Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Developing a Label Propagation Approach for Cancer Subtype Classification Problem(TUBITAK, 2021) Güner, P.; Bakir-Güngör, B.; Coşkun, M.; Şahan, Pınar GünerCancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation-based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches. © 2022 Elsevier B.V., All rights reserved.Article Citation - Scopus: 3Chaos in PID Controlled Nonlinear Systems(Korean Institute of Electrical Engineers, 2015) Ablay, G.Controlling nonlinear systems with linear feedback control methods can lead to chaotic behaviors. Order increase in system dynamics due to integral control and control parameter variations in PID controlled nonlinear systems are studied for possible chaos regions in the closed-loop system dynamics. The Lur’e form of the feedback systems are analyzed with Routh’s stability criterion and describing function analysis for chaos prediction. Several novel chaotic systems are generated from second-order nonlinear systems including the simplest continuous-time chaotic system. Analytical and numerical results are provided to verify the existence of the chaotic dynamics. © 2021 Elsevier B.V., All rights reserved.Article An Extension of Lucas's Theorem(indian Nat Sci Acad, 2025-10-31) Cinkir, Zubeyir; Ozturkalan, AysegulWe give elementary proofs of some congruence criteria to compute binomial coefficients modulo a prime number. These criteria are analogues to the symmetry property of binomial coefficients. We give extended version of Lucas's Theorem by using those criteria. We give applications of these criteria by describing a method to derive identities and congruences involving sums of binomial coefficients.Article Sustainable Stabilization of Peat Soil with Hybrid Geopolymer Jet Grout Columns(Springer Int Publ A.G., 2025-10-15) Yalcin, Hakan; Erol, Aykut; Kaya, Zulkuf; Cadir, Cenk Cuma; Uncuoglu, Erdal; Akin, Muge K.Peat soils present severe challenges in geotechnical engineering due to their low shear strength, high water content, and aggressive chemical environments such as sulfate exposure. While cement-based jet grouting (JG) is widely used, it entails high carbon emissions and energy consumption. Hybrid geopolymer jet grout columns (HGJGCs) are presented in this work as a viable and sustainable alternative. Unlike conventional geopolymer studies that rely on pre-cured molds later exposed to aggressive environments, this research simulates realistic field conditions by injecting fresh geopolymer directly into sulfate-rich peat, where early-age durability and strength are critical. To address early strength limitations commonly seen in aggressive situations, a tiny amount of cement was added to the fly ash/GGBFS-based combination. Crucially, there is no need for high heat because the mechanism cures at room temperature. Physical model testing, laboratory-scale jet grouting, and performance comparisons with conventional JGCs were all carried out. Results show that HGJGCs increased the bearing capacity of peat by 5.5 times, improved compressive strength (5.3-5.7 MPa), and reduced settlement more effectively than JGCs. Additionally, CO2 emissions were reduced by 25.14% due to lower binder-related emissions and energy demand. This work shows that hybrid geopolymer systems are a viable, low-carbon substitute for peat stabilization because they can function well in real-world, chemically demanding situations.Article Citation - WoS: 1Citation - Scopus: 1Interaction of Inula Viscosa (L.) Aiton with IBA1 via Rosmarinic Acid and Rutin: Insights from Computational Models and Biological Effects(Wiley-VCH verlag GmbH, 2025-10-29) Aktas Pepe, Nihan; Acar, Busra; Ceylan Ekiz, Yagmur; Senol, Ayse Merve; Semiz, Gurkan; Sen, Alaattin; Celik Turgut, GurbetInula viscosa (L.) Aiton is a traditional medicinal plant extensively utilized in Mediterranean nations for the treatment of rheumatic pain, inflammatory disorders, diabetes, anemia, and cancer. This study further explored its anti-inflammatory mechanisms through the highest components, chlorogenic acid, rosmarinic acid, and rutin, on the expression of the ionized calcium-binding adapter molecule 1 (Iba1) on monocyte-derived macrophage-like cells. Iba1 is known to contribute pathogenesis of diverse inflammatory diseases. HPLC analysis identified 13 major phenolic compounds, with rosmarinic acid, chlorogenic acid, and rutin as major components. The aqueous extract of the plant and its major components exhibited dose-dependent antiproliferative activity on pTHP-1, RAW264.7, and PCS-201-012 cells. Immunofluorescence staining revealed a significant reduction in Iba1 protein expression, which is associated with inflammation, at the high dose of I. viscosa and rutin. Molecular docking studies indicated that rosmarinic acid and rutin had the strongest predicted interactions with Iba1, with docking scores of -12.403 and -12.301 kcal/mol and MM/GBSA binding energies of -64.47 and -84.20 kcal/mol, respectively. I. visoca and its major components were observed to significantly suppress iNOS activity in LPS-stimulated cells; these findings were also supported by RT-PCR results. Treatment with the high dose of I. viscosa resulted in 9.45% necrotic cells and caused cell cycle arrest in the S phase (59.2 +/- 5.23%). This suggests that it may potentially reduce the proliferation of activated macrophages. In the fibroblast migration assays, the relative wound closure rate was found to be significant 27.06 +/- 18.09% at the low dose of I. viscosa and 31.59 +/- 22.42% at the high dose of I. viscosa. Although the relatively low wound closure rate limits tissue repair, it may benefit chronic wounds and fibrosis by suppressing excessive cell proliferation and inflammation. These results suggest that I. viscosa is a promising natural source of bioactive compounds with potential applications in anti-inflammatory drug development.Article Citation - WoS: 1Citation - Scopus: 1A Comprehensive Review on the Extraction and Recovery of Lithium from Primary and Secondary Sources: Advances Toward Battery-Grade Materials(Wiley, 2025-10-20) Top, Soner; Kursunoglu, Sait; Altiner, MahmutLithium-ion battery (LIB) technologies have become indispensable to modern energy systems, driving global demand for high-purity lithium compounds. This review focuses on lithium recovery and purification strategies for battery-grade lithium carbonate (Li2CO3) and lithium hydroxide (LiOH), addressing both primary sources (brines and minerals) and secondary sources (waste materials). Industrially established processes, such as evaporation-based brine treatment and conventional metallurgical methods, are discussed alongside emerging techniques, including membrane separation, solvent extraction, and CO2-assisted precipitation. Particular attention is given to lithium precipitation mechanisms, the behaviour of co-existing ions during extraction, and the specific quality requirements for cathode material synthesis. By evaluating process scalability, environmental impact, and product purity, this review provides a comprehensive understanding of current practices and future directions. Additionally, it highlights the growing importance of lithium in the context of accelerating electric vehicle (EV) adoption, underscoring the bright and expanding future of the lithium industry.Article Tuning Mechanical Performance of PCL Scaffolds: Influence of 3D Bioprinting Parameters, Polymer Concentration, and Solvent Selection(IOP Publishing Ltd, 2025-09-01) Ceylan, Saniye Aylin; Baltacioglu, Mehmet Furkan; Bal, Burak; Bayram, Ferdi Caner; Isoglu, Ismail AlperThe mechanical performance of three-dimensional (3D) bioprinted scaffolds is susceptible to printing parameters and material formulation. In this study, poly (epsilon-caprolactone) (PCL) scaffolds were fabricated using four different polymer concentrations (10%, 25%, 50%, and 75% w/v) to investigate how these variations, along with process parameters, influence mechanical behavior. Maintaining the structural integrity of bioprinted constructs requires careful optimization of polymer concentration and precise control over parameters such as printing speed, pressure, and infill density. Tensile tests were conducted to evaluate the effects of these variables. Among the tested conditions, a 50% (w/v) concentration allowed for a broader operational window, enabling fabrication across a range of printing speeds and pressures. At a printing speed of 5 mm s-1, PCL-DCM exhibited a Young's modulus of 39.0 MPa, while PCL-CF samples printed at 10 mm s-1 achieved the highest modulus of 32.0 MPa. Notably, when the printing speed was kept constant, applying higher pressures led to an increase in Young's modulus, suggesting that pressure plays a key role in enhancing scaffold stiffness. When comparing the 50% and 75% (w/v) polymer concentrations, the 50% (w/v) formulation stood out by offering both higher elongation and greater stiffness, which makes it particularly suitable for load-bearing applications. These findings provide a quantitative framework for optimizing extrusion-based bioprinting of PCL scaffolds, with implications for customized biomedical implants and regenerative medicine.Article Failure Analysis of Fused Deposition Modeling 3D Printed Poly Lactic Acid Polymer(Sage Publications Ltd, 2025-10-04) Yilmaz, Cagatay; Eltahir, Sara Saeed AbdulrahmanAdditive manufacturing, commonly known as 3D printing (AM), has emerged as one of the most transformative technological advances in the last few decades in global manufacturing, as it allows for the production of intricate components without the use of costly molds. Fused Deposition Modeling (FDM) is widely adopted among various AM techniques due to its accessibility and effectiveness. FDM 3D-printed PLA (Poly Lactic Acid) shows a transversely isotopic symmetry similar to laminated composite structures. Therefore, classical lamination theory can be applied to FDM 3D-printed PLA. This study attempts to expand the knowledge by relying on classical lamination theory and several imposed failure theories like maximum stress, Tsai-Hill, Tsai-Wu, and Hashin to determine how FDM 3D printing of PLA fails. We investigate eight different raster orientations (0 degrees, 10 degrees, 15 degrees, 30 degrees, 45 degrees, 60 degrees, 75 degrees, and 90 degrees) and compare the theoretical prediction of strength with experimental findings. With this comprehensive analysis, we are seeking to better understand the failure analysis of FDM 3D printed PLA. The maximum stress, Tsai-Wu, Tsai-Hill, and Hashin failure theories show good agreement with experimental findings for 0 degrees and 90 degrees raster orientations. As the raster orientation shifts from 0 degrees, the discrepancy between experimental results and theoretical predictions increases, peaks at mid-angles, and then decreases, becoming negligible at 90 degrees.Article Citation - WoS: 1Citation - Scopus: 1Prediction of the Diffusible Hydrogen Concentration After Electrochemical Charging Utilizing Artificial Intelligence(IOP Publishing Ltd, 2025-09-01) Sivesoglu, Abdurrahman; Li, Yang; Bal, BurakThe concentration of diffusible hydrogen in a material is of high importance as it helps to predict the hydrogen embrittlement effect in the material, and the amount of mechanical properties' degradation after reaching a critical concentration. Despite that, a simple experimental setup is not available to measure hydrogen concentration at service. In this paper, a multi-layer perceptron (MLP) model is developed using weight initialization, which can estimate the diffusible hydrogen concentration of Face-Centred-Cubic (FCC) metals after electrochemical charging. The input properties of the model include the electrochemical charging parameters of current density, temperature, and charging time as well as the grain size of the specimen. The MLP model with and without the weight initialization was validated and tested with unseen test dataset. The model in both cases showed an excellent predictive performance with a higher accuracy and faster convergence when using weight initialization. A linear correlation of 89% between the experimental and predicted hydrogen concentration was observed. This demonstrates that for the family of FCC metals under electrochemical charging, the estimation of diffusible hydrogen concentration is a feasible path for material safety design analysis.Article Integrated Quantitative Modelling for the Dimension Stone Quality Evaluation: Implications for Sustainable Resource Management(Springer Heidelberg, 2025-09-30) Koken, Ekin; Strzalkowski, Pawel; Strzałkowski, PawełThe growing demand for dimensional stones in construction and monument conservation requires fast, repeatable and scientifically valid quality assessment procedures. The present study, in this context, established a solid foundation for quantifying the quality of dimension stones by adopting two quantitative methods: the Suitability Index (SI) and Dimension Stone Field Performance Coefficient (DSFPC). Both methods were coded in the MATLAB environment and implemented for 20 different rock types used in various dimension stone applications in Turkey. Evaluations based on the above-mentioned methods demonstrate that the DSFPC provides a more conservative assessment than the SI method. Additionally, engineering interpretations derived from the SI and DSFPC approaches are compared with recently published classification systems developed for the dimension stone industry. Focusing on this comparison, it is concluded that the adopted methods offer a more holistic evaluation framework compared to the approaches based solely on a single input parameter, such as effective porosity (ne), uniaxial compressive strength (UCS), or B & ouml;hme abrasion value (BAV) of rocks. Furthermore, it is concluded that the adopted methods complement each other by yielding supportive outcomes. The coded methods can be adapted to other lithological series and integrated with spatial information systems to support decision-making in mining and construction sectors. From this point of view, the present study may be considered a case study supporting holistic approaches to sustainable resource management in the dimension stone industry.