Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates(Wiley, 2026) Göl, Karan; Ozdarendeli, Aykut; Yetiman, Ahmet E.; Karaman, Melisa Z.; Mujwar, Somdutt; Zanchi, Fernando Berton; Fidan, OzkanThe monkeypox virus (MPXV) has recently risen to be a significant global health threat and currently there are no approved antiviral agents, which makes it necessary to develop new antiviral strategies. In this study, we employed in silico techniques to investigate whether bacteriocins could be potent inhibitors of the MPXV DNA polymerase (MPDP). At first, the MPXV DNA polymerase enzyme chain was extracted from the Cryo-EM structure of MPXV DNA replication complex and was then assessed using SWISS-MODEL/QMEAN for structural quality. The structures of selected bacteriocins were either retrieved from the Protein Data Bank or predicted using AlphaFold. The quality of these predicted models was measured by LGscore. Moreover, the physicochemical properties of the selected bacteriocins, such as Sakacin P and Mundticin KS, were analyzed to assess their molecular stability and compatibility with the molecular docking process. The results of protein-peptide docking simulations on the HADDOCK platform showed that among all the bacteriocins tested, Sakacin P and Mundticin KS had the highest binding affinities toward MPXV DNA polymerase. The analysis of the docking experiments also revealed vital stabilizing interactions, such as the formation of hydrogen bonds, ionic linkages, and pi-pi stacking, which were crucial in the strength of the protein-ligand complexes. Subsequently, the molecular dynamics (MD) simulations further confirmed the stability of the protein-bacteriocin complexes. Our results indicate that bacteriocins, especially Sakacin P and Mundticin KS, can be considered potential antiviral agents against MPXV by interfering with its DNA replication mechanism. The present work shall serve as a reference for future laboratory testing and for the promising innovation of bacteriocin-based drugs targeting MPXV.Conference Object Systematic Evaluation of Data Augmentation Strategies for CNN-Based Image Classification(Institute of Electrical and Electronics Engineers Inc., 2026) Karaköse, Ercan; Kurban, Rifat; Çakiroǧlu, Fatma; Durmuş, AliArticle Stevia Functionalized PVA-Chitosan Membranes as Novel Antimicrobial Wound Dressing Materials(MDPI, 2026) Badem, Merve; Pehlivan, Ilayda; Atakav, Yagmur; Kanbolat, SeydaWound dressings play a crucial role in promoting tissue regeneration while protecting damaged tissue from microbial infections. The aim of this study is to produce antimicrobial PVA-chitosan membranes for wound dressing applications using Stevia rebaudiana Bertoni leaf extract (stevia) as a natural bioactive agent. Although widely recognized as a natural sweetener, stevia contains a high concentration of diterpene glycosides, particularly stevioside and rebaudioside A, together with phenolic compounds that contribute to its biological activities. Therefore, stevia was first evaluated against selected microorganisms and demonstrated effective antimicrobial activity. PVA-chitosan (P/Ch) membranes were prepared by solvent casting method by incorporating different amounts of stevia (P/Ch, P/Ch@20, P/Ch@40, and P/Ch@60). The antimicrobial activity of stevia was also successfully maintained in P/Ch membranes. Good antibacterial activity was observed against Bacillus subtilis and Escherichia coli, whereas the antifungal activity against Candida albicans was comparatively modest. Contact surface analysis showed complete bactericidal activity in Gram-negative and spore-forming bacteria. The cytocompatibility of the membranes was investigated by MTT assay. All formulations maintained a high cell viability (>80%) while the P/Ch@40 membrane increased the metabolic activity to above 100% at higher extract concentrations. In conclusion, stevia-incorporated membranes exhibited high antimicrobial activity, acceptable characteristic properties, and good cytocompatibility, suggesting that they are promising alternative biomaterials for tissue engineering applications.Conference Object Plant Leaf Disease Segmentation Using U-Net++: A Comparative Evaluation with Classical Baselines(Institute of Electrical and Electronics Engineers Inc., 2026) Donmez, Huseyin Cahid; Kurban, Rifat; Ayaz, Vedat; Samet Varel, BurakArticle Overlap Mitigation Versus Classifier Selection in Imbalanced Classification: A Dual-Baseline Analysis(MDPI, 2026) Kaya, Sami; Ünlü, RamazanIn imbalanced binary classification, class overlap forces a familiar fork in the road: refine a preprocessing pipeline, or pivot to classifier selection. Which path dominates has remained empirically open. To address this question, a full factorial experiment was run across 58 KEEL datasets, 11 mitigation techniques, and 10 classifiers (yielding 6960 fitted models in total), with results read through a dual-baseline lens. Against the same classifier without mitigation, the techniques delivered a mean improvement of +4.13 points; gains concentrated on weak learners, with SMOTE and BorderlineSMOTE topping the rankings. Against an honest leave-one-dataset-out (LODO) baseline that selects the strongest standalone classifier from a held-out training pool, mean Delta F1 fell to -4.64 points, and 43.2% of mitigated configurations matched or beat the baseline. Among controllable factors, a Type II ANOVA placed classifier identity at eta(2) = 0.157 against mitigation technique at eta(2) = 0.010, so the choice of algorithm carried roughly sixteen times the explanatory weight of the choice of preprocessing. Dataset characteristics dominated the overall variance at eta(2) = 0.620. The honest LODO selector returned LightGBM on every one of the 58 datasets, suggesting that under typical practitioner conditions, a strong-classifier default is the lower-effort, lower-variance path, with no expected performance cost relative to a pipeline-development investment.Conference Object MACOL-x: Multi-Agent Conflict Learning for xApp Coordination in Open RAN(Institute of Electrical and Electronics Engineers Inc., 2026) Kose, AbdulkadirConference Object Inter-Turn Short Circuit Fault Detection on Permanent Magnet Vernier Machines Through Stray Magnetic Flux(Institute of Electrical and Electronics Engineers Inc., 2026) Atar, Nazif Kerem; Karatepe, Hasan Can; Tekgun, DidemArticle Integrated Virtual Reality Learning Framework with Digital Ecosystem for Enhancing Physics Conceptual Understanding(Cahaya Ilmu Cendekia Publisher, 2026) Nurfitriani, Ressti; Risdianto, Eko; Dewi, Deshinta Arrova; Alshammari, Sultan Hammad; Santos, Joselin; Kuloglu, Esad; Lomerio, NölConference Object Latency-Aware Speaker Identification in Browser Environments: A Comparative Study of Lightweight vs. Deep Architectures(Institute of Electrical and Electronics Engineers Inc., 2026) Cahid Donmez, Huseyin; Varel, Burak Samet; Kurban, Rifat; Ayaz, VedatArticle Genetic Background and Sex Moderate the Effects of Adolescent Nicotine Exposure on Adult Functional Neural Circuits and Behavior(SAGE Publications Ltd, 2026) Zhang, Nanyin; Ünsal, Hayreddin Said; Gould, Thomas J; Novoa, CarlosAdolescence is a critical neurodevelopmental stage marked by heightened plasticity and vulnerability to environmental influences such as nicotine. Nicotine disrupts neural function via nicotinic acetylcholine receptors, leading to long-term impairments in reward processing, cognition, and emotional regulation. While links between adolescent nicotine exposure and adult psychiatric or cognitive deficits are established, the influence of genetics and sex remains unclear. We examined the long-term effects of adolescent nicotine exposure on adult behavior and neural circuitry in male and female C57BL/6J and DBA/2J mice. Nicotine (24 mg/kg/day) or saline was administered via subcutaneous osmotic minipumps from postnatal day 37 for 12 days. Behavioral assessments 4 weeks later included the elevated plus maze for anxiety-related behavior and the open field test for locomotor activity after acute nicotine (0.81 mg/kg). Resting-state functional magnetic resonance imaging evaluated brain connectivity changes. Nicotine exposure altered both behavior and functional connectivity, depending on strain and sex. Adult female C57BL/6J mice exposed to nicotine during adolescence had lower anxiety-like behavior and higher locomotor activity, along with increased striatal-hippocampal connectivity, suggesting adaptations either directly related to nicotine exposure or compensatory adaptations. In contrast, adult female DBA/2J mice exposed to nicotine during adolescence showed widespread disruptions in cortico-striatal-thalamic, polymodal association, and hippocampal networks critical for cognitive and emotional regulation. Overall, greater effects were seen in female mice. Findings reveal that adolescent nicotine exposure drives enduring, strain- and sex-dependent changes in adult brain connectivity and behavior. Considering genetics and sex is essential for tailoring interventions for nicotine addiction and its neuropsychiatric consequences.