Stability and accuracy of central difference method for real-time dynamic substructure testing considering mass participation coefficient

For real-time dynamic substructure testing(RTDST),the influence of the inertia force of fluid specimens on the stability and accuracy of the integration algorithms has never been investigated.Therefore,this study proposes to investigate the stability and accuracy of the central difference method(CDM)for RTDST considering the specimen mass participation coefficient.First,the theory of the CDM for RTDST is presented.Next,the stability and accuracy of the CDM for RTDST considering the specimen mass participation coefficient are investigated.Finally,numerical simulations and experimental tests are conducted for verifying the effectiveness of the method.The study indicates that the stability of the algorithm is affected by the mass participation coefficient of the specimen,and the stability limit first increases and then decreases as the mass participation coefficient increases.In most cases,the mass participation coefficient will increase the stability limit of the algorithm,but in specific circumstances,the algorithm may lose its stability.The stability and accuracy of the CDM considering the mass participation coefficient are verified by numerical simulations and experimental tests on a three-story frame structure with a tuned liquid damper.

Development of a real-time RT-PCR method for the detection of newly emerged highly pathogenic H7N9 influenza viruses

In 2013, a human influenza outbreak caused by a novel H7N9 virus occurred in China. Recently, the H7N9 virus acquired multiple basic amino acids at its hemagglutinin（HA） cleavage site, leading to the emergence of a highly pathogenic virus. The development of an effective diagnostic method is imperative for the prevention and control of highly pathogenic H7N9 influenza. Here, we designed and synthesized three pairs of primers based on the nucleotide sequence at the HA cleavage site of the newly emerged highly pathogenic H7N9 influenza virus. One of the primer pairs and the corresponding probe displayed a high level of amplification efficiency on which a real-time RT-PCR method was established. Amplification using this method resulted in a fluorescent signal for only the highly pathogenic H7N9 virus, and not for any of the H1–H15 subtype reference strains, thus demonstrating high specificity. The method detected as low as 39.1 copies of HA-positive plasmid and exhibited similar sensitivity to the virus isolation method using embryonated chicken eggs. Importantly, the real-time RT-PCR method exhibited 100% consistency with the virus isolation method in the diagnosis of field samples. Collectively, our data demonstrate that this real-time RT-PCR assay is a rapid, sensitive and specific method, and the application will greatly aid the surveillance, prevention, and control of highly pathogenic H7N9 influenza viruses.

检测粪便中GGⅡ型诺如病毒Real-time RT-PCR方法的建立

诺如病毒是世界急性胃肠炎的重要病原之一。为加强其控制，通过序列比对设计出针对GGⅡ型诺如病毒保守序列的特异性引物与探针，建立了TaqMan Real-time RT-PCR方法。结果显示，此方法对诺如病毒核酸检测高度特异，与轮状病毒、腺病毒、甲型肝炎病毒等无交叉反应，最低检出限可达10^2拷贝，线性范围为100～100拷贝，标准曲线的相关系数为-1．00。针对标准品质粒检测的批内实验变异系数为0．28％～1．63％（n=6）、批间实验为0．28％～1．05％（n=3），对同一样品分6次进行RNA提取和逆转录，其变异系数为3增8％。对212份临床腹泻标本分别用常规RT-PCR和本文建立的TaqMan Real-time PCR进行检测，发现后者检出率略高于前者。这些结果提示此研究建立的诺如病毒的TaqMan Real-time RT-PCR检测方法可用于临床腹泻粪便标本的检测。

利用real-time RT-PCR研究大型蚤对铜绿微囊藻毒素合成基因转录水平影响

近年来关于浮游动物与微囊藻相互作用的研究逐渐被关注,其中有的研究认为浮游动物能够诱导产毒细胞毒素含量的变化.微囊藻毒素是由微囊藻毒素合成基因编码翻译的,目前关于浮游动物对微囊藻毒素合成基因相对表达的影响并无报道,本文首次通过实时定量逆转录PCR方法研究铜绿微囊藻PCC7806产毒相关基因mcyB和mcyD在大型蚤胁迫下相对表达变化.结果显示微囊藻mcyB、mcyD基因相对表达均有上调,表明铜绿微囊藻PCC7806通过上调产毒基因的转录水平达到对大型蚤的诱导防御,从而为浮游动物与微囊藻相互作用研究提供新的依据.

TaqMan MGB Real-time RT-PCR检测西尼罗病毒方法的建立

目的建立一种灵敏、特异、高效的西尼罗病毒(West Nile virus,WNV)感染诊断和流行病学调查的实验室检测方法。方法用C6/36细胞培养WNV并用Vero细胞蚀斑法滴定病毒浓度;根据WNVC蛋白基因组保守序列,设计一套特异性引物和TaqMan MGB探针,用细胞培养病毒液进行方法的条件优化;用不同病毒评价方法的特异性,用系列浓度病毒稀释液和染毒蚊子评价方法的灵敏性。结果建立的TaqMan MGB Real-time RT-PCR方法可检出低于0.01PFU的WNVRNA,并可检出只含3只染毒蚊的标本;用该方法检测4种血清型登革病毒标准毒株、日本脑炎病毒、麻疹病毒、基孔肯亚病毒均为阴性。结论新建TaqMan MGB Real-time RT-PCR方法具有极高的特异性和灵敏性,是实验室早期诊断WNV感染和调查媒介携带WNV情况的理想方法。

猴逆转录病毒RT-PCR和Real-time RT-PCR检测方法的建立

猴逆转录病毒(Simian type D retrovirus,SRV)是引起猴获得性免疫缺陷综合征(Simian acquired immunodeficiency syndrome,SAIDS)的病原之一,其严重危害猴的健康,并威胁与猴接触人员的健康,是无特定病原体(SPF)猴必须排除的病毒之一。为了应对口岸对进出境野生及实验用灵长类动物SRV感染情况的监测和流行病学调查的需要,建立了RT-PCR和real-time RT-PCR检测SRV的方法,并对方法的特异性、敏感性和稳定性进行了验证。

鸡传染性支气管炎病毒Real-time RT-PCR检测方法的建立及应用

为定量检测鸡传染性支气管炎病毒(IBV)载量,建立IBV的Real-timeRT-PCR方法。用RT-PCR方法扩增出IBV的N基因片段,并克隆到pEASY-T3载体中,构建成含有N基因片段的重组质粒。应用该重组质粒进行SYBRGreenⅠReal-timePCR,建立了定量检测IBV核酸的标准曲线与直线回归方程,该方法显示:特异性强,检测下限至少达到5.58×102拷贝/μL,其重复性试验的变异系数小于3.2%;用建立的方法对实验接种IBVM41株的雏鸡组织中的病毒核酸进行了定量检测,检测结果显示:攻毒后肾脏中IBV含量高于支气管和肺脏,支气管和肺脏中病毒含量在攻毒后第3天高于攻毒后第7、10天,并证实临床表现与病毒载量之间存在密切关系。研究结果表明,建立的Real-timeRT-PCR检测方法特异性强、灵敏度高、可重复性好,可用于IBV的定量检测。

利用Real-time RT-PCR法检测抗病毒活性物质对CMV复制的影响

为准确检测经活性物质处理后的烟草体内病毒含量,建立了real-time RT-PCR检测体系。从烟田中分离到1株对CMV有拮抗作用的细菌B6,经分离纯化得到拮抗CMV的活性物质B6p,其分子量为40.6 kDa。利用叶圆片法,分析了活性物质处理后寄主体内病毒的复制特点,结果表明寄主体内的病毒复制作用受到了拮抗活性物质的抑制,并且随着拮抗活性物质浓度的增加病毒的复制作用减弱。

应用Real-Time RT-PCR鉴定2个水稻品种(品系)对水稻条纹病毒的抗性差异

应用Real-time RT-PCR检测了水稻条纹病毒(Rice stripe virus,RSV)在2种水稻品种(品系)武育粳3号和KT95-418的悬浮细胞内复制变化和相对含量的差异,结合传统生物学接种试验,确定了这2个品种(品系)对RSV抗性的差异.结果表明,RSV在武育粳3号的悬浮细胞内24 h达到复制高峰,病毒含量为侵染初期的7.46倍.而在KT95-418的悬浮细胞内,RSV达到复制高峰需要36 h,病毒含量为侵染初期的4.51倍.利用病毒生物学接种的方法,武育粳3号发病率达91.7%,而KT95-418仅为36.0%.由此可见,KT95-418较武育粳3号对RSV具有较高的抗病性.因此,Real-time RT-PCR方法与传统生物学接种试验方法相比,具有更高的准确性和灵敏性,可以作为传统品种抗病性鉴定的验证手段.

Real-time RT-PCR检测J亚群禽白血病病毒的研究

为了建立检测J亚群禽白血病病毒(ALV-J)的方法,试验采用Real-time RT-PCR,通过1对ALV-J特异性引物对ALV-J山东分离株(命名为ALV-JSD株)进行特异性、敏感性和重复性试验;然后用ALV-JSD株感染1日龄SPF鸡,感染8周后剖检取各组织,用已建立的方法检测ALV-LSD株的感染情况。结果表明:特异性试验中只有以ALV-JSD株cDNA为模板的反应管中能够检测到扩增曲线;敏感性试验测得反应灵敏度达到3.01×1010 copies/μL,比普通PCR灵敏100多倍;对人工感染鸡的不同组织样品进行3次重复检测,病毒检出率为100%;经重复性和实际临床样本检验证实,该方法稳定、可靠,为ALV-J的早期快速诊断建立了特异、灵敏、廉价的定量检测方法。

流感病毒Real-time RT-PCR核酸检测及流行情况分析

目的:分析鄂尔多斯市2012年流感检测结果,为本地区流感预防控制提供科学依据。方法采用Real-time RT-PCR法对哨点医院采集的流感样病例咽拭子标本进行病毒核酸检测。结果共检测流感咽拭子标本281份,流感病毒核酸阳性35份,总阳性率为12.46%。其中乙型16份,占5.69%,季节性H3亚型15份,占5.34%,甲型H1N12份,占0.71%,甲型未分型2份,占0.71%。2012年1月~3月阳性率分别为11.36%、27.50%、37.50%,10月和12月阳性率均为5.00%,其它月份未检出阳性。结论监测显示鄂尔多斯地区流感流行季节主要为冬春季,流行毒株主要是乙型和季节性H3亚型。

Real-time localization for underwater equipment using an extremely low frequency electric field

A new real-time underwater equipment location method adopting an electric field induced by a standard current source is proposed.Our goals were real-time tracking and location of stationary or moving underwater equipment both in shallow and deep seas,under noisy conditions.The main features of this method are as follows:(1)a standard current source on the water surface,which can be towed by a vehicle,consisting of two electrodes,a signal generator,and a GPS unit;(2)measurement of the extremely low frequency(ELF)electric field emitted by the current source,made possible by electric field sensors on the underwater equipment;(3)position of the underwater equipment is estimated in real time based on a progressive update extended Kalman filter(PUEKF),which is carried out using the propagation model of an ELF electric field because the electric field at the position of the underwater equipment and the current source position are known.We verified the accuracy of our method and confirmed real-time location feasibility through numerical,physical scale,and real-time sea experiments.Through numerical experiments,we verified that our method works for underwater equipment location in real-world conditions,and the location error can be less than 0.2 m.Next,real-time location experiments for stationary underwater measuring equipment in water tank were conducted.The result shows that the location error can be less than 0.1 m.We also confirmed real-time location feasibility through the use of offshore experiment.We expect that our method will complement conventional underwater acoustic location methods for underwater equipment in acoustically noisy environments.

Quantitative real-time RT-PCR detection for CEA, CK20 and CK19 mRNA in peripheral blood of colorectal cancer patients

This study is aimed at establishing a sensitive approach to detect disseminated tumor cells in peripheral blood and evaluate its clinical significance. A total of 198 blood samples including 168 from colorectal carcinoma (CRC) patients and 30 from healthy volunteers were examined by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) to evaluate the expression of carcinoembryonic antigen (CEA), cytokeratin 20 (CK20) and cytokeratin 19 (CK19) mRNA. CEA mRNA was detected in 35.8% of patients and 3.3% of controls, CK20 mRNA in 28.3% of patients and 6.7% of controls, and CK19 mRNA in 41.9% of patients and 3.3% of controls. CEA and CK20 mRNA positive ratio increased with the advancing Dukes stages, but there was no significant difference in positive ratio between any two stages (P>0.05). Also, relatively high positive ratio of CEA, CK20 and CK19 mRNA expression was observed in some CRC patients with earlier Dukes stages. A higher positive ratio was obtained when two or three detection markers were combined compared to a single marker. Our study indicates that quanti-tative real-time RT-PCR detection for CEA, CK20 and CK19 mRNA in peripheral blood is a valuable tool for monitoring early stage dissemination of CRC cells in blood circulation.

Expression of Eph-Ephrin A Molecules in Endometrium During Swine Embryo Implantation Examined Using Real-Time RT-PCR

Erythropoietin-producing hepatocellular receptor and its membrane-bound ligands （Eph-Ephrin） system could regulate some mammalian blastocyst attachment and spreading. In order to investigate the involvement of the Eph-Ephrin system in swine embryo attachment, mRNA expression of Eph-Ephrin molecules in endometrium was examined by real-time RT- PCR during embryo implantation in pigs. The results indicated that mRNA expressions of Eph A5, A7 and Ephrin A5 all continually increased from pregnancy day 13 to 24. Ephrin A3 mRNA expression significantly increased from day 13 to 18 and decreased from day 18 to 24, and the expression was the lowest on pregnancy day l 3 and the highest on day 18. However, Ephrin A4 mRNA expression was the lowest on pregnancy day 18 and the highest on day 24, and the expression decreased from day 13 to 18 and increased from day 18 to 24. Furthermore, mRNA expressions of Eph A5 and A7 were both found in other tissues, such as brain, muscle, intestine, stomach, etc. These findings suggest that the Eph-Ephrin system may play an important role in regulating the contact between blastocysts and endometrium during swine embryo implantation.

TaqMan Real-time RT-PCR Assay for Detecting and Differentiating Japanese Encephalitis Virus

Objective To detect Japanese encephalitis virus（JEV） rapidly and distinguish its genotypes, a TaqMan-based reverse transcriptase quantitative polymerase chain reaction（RT-PCR） detection system was developed.Methods By aligning the full-length sequences of JEV（G1-G5）, six sets of highly specific TaqMan real-time RT-PCR primers and probes were designed based on the highly conserved NS1, NS2, and M genes of JEV, which included one set for non-specific JEV detection and five sets for the detection of specific JEV genotypes. Twenty batches of mosquito samples were used to evaluate our quantitative PCR assay.Results With the specific assay, no other flavivirus were detected. The lower limits of detection of the system were 1 pfu/mL for JEV titers and 100 RNA copies/μL. The coefficients of variation of this real-time RT-PCR were all 〈 2.8%. The amplification efficiency of this method was between 90% and 103%.Conclusion A TaqMan real-time RT-PCR detection system was successfully established to detect and differentiate all five JEV genotypes.

Multiplex real-time RT-PCR for detecting chikungunya virus and dengue virus

Objective:To develop diagnostic test for detection chikungunya virus(CHIKV and Dengue virus (DENV) infection.Methods:We have performed a rapid,accurate laboratory confirmative method to simultaneously detect,quantify and differentiate CHIKV and DENV infection by single-step multiplex real-time RT-PCR.Results:The assay’s sensitivity was 97.65%,specificity was 92.59% and accuracy was 95.82%when compared to conventional RT-PCR.Additionally,there was no cross-reaction between CHIKV,DENV,Japanese encephalitis virus,hepatitis C,hepatitis A or hepatitis E virus.Conclusions:This rapid and reliable assay provides a means for simultaneous early diagnosis of CHIKV and DENV in a single-step reaction.

Real-time embedded software testing method based on extended finite state machine

The reliability of real-time embedded software directly determines the reliability of the whole real-time embedded sys- tem, and the effective software testing is an important way to ensure software quality and reliability. Based on the analysis of the characteristics of real-time embedded software, the formal method is introduced into the real-time embedded software testing field and the real-time extended finite state machine （RT-EFSM） model is studied firstly. Then, the time zone division method of real-time embedded system is presented and the definition and description methods of time-constrained transition equivalence class （timeCTEC） are presented. Furthermore, the approaches of the testing sequence and test case generation are put forward. Finally, the proposed method is applied to a typical avionics real- time embedded software testing practice and the examples of the timeCTEC, testing sequences and test cases are given. With the analysis of the testing result, the application verification shows that the proposed method can effectively describe the real-time embedded software state transition characteristics and real-time requirements and play the advantages of the formal methods in accuracy, effectiveness and the automation supporting. Combined with the testing platform, the real-time, closed loop and automated simulation testing for real-time embedded software can be realized effectively.

A novel real-time RT-PCR with TaqM an-MGB probes and its application in detecting BVDV infections in dairy farms

A real-time RT-PCR assay using Taq Man-MGB probes was developed to detect and type the bovine viral diarrhea virus（BVDV） in cattle.Universal primers and Taq Man-MGB probes were designed from the 5′-untranslated region of known pestiviral sequences.Prior to optimizing the assay, c RNAs were transcribed in vitro from the BVDV 1 and BVDV 2 RTPCR products to make standard curves.The detection limit of the assay was 1.72×102 copies for BVDV 1 and 2.14×102copies for BVDV 2.The specificity of the assay evaluated on several BVDV strains including bovine herpesvirus 1（BHV 1）, foot and mouth disease virus（FMDV） and several classical swine fever virus（CSFV） strains showed specific detection of the positive virus over 40 cycles.The assay was highly reproducible with the coefficient of variance ranging from 1.04 to 1.33% for BVDV 1 and from 0.83 to 1.48% for BVDV 2, respectively.Using this method, we tested a total of 2 327 cattle from three dairy farms for the presence of BVDV persistently infected（PI） animals.In this assay, each RT-PCR template contained a mixture of ten samples from different animals.The occurrence rate of PI cattle in three farms ranging from 0.9 to 2.54% could represent partly the PI rates in cattle farm in China.In conclusion, using our real-time PCR assay, we could effectively detect and type BVDV and identify PI cattle in a rapid and cost-effective manner.

Real-time RT-PCR Assay for the detection of Tahyna Virus

A real-time RT-PCR （RT-qPCR） assay for the detection of Tahyna virus was developed to monitor Tahyna virus infection in field-collected vector mosquito samples. The targets selected for the assay were S segment sequences encoding the nucleocapsid protein from the Tahyna virus. Primers and probes were selected in conserved regions by aligning genetic sequences from various Tahyna virus strains available from GenBank. The sensitivity of the RT-qPCR approach was compared to that of a standard plaque assay in BHK cells. RT-qPCR assay can detect 4.8 PFU of titrated Tahyna virus. Assay specificities were determined by testing a battery of arboviruses, including representative strains of Tahyna virus and other arthropod-borne viruses from China. Seven strains of Tahyna virus were confirmed as positive; the other seven species of arboviruses could not be detected by RT-qPCR. Additionally, the assay was used to detect Tahyna viral RNA in pooled mosquito samples. The RT-qPCR assay detected Tahyna virus in a sensitive, specific, and rapid manner; these findings support the use of the assay in viral surveillance.