Genotypic variation in CYP2E1, GCKR, and PNPLA3 among nonalcoholic steatohepatitis patients of Turkish origin.

BACKGROUND: This study examines genetic variations in CYP2E1 (rs6413432, rs3813867), GCKR (rs780094, rs1260326), and PNPLA3 (rs738409) among Turkish patients to assess their influence on nonalcoholic steatohepatitis. METHODS: Allele and genotype frequencies were compared between 245 NASH patients and 120 healthy controls using SNP genotyping via polymerase chain reaction-restriction fragment length polymorphism. Additionally, the deviation of the observed genotype frequencies from Hardy-Weinberg proportion was examined. RESULTS: No significant differences were found in the allelic and genotypic distributions of rs6413432, rs3813867, and rs780094 between NASH patients and healthy controls. However, significant disparities were noted for rs1260326 and rs738409. Gender and age-specific distributions showed no notable differences. The only observed deviation from Hardy-Weinberg proportion was in the genotype frequency of rs738409. CONCLUSIONS: Variants in GCKR (rs1260326) and PNPLA3 (rs738409) are significantly associated with increased NASH risk in the Turkish population, with the rs738409 variant potentially playing a more prominent role in NASH development.

Optimization of a rapid and sensitive nucleic acid lateral flow biosensor for hepatitis B virus detection.

BACKGROUND AND OBJECTIVE: The utilization of direct amplification of nucleic acid from lysate has attracted interest in the advancement of straightforward and economical point-of-care assays. Consequently, this study primarily focuses on the development of a rapid, precise, and cost-effective lateral flow biosensor for the convenient detection of HBV nucleic acid at the point-of-care. Furthermore, the study evaluates the effectiveness of the direct amplification method in comparison to purified nucleic acid samples within the context of LAMP-LF biosensing approaches. METHODS: The experiments conducted in this study utilized clinical serum samples that were confirmed as HBV-positive through real-time PCR assays. Sample preparation involved employing spin column nucleic acid purification and serum heat treatment. To amplify a 250 bp fragment of the HBV polymerase gene, three pairs of specific LAMP primers were utilized, which were biotin-labeled and FITC-labeled for detection purposes. Various incubation temperatures (ranging from 64 to 68 °C) and durations (30 min, 45 min, and 1 h) were investigated to determine the optimal conditions for the LAMP assay. The results were subsequently assessed through fluorometric analysis, white turbidity measurements, and lateral flow assay. Milenia HybriDetect1 strips, designed for immediate use, were employed to visualize the LAMP amplicons. Furthermore, the performance of the lateral flow biosensor was evaluated using 10-fold serial dilutions of a secondary standard containing a viral load of 108 IU/ml. RESULTS: The optimization of the LAMP reaction was achieved at a temperature of 67 °C, resulting in significant turbidity after a 30-minute incubation period. When the spin column purification method was employed, varying test bands were observed for templates ranging from 108 IU/ml to 101 IU/ml viral load. However, when serum samples underwent heat treatment and the resulting supernatant was directly used for LAMP, the lateral flow assay was capable of detecting a minimum viral load of 103 IU/ml. CONCLUSION: In resource-limited settings, the LAMP-LF assay presents a promising solution for HBV testing. However, it is important to note that direct amplification without DNA purification may diminish the performance of the approach.

Unveiling the etiological impact of GST-M1, GST-T1, and P53 genotypic variations on brain carcinogenesis.

BACKGROUND: Functional variants of glutathione-S-transferase (GST)-M1, GST-T1, p53 might modulate brain cancer risk by altering the rate of metabolism and clearance of carcinogens from the brain tissue. In this study, the role of GST-M1, GST-T1, p53 polymorphisms on brain tumor was investigated. METHODS AND RESULTS: Brain tumor tissues of 143 patients were obtained from the Gulhane Training and Research Hospital, Department of Neurosurgery between 2019 and 2020. In the xenobiotic mechanism, the null allele frequency in the GST-T1, GST-M1 gene regions of Phase II enzymes by qPCR method were investigated. Single nucleotide polymorphism encoding Arg/Pro conversion in the p53 gene region was analyzed in 120 cases by sequence analysis method. The data were analyzed statistically with patient's demographic and clinical data. GST-M1, GST-T1, p53 genotypes of the patient group were determined. The most frequent genotype was null genotype (0/0) for GST-M1 (χ2 = 39.756, p < 0.001). GST-M1 genotype frequencies were 30.8%, 23.1%, 44.3% for 1/1, 1/0, 0/0, respectively. The most frequent genotype was GST-T1 1/1 following by GST-T1 1/0 (χ2 = 0.335, p = 0.846). GST-T1 genotype frequencies were 64.3%, 30.8%, 4.9% for 1/1, 1/0, 0/0, respectively. GST-M1 null genotype might be associated with the development of brain tumors. Genotype distribution obtained in p53 exon 4 codon 72; Arg/Arg was determined as 31 (25.8%), Arg/Pro 70 (58.3%), and Pro/Pro 19 (15.8%) in the case group, while there were 18 (38.3%), 23 (48.9%), and 6 (12.8%) respectively in the control group. However, the genotype distribution of p53 exon 4 codon 72 among tumorous tissue did not significantly vary from healthy control tissues (χ²=2.536, p = 0.281). CONCLUSION: The null allele frequency encountered in the GST-M1, GST-T1 gene regions is consistent with the rates in the gene pool called Caucasian in the literature. GST-M1 gene polymorphism may play a crucial role in brain carcinogenesis in Turkish patients. This study based on clinical data is thought to help to understand the important epidemiological features of brain tumors.

Epidemiology of blood-borne viral infections in Afghanistan.

Although a few studies have been done on transmissible blood-borne viral infections in high-risk groups, little attention has been given to assessing the infection status of the general population in Afghanistan. To investigate the epidemiological status in the general population, we tested the serological markers of hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis delta virus (HDV), human immunodeficiency virus 1 (HIV-1) and human T-cell leukemia virus (HTLV) infections. In total, 492 samples were selected randomly from Nangarhar, Herat, Mazar-e Sharif, Kandahar, and Kabul from subjects between 25 and 70 years old. The samples were tested for the presence of HBsAg, anti-HBs, anti-HBc, anti-HDV, anti-HCV, anti-HIV-1 and anti-HTLV I/II antibodies using chemiluminescent immunoassays on Abbott Architect automated platforms. In addition, 220 HBsAg-positive samples identified among 5897 samples from the general population of the same regions of Afghanistan were included in the study and tested for both HBsAg and anti-HDV to investigate HDV prevalence in the country. Viral loads of HBV, HCV and HDV were determined in all seropositive samples using Ampliprep/Cobas TaqMan HBV, HCV, Test Roche (CA, USA), and an in-house method, respectively. Out of 492 samples, 31 (6.3%), 136 (27.6%) and 149 (30.3%) were found to be positive for HBsAg, anti-HBs and anti-HBc, respectively. Anti-HDV positivity was detected in five (2.1%) out of 234 HBsAg-positive samples (including 14 of the randomly selected samples that were not among the 220 previously identified as HBsAg positive). Only eight out of 492 (1.6%) subjects were positive for anti-HCV antibodies. Seven out of 489 (1.4%) were positive for anti-HIV-1 antibodies, and three out of 466 cases (0.6%) were positive for anti-HTLV I/II antibodies. These results suggest that Afghanistan is an intermediate endemic region for HBV, HDV and HCV infection. The prevalence of HIV-1 seems to be significantly higher than the global prevalence and that of the eastern Mediterranean region. In addition, the HTLV I/II screening results suggest that these viruses should be monitored in Afghanistan to confirm the trend observed in the current study.

Developing a surface acoustic wave-induced microfluidic cell lysis device for point-of-care DNA amplification.

We developed a microchip device using surface acoustic waves (SAW) and sharp-edge glass microparticles to rapidly lyse low-level cell samples. This microchip features a 13-finger pair interdigital transducer (IDT) with a 30-degree focused angle, creating high-intensity acoustic beams converging 6 mm away at a 16 MHz frequency. Cell lysis is achieved through centrifugal forces acting on Candida albicans cells and glass particles within the focal area. To optimize this SAW-induced streaming, we conducted 42 pilot experiments, varying electrical power, droplet volume, glass particle size, concentration, and lysis time, resulting in optimal conditions: an electrical signal of 2.5 W, a 20 µL sample volume, glass particle size below 10 µm, concentration of 0.2 µg, and a 5-min lysis period. We successfully amplified DNA target fragments directly from the lysate, demonstrating an efficient microchip-based cell lysis method. When combined with an isothermal amplification technique, this technology holds promise for rapid point-of-care (POC) applications.

Sonographic cortical bone thickness measurement: can it predict bone mineral density in the pediatric population?

PURPOSE: To explore sonographic cortical bone thickness (CoT) as a potential indicator of bone mineral density (BMD) measured by dual-energy X-ray absorptiometry for screening and diagnosing pediatric osteoporosis. METHODS: A prospective study included 41 osteopenic or osteoporotic patients and 52 healthy children. Radius cortical thickness (R-CoT), tibial cortical thickness (T-CoT), and second metatarsal cortical thickness (M-CoT) were measured by B-mode ultrasound; CoT values were compared between groups and the correlation between BMD and CoT was examined. RESULTS: There were no significant differences in R-CoT (P = 0.433), T-CoT (P = 0.057), and M-CoT (P = 0.978) values between the patient and control groups. No significant correlations were found between BMD T-scores and R-CoT (r = -0.073, P = 0.490), T-CoT (r = -0.154, P = 0.141), and M-CoT (r = 0.047, P = 0.657) values. CONCLUSION: Sonographic CoT values in children do not correlate with BMD values. Unlike in adults, sonographic CoT measurements do not appear to have a role in assessing BMD in the pediatric population.

Phylogenetic analysis and prevalence of Delta hepatitis among HBsAg carriers in Afghanistan.

The molecular profile of hepatitis Delta in Afghanistan remains unclear yet, therefore this study addresses the genotype of HDV among HBsAg carriers in Afghanistan. In total 234 HBsAg-positive sera were examined by chemiluminescent micro-particle immunoassay to detect Anti-HDV antibodies. Serologically positive samples were later approved via real-time PCR test and subsequently, a 731 bp segment of the HDV Delta antigen RNA region was sequenced in the Illumina platform. The isolates were genotyped via distance matrix/UPGMA analysis using Kimura 2-parameter by MEGA7 software package program. The HBV/HDV coinfection rate among HBsAg carriers in Afghanistan was 2.1%. Finally, 4 samples successfully amplified Hepatitis delta antigen (HDAg) which Later in phylogenetic analysis, all resided in branch genotype I and were stored at GenBank with accession numbers MK799645, MK799646, MK799647, MK799648. The HDV genotypic variations in the Afghan HBsAg carriers may be homogenous and HDV-1 may be the predominant genotype in Afghanistan.

Maternal health literacy and pregnancy outcomes in Afghanistan.

BACKGROUND: A healthy pregnancy and its outcomes are highly dependent on maternal health literacy. This is the first study that targets the association between maternal health literacy and pregnancy outcomes of women in Afghanistan. MATERIALS AND METHODS: This is a cross-sectional study on 200 women who received a prenatal care program and have given birth at Barchi National - 100 beds hospital in Kabul, the capital city of Afghanistan. As a convenient sample, they answered Maternal Health Literacy and Pregnancy Outcome Questionnaire with 5-point Likert scales. We tested the correlation between maternal health literacy and pregnancy outcome scores via the Pearson's correlation coefficient. The potential association of socio-demographic and fertility variables with both maternal health literacy and pregnancy outcome was tested via independent samples t-test or one-way ANOVA. All analysis was performed with a 95% confidence level and a significant level was defined as a P value ≤0.05. RESULTS: The maternal health literacy of Afghan women is inadequate. Maternal health literacy is linked to pregnancy outcome, and both were associated with education level, age, number of gravidities, number of received care, and time that onset the prenatal care. Nutshell, we found evidence of a positive and significant correlation between maternal health literacy and pregnancy outcome. CONCLUSION: This study brings forth the novel data on maternal health literacy of Afghan women, the members of society that face health crises for more than half a century. This study calls for recognition that inadequate maternal health literacy in Afghanistan significantly influences prenatal care quality and perpetuates the biggest challenge for maternal and child health through pregnancy outcomes.

A machine-learning approach for nonalcoholic steatohepatitis susceptibility estimation.

BACKGROUND: Nonalcoholic steatohepatitis (NASH), a severe form of nonalcoholic fatty liver disease, can lead to advanced liver damage and has become an increasingly prominent health problem worldwide. Predictive models for early identification of high-risk individuals could help identify preventive and interventional measures. Traditional epidemiological models with limited predictive power are based on statistical analysis. In the current study, a novel machine-learning approach was developed for individual NASH susceptibility prediction using candidate single nucleotide polymorphisms (SNPs). METHODS: A total of 245 NASH patients and 120 healthy individuals were included in the study. Single nucleotide polymorphism genotypes of candidate genes including two SNPs in the cytochrome P450 family 2 subfamily E member 1 (CYP2E1) gene (rs6413432, rs3813867), two SNPs in the glucokinase regulator (GCKR) gene (rs780094, rs1260326), rs738409 SNP in patatin-like phospholipase domain-containing 3 (PNPLA3), and gender parameters were used to develop models for identifying at-risk individuals. To predict the individual's susceptibility to NASH, nine different machine-learning models were constructed. These models involved two different feature selections including Chi-square, and support vector machine recursive feature elimination (SVM-RFE) and three classification algorithms including k-nearest neighbor (KNN), multi-layer perceptron (MLP), and random forest (RF). All nine machine-learning models were trained using 80% of both the NASH patients and the healthy controls data. The nine machine-learning models were then tested on 20% of both groups. The model's performance was compared for model accuracy, precision, sensitivity, and F measure. RESULTS: Among all nine machine-learning models, the KNN classifier with all features as input showed the highest performance with 86% F measure and 79% accuracy. CONCLUSIONS: Machine learning based on genomic variety may be applicable for estimating an individual's susceptibility for developing NASH among high-risk groups with a high degree of accuracy, precision, and sensitivity.

Molecular epidemiology of Hepatitis B virus, Hepatitis C virus, and Hepatitis D virus in general population of Afghanistan.

BACKGROUND/AIMS: This study gives a clue about genotypes, subgenotypes and subtypes of HBV, HCV and HDV viruses in general population of Afghanistan. MATERIALS AND METHODS: A total of 234 HBsAg, 44 anti-HCV and 5 Anti-Delta positive patients belong to 25-70 age group were obtained through a rapid screening test among 5898 residents of Afghanistan. After quantifying viral load, genotyping of 61 HBV, 29 HCV and 1 HDV samples were accomplished by sequencing of a segment of the HBV Pre S, HCV NS5B, and HDV Delta antigen regions respectively. Clinically important variants of the HBV polymerase gene, the "a" determinant of HBsAg, HCV NS5B and NS3 regions were assessed. RESULTS: All HBV isolates were dispersed throughout the genotype D branch and ayw2 was the only subtypes found. The anti-HDV prevalence among HBsAg positive individuals was 2.2% and the single HDV sample, belonged to HDV genotype I. Analysis of HCV isolates revealed subtype HCV-1b in 75.86%, HCV-3a in 20.69% and HCV-3b in 3.44% patients. The observed mutant variants in the MHR of HBsAg were Y100 15%, Q101 5%, G102 15%, T115 45%, P120 5%, T131 5%. Likewise, S213T 10%, Q215P 5% and N248H 100% mutations were detected in the HBV polymerase region. C316N mutation was prevalent in 72.7% of HCV 1b participants. CONCLUSION: Genotypic variation in Afghan patients is in line with the ones existing in neighboring countries and regions. HBV genotypes D1, subtype ayw2, HDV RNA type I, and HCV RNA genotype 1b are likely to be dominant in Afghan patients.