Evaluation of three Polymerase chain reaction tests targeting morphological transforming region II, UL-83 gene and glycoprotein O gene for the detection of Human Cytomegalovirus genome in clinical specimens of immunocompromised patients in Chennai, India

BACKGROUND: Human Cytomegalovirus (HCMV) continues to be an important cause of morbidity and occasional mortality in immunocompromised patients. Polymerase chain reaction (PCR) is the most sensitive and commonly used method for the assessment of HCMV infection in the immunocompromised patients at risk from severe associated clinical manifestations. However, there is little consistency in the qualitative PCR used for different regions of HCMV genome. Therefore, the performance of three Qualitative PCR tests to detect HCMV genome in clinical specimens from immunocompromised patients was evaluated. With pp65 antigenemia assay as the "gold standard", nested PCR for morphological transforming region II (mtr II) and glycoprotein O (gO) gene and uniplex PCR for UL 83 gene were applied on 92 consecutive clinical specimens obtained from 74 immunocompromised patients with clinically suspected HCMV disease. Virus isolation was attempted on 12 clinical specimens from six pp65 antigenemia positive patients. Based on the pp 65 antigenemia results as "gold standard", the sensitivity, specificity, positive predictive value and negative predictive value for each PCR was calculated. RESULTS: The PCR targeting mtr II region showed a higher sensitivity (100%) and negative predictive value (100%) than the other two PCRs in detecting HCMV DNA from clinical specimens obtained from different immunocompromised patient population of Chennai region, India. CONCLUSION: The results suggests that the optimal method of detection of HCMV DNA could be achieved by PCR using primer sequences targeting mtr II region of genome of HCMV in Chennai region, India

Effect of temperature and time delay in centrifugation on stability of select biomarkers of nutrition and non-communicable diseases in blood samples

Introduction: Preanalytical conditions are critical for blood sample integrity and poses challenge in surveys involving biochemical measurements. A cross sectional study was conducted to assess the stability of select biomarkers at conditions that mimic field situations in surveys. Material and methods: Blood from 420 volunteers was exposed to 2 – 8 °C, room temperature (RT), 22 – 30 °C and > 30 °C for 30 min, 6 hours, 12 hours and 24 hours prior to centrifugation. After different exposures, whole blood (N = 35) was used to assess stability of haemoglobin, HbA1c and erythrocyte folate; serum (N = 35) for assessing stability of ferritin, C-reactive protein (CRP), vitamins B12, A and D, zinc, soluble transferrin receptor (sTfR), total cholesterol, high density lipoprotein cholesterol (HDL), low density lipoprotein cholesterol (LDL), tryglicerides, albumin, total protein and creatinine; and plasma (N = 35) was used for glucose. The mean % deviation of the analytes was compared with the total change limit (TCL), computed from analytical and intra-individual imprecision. Values that were within the TCL were deemed to be stable. Result: Creatinine (mean % deviation 14.6, TCL 5.9), haemoglobin (16.4%, TCL 4.4) and folate (33.6%, TCL 22.6) were unstable after 12 hours at 22- 30°C, a temperature at which other analytes were stable. Creatinine was unstable even at RT for 12 hours (mean % deviation: 10.4). Albumin, CRP, glucose, cholesterol, LDL, triglycerides, vitamins B12 and A, sTfR and HbA1c were stable at all studied conditions. Conclusion: All analytes other than creatinine, folate and haemoglobin can be reliably estimated in blood samples exposed to 22-30°C for 12 hours in community-based studies

Relative efficiency of polymerase chain reaction and enzyme-linked immunosorbant assay in determination of viral etiology in congenital cataract in infants

<b>Background:</b> Perinatal viral infections of fetus are among the leading causes of congenital cataract and identifying the viral etiology is important. Objectives: To detect the presence of Rubella virus (RV), herpes simplex virus (HSV) and cytomegalovirus (CMV) in lens aspirate specimens obtained from patients with congenital cataract and relate the results with serology. <b>Setting and Design:</b> Prospective study carried out in tertiary care hospital. <b>Materials and Methods:</b> Fifty lens aspirates from 50 infants with congenital cataract were subjected to HSV, RV isolation and polymerase chain reaction (PCR) for detection of HSV and CMV. Reverse transcription polymerase chain reaction (RT-PCR) was applied for RV detection. Peripheral blood specimens were screened for anti-HSV, RV and CMV antibodies by enzyme-linked immunosorbant assay (ELISA). <b>Results: </b> Rubella virus was detected in nine (18&#x0025;) lens aspirates, by nRT-PCR which includes six positive by culture. HSV-2 DNA was detected in nine other lens aspirates, while CMV was not detected by PCR. Serological results did not correlate with the presence of viruses in the lens aspirates. This is the first report of detection of HSV-2 DNA in cases of congenital cataract. <b>Conclusions:</b> Cytomegalovirus may not be playing a significant role in causation of congenital cataract. The role of serology in identifying causative viral infection for congenital cataract needs to be re-evaluated

Relative efficiency of polymerase chain reaction and enzyme-linked immunosorbant assay in determination of viral etiology in congenital cataract in infants

Background: Perinatal viral infections of fetus are among the leading causes of congenital cataract and identifying the viral etiology is important. Objectives: To detect the presence of Rubella virus (RV), herpes simplex virus (HSV) and cytomegalovirus (CMV) in lens aspirate specimens obtained from patients with congenital cataract and relate the results with serology. Setting and Design: Prospective study carried out in tertiary care hospital. Materials and Methods: Fifty lens aspirates from 50 infants with congenital cataract were subjected to HSV, RV isolation and polymerase chain reaction (PCR) for detection of HSV and CMV. Reverse transcription polymerase chain reaction (RT-PCR) was applied for RV detection. Peripheral blood specimens were screened for anti-HSV, RV and CMV antibodies by enzyme-linked immunosorbant assay (ELISA). Results: Rubella virus was detected in nine (18%) lens aspirates, by nRT-PCR which includes six positive by culture. HSV-2 DNA was detected in nine other lens aspirates, while CMV was not detected by PCR. Serological results did not correlate with the presence of viruses in the lens aspirates. This is the first report of detection of HSV-2 DNA in cases of congenital cataract. Conclusions: Cytomegalovirus may not be playing a significant role in causation of congenital cataract. The role of serology in identifying causative viral infection for congenital cataract needs to be re-evaluated

Efficient FPGA Implementation of an RFIR Filter Using the APC–OMS Technique with WTM for High-Throughput Signal Processing

Nowadays, Finite Impulse Response (FIR) filters are used to change the attributes of a signal in the time or frequency domain. Among FIR filters, a reconfigurable filter has the advantage of changing the coefficient in real-time, while performing the operation. In this paper, the Anti-Symmetric Product Coding (APC) and Odd Multiple Storage (OMS) modules are utilized to implement the reconfigurable FIR filter (RFIR–APC–OMS). Herein, the APC–OMS module is used to reduce the area of the RFIR architecture. The performance of the RFIR–APC–OMS is analyzed in terms of: area, power, delay, LUT, flip flop, slices, and frequency. RFIR–APC–OMS has reduced 3.44% of area compared to the existing RFIR architecture employing the Dynamic Reconfigurable Partial Product Generator (DRPPG) module

FPGA-Based Reconfigurable Convolutional Neural Network Accelerator Using Sparse and Convolutional Optimization

Nowadays, the data flow architecture is considered as a general solution for the acceleration of a deep neural network (DNN) because of its higher parallelism. However, the conventional DNN accelerator offers only a restricted flexibility for diverse network models. In order to overcome this, a reconfigurable convolutional neural network (RCNN) accelerator, i.e., one of the DNN, is required to be developed over the field-programmable gate array (FPGA) platform. In this paper, the sparse optimization of weight (SOW) and convolutional optimization (CO) are proposed to improve the performances of the RCNN accelerator. The combination of SOW and CO is used to optimize the feature map and weight sizes of the RCNN accelerator; therefore, the hardware resources consumed by this RCNN are minimized in FPGA. The performances of RCNN-SOW-CO are analyzed by means of feature map size, weight size, sparseness of the input feature map (IFM), weight parameter proportion, block random access memory (BRAM), digital signal processing (DSP) elements, look-up tables (LUTs), slices, delay, power, and accuracy. An existing architectures OIDSCNN, LP-CNN, and DPR-NN are used to justify efficiency of the RCNN-SOW-CO. The LUT of RCNN-SOW-CO with Alexnet designed in the Zynq-7020 is 5150, which is less than the OIDSCNN and DPR-NN

Efficient FPGA Implementation of an RFIR Filter Using the APC&ndash;OMS Technique with WTM for High-Throughput Signal Processing

Nowadays, Finite Impulse Response (FIR) filters are used to change the attributes of a signal in the time or frequency domain. Among FIR filters, a reconfigurable filter has the advantage of changing the coefficient in real-time, while performing the operation. In this paper, the Anti-Symmetric Product Coding (APC) and Odd Multiple Storage (OMS) modules are utilized to implement the reconfigurable FIR filter (RFIR&ndash;APC&ndash;OMS). Herein, the APC&ndash;OMS module is used to reduce the area of the RFIR architecture. The performance of the RFIR&ndash;APC&ndash;OMS is analyzed in terms of: area, power, delay, LUT, flip flop, slices, and frequency. RFIR&ndash;APC&ndash;OMS has reduced 3.44% of area compared to the existing RFIR architecture employing the Dynamic Reconfigurable Partial Product Generator (DRPPG) module

Application of polymerase chain reaction to differentiate herpes simplex virus 1 and 2 serotypes in culture negative intraocular aspirates

Purpose: To standardize and apply a polymerase chain reaction (PCR) on the glycoprotein D gene to differentiate Herpes simplex virus (HSV) 1 & 2 serotypes in culture negative intraocular specimens. Methods: Twenty-one intraocular fluids collected from 19 patients were subjected to cultures for HSV and uniplex PCR (uPCR) for DNA polymerase gene. To differentiate HSV serotypes, as 1 & 2, a seminested PCR (snPCR) targeting the glycoprotein D gene was standardised and applied onto 21 intraocular fluids. The specificity of the snPCR was verified by application onto ATCC strains of HSV 1 and 2, clinical isolates and DNA sequencing of the amplified products. All specimens were also tested for the presence of cytomegalovirus (CMV) and varicella zoster virus (VZV) by nucleic acid amplification methods. Results: Four of the 21 intraocular fluids were positive for HSV by uPCR. snPCR detected HSV in three additional specimens (total of seven specimens), and identified three as HSV 1 and four as HSV 2. DNA sequencing of PCR products showed 100% homology with the standard strains of HSV 1 and 2 respectively. None of the samples were positive in culture. Among the other patients, CMV DNA was detected in two and VZV DNA in five others. Conclusions: The standardized snPCR can be applied directly onto the culture negative specimens for rapid differentiation of HSV serotypes