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, Amin
    The 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, Volkan
    Neu1 (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
    Liposomal Encapsulation of a Synthetic Bromophenol for Antitumor Efficacy and Apoptotic Activity in Cancer Cells
    (Springer, 2026) Oztanrikulu, Bercem Dilan; Ozdemir, Ekrem; Avci, Bahri; Goksu, Suleyman; Bayrakceken, Handan Uguz; Askin, Hakan
    A novel synthetic bromophenol (BP), inspired by marine-derived natural bromophenols, was evaluated for its antitumor activity and for the enhancement of its in vitro performance through liposomal encapsulation (LipoBP). Etoposide was used as a reference in characterization, release, and loading studies. PEGylated liposomes were employed to improve BP's solubility, bioavailability, and therapeutic potential. The cytotoxicity, apoptosis, and gene expression effects of free BP and LipoBP were assessed in A549 (lung) and MCF-7 (breast) cancer cell lines. WST-8 assays showed that encapsulation significantly increased BP's cytotoxic activity, particularly in A549 cells, while flow cytometry and Annexin V-FITC/PI analyses indicated more pronounced apoptotic induction by LipoBP compared with free BP. qRT-PCR analyses revealed upregulation of proapoptotic genes (BAX, CASP6, CASP3 and CASP9) and downregulation of antiapoptotic/survival genes (BCL-XL, IQSEC2) in both cell lines, indicating activation of intrinsic apoptotic pathways. Plain liposomes exhibited minimal cytotoxicity, confirming their biocompatibility. Liposomal bromophenol, which we have introduced to the literature for the first time, is expected to be a promising nanocarrier system that could be effective in cancer treatment by improving the therapeutic index of new drug candidates such as marine bromophenols.
  • Article
    Fluid-CO2 Injection in a Hypersaline Volcanic Systems: A Reactive Transport and Experimental Evaluation with Application to the Tuzla Geothermal Field, Turkiye
    (Springer, 2026) Tonkul, Serhat; Erol, Selcuk; Baba, Alper; Regenspurg, Simona
    This study evaluates the CO2 sequestration capability of the Tuzla Geothermal Field (TGF) in northwest T & uuml;rkiye under reservoir conditions (200 degrees C and 4.4 MPa). While ongoing studies at TGF have investigated CO2 co-injection primarily for geothermal heat extraction, the present study focuses on the associated potential for long-term CO2 storage. To this end, CO2-brine-rock interactions were examined through batch reactor experiments and reaction path modeling using the PhreeqC geochemical tool. The experiments revealed complex dissolution/precipitation reactions that altered reservoir properties, with mineralogical analyses (XRD, XRF, SEM, and EDS) showing the formation of secondary phases such as calcite, kaolinite, and Ca-rich aluminosilicates. These results indicate that the Tuzla reservoir rocks provide sufficient divalent cations to support mineral trapping under reservoir conditions. Overall, our findings highlight that, in addition to its promise for heat extraction, CO2 co-injection at TGF offers an opportunity for permanent geological storage, thereby strengthening the dual benefits of this approach.
  • 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, Volkan
    Tay-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.
  • Correction
    Automating Software Size Measurement From Python Code Using Language Models (Vol 33, 19, 2026)
    (Springer, 2025) Tenekeci, Samet; Unlu, Huseyin; Gul, Bedir Arda; Keles, Damla; Kucuk, Murat; Demirors, Onur
  • 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 Baris
    The 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, Onur
    Software 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
    Performance of Sheet Pile Walls With Rubber-Modified Backfill
    (Springer, 2025) Ecemis, Nurhan; Kadekeshova, Kuralay; Khlaif, Ali Hamid
    This 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.