011;31(6):394-399
ObjectiveTo evaluate the diagnostic performance of CTCA in predicting myocardial perfusion defects through comparative analysis between MPI defects and severity of coronary stenosis on CTCA.MethodsFour hundred and seventy-eight patients who underwent CTCA and 99Tcm-MIBI MPI in the same period were analyzed retrospectively.According to the severity of coronary stenosis judged by visual evaluation of the vessel diameter,the patients were divided into five groups:no stenosis,mild stenosis,moderate stenosis,severe stenosis and total occlusion.MPI results were classified as negative or positive for perfusion defects,and the prevalence of perfusion defects in every group was calculated per-patient and per-vessel basis.The cut-off of stenotic severity for predicting myocardial perfusion defects was designated as 50% or 75%,with MPI as standard reference.True positive,true negative,false positive and false negative statistics were thus determined separately on patient and vessel basis.The diagnostic performance for CTCA were calculated and compared.Pearson Chi-square and its partition tests or Fisher exact test were used to compare ordinal variables.ResultsFifty-eight patients showed myocardial perfusion defects.Either by patientbased or vessel-based analysis,the prevalence of myocardial perfusion defects showed an increasing trend with greater coronary artery stenosis in each group,and there were statistical differences among them (x2 =116.62 and 483.83,both P < 0.05).On patient-based analysis,sensitivity ( SN),specificity ( SP),positive predictive value( PPV),negative predictive value(NPV) and accuracy (AC) for CTCA predicting myocardial perfusion defects were 62.1 % ( 36/58 ) and 34.5% ( 20/58 ) (x2 =8.84,P < 0.05 ),84.5%(355/420) and 97.1% (408/420) (x2 =40.16,P <0.05),35.6% (30/101) and 62.5% (20/32) (x2 =7.19,P<0.05),94.2% (355/377) and 91.5% (408/446) (x2 =2.18,P >0.05),81.8% (391/478)and 89.5 % (428/478) (x2 =11.66,P < 0.05 ) when the cutoff was set to 50% and 75%,respectively.On vessel-based analysis,the SN,SP,PPV,NPV and AC for CTCA predicting myocardial perfusion defects were 58.8% (40/68) and 30.9% (21/68) (x2 =10.73,P < 0.05),95.9% (1768/1844) and 99.0% (1826/1844) (x2 =36.72,P < 0.05 ),34.5% (40/116) and 53.8% (21/39) (x2 =4.59,P <0.05 ),98.4% (1768/1796) and 97.5% ( 1826/1873 ) (x2 =4.14,P < 0.05 ),94.6% ( 1808/1912 ) and 96.6% ( 1847/1912 ) (x2 =10.31,P < 0.05 ),respectively.ConclusionsThe prevalence of myocardial perfusion defects correlates positively with the severity of coronary stenosis seen on CTCA.CTCA may predict perfusion defects with high SP and NPV.However,the PPV of CTCA in predicting myocardial perfusion defects is poor when the stenosis cut-off is set at 50%.It is significantly improved when the cutoff value is set at 75 %.
3.Automated classification of ICD-O-3 morphology code from pathology reports using text-mining and support vector machine
PAN Jin ; GONG Wei Wei ; FEI Fang Rong ; WANG Meng ; ZHOU Xiao Yan ; HU Ru Ying ; ZHONG Jie Ming
Journal of Preventive Medicine 2021;33(3):255-258
Objective:
To evaluate the accuracy of automated classification of ICD-O-3 morphology code from pathology reports by text-mining and support vector machine ( SVM ) , in order to provide basis for automated tumor coding in Chinese.
Methods:
The tumor report cards of Zhejiang residents from 2017 to 2019 were collected from Chronic Disease Surveillance Information Management System of Zhejiang Province. According to ICD-O-3, the keywords of the pathology reports were extracted, and SVM was used for automatic classification. The classification results were compared with those of 16 professionals with more than two years of experience in tumor coding, and the accuracy rate, recall rate and F-score were calculated for effect evaluation.
Results:
Totally 83 082 cases from 2017 to 2019 were included and were categorized into 17 morphological classifications, with 52 877 ( 63.65% ) cases of adenocarcinoma, squamous carcinoma and transitional cell carcinoma. A total of 1 090 keywords were enrolled into main corpus. The total F-score, accuracy rate and recall rate are 85.69, 77.20% and 96.27%, respectively.
Conclusion
Text-mining combined with SVM can improve the efficiency of ICD-O-3 morphology coding; however, the accuracy needs to be further improved.
4.Total fluid intake, urination frequency and risk of bladder cancer: a population-based case-control study in urban Shanghai
Wei ZHANG ; Yong-Bing XIANG ; Ru-Rong FANG ; Jia-Rong CHENG ; Jian-Min YUAN ; Yu-Tang GAO
Chinese Journal of Epidemiology 2010;31(10):1120-1124
Objective To evaluate the association between total fluid intake and the time of urination per day and the risk of bladder cancer. Methods A population-based case-control study was conducted in urban Shanghai, China, during January 1996 to December 1998. The study included 608 incident cases of bladder cancer and 607 age- and sex-matched controls. Unconditional logistic regression models were used to estimate the odds ratios(ORs)and their corresponding 95%confidence intervals(95%CIs)for bladder cancer associated with frequency of urination, after adjusted for age, gender, smoking status, history of occupation with high risk, history of bladder infections, body mass index and other confounding factors. The level of statistical significance was set at 0.05(two-sided). Results No significant trend was observed for the association between total fluid intake, time of nighttime urination and the risk of bladder cancer. Increasing time of urination during daytime was associated with decreased risk of bladder cancer(P for trend=0.014). ORs(95%CIs)for subjects who voided 4 times, 5 times and 6 or more times per day[0.72(0.49-1.05),0.60(0.41-0.87)and 0.62(0.43-0.90), respectively], when compared with those with less than 4times per day after adjustment of confounding factors. Data showed that smokers and nonsmokers who voided at least 6 times per day had the ORs of 0.72(95%CI: 0.45-1.15)and 0.46(95%CI:0.25-0.87)when compared to their counterparts who voided 3 times or less per day during the daytime. Subjects who urinated at least 6 times per day and consumed more than 1500 ml of total fluid per day experienced a significant 57% reduction in risk compared to subjects who urinated 3 times or less and consumed less than 750 ml of total daily fluid intake. Conclusion Increased urination frequency and total fluid intake, especially among those who never smoked might be associated with a reduced risk of bladder cancer.
5.Human metapneumoviruses were isolated from infants and children with acute respiratory infections in Beijing.
Fang WANG ; Ru-nan ZHU ; Yuan QIAN ; Jie DENG ; Lin-qing ZHAO ; Yu SUN ; Li SHA ; Bin LIAO ; Rong-yan HUANG
Chinese Journal of Pediatrics 2010;48(11):820-823
OBJECTIVETo obtain isolated human metapneumovirus (HMPV) strains from clinical specimens collected from infants and children in Beijing and to promote the investigation on this important respiratory pathogen.
METHODClinical specimens including throat swabs from outpatients and nasopharyngeal aspirates from hospitalized children were collected from infants and children visited the affiliated children's hospital for acute respiratory infections during May 2008 to April 2009. HMPV positive specimens identified by RT-PCR and/or direct immunofluorescent assay with monoclonal antibody against HMPV were inoculated to LLC-MK(2) cells and incubated at 37°C and 33°C, respectively. The replication of the virus in the cells was detected by direct immunofluorescent assay followed by RT-PCR. The genotypes of the isolated virus strains were identified by RT-PCR.
RESULTOut of 1092 clinical specimens, 81 were HMPV positive by RT-PCR, the positive rate was 7.4% (81/1092). Among these positive specimens, 33 were inoculated to LLC-MK(2) cells and the replication of HMPV was revealed by antigen detection and RT-PCR from 5 out of these 33 inoculates. These isolated viruses could be passed in LLC-MK(2) cells and were not cross-reacted with other common respiratory viruses, such as ADV, RSV and Parainfluenza viruses 1/2/3 by monoclonal antibodies against these viruses in direct immunofluorescent assay. The HMPV was more likely to be isolated from fresh specimens within 24 hours after the collection of specimens which were not frozen. Four of the 5 isolated strains were identified as genotype A and 1 as genotype B. Unlike other respiratory viruses, these isolated HMPV did not show specific CPE in cell culture and the replication of the virus was identified by antigen detection and RT-PCR.
CONCLUSIONHMPV of both genotypes were isolated from infants and children with acute respiratory infections in Beijing which will accelerate the investigation of this important virus.
Acute Disease ; Child ; China ; Genes, Viral ; genetics ; Genotype ; Humans ; Infant ; Metapneumovirus ; isolation & purification ; Respiratory Tract Infections ; virology
6.The Invigoration Effect of Halophilic Bacterium and Its Bio-augmention in High-sality Organic Wastewater Treatment
Wei-Guo LI ; Zhong XU ; Da-Wei ZHANG ; Guang-Yu WANG ; Feng LIU ; Mei-Rong MA ; Hui-Ru YANG ; Fang MA ;
Microbiology 1992;0(04):-
Be subjected to study the application in the hypersaline organic wastewater treatment,A moder-ately halophilic bacterium YS-1 was isolated from the salty water of a Ludaokou salina of Weihai in China.The polyphasic taxonomy study was processed through identifying its morphological features by AFM,researched the features of culture and measured physiologic-biochemical index,analyzed 16S rDNA se-quence homology Phylogenetic analysis based on 16S rDNA gene sequences showed that the closest relative of the strain was Halomonas sp.(AB167061).Experimented of intensifying hypersaline organic wastewater treatmented processing in the SBR demonstrate a significant result.The wastewater salt content of initial wastewater was 12% and initial CODcr was 1494 mg/L.After 72 h,the removal efficiency of CODcr achieved 90.0% and after 120 h,it achieved 98.1%.The experiments also showed the hypersaline organic wastewater treatment and presented the feasibility of acclimating of halophilic bacteria and running of proc-essing system.
7.Research on improved dispensing technology to reduce infusion particle pollution and raise infusion security
Mei-Fang XU ; Hui-Rong YANG ; Yan BAI ; Rui-Zhi RU ; Li-Zhu LIANG
Chinese Journal of Modern Nursing 2011;17(10):1215-1217
Objective To investigate the optimal method of dispensing safety, and increase work efficacy. Methods The experimental group and control group were collected with 30 cases respectively. The control group was treated with conventional dispensing methods, experimental group improved dispensing method. The number of insoluble particles was observed between the two groups. Results The experimental group showed ≥ 10 microns (a/ml), and ≥ 25 microns (a/ml) than in the control group (P < 0. 01), but both failed to meet the standards of the Chinese Pharmacopoeia. Conclusions The modified method can reduce the transfusion of dispensing particulate pollution, but the establishment of intravenous infusion center or install clean benches pharmacy dispensing is necessary.
8.Analysis on Incidence and Mortality Characteristics of Thyroid Cancer during 2007 to 2011 in Zhejiang Province
Wei-Wei GONG ; Ru-Ying HU ; Sheng-Lan LUO ; Jin PAN ; Fang-Rong FEI ; Qing-Fang HE ; Zhi-Tong ZHANG ; Min YU
Journal of Preventive Medicine 2014;(5):433-437
Objective To analyze the characteristics and trend of incidence and mortality of thyroid cancer in Zhejiang Province from 2007 to 2011.Methods Data from cancer registry and death registry in Zhejiang province were used to calculate the crude incidence and mortality,age -specific incidence and mortality,China - and World -standardized incidence and mortality of thyroid cancer.Trend Chi -square test was used to analyze the trend of incidence and mortality. Results From 2007 to 2011,the reported incidence rate of thyroid cancer in Zhejiang Province was 8.37 /100,000 (China -and World -standardized incidence were 5.28 /100,000 and 6.14 /100,000 respectively).The mortality rate was 0.34 /100,000 (China -and World -standardized mortality were 0.17 /100,000 and 0.24 /100,000 respectively). The incidence and mortality were both significantly higher in females and urban residents than in males and rural residents (both P <0.01).With age increased,the mortality increased.However,the incidence increased at the beginning and then declined with a peak age of 30 -59.From 2007 to 2011,the incidence of thyroid cancer increased rapidly with a speed of 29.95% per year while the mortality did not show the similar trend.Conclusion The incidence of thyroid cancer in Zhejiang Province is growing rapidly and the relative risk factors should be taken into consideration in future researches.
9.Identification and typing of adenoviruses from pediatric patients with acute respiratory infections in Beijing from 2003 to 2008.
Jie DENG ; Yuan QIAN ; Lin-qing ZHAO ; Ru-nan ZHU ; Fang WANG ; Yu SUN ; Bin LIAO ; Rong-yan HUANG ; Yi YUAN ; Dong QU ; Xiao-xu REN
Chinese Journal of Pediatrics 2010;48(10):739-743
OBJECTIVEAdenovirus (ADV) is one of the most common causes of acute respiratory infections in infants and children. The objective of this study was to investigate the prevalence of adenovirus infection among pediatric patients with acute respiratory infections in Beijing and the types of the adenoviruses circulating in Beijing on the molecular bases.
METHODClinical specimens including throat swabs from outpatients and nasopharyngeal aspirates from hospitalized patients were collected from patients with acute respiratory infections in a consecutive period of 6 years from Jan 2003 to Dec 2008. Adenoviruses were identified from the collected clinical specimens by tissue culture and/or immunofluorescence assay and typed by nested-PCR based on the sequence of the encoding gene of hexon. Primers were designed for PCR amplification using hexon gene of adenovirus as target. One primer pair was designed as universal primers for amplifying a 1278 bp gene fragment located at the hexon gene of adenovirus types 3, 7, 11 and 21. Four primer pairs with the sequences located within the region of this 1278 bp fragment were designed specifically for amplifying adenoviruses types 3, 7, 11 or 21, respectively, which were used for a multiplex nest-PCR in a single tube. The products from this multiplex nest-PCR were 502 bp (for type 3), 311 bp (for type 7), 880 bp (for type 11) and 237 bp (for type 21), respectively, and the type of the adenovirus tested can be determined after agarose electrophoresis analysis of the PCR products. For those strains which could not be typed by the multiplex nest-PCR, the gene fragment was amplified by a universal primer pair for all adenovirus types from group A to F and the PCR products were sequenced directly.
RESULTOut of 17 941 clinical specimens collected, including 4378 throat swabs from outpatients and 13 563 nasopharyngeal aspirates from hospitalized patients, 304 were adenovirus positive by tissue culture and/or immunofluorescence assay, the overall positive rate was 1.69% (304/179 41). Among these 304 adenovirus positive specimens, 184 were by virus isolation and 184 by immunofluorescence assay, among which 64 were positive by both methods. The types of the adenoviruses were tested for 285 patients including 174 viral isolates and 111 clinical specimens. By using the multiplex nest-PCR, 272 were typable, including 174 (61.1%, 174/285) for ADV3, 92 (32.3%, 92/285) for ADV7, 6 for ADV11 (2.1%, 6/285) and no adenovirus type 21 was detected. Sequence analysis for those 13 nontypable specimens by the multiplex nest-PCR showed that 9 were ADV2 (3.2%, 9/285), 2 were ADV6 (0.7%, 2/285), 1 was ADV1 (0.4%, 1/285) and 1 was ADV5 (0.4%, 1/285). Most of the patients positive for adenovirus were under 5 years of age and 64.4% were from patients with lower respiratory infections, such as bronchiolitis and pneumonia. All the 5 cases of severe pneumonia with pulmonary failure were caused by ADV7 infection.
CONCLUSIONAdenovirus is still an important pathogen for acute respiratory infection in infants and young children and most of the adenoviruses associated with acute respiratory infections in children in Beijing from 2003 to 2008 were ADV3 and ADV7. ADV7 could cause severe lower respiratory infections.
Acute Disease ; Adenoviridae ; classification ; isolation & purification ; Adenoviridae Infections ; epidemiology ; prevention & control ; Adolescent ; Child ; Child, Preschool ; China ; epidemiology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Prevalence ; Respiratory Tract Infections ; epidemiology ; prevention & control ; virology
10.Sequence analysis of the HA1 regions of hemagglutinin gene from influenza viruses (H3N2) isolated from children in Beijing in 2004 indicated antigenic variation.
Ru-nan ZHU ; Hong XU ; Yuan QIAN ; Fang WANG ; Jie DENG ; Lin-qing ZHAO ; Bin LIAO ; Rong-yan HUANG
Chinese Journal of Pediatrics 2005;43(9):653-656
OBJECTIVETo identify variations in hemagglutinin genes from influenza viruses (H3N2) isolated from infants and young children with acute respiratory infection (ARI) between March, 2004 and April 2005.
METHODSRNAs from influenza A virus strains (subtype H3) isolated from specimens collected from ARI children were extracted followed by amplification for HA1 fragments from hemagglutinin (HA) genes by RT-PCR. The sequences of the fragments were defined by direct sequencing for the PCR products or the target inserts after the PCR fragments were cloned into the TA-cloning vector pBS-T and analyzed by bioinformatic software.
RESULTSFragments of 987 bps of HA1 (encoding 329 amino acids) from a total of 32 strains of influenza A virus (subtype H3) isolated from the 2004 season and 1 from the 2003 season were amplified and the sequences were compared with vaccine reference strains recommended by WHO which were used in recent years. There were several consistent amino acid variations which involved in both antigenic epitopes A and B and receptor binding site (RBS) for isolated strains in the 2004 influenza season compared with the vaccine strains used during the recent years and the virus strains isolated in March 2004, indicated the antigenic drift of the viruses isolated in 2004 influenza season may lead to variant viruses.
CONCLUSIONThe variations of the HA genes from influenza virus (subtype H3) strains in the 2004-2005 influenza season were confirmed by sequence analysis for the HA1 regions of the hemagglutinin genes, which indicate that the antigenic drift would have been caused by the diversification of the genes and the efficacy of the recently used vaccines should be kept under close watch.
Antigenic Variation ; Child ; China ; epidemiology ; Evolution, Molecular ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; Humans ; Influenza A Virus, H3N2 Subtype ; genetics ; immunology ; isolation & purification ; Influenza, Human ; epidemiology ; immunology ; virology ; RNA, Viral ; genetics ; Sequence Analysis, RNA