Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article FW-S3PFCM: Feature-Weighted Safe-Semi Possibilistic Fuzzy C-Means Clustering(Springer, 2026) Khezri, Shirin; Aghazadeh, Nasser; Hashemzadeh, Mahdi; Golzari Oskouei, AminThe safe semi-supervised fuzzy c-means clustering (S3FCM) method is a well-known clustering method that can produce successful results by incorporating prior knowledge of the class distribution. Its process is fast and simple but still has two limitations. The first issue is that it gives equal weight to all data features, while in real-world applications, different features usually have different importance. Secondly, S3FCM is very sensitive to noise and outliers. This paper proposes an extension of the S3FCM, entitled FW-S3PFCM, to mitigate these shortcomings. The proposed method uses a local feature weighting scheme to consider the different feature weights in the clustering process. Additionally, a possibilistic version of the S3FCM is designed to reduce the sensitivity to noise and outliers. The effectiveness of the proposed method is comprehensively evaluated on various benchmark datasets, and its performance is compared with the state-of-the-arts methods. To practically asses the FW-S3FCM, a real-world dataset of brain MRI images and its segmentation performance are analyzed as well. The average Accuracy, F1-score, Sensitivity, and Precision measures obtained by FW-S3FCM are 0.9682, 0.9826, 0.9743, and 0.9925, respectively, which are better than the competitors' performance.Article Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice(Springer, 2026) Ada, Ebru; Seyrantepe, VolkanNeu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.Article Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We(Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, MalihehInvestigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.Article Mn2+ Removal From Water Using a Strong Acidic Shallow Shell Resin: Performance and Response Surface Optimization(Springer, 2026) Gucur, G.; Recepoglu, Y. K.; Ozcan, D. O.; Arar, O.The removal of manganese ions (Mn2+) from aqueous solutions using a strong acid cation-exchange resin, Purolite SST60, was investigated in the present study. The influences of resin dosage, temperature, and pH on Mn2(+) removal were optimized using Response Surface Methodology based on a Central Composite Design. Results showed that removal efficiency was highly pH-dependent, increasing from 63% at pH 1.0 to over 99% at pH 3.0 and above. Even with only 0.01 g of resin, 98% removal was achieved, indicating high performance at low dosages. Equilibrium data aligned with the Langmuir isotherm, indicating monolayer sorption with a maximum capacity of 91.06 mg/g. Kinetic data followed a pseudo-second-order model. Thermodynamic analysis confirmed a spontaneous and exothermic process, supported by a negative enthalpy change and positive entropy change, likely due to dehydration of Mn2+ ions upon binding. Competitive ion studies revealed that divalent ions, particularly calcium and magnesium, significantly hinder Mn2+ removal, whereas monovalent ions had minimal impact. Complete desorption of Mn2+ was achieved using hydrochloric or nitric acid at concentrations of 0.5 mol/L and above, confirming the resin's reusability. Overall, Purolite SST60 offers an efficient, regenerable, and robust solution for manganese removal in water treatment applications.Article Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions(Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, VolkanTay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.Article Comparative Optimization of Hot Water and Citric Acid Extraction Methods for Sericin Recovery From Silk Cocoons: In Vitro Antioxidant and Antidiabetic Activities(Springer, 2026) Sincar, Bahar; Ozdemir, Feyza; Bicakci, Beyza Tutku; Erdem, Cansu; Yalcin, Dilek; Alamri, Abdulhakeem S.; Bayraktar, OguzSilk sericin, a hydrophilic protein derived from Bombyx mori cocoons, has attracted increasing interest due to its antioxidant, moisturizing, and enzyme-inhibitory properties. Efficient extraction is essential to preserve its biofunctional potential. In this study, sericin was extracted using hot water and 1.25% (w/v) citric acid using autoclave-based heating to achieve pressurized conditions above 100 degrees C. A Box-Behnken Response Surface Methodology (RSM) was applied to systematically evaluate the effects of extraction parameters (temperature and time) and to optimize five key response variables: yield, purity, molecular weight and polydispersity index (PDI), total antioxidant capacity (ABTS), and alpha-glucosidase inhibition activity. The results revealed that higher temperatures (125 degrees C) produced the maximum sericin yield, while moderate conditions (115 degrees C for 45 min) ensured better preservation of antioxidant and antidiabetic activities. Hot acid extraction resulted in significantly enhanced purity and enzymatic inhibition compared to hot water extraction. Sericin fractions above 7 kDa exhibited the strongest bioactivity, as reflected by lower IC50 values in both ABTS and alpha-glucosidase inhibition assays. The optimized hot water citric acid-based method yielded 24.00% sericin with 100.00% purity and an IC50 of 0.67 mg/mL for alpha-glucosidase inhibition. This study compares hot water and hot acid autoclave extractions using Box-Behnken design and evaluates their effects on sericin yield, purity, and bioactivities. Citric acid-based extraction produced higher purity and stronger alpha-glucosidase inhibition, while hot water extraction preserved antioxidant potential more effectively. These findings support the use of citric acid as an eco-friendly and scalable extraction agent and highlight the potential of sericin in biomedical and nutraceutical applications.Article Sainfoin (Onobrychis Viciifolia L.) Protein Isolate as a New Source of Alternative Plant-Based Protein: Cytotoxicity, Immunoreactivity, Nutritional and Functional Properties(Springer, 2025) Korkmaz, Fatma; Gungor, Sevde Nur; Gulec, Sukru; Sakarya, Fatma Betul; Andac, Ali Emre; Yilmaz Tuncel, Nese; Tuncel, Necati BarisThe objective of this research was to develop an alternative plant-based protein isolate using sainfoin (Onobrychis viciifolia L.) seeds. The extraction process was optimized using response surface methodology (RSM) based on the Box-Behnken Design, which examined the effects of key parameters: solvent/solid ratio (10-50 mL/g), pH (8-11), temperature (20-50 degrees C), and extraction time (30-120 min), aiming to maximize protein yield. The optimal extraction conditions identified were a solvent/solid ratio of 49.96 mL/g, pH of 10.99, temperature of 20 degrees C, and a duration of 38.55 min, achieving a protein yield of 56.36%. Additionally, the amino acid composition, cytotoxicity, immunoreactivity, and functional properties of the sainfoin seed protein isolate (SPI) were evaluated. SPI exhibited a high crude protein content of 91.44%, with arginine being the most abundant amino acid at 158.20 mg/g. The protein isolate comprised a remarkable value of 50.26% essential amino acids. Additionally, SPI demonstrated desirable functional properties, including solubility of 53.95% at neutral pH, water holding capacity of 2.36 g/g, and oil binding capacity of 4.68 g/g. Its emulsifying performance was notable, with emulsion activity and stability values of 66.67% and 77.50%, respectively. Moreover, in vitro cell culture studies demonstrated that sainfoin seed protein exhibited no adverse effects on cellular toxicity or immunoreactivity. This study highlights the potential of SPI as a novel, high-quality plant protein source with promising nutritional and functional properties and demonstrates its potential as a functional ingredient in the formulation of plant-based foods, meat analogs, and dietary supplements.Article Automating Software Size Measurement from Python Code Using Language Models(Springer, 2025) Tenekeci, Samet; Unlu, Huseyin; Gul, Bedir Arda; Keles, Damla; Kuuk, Murat; Demirors, OnurSoftware size is a key input for project planning, effort estimation, and productivity analysis. While pre-trained language models have shown promise in deriving functional size from natural-language requirements, measuring size directly from source code remains under-explored. Yet, code-based size measurement is critical in modern workflows where requirement documents are often incomplete or unavailable, especially in Agile development environments. This exploratory study investigates the use of CodeBERT, a pre-trained bimodal transformer model, for measuring software size directly from Python source code according to two measurement methods: COSMIC Function Points and MicroM. We construct two curated datasets from the Python subset of the CodeSearchNet corpus, and manually annotate each function with its corresponding size. Our experimental results show that CodeBERT can successfully measure COSMIC data movements with up to 91.4% accuracy and generalize to the functional, architectural, and algorithmic event types defined in MicroM, reaching up to 81.5% accuracy. These findings highlight the potential of code-based language models for automated functional size measurement when requirement artifacts are absent or unreliable.Article Ranking Circularity Levels in Industrial Parks: A Holistic Approach Incorporating Environmental, Economic and Social Indicators(Springer, 2025) Berk, I.; Ediger, V.Ş.; Öztürk, E.B.; Uctug, F.G.; Kucuker, M.A.; Inan, A.; Aktuna, G.B.This study introduces a circularity ranking system at the meso-level, specifically targeting industrial parks, through the development of the Circular Economy Sustainability Index (CESI). The index comprises five economic-environmental indicators: energy intensity, emission intensity, water intensity, waste intensity, and recycling ratio, as well as a social indicator as a sixth dimension. We utilize CESI to evaluate the circular economy performance of 22 manufacturing firms in the Adana Hacı Sabancı Organized Industrial Zone (AOSB). AOSB, one of the most prominent industrial parks in Türkiye, serves as an excellent case study to assess companies’ circularity performance and identify areas for improvement in the country’s green industrial transformation endeavor. Our findings reveal that waste and recycling indicators are pivotal in determining circularity, contributing 34.6% to the overall score, while the social indicator adds another 16.3%. These results underscore the significance of effective waste management and social responsibility in enhancing circularity. © 2025 Elsevier B.V., All rights reserved.Article Performance of Sheet Pile Walls With Rubber-Modified Backfill(Springer, 2025) Ecemis, Nurhan; Kadekeshova, Kuralay; Khlaif, Ali HamidThis study investigates the behavior of clean sand and sand-rubber mixtures used as backfill materials behind sheet pile walls under vertical loads. Physical model experiments were conducted to assess lateral displacement and pressure for backfills containing 10% granulated rubber (2.5-5 mm) under both dry and saturated conditions, and across varying backfill inclination angles. To complement the experiments, discrete element method (DEM) simulations were performed to capture the micromechanical behavior of sand-rubber mixtures, enabling analysis of particle-scale interactions. Material stiffness and friction parameters were calibrated through direct shear tests to ensure computational efficiency and accurate representation. Comparative analyses were conducted between the DEM simulations and the physical sheet pile tests across various sand-rubber backfill configurations. The results suggest that sand-rubber mixtures offer a practical and sustainable alternative for backfill applications, improving both mechanical performance and pressure mitigation. Furthermore, force chain development and deformation patterns were thoroughly examined to understand the role of micro parameters; such as particle contact behavior, porosity, internal friction, and stiffness of the rubber-sand composite backfill in reducing active earth pressure against sheet pile walls.