Prediction of hepatitis B virus lamivudine resistance based on YMDD sequence data using an artificialneural network model

Hepatitis B virus [HBV] infection is an important health problem worldwide with critical outcomes. The nucleoside analog lamivudine [LMV] is a potent inhibitor of HBV polymerase and impedes HBV replication in patients with chronic hepatitis B. Treatment with LMV for long periods causes the appearance and reproduction of drug-resistant strains, rising to more than 40% after 2 years and to over 50% and 70% after 3 and 4 years, respectively. Artificial neural networks [ANNs] were used to make predictions with regard to resistance phenotypes using biochemical and biophysical features of the YMDD sequence. The study population comprised patients who were intended for surgery in various hospitals in Tehran-Iran. An ACRS-PCR method was performed to distinguish mutations in the YMDD motif of HBV polymerase. In the training and testing stages, these parameters were used to identify the most promising optimal network. The ideal values of RMSE and MAE are zero, and a value near zero indicates better performance. The selection was performed using statistical accuracy measures, such as root mean square error [RMSE], coefficient of determination [R2], and mean absolute error [MAE]. The main purpose of this paper was to develop a new method based on ANNs to simulate HBV drug resistance using the physiochemical properties of the YMDD motif and compare its results with multiple regression models. The results of the MLP in the training stage were 0.8834, 0.07, and 0.09 and 0.8465, 0.160.04 in the testing stage; for the total data, the values were 0.8549, 0.115, and 0.065, respectively. The MLP model predicts lamivudine resistance in HBV better than the MLR model. The ANN model can be used as an alternative method of predicting the outcome of HBV therapy. In a case study, the proposed model showed vigorous clusterization of predicted and observed drug responses. The current study was designed to develop an algorithm for predicting drug resistance using chemiophysical data with artificially created neural networks. To this end, an intelligent and multidisciplinary program should be developed on the basis of the information to be gained on the essentials of different applications by similar investigations. This program will help design expert neural network architectures for each application automatically

[Sero prevalence of CMV in women's with spontaneous abortion in kowsar hospital, ilam during 2007-2008]

Human CMV is the most causative agent of a very common viral infection contacted by most adults that have no noticeable or with only mild uncharacteristic symptoms. However when a pregnant women is infected with CMV as a primary infection, there is a risk for transmission of virus to the fetus as well as reactivation of virus in rare case. HCMV antibodies were already described in spontaneous abortion and fetal abnormalities cases. Also antibodies against HCMV in fetal abnormalities as well as abortion had been reported by several studies in different part of the world. Due to lack of published data about CMV epidemiology in Ilam, the aim of current study was to determine the seroprevalence of specific viral IgM and IgG in spontaneous abortion cases as well as the age and socioeconomic status in the studied population in Ilam. Sera sample from 42 patients in abortion process as well as 30 healthy pregnant and 30 healthy women as negative control were collected and quantitative serological test to assess IgM/IgG against HCMV was performed using a commercial ELISA assay. SPSS software was used to analysis the results and demographic information. Among 42 patients in abortion process, IgG was found in 6 [14.28%] patients and IgM in 12 [28.58%] cases. Based on demographical information, it was showed that IgG seropositivity correlate with the increase of age, but there is no correlation between IgM and age of patients. The results showed that there is a high seroPrevalence of HCMV IgM than IgG among pregnant women in the process of abortion in Ilam; correlation between Age and IgG anti body seroPrevalence was same as other reported. Based on the current studies, it seems that more sensitive and specific method such as NAT method is needed for determination of CMV and abortion procces

[Development of a new-fast and sensitive one step/one tube nested RT-PCR method in a closed system by double-joint primer for detecting HCV]

Polymerase chain reaction [PCR] is one of the most important progress in the field of molecular biology and diagnosis. Despite simplicity in concept, the reaction needs complex interaction between target sequence, primers, dNTPs and DNA polymerase for a successful amplification and diagnosis. For the detection of RNA viruses highly sensitive and specific technique is required. Hence amplification based on Nested PCR would improve sensitivity, and also use of one step reaction would decrease probable contaminations as reported previously in several studies. The aim of the current study was to develop a new, rapid and sensitive one step-one tube Nested PCR in a closed system, by using two novel coherent primers. In this study, a novel and special primer development method was used for one step-one tube reaction. After development and optimization, the assay was evaluated with known positive and negative controls. The developed assay was performed on 50 HCV positive samples and 10 negative controls and 5 samples from each HIV, HBV, TTV [Torque Teno Virus] and GBV-C [Hepatitis G Virus: HGV]. Based on the obtained results, sensitivity and specifity was calculated. 48 out of 50 HCV positive samples showed expected band while none of the negative controls gave any band. Based on the specific primer design system which has been used in the current study; the inner primer was synthesized as complementary of routine PCR primers and was bound to the outer primers. Therefore, there is no probability for false priming in the both rounds of the reaction, hence there would be no nonspecific amplifications. Other advantages of this assay system were prevention of contamination which was due to one step-one tube reaction, decrease in duration and the cost of the reaction