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Öğe Comprehensive Review of Transcriptomics (RNAs) Workflows from Blood Specimens(Taylor & Francis Inc, 2022) Husseini, Abbas Ali; Derakhshandeh, Masoud; Tatlisu, Nevruz BernaBlood is the most interesting tissue for molecular analysis in a wide range of diseases since it provides accumulative information of the whole body state. Transcriptomic analysis of the blood is one of the most favorable omics approaches for clinical and research purposes. However, blood sample preparation for RNA analyses is highly diverse encompassing specific methodology and application. In this study, we review the common sample preparation maneuvers including RNA handling techniques, sample collection and stabilization, blood cell sorting, extracellular vesicle enrichment, RNA extraction, globin/ribosomal RNA reduction, and RNA concentration and quality assessment. These techniques are the most prevalent procedures of blood sample preparation in RNA transcriptomic analyses. The methodologies, technical challenges of the current approaches, and latest advances in the field are discussed in detail.Öğe COVID-19 Disease and Interferon-gamma: Has it a Protective Impact on Mortality?(ERCIYES UNIV SCH MEDICINE, ERCIYES UNIV TIP FAK 38039 MELIKGAZI, KAYSERI 00000, TURKEY, 2021) Husseini, Abbas Ali; Kamil, Anton Abdulbasah; Aloudal, Mohammad RezaThe complex coincidence of several immunopathological, socio-cultural, and health infrastructure factors may affect the COVID-19 related mortality among different populations. The impact of the age on disease progression has been confirmed in several studies. Recently limited ecological and clinical studies have sparked controversy among researchers about the protective impact of the non-specific effect of routinely used Bacille Calmette-Guerin (BCG), Hepatitis A virus (HAV), and influenza (Flu) vaccines or their natural infections against COVID-19. In the present study, variables, including BCG vaccination coverage, HAV prevalence, and population age distributions, from 59 countries were analyzed to examine their potential association with COVID-19 infection and related mortality rate. Concerning COVID-19 cases/million population (1MP) and mortality, there are significant differences between countries with and without BCG vaccination programs (p-value <0.001). A significant negative correlation between both BCG coverage and HAV prevalence with COVID-19 related mortality was also found (r (59)=-0.4, p-value <0.05), (r (59) =-0.3, p-value <0.01). Based on the results of the present study, previous ecological analyses and available epidemiological evidence, along with knowledge of the immune response to BCG, HAV and influenza vaccination, as well as COVID-19 infection progression, the current study suggest a hypothesis that IFN-? induced immune response which could be triggered by BCG, HAV, and flu vaccination or natural infections may have a protective effect against COVID-19 related mortality.Öğe Developing a surface acoustic wave-induced microfluidic cell lysis device for point-of-care DNA amplification(Wiley, 2024) Husseini, Abbas Ali; Yazdani, Ali Mohammad; Ghadiri, Fatemeh; Sisman, AlperWe 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 mu L sample volume, glass particle size below 10 mu m, concentration of 0.2 mu g, 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.Öğe Development of an Ultra-Sensitive Magnetic-Based Biosensor; a Simulation Study(Institute of Electrical and Electronics Engineers Inc., 2023) Yahya, Khalid; Husseini, Abbas Ali; Dirican, Onur; Attar, Hani; Aldababsa, Mahmoud; Hafez, MohamedThis study presents an advanced magnetic biosensor design incorporating an L-shaped ferromagnetic core with UL dimensions and an air gap replaced by highly porous aluminum or copper foam later-filled biological samples containing high-permeability ferromagnetic nanoparticles. The sensor detects specific biological molecules through magnetic field interactions. The system's electrical parameters were methodically optimized for enhanced performance. The research investigated the impact of various materials on the air gap's magnetic properties and assessed the relationships between permeability, output-induced voltage, input voltage, and input frequency. Findings indicate that using materials with higher magnetic permeability, such as Magnetite (Fe304) or Cobalt ferrite (CoFe2O4) ferrofluids, considerably improved the biosensor's performance by optimizing magnetic coupling between primary and secondary windings. This innovative magnetic biosensor holds potential for diverse applications, including medical diagnostics, environmental monitoring, and industrial process control. The study offers valuable insights into magnetic biosensor design and optimization, facilitating heightened sensitivity and selectivity in detecting target molecules. © 2023 IEEE.Öğe Estimating COVID-19 Dynamics in Afghanistan(ERCİYES ÜNİVERSİTESİ TIP FAKÜLTESİ, 2020) Husseini, Abbas Ali; Kamil, Anton AbdulbasahLittle reliable information on novel coronavirus (COVID-19) outbreak is available from war-torn countries, including Afghanistan. The current study estimates the pandemic features based on currently available data to forecasting future challenges of preventive strategies and emergency response using mathematical modeling. The infection fatality and recovery rates were estimated by 1.8% and 20.8%, respectively. The average growth rates of infection, death, and recovery among the Afghanistan population were estimated as 0.2, 0.2, and 0.5, respectively. Also, it was estimated that approximately 6 million people infected in the urban area, which may lead to approximately 11 thousand deaths. However, the features of the pandemic, marks that Afghanistan needs more time to pass the pandemic. Along with this, inadequate community engagement and low abiding to health advice, including social distancing, lack of personnel and testing capacities in the provinces, shortage of laboratory testing supplies, insufficient infection prevention, and control measures in health facilities in some of the provinces, limited access to and response capacities are the main challenges to fight against COVID-19. Therefore, the majority of infected cases and deaths may not be reported, and preventive strategies effectively in Afghanistan could severely be disrupted by several socio-cultural, financial, political, and administrative obstacles.Öğe Genotypic variation in CYP2E1, GCKR, and PNPLA3 among nonalcoholic steatohepatitis patients of Turkish origin(Springer, 2024) Husseini, Abbas AliBackgroundThis study examines genetic variations in CYP2E1 (rs6413432, rs3813867), GCKR (rs780094, rs1260326), and PNPLA3 (rs738409) among Turkish patients to assess their influence on nonalcoholic steatohepatitis.MethodsAllele 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.ResultsNo 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.ConclusionsVariants 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.Öğe A machine-learning approach for nonalcoholic steatohepatitis susceptibility estimation(SPRINGER INDIA, 7TH FLOOR, VIJAYA BUILDING, 17, BARAKHAMBA ROAD, NEW DELHI 110 001, INDIA, 2022) Ghadiri, Fatemeh; Husseini, Abbas Ali; Öztaş, OğuzhanBackground 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 highrisk 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 patatinlike 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.Öğe Maternal health literacy and pregnancy outcomes in Afghanistan(WOLTERS KLUWER MEDKNOW PUBLICATIONS, WOLTERS KLUWER INDIA PVT LTD, A-202, 2ND FLR, QUBE, C T S NO 1498A-2 VILLAGE MAROL, ANDHERI EAST, MUMBAI, Maharashtra 400059, INDIA, 2022) Rostamzadeh, Mehran; Ezadi, Zainab; Hosseini, Maryam; Husseini, Abbas AliBACKGROUND: 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.Öğe Molecular epidemiology of Hepatitis B virus, Hepatitis C virus, and Hepatitis D virus in general population of Afghanistan(AVES, BÜYÜKDERE CAD 105-9, MECİDİYEKÖY, ŞİŞLİ, ISTANBUL 34394, TURKEY, 2020) Husseini, Abbas Ali; Saeed, Khwaja Mir Islam; Yurdcu, Esra; Bozdayı, A. MithatBackground/Aims: This study gives a clue about genotypes, subgenotypes, and subtypes of hepatitis B (HBV), Hepatitis C (HCV), and Hepatitis D (HDV) viruses in general population of Afghanistan. Materials and Methods: A total of 234 Hepatitis B surface antigen (HBsAg), 44 anti-HCV, and 5 antidelta positive patients from 25–70- age group were studied 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, from HDV genotype I. Analysis of HCV isolates revealed subtype HCV genotype 1b (HCV-1b) in 75.86%, HCV-3a in 20.69%, and HCV-3b in 3.44% patients. The observed mutant variants in the major hydrophilic region (MHR) of HBsAg were Y100 15%, Q101 5%, G102 15%, T115 45%, P120 5%, and 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.Öğe Optimization of a rapid and sensitive nucleic acid lateral flow biosensor for hepatitis B virus detection(Springer, 2023) Husseini, Abbas Ali; Baydar, Serap YesilkirBackground and objectiveThe 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.MethodsThe 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 & DEG;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 10(8) IU/ml.ResultsThe optimization of the LAMP reaction was achieved at a temperature of 67 & DEG;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 10(8) IU/ml to 10(1) 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 10(3) IU/ml.ConclusionIn 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.Öğe Phylogenetic analysis and prevalence of Delta hepatitis among HBsAg carriers in Afghanistan(Shiraz University, 2022) Husseini, Abbas Ali; Rostamzadeh, MehranThe 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 © 2022, Molecular Biology Research Communications.All Rights Reserved.Öğe Sonographic cortical bone thickness measurement: can it predict bone mineral density in the pediatric population?(Turkish Soc Radiology, 2024) Isin, Ugur Ufuk; Cakmakci, Emin; Bulus, Ayse Derya; Yasartekin, Yuksel; Unal, Oznur; Dirican, Onur; Husseini, Abbas AliPURPOSE 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.Öğe Synthesis, Molecular Modeling and Biological Assessment of Aryloxymethyl 1,3,4-Thiadiazole and 1,2,4-Triazole-5-Thione Derivatives as Potential Cox Inhibitors(Springer, 2024) Shirzad, Mohammad Musa; Ozadali-Sari, Keriman; Unsal-Tan, Oya; Husseini, Abbas Ali; Palaska, ErhanThiadiazole and triazole-5-thione derivatives are five membered heterocyclic compounds showing cyclooxygenase inhibition activities. Based on this observation a series of novel aryloxymethyl 1,3,4-thiadiazole and 1,2,4-triazole-5-thione derivatives were synthesized and their biological activities evaluated. The suggested chemical structure of synthesized compounds was confirmed using FT-IR, Mass, 1H-NMR, and 13C-NMR spectrometric methods and elemental analysis. The biological activity or potency of synthesized compounds was evaluated using a COX inhibitor screening assay kit (Cayman Chemical Company), and indomethacin and NS398 as standard compounds. Compounds 2b and 3b showed good inhibitory activity against COX-2 and COX-1 enzymes respectively. The obtained data indicate that compound 2b is more selective to COX-2 and compound 3b is more selective to COX-1 compared with other synthesized compounds. These two compounds show promising selectivity and could be a starting point for future research in this area.Öğe Unveiling the etiological impact of GST-M1, GST-T1, and P53 genotypic variations on brain carcinogenesis(SPRINGERVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS, 2024) Dirican, Onur; Kaygın, Pınar; Oğuztüzün, Serpil; Husseini, Abbas Ali; Yılmaz Sarıaltın, Sezen; Yılmaz, Can; Ünlü, Nihan; İzci, YusufBackground 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, GSTT1, 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 (?2=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 (?2=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 (?²=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.
