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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: 4Citation - Scopus: 4The Effect of Cerium Oxide (ceo2) on Ischemia-Reperfusion Injury in Skeletal Muscle in Mice With Streptozocin-Induced Diabetes(Mdpi, 2024) Ozer, Abdullah; Sengel, Necmiye; Kucuk, Ayseguel; Yigman, Zeynep; Ozdemir, Cagri; Kilic, Yigit; Arslan, MustafaObjective: Lower extremity ischemia-reperfusion injury (IRI) may occur with trauma-related vascular injury and various vascular diseases, during the use of a tourniquet, in temporary clamping of the aorta in aortic surgery, or following acute or bilateral acute femoral artery occlusion. Mitochondrial dysfunction and increased basal oxidative stress in diabetes may cause an increase in the effects of increased reactive oxygen species (ROS) and mitochondrial dysfunction due to IRI. It is of great importance to examine therapeutic approaches that can minimize the effects of IRI, especially for patient groups under chronic oxidative stress such as DM. Cerium oxide (CeO2) nanoparticles mimic antioxidant enzymes and act as a catalyst that scavenges ROS. In this study, it was aimed to investigate whether CeO2 has protective effects on skeletal muscles in lower extremity IRI in mice with streptozocin-induced diabetes. Methods: A total of 38 Swiss albino mice were divided into six groups as follows: control group (group C, n = 6), diabetes group (group D, n = 8), diabetes-CeO2 (group DCO, n = 8), diabetes-ischemia/reperfusion (group DIR, n = 8), and diabetes-ischemia/reperfusion-CeO2 (group DIRCO, n = 8). The DCO and DIRCO groups were given doses of CeO2 of 0.5 mg/kg intraperitoneally 30 min before the IR procedure. A 120 min ischemia-120 min reperfusion period with 100% O-2 was performed. At the end of the reperfusion period, muscle tissues were removed for histopathological and biochemical examinations. Results: Total antioxidant status (TAS) levels were found to be significantly lower in group DIR compared with group D (p = 0.047 and p = 0.022, respectively). In group DIRCO, total oxidant status (TOS) levels were found to be significantly higher than in group DIR (p < 0.001). The oxidative stress index (OSI) was found to be significantly lower in group DIR compared with group DCO (p < 0.001). Paraoxanase (PON) enzyme activity was found to be significantly increased in group DIR compared with group DCO (p < 0.001). The disorganization and degeneration score for muscle cells, inflammatory cell infiltration score, and total injury score in group DIRCO were found to be significantly lower than in group DIR (p = 0.002, p = 0.034, and p = 0.001, respectively). Conclusions: Our results confirm that CeO2, with its antioxidative properties, reduces skeletal muscle damage in lower extremity IRI in diabetic mice.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 - Scopus: 2Comparison of the Effectiveness of Kinesiology Taping and Rigid Taping on Ankle Kinematics During Drop Landing in Individuals With Lateral Ankle Injury(American Podiatric Medical Association, 2022) Korkusuz,S.; Kilic,R.T.; Aritan,S.; Ozgoren,N.; Sozay,S.; Kibar,S.; Yosmaoglu,H.B.Background: Lateral ankle sprain is an injury that often occurs during sports or daily life activ-ities. Athletic tape and kinesiology tape applications are among the external support treatment options especially for athletes to support the ankle and protect it from recurrent sprains. We sought to compare the kinematic stabilization effects of different ankle taping applications on the ankle joint during drop landing in individuals with a history of unilateral lateral ankle injury. Methods: In this randomized controlled study, 30 volunteers with unilateral ankle injury were evaluated. The participants were asked to land on one leg on the involved side and the contralateral side from a 30-cm-high platform. The same practice was repeated after apply-ing kinesiology tape and rigid tape to the injured foot. Kinematic analysis of the foot and ankle was performed by recording three-dimensional spatial position information at a speed of 240 frames per second using infrared cameras. Results: The highest inversion angles of the involved foot at initial contact and 150 msec after initial contact were higher than those of the uninvolved side (P = .03 and P = .04, respec-tively). There was no significant difference in ankle kinematic values in the involved foot among kinesiology taping, athletic taping, and no taping applications (P = .74). Conclusions: People with lateral ankle sprains show reduced inversion during landing. There were no significant differences among kinesiology taping, athletic taping, and no taping on the injured foot in terms of ankle kinematics. Care should be taken when using taping materials as protective measures for sports activities. © 2022, American Podiatric Medical Association. All rights reserved.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: 33Citation - Scopus: 36Comparison of Biomechanical Behaviour of Maxilla Following Le Fort I Osteotomy With 2-Versus 4-Plate Fixation Using 3d-Fea. Part 1: Advancement Surgery(Churchill Livingstone, 2008) Atac, M. S.; Erkmen, E.; Yucel, E.; Kurt, A.The study aimed to calculate the location and intensity of the maximum stress fields on the fixation plates and surrounding maxilla following Le Fort I osteotomies after advancement procedures using three-dimensional finite element analysis. The models were generated using skull CT scan data. Le Fort I osteotomy Simulations were made and two separate impacted maxillary models were designed. The ADV-2 model has 2 plate fixations bilaterally at the piriform rims, the ADV-4 model has 4 plate fixations at the zygomatic buttresses and piriform rims. The stress fields on bone, plate and screws were computed for each model. Posterior occlusal loads were simulated on one side in the molar-premolar region, in all three directions, reflecting the chewing forces. The increased locations of highest Von Mises stresses on the plates and highest maximum principle stresses on the bones were determined in ADV-2 models especially Under horizontal and oblique loads when compared with ADV-4 models. Evaluation of the highest Von Mises Stress Values and maximum principal stress revealed that oblique load in the ADV-2 model received the highest values. 4-plate fixation following Le Fort I advancement Surgery exerts less stress on the maxillary bones and fixation materials than 2-plate fixation.
