Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 2Citation - Scopus: 2Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration(Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, FundaIn recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.Article Machinability Investigation on Cnc Milling of Recycled Short Carbon Fiber Reinforced Magnesium Matrix Composites(Iop Publishing Ltd, 2024) Atasoy, Sahin; Kandemir, SinanThis study investigates the machinability of magnesium matrix composites reinforced with short carbon fibers, which represent novel materials in the field. AZ91 alloy and its composites containing 2.5 and 5 wt% recycled carbon fiber (rCF) reinforcements were used as workpieces. Face milling was conducted using uncoated carbide cutting tools under dry cutting conditions with varied cutting speeds (480-560-640 m min(-1)) and feed rates (0.65-0.8-0.95 mm min(-1)). The experimental design was based on the Taguchi L-9 (3(3)) orthogonal array. Analysis included cutting forces, surface roughness, wear on cutting inserts, and chip morphology to assess machinability. Taguchi, analysis of variance, and regression methods were employed to analyze cutting force and surface roughness results. Findings indicated satisfactory machinability for AZ91 alloy and comparatively poorer performance for the 5 wt% rCF reinforced composite, with increased reinforcement content correlating with higher cutting force and surface roughness. SEM and EDX analyses revealed significant built-up layer formation on cutting inserts, with predominantly spiral-shaped continuous chips observed in the experiments. Overall, the study affirmed the machinability of the composites and identified suitable cutting parameters for further investigations.Article Citation - WoS: 1Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems(Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide AlsoyIn this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.Article Effect of Random Structural Variations on the Optical Properties of Honeycomb Photonic Crystals(Taylor & Francis Ltd, 2024) Tuncturk, Yigit; Sozuer, H. SamiPeriodic dielectric structures called photonic crystals are being used in various sensors and devices. Since photonic crystals are designed to operate within certain frequency ranges, accuracy in structure becomes important. In this work, we investigate the effects of two types of randomness, surface roughness and positional randomness, on the optical properties of the honeycomb photonic crystal. We employed the plane wave expansion method to investigate the effects of random perturbations of the shape and the position of the structure on the density of states. We also employ the finite-difference time-domain method to calculate the transmission spectrum as a consistency check. We find that both surface roughness and positional imperfections cause significant changes in the DOS. As the degree of randomness is increased, transverse electric and transverse magnetic gaps are narrowed and complete gaps totally disappear at $ 45\% $ 45% of surface roughness.Article Regression Via Classification for Fingerprint Orientation Estimation(Ieee-inst Electrical Electronics Engineers inc, 2024) Erdogmus, NesliEstimating the direction in which the ridges and valleys of the fingerprint pattern are aligned often serves as a pivotal first step in fingerprint recognition systems. The ridge orientation map is a fundamental reference for subsequent processing stages, such as image enhancement, feature extraction, and matching. Therefore, its accuracy is essential to achieve high recognition rates. Ridge orientation estimation entails a regression problem since the task is to estimate an angle between 0 degrees and 180 degrees for each sub-region in the fingerprint image. However, the majority of the approaches in the literature pivot towards framing this regression task as a classification problem. This paper systematically analyzes the regression via classification methodology for fingerprint orientation estimation, exploring various discretization and encoding strategies. Specifically, we examine single and multiple discretization schemes designed to ensure that resulting bins maintain uniform length or uniform probability or are allocated randomly, paired with one-hot, ordinal, and cyclic encoding techniques. Our experiments are conducted on the FOE-TEST database from FVC-onGoing, the sole publicly available fingerprint orientation dataset. The findings highlight the efficacy of cyclic encoding over the one-hot encoding prevalent in prior research, while equal-length and equal-probability discretization strategies yield comparable results.Article Citation - WoS: 4Citation - Scopus: 3An Investigation of Rna Methylations With Biophysical Approaches in a Cervical Cancer Cell Model(Mdpi, 2024) Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, Azime; Ceylan, Cagatay; Guler, Gunnur; Akgul, BunyaminRNA methylation adds a second layer of genetic information that dictates the post-transcriptional fate of RNAs. Although various methods exist that enable the analysis of RNA methylation in a site-specific or transcriptome-wide manner, whether biophysical approaches can be employed to such analyses is unexplored. In this study, Fourier-transform infrared (FT-IR) and circular dichroism (CD) spectroscopy are employed to examine the methylation status of both synthetic and cellular RNAs. The results show that FT-IR spectroscopy is perfectly capable of quantitatively distinguishing synthetic m(6)A-methylated RNAs from un-methylated ones. Subsequently, FT-IR spectroscopy is successfully employed to assess the changes in the extent of total RNA methylation upon the knockdown of the m(6)A writer, METTL3, in HeLa cells. In addition, the same approach is shown to accurately detect reduction in total RNA methylation upon the treatment of HeLa cells with tumor necrosis factor alpha (TNF-alpha). It is also demonstrated that m(1)A and m(6)A methylation induce quite a distinct secondary structure on RNAs, as evident from CD spectra. These results strongly suggest that both FT-IR and CD spectroscopy methods can be exploited to uncover biophysical properties impinged on RNAs by methyl moieties, providing a fast, convenient and cheap alternative to the existing methods.Review Citation - WoS: 13Citation - Scopus: 18Review of Cell Level Battery (calendar and Cycling) Aging Models: Electric Vehicles(Mdpi, 2024) Yarimca, Gulsah; Cetkin, ErdalElectrochemical battery cells have been a focus of attention due to their numerous advantages in distinct applications recently, such as electric vehicles. A limiting factor for adaptation by the industry is related to the aging of batteries over time. Characteristics of battery aging vary depending on many factors such as battery type, electrochemical reactions, and operation conditions. Aging could be considered in two sections according to its type: calendar and cycling. We examine the stress factors affecting these two types of aging in detail under subheadings and review the battery aging literature with a comprehensive approach. This article presents a review of empirical and semi-empirical modeling techniques and aging studies, focusing on the trends observed between different studies and highlighting the limitations and challenges of the various models.Article On the Rings Whose Injective Right Modules Are Max-Projective(World Scientific Publ Co Pte Ltd, 2024) Alagoz, Yusuf; Buyukasik, Engin; Yurtsever, Haydar BaranRecently, right almost-QF (respectively, max-QF) rings that is the rings whose injective right modules are R-projective (respectively, max-projective) were studied by the first two authors. In this paper, our aim is to give some further characterizations of these rings over more general classes of rings, and address several questions about these rings. We obtain characterizations of max-QF rings over several classes of rings including local, semilocal right semihereditary, right non-singular right Noetherian and right non-singular right finite dimensional rings. We prove that for a ring R being right almost-QF and right max-QF are not left-right symmetric. We also show that right almost-QF and right max-QF rings are not closed under factor rings. This leads us to consider the rings all of whose factor rings are almost-QF and max-QF.Article Citation - WoS: 1Citation - Scopus: 1Application of a Size Measurement Standard for Data Warehouse Projects(Wiley, 2024) Unlu, Hueseyin; Yueruem, Ozan Rasit; Yildiz, Ali; Demirors, OnurMethodologyIn this research, we conducted a case study to establish a foundation for size measurement and effort estimation in DWH projects. We first applied a productivity-based estimation approach using linear regression with the ISBSG repository to assist organizations without historical data. We then evaluated various machine learning algorithms to improve estimation accuracy. Finally, we tested a combined model that integrates both approaches for estimating effort in external projects.ResultsUsing the ISBSG dataset, linear regression models based on productivity achieved a Mean Magnitude of Relative Error (MMRE) of 0.285. Machine learning algorithms improved accuracy by 22.81%, reducing the MMRE to 0.220. The final model, applied to external projects, yielded MRE values between 0.010 and 0.245.ConclusionThe ISBSG repository is a valuable resource for effort estimation in DWH projects. Combining productivity-based estimation with machine learning enhances accuracy and predictive performance, making it a more reliable approach than traditional models.Article Citation - Scopus: 1Dynamic Frequent Subgraph Mining Algorithms Over Evolving Graphs: a Survey(PeerJ Inc., 2024) Bostanoğlu, B.E.; Abuzayed, N.Frequent subgraph mining (FSM) is an essential and challenging graph mining task used in several applications of the modern data science. Some of the FSM algorithms have the objective of finding all frequent subgraphs whereas some of the algorithms focus on discovering frequent subgraphs approximately. On the other hand, modern applications employ evolving graphs where the increments are small graphs or stream of nodes and edges. In such cases, FSM task becomes more challenging due to growing data size and complexity of the base algorithms. Recently we see frequent subgraph mining algorithms designed for dynamic graph data. However, there is no comparative review of the dynamic subgraph mining algorithms focusing on the discovery of frequent subgraphs over evolving graph data. This article focuses on the characteristics of dynamic frequent subgraph mining algorithms over evolving graphs. We first introduce and compare dynamic frequent subgraph mining algorithms; trying to highlight their attributes as increment type, graph type, graph representation, internal data structure, algorithmic approach, programming approach, base algorithm and output type. Secondly, we introduce and compare the approximate frequent subgraph mining algorithms for dynamic graphs with additional attributes as their sampling strategy, data in the sample, statistical guarantees on the sample and their main objective. Finally, we highlight research opportunities in this specific domain from our perspective. Overall, we aim to introduce the research area of frequent subgraph mining over evolving graphs with the hope that this can serve as a reference and inspiration for the researchers of the field. © (2024), (PeerJ Inc.). All rights reserved.