Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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  • Article
    A New Discrete Differential Evolution Algorithm Coupled With Simulation–optimization Model for Groundwater Management Problems
    (Springer Science and Business Media Deutschland GmbH, 2024) Şahin, O.G.; Gurarslan, G.; Gündüz, O.
    Discrete differential evolution (DDE) is a promising algorithm specifically developed to solve discrete problems. In this study, we aim to apply DDE to groundwater management problems and to compare its performance and discrete space search capabilities with the well-known genetic algorithm (GA) techniques. Local search process was used to enhance the performance of GA algorithm. Metaheuristic algorithms are used for finding location of wells as a hybrid optimization procedure. Two examples from the groundwater management literature were selected to test the performance of the algorithm. The main novelty and objective of this study lie in the comparison of the discrete space search capabilities of the mentioned metaheuristics algorithms using the groundwater management problems. In the first test example, discrete space search performances of algorithms are 15% and 93% for GA and DDE, respectively. In the second test example, DDE exhibited a significantly higher test results (77%) compared to GA (1%). The analysis revealed that GA often prematurely converged and was insufficient to produce the optimum result. DDE reaches the solution considerably faster than the other algorithms. The results showed the superior performance of DDE in the discrete space. As the problem becomes more discrete, the performance of the DDE algorithm in finding the optimum solution increases considerably. Thus, it can be revealed that DDE can also be applied to a wider range of water resource management problems as an effective discrete optimization algorithm. © The Author(s), under exclusive licence to Springer-Verlag London Ltd., part of Springer Nature 2024.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Fabrication 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, Funda
    In 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
    Citation - WoS: 7
    Citation - Scopus: 7
    Bond-Based Peridynamic Fatigue Analysis of Ductile Materials With Neuber's Plasticity Correction
    (Springer, 2024) Altay, Ugur; Dorduncu, Mehmet; Kadioglu, Suat; Madenci, Erdogan
    This study introduces an approach for performing bond-based (BB) peridynamic (PD) fatigue analysis of ductile materials. Existing BB PD fatigue models do not account for the effect of plastic deformation. The current approach addresses this by incorporating Neuber's plasticity correction concept into the fatigue model. Neuber's correction adjusts the stress and strain predictions of the PD elastic solution to account for local plastic deformation around crack tips. The PD fatigue simulations demonstrate the effectiveness of this method and improvements in fatigue life predictions by considering local plasticity effects. The numerical results first examine the response of a ductile plate without a crack under quasi-static monotonic loading. Subsequently, specimens exhibiting Mode I and mixed-mode crack propagation paths due to cyclic loading are analyzed. The PD predictions accurately capture the test data. Additionally, the model specifically investigates the effect of a stop hole on fatigue life.
  • Article
    Citation - WoS: 7
    Citation - Scopus: 7
    Development of a Dopamine-Based Surface Modification Technique To Enhance Protein Fouling Resistance in Commercial Ultrafiltration Membranes
    (Elsevier, 2025) Onuk, Ecem; Gungormus, Elif; Cihanoglu, Aydin; Altinkaya, Sacide Alsoy
    This study introduces a new method for modifying ultrafiltration membranes using dopamine polymerization to overcome issues such as prolonged polymerization times, potential pore narrowing, and insufficient formation of hydrophilic groups. The technique involves continuously supplying oxygen (O2) gas from the porous backside of the membrane while simultaneously applying an aqueous dopamine solution to the active top surface. TGA and XPS analyses revealed that 10 kDa commercial polysulfone (PSF) membranes coated with O2 backflow contained more dopamine than those modified using the classical method. Additionally, changes in contact angle and zeta potential values were more pronounced with the O2 backflow method. Dopamine coating for 10 and 20 min improved the pure water permeance of the PSF membrane, whereas a 40-min coating decreased it. Notably, the reduction in permeance was 2.5 times less with the O2 backflow method than with the classical method. The classical dopamine coating method did not enhance the PSF membrane's resistance to fouling during whey filtration; in fact, 20 and 40-min coatings caused more significant flux declines compared to the unmodified membrane. Conversely, 10 and 20 min of PDA coating under O2 backflow improved fouling resistance, though this benefit disappeared with a 40-min coating.
  • Article
    Citation - WoS: 1
    Comparison 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 Alsoy
    In 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
    Regression Via Classification for Fingerprint Orientation Estimation
    (Ieee-inst Electrical Electronics Engineers inc, 2024) Erdogmus, Nesli
    Estimating 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: 4
    Citation - Scopus: 3
    An 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, Bunyamin
    RNA 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.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Application of a Size Measurement Standard for Data Warehouse Projects
    (Wiley, 2024) Unlu, Hueseyin; Yueruem, Ozan Rasit; Yildiz, Ali; Demirors, Onur
    MethodologyIn 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: 1
    Dynamic 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.
  • Article
    Citation - Scopus: 6
    Lithium Extraction From Geothermal Brine Using Γ-Mno2: a Case Study for Tuzla Geothermal Power Plant
    (Elsevier Ltd, 2024) Toprak, S.; Yılmaz, Selahattin; Öncel, Ç.; Baba, Alper; Yılmaz, S.; Demir, Mustafa Muammer; Baba, A.; Koç, G.A.; Demir, M.M.
    Geothermal brines contain high concentrations of ions and form a source of various valuable elements. The isolation of the elements from their water systems is a great challenge when the gradual depletion of ores in mining is considered. Attempts have been made for a long time to isolate valuable elements from aqueous mixtures prepared in the laboratory. However, those studies might not reflect the complexity of natural systems and might yield results that deviate significantly from the performance in real field systems. In this study, sorption is used to extract lithium ions from a representative field, Tuzla Geothermal Power Plant (TGPP) Turkey, using a mini-pilot reactor introduced to the reinjection well of the plant. Electrolytic manganese dioxide (γ-MnO2), a relatively inexpensive material widely used as the cathode material in lithium-ion batteries, was employed as a sorbent material for lithium. The sorption/desorption performance of the novel γ-MnO2 was investigated under various conditions. Sorption is performed at 360K and 2 bars. The maximum sorption performance was obtained at 1 h in Tuzla GPP. The desorption experiments were performed in acidic solutions. The concentration of Li+ in the desorption solution was found to be 25 mg/L on average when 10 g of γ-MnO2 was dispersed into 30 mL of the acidic aqueous solution. The first desorption solution was used consecutively for collecting more Li+ ions through the desorption of fresh brine-treated powder samples (cumulative desorption). By repeating this process four times consecutively, 230 mg/L of Li+ was obtained in the desorption solution. Moreover, the reusability of the γ-MnO2 sorbent was examined. The sorbent powder showed almost 40% performance efficiency compared to virgin powder under the conditions employed in this study. The use of electrolytic γ-MnO2 sorbent for lithium adsorption was found to be a promising process for practical use in the separation of lithium from geothermal brines. © 2024