Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article On the Construction of Xor-Magic Graphs(Elsevier, 2026) Batal, AhmetA simple connected graph of order 2nis defined as a xor-magic graph of power n if its vertices can be labeled with vectors from Fn2 in a one-to-one manner such that the sum of labels in each closed neighborhood set of vertices equals zero. In this paper, we introduce a method called the self-switching operation, which, when properly applied to an odd xor-magic graph of power n, generates a xor-magic graph of power n + 1. We demonstrate the existence of a proper self-switching operation for any given odd xor-magic graph and provide a characterization of the cut space of a connected graph in the process. We also observe that the Dyck graph can be obtained from the complete graph of order 4 by applying three successive self-switching operations. Additionally, we investigate various graph products, including Cartesian, tensor, strong, lexicographical, and modular products. We observe that these products allow us to generate xor-magic graphs by selecting appropriate factor graphs. Notably, we discover that a modular product of graphs is always a xor-magic graph when the orders of its factors are powers of 2 (except for 2 itself). In the process, we realize that the Clebsch graph is the modular product of the cycle graph and the empty graph, each of order 4. By combining the self-switching operation with the modular product, we establish the existence of k-regular xor-magic graphs of power n for all n >= 2 and for all k is an element of {3, 5, 7, ... , 2n-5}boolean OR{2n-1}. We also prove that there is no (2n-3)-regular xor-magic graph of power n. Lastly, we introduce two more methods to produce xor-magic graphs. One method utilizes Cayley graphs and the other utilizes linear algebra. (c) 2025 Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.Article Advancements in Oil-Water Separation: the Role of Molybdenum and Tungsten Disulfide as Cutting-Edge 2D Nanomaterials(Elsevier, 2025) Recepoglu, Yasar Kemal; Goren, Ayseguel YagmurThis article reviews recent strides in synthesizing, functionalizing, and utilizing molybdenum disulfide (MoS2) and tungsten disulfide (WS2) nanomaterials owing to their exceptional wetting properties, which facilitate oilwater separation. Among various materials explored, they have also emerged as particularly promising candidates due to their high surface area, tunable surface chemistry, and unique layered structure. The twodimensional (2D) morphology offers abundant active sites, enhanced interaction with water molecules, and the ability to engineer surface wettability at the nanoscale, all of which are highly advantageous for efficient oilwater separation. Distinct separation mechanisms, performance benchmarks, and potential integration into practical separation setups were meticulously surveyed and analyzed. Furthermore, to elucidate the superiority of MoS2 and WS2 2D nanomaterials over alternative methodologies for oil-water separation, we comprehensively examined other techniques, including membrane processes, electrocoagulation, adsorption with modified materials, and biological methods. For instance, the high membrane, operational, and maintenance costs, scaling, fouling, expensive production steps, high energy consumption, and complex operations are significant limitations of other processes for oil-water separation. On the other hand, the MoS2 and WS2 nanomaterials provide sustainable and effective oil-water separation performance compared to other processes owing to their unique properties, such as superior reusability, high separation efficiency, excellent hydrophobicity (water-repelling) and oleophilicity (oil-attracting) features, significant chemical and thermal stability, and enhanced photocatalytic properties. This review showed that the oil-water separation efficiency of the MoS2 and WS2-based materials was 70-100 %. The highest oil-water separation efficiency of 100 % is observed using cellulose acetate -MoS2 fibrous sponge from a toluene-water mixture at a pH of 8. Nevertheless, while MoS2 and WS2 nanomaterials promise oil-water separation owing to their unique properties, their limitations, such as cost, scalability, environmental concerns, agglomeration, regeneration challenges, and potential toxicity, must be carefully addressed. Consequently, further research and development are necessary to overcome these hurdles and fully realize their potential in practical applications.Article Residue-Specific Pathways in Peptide Fragmentation: the Role of Aromatic Side Chain in A3 Ion Formation From B3 Ion(Elsevier, 2025) Atik, A. Emin; Yalçın, Talat; Karaca, Sila; Yalcin, TalatPeptide fragmentation chemistry is essential for the sequence elucidation of proteins through tandem mass spectrometry (MS/MS). In this study, we examine the gas-phase fragmentation of b3 ions from model tripeptides under low-energy CID conditions, focusing on the pathway leading to the stable formation of a3 ions from b3 ions. The study utilized C-terminal amidated model tripeptides, including YGG-NH2, GYG-NH2, and GGX-NH2, where X represents D, E, H, Q, C, S, F, and Y. Our results reveal that only tripeptides with phenylalanine (F) and tyrosine (Y) as the third residue yield a3 ions upon b3 ion fragmentation under the applied experimental conditions, suggesting a unique stabilizing role of aromatic side chains in facilitating this pathway. Our theoretical studies indicate that the a3 ions from GGF-NH2 and GGY-NH2 preferentially adopt an energetically favored linear imineprotonated isomer, which is lower in energy by 3.29 kcal/mol and 4.17 kcal/mol, respectively, compared to their 7-membered ring isomers protonated at the ring imine. The latter structure has been previously assigned for the GGG sequence as a predominant structure, supported by IR spectroscopy and DFT calculations (JACS, 2010, 132, 14,766-14779). We proposed a plausible fragmentation mechanism for the a3 ions based on the linear imineprotonated structure. These findings provide insights into residue-specific fragmentation mechanisms and enhance our understanding of peptide ion dissociation, particularly in small peptides.Conference Object Citation - WoS: 1Citation - Scopus: 1A Mixed-Integer Dynamic and Stochastic Algae Process Optimization(Elsevier, 2024) Kivanc, Sercan; Deliismail, Özgün; Şıldır, HasanWith increased energy demand as it gets scarcer, a great deal of research is being carried out into alternatives to non - renewable energy resources. One of the promising studies is the biofuel production from micro algae. Microalgae are photosynthetic organisms and capture carbon dioxide, reducing emissions and providing valuable products (fuel, fertilizer, etc.). Thus, efficiency in the design and optimization of process related units are important. In this study, the optimal experimental conditions for Nannochloropsis Oculata were calculated under the constraints of the model equations and other process related constraints through simultaneous optimization approach. The economic evaluation of the process is also handled by introducing the uncertainty in the economic measures sampled from normal distribution to maximize the average profit. Unlike traditional approaches, the MINLP formulation, which is solved stochastically, dynamically, and simultaneously, provides more robust and reliable results, flexibility, improved decision making, reduced risks to be taken and a better understanding of risk factors. Copyright (C) 2024 The Authors. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/)Article Citation - WoS: 1Citation - Scopus: 1Canine Oocyte Nuclear Maturation With Nano-Ozone (nzs) Supplementation: the Alterations of Antioxidant, and Oxidant Status and Cdk1, Cyclin B1 Expressions(Elsevier, 2024) Bari, O.; Sabanci, A. U.; Avci, G.; Bozkurt, B.; Ustuner, B.; Denk, B.; Ozalp, G. R.This study aims to evaluate the effects of nano-ozone solution (NZS) on canine oocyte nuclear maturation, associated with the alterations of antioxidant and oxidant status and cyclin-dependent kinase 1 (CDK1), cyclin B1 gene expressions. Oocytes were cultured in four distinct concentrations of NZS (0.5, 1, 2, and 5 mu g/mL) and parthenogenetically activated. The rates of oocytes arrested at the Germinal Vesicle (GV), Germinal Vesicle Breakdown (GVBD), Metaphase I (MI), and Metaphase II (MII) stages were statistically different among groups (P < 0.05). The oocytes cultured in 1 <mu>g/mL NZS yielded the best oocyte maturation rate at the MI and MII stages; however, the lowest maturation and high degeneration rates were observed in Group E. The measurements of Malondialdehyde (MDA), reduced Glutathione (GSH), Superoxide Dismutase (SOD), and Ferric Reducing/Antioxidant Power assay (FRAP) were performed from IVM culture media. No statistical difference was observed in SOD and MDA results (P > 0.05). GSH levels were statistically significant between Group AGroup E (p = 0.003), Group B-Group E (p = 0.045), and Group E-Group D (p = 0.021). The culture media in Group D and Group E had high FRAP concentrations and significantly differed between groups (P < 0.05). CDK1, and cyclin B1 genes, which are subunits of maturation-promoting factor (MPF), are upregulated in Group B and Group C, while are downregulated in oocytes of Group E. This study showed that low, controlled doses of NZS (1 <mu>g/mL) supplementation could improve the meiotic competence of canine oocytes and lead to positive response in expressions of CDK1 and cyclin B1 on the gene level.Letter Citation - WoS: 1Citation - Scopus: 1Evaluating Ethanol Concentrations Against Staphylococcus Spp: a Proposal for Improving Nosocomial Bacteria Control(Elsevier, 2024) Soyer, Ferda; Özdemir, Özgün Öykü; Polat, Bengi; Ekenel, Nil HazalDear Editor, Nosocomial infections originating from commonly encountered pathogenic bacteria, notably Staphylococcus species, persist as a prominent global public health issue. This phenomenon exerts consequential impacts on both the well-being of patients and the healthcare personnel within hospital environments. Hospital-acquired infections from common bacteria like Staphylococcus remain a global public health concern. The European Centre for Disease Prevention and Control reports prevalence rates of 4.5% in the USA and 7.1% in Europe [1]. An estimated 8.9 million healthcare-associated infections occur annually in European hospitals and long-term care facilities [1]. According to the World Health Organization, although 10% of patients get healthcare-associated infections, at least a 30% reduction can be achieved through adequate infection prevention and control [2]. The efficacy of disinfection methodologies employed in healthcare institutions assumes critical significance in mitigating this threat.Article Citation - WoS: 1Citation - Scopus: 1Hdac9/P300 Immunoexpression and Migration Analysis for Malignant Melanoma Stem Cell(Elsevier, 2023) Özdil, Berrin; Asker Abdikan, Cemile Sinem; Özdemir, Merve; Erişik, Derya; Yesin, Taha Kadir; Avcı, Çığır Biray; Kurkutçu, Yeşim; Güler, Günnur; Aktuğ, HüseyinMelanoma is an aggressive tumor with a poor prognosis that worsens in the metastatic phase. Distruptions of epigenetic mechanisms is known to effect cancer stem cells (CSCs) activity. Malignant melanoma (MM) progression may be promoted by changes in the genetic structure of CSC. Thus, treatments that target epigenetic modifications could be a promising weapon, especially in melanoma. Here, we compared p300, HDAC9, and Factin proteins in melanoma CSCs (CD133+), non-CSCs (CD133-) and CHL-1 cell line, as well as cell migration and division rates. At 4 and 6 h, P300 protein levels in CHL-1 and CD133 + were remarkably similar, and the CD133- showed increases in expression levels as the incubation period lengthened. HDAC9 protein intensity decreased in CHL-1, increased in the CD133-, and remained relatively unchanged in the CD133+ as the incubation period lengthened. The mean value of F-actin expression level increased in all cell group with time, when the highest increase observed in CHL-1. In conclusion, our studies contribute to the management of metastatic diseases in the future and offer new insight into the molecular basis of the initiation and progression of MM.Article Arithmetic Progressions in Certain Subsets of Finite Fields(Elsevier, 2023) Eyidoğan, Sadık; Göral, Haydar; Kutlu, Mustafa KutayIn this note, we focus on how many arithmetic progressions we have in certain subsets of finite fields. For this purpose, we consider the sets Sp = {t2 : t & ISIN; Fp} and Cp = {t3 : t & ISIN; Fp}, and we use the results on Gauss and Kummer sums. We prove that for any integer k & GE; 3 and for an odd prime number p, the number of k-term arithmetic progressions in Sp is given by p2 2k + R, where and ck is a computable constant depending only on k. The proof also uses finite Fourier analysis and certain types of Weil estimates. Also, we obtain some formulas that give the exact number of arithmetic progressions of length in the set Sp when & ISIN; {3,4, 5} and p is an odd prime number. For = 4, 5, our formulas are based on the number of points onArticle Citation - WoS: 8Citation - Scopus: 9Dynamic Computational Wear Model of Peek-On Bearing Couple in Total Hip Replacements(Elsevier, 2023) Alpkaya, Alican Tuncay; Mihçin, ŞenayUnderstanding wear mechanisms is a key factor to prevent primary failures causing revision surgery in total hip replacement (THR) applications. This study introduces a wear prediction model of (Polyetheretherketone) PEEK-on-XLPE (cross-linked polyethylene) bearing couple utilized to investigate the wear mechanism under 3D-gait cycle loading over 5 million cycles (Mc). A 32-mm PEEK femoral head and 4-mm thick XLPE bearing liner with a 3-mm PEEK shell are modeled in a 3D explicit finite element modeling (FEM) program. The volumetric and linear wear rates of XLPE liner per every million cycles were predicted as 1.965 mm3/Mc, and 0.0032 mm/Mc respectively. These results are consistent with the literature. PEEK-on-XLPE bearing couple exhibits a promising wear performance used in THR application. The wear pattern evolution of the model is similar to that of conventional polyethylene liners. Therefore, PEEK could be proposed as an alternative material to the CoCr head, especially used in XLPE-bearing couples. The wear prediction model could be utilized to improve the design parameters with the aim of prolonging the life span of hip implants. © 2023Article Citation - WoS: 5Citation - Scopus: 5Thickness-Dependent Piezoelecticity of Black Arsenic From Few-Layer To Monolayer(Elsevier, 2023) Akgenç Hanedar, Berna; Ersan, Fatih; Altalhi, Tariq; Yağmurcukardeş, Mehmet; Yakobson, BorisUltra-thin forms of black phosphorus (b-P) have been widely investigated due to its unique properties arising from the in-plane anisotropy in its crystal structure. Recently, two-dimensional (2D) forms of black arsenic (b-As) have also been added to the 2D family. In this study, the thickness-dependent structural, electronic, and piezoelectric properties of layered b-As are investigated by means of ab-initio calculations. The structural optimizations confirm the van der Waals type layered structure for both these structures. In addition, increasing the thickness is shown to result in the decreasing of the band gap arising from the confinement of electrons in the layers. In contrast to the case of b-P, it is revealed that a transition from indirect-to-direct band gap behavior can be found in b-As which can be important for optically identifying the single-layer structure. Moreover, the piezoelectric properties are investigated as a function of the number of layers. It is shown that while a single-layer of b-As does not exhibit piezoelectric features, even in the case of bilayer structures the piezoelectricity is created. Our results revealed the strong in-plane anisotropy in piezoelectric coefficients for the three-layer and thicker structures. We have shown that the out-of-plane piezoelectric properties can be achieved by non-centrosymmetric features in the out-of-plane direction in thicker structures of b-As.
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