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Article Citation - WoS: 6Synthesis and Biological Study of Novel Indole-3 Derivatives as Src Kinase and Glutathione S-Transferase Inhibitors(Bentham Science Publ Ltd, 2013) Kurt, Z. Kilic; Aydin, D.; Isgor, Y. G.; Isgor, B. S.; Olgen, S.The aim of this study is to design and synthesize novel dual inhibitors of Src protein tyrosine kinase (PTK) and Glutathione S-transferases (GSTs), as a potential drug lead with therapeutic efficacy on cancer and immune disorders. The biological activity profiling of small molecule inhibitors via miniaturized biochemical techniques compatible with medium throughput screening and focused screening methodologies were performed. To determining the effects of small molecule inhibitors on Src kinase and Phase II detoxification enzyme GST isozymes in liver homogenates used to verify their roles in drug resistance mechanism for cancer chemotherapeutics. In this study, 14 indole-3-imine-2-on and N-benzyl indole-3-imine-2-on derivatives were synthesized for dual activities against Src and GST. The chemical structures and purities of compounds were verified by IR, H-1 NMR, MASS spectroscopy, and elemental analysis. The compounds 2, 3 and 9 are found slightly active against both enzyme Src and GST.Article Comparison of Amiodarone Loading Dosage in the Treatment of Postoperative Atrial Fibrillation: High Versus Standard Dose Treatment(Bentham Science Publ Ltd, 2024) Sarıçam, E.; Öcal, A.; Iscanlı, M.D.; Bozkurt, E.; Ilkay, E.; Cantekin, ÖF.BACKGROUND: Postoperative atrial fibrillation (POAF) is associated with poor outcomes, including hemodynamic instability, stroke, myocardial infarction, and death. In hemodynamic stable patients, the rhythm-control strategy is more advantageous than rate control. Current standard intravenous amiodarone administration has limited success and a delayed effect; the acute success rate is 44% (8-12 h to several days). PURPOSE: The aim of this study was to evaluate the effectiveness of higher amiodarone loading dosage to restore sinus rhythm in patients with POAF after noncardiac surgery. METHODS: This is a prospective, randomized, controlled single-center study. The study included 39 patients with POAF, divided into group I (n=27) (intravenous 600 mg amiodarone loading dosage over 2 h and infusion of 50 mg/h over a 24-h period) and group II (n=12) (standard protocol; 300 mg of bolus intravenously in 30 min and infusion of 50 mg/h over a 24-h period). The primary endpoint of the study was a restoration of sinus rhythm at the 24th hour. RESULTS: Baseline clinical, laboratory and echocardiographic characteristics of both groups were similar. The patients with higher loading amiodarone dosage had earlier restoration of sinus rhythm (2.38 ± 1.41 vs 8.66 ± 2.87 h, respectively; p=0.015). There was no significant difference in achieving sinus rhythm at the 24th hour between both groups. CONCLUSION: Higher loading amiodarone dosage increased early conversions to sinus rhythm compared with standard amiodarone protocol in patients with POAF. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.Article Citation - WoS: 3Citation - Scopus: 3Predicted Sars-Cov Mirnas Associated With Epigenetic Viral Pathoge-Nesis and the Detection of New Possible Drugs for Covid-19(Bentham Science Publ Ltd, 2021) Cetin, Zafer; Bayrak, Tuncay; Ogul, Hasan; Saygili, Eyup Ilker; Akkol, Esra KupeliObjective: The outbreak of COVID-19 caused by SARS-CoV-2 has promptly spread worldwide. This study aimed to predict mature miRNA sequences in the SARS-CoV-2 genome, their effects on protein-protein interactions in the affected cells, and gene-drug relationships to detect possible drug candidates. Methods: Viral hairpin structure prediction, classification of hairpins, mutational examination of precursor miRNA candidate sequences, Minimum Free Energy (MFE) and regional entropy analysis, mature miRNA sequences, target gene prediction, gene ontology enrichment, and Protein-Protein Interaction (PPI) analysis, and gene-drug interactions were performed. Results: A total of 62 candidate hairpins were detected by VMir analysis. Three hairpin structures were classified as true precursor miRNAs by miRBoost. Five different mutations were detected in precursor miRNA sequences in 100 SARS-CoV-2 viral genomes. Mutations slightly elevated MFE values and entropy in precursor miRNAs. Gene ontology terms associated with fibrotic pathways and immune system were found to be enriched in PANTHER, KEGG and Wiki pathway analysis. PPI analysis showed a network between 60 genes. CytoHubba analysis showed SMAD1 as a hub gene in the network. The targets of the predicted miRNAs, FAM214A, PPM1E, NUFIP2 and FAT4, were downregulated in SARS-CoV-2 infected A549 cells. Conclusion: miRNAs in the SARS-CoV-2 virus genome may contribute to the emergence of the Covid-19 infection by activating pathways associated with fibrosis in the cells infected by the virus and modulating the innate immune system. The hub protein between these pathways may be the SMAD1, which has an effective role in TGF signal transduction.Article Citation - WoS: 9Citation - Scopus: 9Benchmarking Classification Models for Cell Viability on Novel Cancer Image Datasets(Bentham Science Publ Ltd, 2019) Ozkan, Akin; Isgor, Sultan Belgin; Sengul, Gokhan; Isgor, Yasemin GulgunBackground: Dye-exclusion based cell viability analysis has been broadly used in cell biology including anticancer drug discovery studies. Viability analysis refers to the whole decision making process for the distinction of dead cells from live ones. Basically, cell culture samples are dyed with a special stain called trypan blue, so that the dead cells are selectively colored to darkish. This distinction provides critical information that may be used to expose influences of the studied drug on considering cell culture including cancer. Examiner's experience and tiredness substantially affect the consistency throughout the manual observation of cell viability. The unsteady results of cell viability may end up with biased experimental results accordingly. Therefore, a machine learning based automated decision-making procedure is inevitably needed to improve consistency of the cell viability analysis. Objective: In this study, we investigate various combinations of classifiers and feature extractors (i.e. classification models) to maximize the performance of computer vision-based viability analysis. Method: The classification models are tested on novel hemocytometer image datasets which contain two types of cancer cell images, namely, caucasian promyelocytic leukemia (HL60), and chronic myelogenous leukemia (K562). Results: From the experimental results, k-Nearest Neighbor (KNN) and Random Forest (RF) by combining Local Phase Quantization (LPQ) achieve the lowest misclassification rates that are 0.031 and 0.082, respectively. Conclusion: The experimental results show that KNN and RF with LPQ can be powerful alternatives to the conventional manual cell viability analysis. Also, the collected datasets are released from the "biochem.atilim.edu.tr/datasets/ " web address publically to academic studies.Article Toxoplasma gondii Coinfection in HIV-Positive Patients at a Tertiary Care Hospital(Bentham Science Publ Ltd, 2025) Kurkcu, Muhammed Furkan; Bakir, Ayfer; Kaba, Semiha Berra Topsakal; Kusabbi, Ilknur Alkan; Usluca, SelmaIntroduction: Toxoplasma gondii (T. gondii) can cause serious complications in both immunocompetent and immunosuppressed individuals. This study aims to assess the seroprevalence of T. gondii among HIV-positive individuals and to investigate its association with age, sex, CD4+ T cell count, HIV RNA levels, and hematological parameters. Methods: This study included 247 HIV-positive individuals followed up at a tertiary care hospital between November 1, 2022, and November 30, 2024. We analyzed serum samples for T. gondii IgG antibodies using electrochemiluminescent microparticle immunoassay. Results: The prevalence of T. gondii IgG seropositivity was found to be 32.8% (n=81; 95% CI: 26.9-39). The median age of seropositive individuals was 52 years (IQR: 42-61), which was significantly higher compared to seronegative individuals (p<0.001). The highest IgG seropositivity rate (66.7%) was observed in the 61-80 age group. Hemoglobin levels were significantly lower in IgG seropositive individuals (p=0.040). Logistic regression analysis indicated an increased risk of T. gondii infection with advancing age. The odds ratio for the 41-60 age group was 13.3 (95% CI: 1.6-106, p=0.02), while for the 61-80 age group, it was 28 (95% CI: 3.3-240, p=0.002). Discussion: The seroprevalence of T. gondii in HIV-positive individuals was lower than both global and regional averages. Age was identified as an independent risk factor for T. gondii seropositivity. Additionally, hematological alterations associated with anemia were observed in seropositive individuals. Further large-scale, multi-center, and regionally representative studies are required to optimize T. gondii infection management and screening strategies in people living with HIV. Conclusion: These findings suggest that T. gondii infection in HIV-positive individuals increases with age and may be associated with anemia, highlighting the need for age-focused screening and management strategies.Article Clinical and Laboratory Evaluation of Acute Pericarditis Associated With Antinuclear Antibodies Positivity(Bentham Science Publ Ltd, 2023) Dursun, Ali Dogan; Saricam, Ersin; Erdem, Hakan; Sariyildiz, Gulcin Turkmen; Ozyer, Esref Umut; Bozkurt, Engin; Cantekin, Omer FarukBackground Up to 30% of patients with acute pericarditis develop recurrent pericarditis. Acute pericarditis may be a manifestation of an underlying systemic autoimmune disease. Therefore, we evaluated the characteristics of patients with acute pericarditis according to antinuclear antibodies (ANA) positivity/negativity. Methods Participants with acute pericarditis and negative ANA (n=29), recurrent pericarditis with positive ANA (n=30) and healthy controls (n=11) were examined. The groups were compared using serum parameters (ANA, C-reactive protein, leucocyte count, erythrocyte sedimentation rate, total antioxidant status, nitric oxide (NO), and oxidative stress index (OSI)) and imaging techniques (electrocardiogram, echocardiography, cardiovascular magnetic resonance, and venous Doppler ultrasound). Results In females, acute pericarditis associated with ANA occurred more frequently (p<0.001). ANA-positive acute pericarditis had significantly lower NO and OSI (p<0.05 and p<0.001, respectively) and pericardial inflammation on magnetic resonance. We found a pulmonary embolism in one patient with positive ANA. Slow venous flow (SVF) occurred more often in acute pericarditis associated with ANA than in the ANA-negative group on venous ultrasound (p<0.05). The prevalence of positive ANAs was 1.6 times higher among SVF patients than in controls. Conclusion This study suggests that acute pericarditis associated with ANA is more common in middle-aged females. SVF and lower oxidative stress tests were more common in patients with ANA-associated acute pericarditis. Acute pericarditis associated with ANA could be considered as a hypercoagulable state. Therefore, all newly diagnosed pericarditis patients (especially females) should be checked for ANA positivity. Awareness of this coexistence should be promptly addressed to establish management strategies.
