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Article Citation - WoS: 5Citation - Scopus: 6A Novel Deep Learning-Based Framework With Particle Swarm Optimisation for Intrusion Detection in Computer Networks(Public Library Science, 2025) Yilmaz, Abdullah AsimIntrusion detection plays a significant role in the provision of information security. The most critical element is the ability to precisely identify different types of intrusions into the network. However, the detection of intrusions poses a important challenge, as many new types of intrusion are now generated by cyber-attackers every day. A robust system is still elusive, despite the various strategies that have been proposed in recent years. Hence, a novel deep-learning-based architecture for detecting intrusions into a computer network is proposed in this paper. The aim is to construct a hybrid system that enhances the efficiency and accuracy of intrusion detection. The main contribution of our work is a novel deep learning-based hybrid architecture in which PSO is used for hyperparameter optimisation and three well-known pre-trained network models are combined in an optimised way. The suggested method involves six key stages: data gathering, pre-processing, deep neural network (DNN) architecture design, optimisation of hyperparameters, training, and evaluation of the trained DNN. To verify the superiority of the suggested method over alternative state-of-the-art schemes, it was evaluated on the KDDCUP'99, NSL-KDD and UNSW-NB15 datasets. Our empirical findings show that the proposed model successfully and correctly classifies different types of attacks with 82.44%, 90.42% and 93.55% accuracy values obtained on UNSW-B15, NSL-KDD and KDDCUP'99 datasets, respectively, and outperforms alternative schemes in the literature.Article Citation - WoS: 58Two-Dimensional Fluorinated Boron Sheets: Mechanical, Electronic, and Thermal Properties(Amer Chemical Soc, 2018) Pekoz, Rengin; Konuk, Mine; Kilic, M. Emin; Durgun, EnginThe synthesis of atomically thin boron sheets on a silver substrate opened a new area in the field of two-dimensional systems. Similar to hydrogenated and halogenated graphene, the uniform coating of borophene with fluorine atoms can lead to new derivatives of borophene with novel properties. In this respect, we explore the possible structures of fluorinated borophene for varying levels of coverage (BnF) by using first-principles methods. Following the structural optimizations, phonon spectrum analysis and ab initio molecular dynamics simulations are performed to reveal the stability of the obtained structures. Our results indicate that while fully fluorinated borophene (BF) cannot be obtained, stable configurations with lower coverage levels (B4F and B2F) can be attained. Unveiling the stable structures, we explore the mechanical, electronic, and thermal properties of (BnF). Fluorination significantly alters the mechanical properties of the system, and remarkable results, including direction-dependent variation of Young's modulus and a switch from a negative to positive Poisson's ratio, are obtained. However, the metallic character is preserved for low coverage levels, and metal to semiconductor transition is obtained for B2F. The heat capacity at a low temperature increases with an increasing F atom amount but converges to the same limiting value at high temperatures. The enhanced stability and unique properties of fluorinated borophene make it a promising material for various high-technology applications in reduced dimensions.Article Citation - WoS: 9Citation - Scopus: 15Therapeutic Efficacy of Boric Acid Treatment on Brain Tissue and Cognitive Functions in Rats With Experimental Alzheimer's Disease(Dove Medical Press Ltd, 2023) Ozdemir, Cagri; Arslan, Mustafa; Kucuk, Aysegul; Yigman, Zeynep; Dursun, Ali DoganIntroduction: Oxidative stress has an important role in the pathophysiology of Alzheimer's disease (AD), the most common type of dementia. Boric acid (BA) contributes significantly to the protection of the brain by reducing lipid peroxidation and supporting antioxidant defense. We aimed to evaluate the therapeutic potential of BA treatment in AD rats. Materials and Methods: Four groups were formed as Control (C), Alzheimer's (A), Alzheimer's + Boric acid (ABA), Boric acid (BA). Intracerebroventricular injection of Streptozotocin (STZ) was preferred to create an AD. After 4 weeks, BA was applied 3 times every other day. The Radial Arm Maze Test (RAMT) was used to evaluate memory and learning abilities. Biochemical and histopathological evaluations were made in the hippocampus. Results: Initial RAMT inlet/outlet (I/O) numbers were similar. Two weeks after STZ injection, I/O numbers decreased in group A and ABA compared to group C and BA (p<0.05). After the second BA application, I/O numbers increased in the ABA group compared to the A group (p<0.05). In group A, PON-1, TOS and OSI levels were higher and TAS levels were lower than in groups BA and C. After BA treatment, PON-1 and OSI levels were lower in the ABA group than in the A group (p<0.05). Although there was an increase in TAS value and a decrease in TOS, this did not make a statistical difference. The thickness of the pyramidal cell in CA1 and the granular cell layers in the dentate gyrus, and the number of intact and degenerated neurons in the pyramidal cell layer were similar between the groups. Discussion: Significant improvement in learning and memory abilities after BA application is promising for AD. Conclusion: These results show that BA application positively affects learning and memory abilities, and reduces oxidative stress. More extensive studies are required to evaluate histopathological efficacy.Article Effects of Pomegranate Seed Oil on Lower Extremity Ischemia-Reperfusion Damage: Insights into Oxidative Stress, Inflammation, and Cell Death(MDPI, 2025) Bozok, Ummu Gulsen; Ergorun, Aydan Iremnur; Kucuk, Aysegul; Yigman, Zeynep; Dursun, Ali Dogan; Arslan, MustafaAim: This study sought to clarify the therapeutic benefits and mechanisms of action of pomegranate seed oil (PSO) in instances of ischemia–reperfusion (IR) damage in the lower extremities. Materials and Methods: The sample size was determined, then 32 rats were randomly allocated to four groups: Control (C), ischemia–reperfusion (IR), low-dose PSO (IR + LD, 0.15 mL/kg), and high-dose PSO (IR + HD, 0.30 mL/kg). The ischemia model in the IR group was established by occluding the infrarenal aorta for 120 min. Prior to reperfusion, PSO was delivered to the IR + LD and IR + HD groups at doses of 0.15 mL/kg and 0.30 mL/kg, respectively, followed by a 120 min reperfusion period. Subsequently, blood and tissue specimens were obtained. Statistical investigation was executed utilizing Statistical Package for the Social Sciences version 20.0 (SPSS, IBM Corp., Armonk, NY, USA). Results: Biochemical tests revealed significant variations in total antioxidant level (TAS), total oxidant level (TOS), and the oxidative stress index (OSI) across the groups (p < 0.0001). The IR group had elevated TOS and OSI levels, whereas PSO therapy resulted in a reduction in these values (p < 0.05). As opposed to the IR group, TASs were higher in the PSO-treated groups. Histopathological analysis demonstrated muscle fiber degeneration, interstitial edema, and the infiltration of cells associated with inflammation in the IR group, with analogous results noted in the PSO treatment groups. Immunohistochemical analysis revealed that the expressions of Tumor Necrosis Factor-alpha (TNF-α), Nuclear Factor kappa B (NF-κB), cytochrome C (CYT C), and caspase 3 (CASP3) were elevated in the IR group, while PSO treatment diminished these markers and attenuated inflammation and apoptosis (p < 0.05). The findings demonstrate that PSO has a dose-dependent impact on IR injury. Discussion: This research indicates that PSO has significant protective benefits against IR injury in the lower extremities. PSO mitigated tissue damage and maintained mitochondrial integrity by addressing oxidative stress, inflammation, and apoptotic pathways. Particularly, high-dose PSO yielded more substantial enhancements in these processes and exhibited outcomes most comparable to the control group in biochemical, histological, and immunohistochemical investigations. These findings underscore the potential of PSO as an efficacious natural treatment agent for IR injury. Nevertheless, additional research is required to articulate this definitively.Article Citation - WoS: 2Citation - Scopus: 2Potential Role of SGLT-2 Inhibitors in Improving Allograft Function and Reducing Rejection in Kidney Transplantation(Wiley, 2025) Demir, Mehmet Emin; Helvaci, Ozant; Yildirim, Tolga; Merhametsiz, Ozgur; Sezer, SirenSodium-glucose cotransporter-2 inhibitors (SGLT-2i) have demonstrated renoprotective and cardioprotective benefits beyond their antiglycemic effects. Their potential utility in kidney transplant recipients (KTRs) for preserving graft function and reducing rejection risk is currently under active investigation. Preliminary studies indicate that SGLT-2i therapy stabilizes estimated glomerular filtration rate (eGFR), decreases glomerular hyperfiltration, and improves metabolic outcomes in KTRs. Emerging clinical evidence also suggests that SGLT-2i may be associated with reduced rates of acute rejection, although direct immunosuppressive actions remain unclear. Experimental findings further suggest that SGLT-2i modulates gene regulation pathways involved in inflammation, oxidative stress, and fibrosis, contributing to improved allograft outcomes. Current safety data in KTRs are reassuring, without significant increases in urinary tract infections or adverse graft events. Nevertheless, long-term prospective studies specific to transplant populations are lacking. This review summarizes available evidence regarding the mechanisms of action, clinical efficacy, and safety profile of SGLT-2i in kidney transplantation, emphasizing their metabolic, hemodynamic, inflammatory, and immunomodulatory effects.Article Citation - WoS: 23Citation - Scopus: 26Reconstruction of 3d Object Shape Using Hybrid Modular Neural Network Architecture Trained on 3d Models From Shapenetcore Dataset(Mdpi, 2019) Kulikajevas, Audrius; Maskeliunas, Rytis; Damasevicius, Robertas; Misra, SanjayDepth-based reconstruction of three-dimensional (3D) shape of objects is one of core problems in computer vision with a lot of commercial applications. However, the 3D scanning for point cloud-based video streaming is expensive and is generally unattainable to an average user due to required setup of multiple depth sensors. We propose a novel hybrid modular artificial neural network (ANN) architecture, which can reconstruct smooth polygonal meshes from a single depth frame, using a priori knowledge. The architecture of neural network consists of separate nodes for recognition of object type and reconstruction thus allowing for easy retraining and extension for new object types. We performed recognition of nine real-world objects using the neural network trained on the ShapeNetCore model dataset. The results evaluated quantitatively using the Intersection-over-Union (IoU), Completeness, Correctness and Quality metrics, and qualitative evaluation by visual inspection demonstrate the robustness of the proposed architecture with respect to different viewing angles and illumination conditions.Article Citation - WoS: 3Citation - Scopus: 3Characterization of Mesenchymal Stem Cells in Mucolipidosis Type Ii (i-Cell Disease)(Tubitak Scientific & Technological Research Council Turkey, 2019) Köse, Sevil; Kaya, Fatima Aerts; Kuşkonmaz, Bülent Barış; Çetinkaya, Duygu UçkanMucolipidosis type II (ML-II, I-cell disease) is a fatal inherited lysosomal storage disease caused by a deficiency of theenzyme N-acetylglucosamine-1-phosphotransferase. A characteristic skeletal phenotype is one of the many clinical manifestationsof ML-II. Since the mechanisms underlying these skeletal defects in ML-II are not completely understood, we hypothesized that adefect in osteogenic differentiation of ML-II bone marrow mesenchymal stem cells (BM-MSCs) might be responsible for this skeletalphenotype. Here, we assessed and characterized the cellular phenotype of BM-MSCs from a ML-II patient before (BBMT) and afterBM transplantation (ABMT), and we compared the results with BM-MSCs from a carrier and a healthy donor. Morphologically, wedid not observe differences in ML-II BBMT and ABMT or carrier MSCs in terms of size or granularity. Osteogenic differentiation wasnot markedly affected by disease or carrier status. Adipogenic differentiation was increased in BBMT ML-II MSCs, but chondrogenicdifferentiation was decreased in both BBMT and ABMT ML-II MSCs. Immunophenotypically no significant differences were observedbetween the samples. Interestingly, the proliferative capacity of BBMT and ABMT ML-II MSCs was increased in comparison to MSCsfrom age-matched healthy donors. These data suggest that MSCs are not likely to cause the skeletal phenotype observed in ML-II, butthey may contribute to the pathogenesis of ML-II as a result of lysosomal storage-induced pathology.Article Citation - WoS: 9Citation - Scopus: 13The Evaluation of Oxidative Stress in the Young Adults With Covid-19 Mrna Vaccines Induced Acute Pericarditis- Myopericarditis(Dove Medical Press Ltd, 2022) Dursun, Ali Dogan; Saricam, Ersin; Sariyildiz, Gulcin Turkmen; Iscanli, Murat Dogan; Cantekin, Omer FarukBackground: During COVID-19 pandemic, several vaccines have been developed such as mRNA vaccines. However, acute pericarditis and myocarditis/myopericarditis cases have been described after mRNA vaccination. The mechanism for the development of cardiac involvement is unknown. Potential mechanism for oxidative stress associated with vaccine-induced heart involvement is unidentified. This study aimed to examine the role of oxidative stress and the heart involvement in young adults vaccinated with COVID-19 mRNA vaccines. Methods: In this cross-sectional study, a total of 23 participants were included and 10 of these participants were asymptomatic patients (control group). Comparison of the cardiac involvement and control group was made by using troponin I, C-reactive protein (hsCRP), D-dimer levels, and oxidative stress tests including nitric oxide, and imaging techniques (ECG, echocardiography, cardiovascular magnetic resonance). Results: The median age of acute pericarditis group (10 patients) was 22 years (Q1-Q3: 18.5-31), and the mean age was 24.4 +/- 7.5 years. The median age of myopericarditis group (3 patients) was 22 years (Q1-Q3 18.0-25.0), and the mean age was 21.6 +/- 3.5 years. All the myopericarditis cases were male. The patients with myopericarditis had higher troponin I level, hsCRP, and D-dimer levels (troponin I level; 1600.00 ng/mL; D-dimer; 1.20 mu g/mL, hsCRP; 3.0 mg/L, respectively; p < 0.05). Serum nitric oxide levels and OSI (total oxidant status, H2O2/total antioxidant status) were lower in myopericarditis group than the control and acute pericarditis group (p < 0.05). This shows inflammatory and procoagulant state. Conclusion: Vaccine-induced myopericarditis cases are associated with oxidative stress test abnormality (abnormal NO, OSI levels). However, there is no relationship between NO levels and other oxidative stress tests difference in vaccine-induced acute pericarditis. It is thought that vaccine-induced pericarditis and myopericarditis could have different pathogenesis. This could make it necessary to reassess the second dose of vaccination for vaccine-induced cardiac involvement cases.Article Citation - WoS: 5Citation - Scopus: 5Maternal Pain Management at Home in Children with Cancer: A Turkish Sample(Elsevier Science inc, 2020) Boztepe, Handan; Ay, Ayse; Akyuz, CananPurpose: The purpose of the present study was to examine maternal pain management in children with cancer and the associated factors. Design and methods: The present work is a descriptive and cross-sectional study. Data for the study were obtained from mothers of children in the age group of 0 to 18 years undergoing treatment for solid tumors in Pediatric Oncology Service and Outpatient Clinics (n = 112 ). We used a questionnaire on parental pain management practices at home, the knowledge about pain and analgesic drugs, Spielberger State-Trait Anxiety Inventory (STAI), and Pain Catastrophizing Scale (PCS) to collect the data. Results: Several mothers taking part in the study reported various misconceptions about the assessment of children's pain, analgesic drugs, and usage of limited non-pharmacological methods for managing pain in children with cancer. No significant relationships were found between mothers' pain management practices, knowledge of pain assessment and analgesic drugs, and mothers' and children's sociodemographic characteristics or mothers' pain catastrophizing and anxiety about their own pain. Conclusions: The findings of the study revealed that the majority of mothers of children with cancer had misconceptions regarding knowledge of pain assessment and analgesic drugs; these misconceptions potentially lead to manage children's pain associated with cancer ineffectively. Findings indicate mothers' information and support needs for children's cancer pain management in the home settings. Practice implications: A further understanding of barriers to parental pain management in children with cancer in the home setting will contribute immensely in developing appropriate management practices. (C) 2019 Elsevier Inc. All rights reserved.Article Citation - WoS: 8Citation - Scopus: 12Protective Effects of BPC 157 on Liver, Kidney, and Lung Distant Organ Damagein Rats with Experimental Lower-Extremity Ischemia–Reperfusion Injury(MDPI, 2025) Demirtas, Hueseyin; Ozer, Abdullah; Yildirim, Alperen Kutay; Dursun, Ali Dogan; Sezen, Saban Cem; Arslan, MustafaBackground and Objectives: Ischemia–reperfusion (I/R) injury can affect multiple distant organs following I/R in the lower extremities. BPC-157’s anti-inflammatory and free radical-neutralizing properties suggest its potential in mitigating ischemia–reperfusion damage. This study evaluates the protective effects of BPC-157 on remote organ damage, including the kidneys, liver, and lungs, in a rat model of skeletal muscle I/R injury. Materials and Methods: A total of 24 male Wistar albino rats were randomly divided into four groups: sham (S), BPC-157(B), lower extremity I/R(IR) and lower extremity I/R+BPC-157(I/RB). Some 45 min of ischemia of lower extremity was followed by 2 h of reperfusion of limbs. BPC-157 was applied to groups B and I/RB at the beginning of the procedure. After 2 h of reperfusion, liver, kidney and lung tissues were harvested for biochemical and histopathological analyses. Results: In the histopathological examination, vascular and glomerular vacuolization, tubular dilation, hyaline casts, and tubular cell shedding in renal tissue were significantly lower in the I/RB group compared to other groups. Lung tissue showed reduced interstitial edema, alveolar congestion, and total damage scores in the I/RB group. Similarly, in liver tissue, sinusoidal dilation, necrotic cells, and mononuclear cell infiltration were significantly lower in the I/RB group. Additionally, the evaluation of TAS, TOS, OSI, and PON-1 revealed a statistically significant increase in antioxidant activity in the liver, lung, and kidney tissues of the I/RB group. Conclusions: The findings of this study demonstrate that BPC-157 exerts a significant protective effect against distant organ damage in the liver, kidneys, and lungs following lower extremity ischemia–reperfusion injury in rats.
