Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
Browse
369 results
Filters
Settings
Search Results
Article Self-Assembled Peptide Hydrogels with Cell Attachment Motifs for 3D Lung Cancer Model: Evaluation of Cell-Matrix Interactions and Drug Response(John Wiley and Sons Inc, 2026) Sırma Tarım, B.; Tamburaci, S.; Top, A.3D cancer models can mimic the tumor microenvironment, serving as a physiologically relevant platform to investigate the behavior of tumors and test anticancer therapeutics. Although bioactive peptide hydrogels have been widely evaluated for tissue engineering applications, their potential in 3D cancer models has been confirmed in only a few studies. In this study, self-assembling peptide hydrogels containing LDV (IBP1) and LDV and IKVAV cell attachment motifs (IBP2), and the control hydrogel without adhesion units (KLEI) were used for lung cancer modeling. The peptides self-assembled into hydrogels in a cell culture medium with storage moduli of ∼700–1500 Pa. The IBP1 and IBP2 hydrogels enhanced A549 cell proliferation and induced the formation of spheroids with average diameters between ∼70 and ∼150 µm. The cells in KLEI hydrogel with the highest stiffness exhibited mesenchymal-type migration, independent of the cell population, whereas transformation to mesenchymal migration necessitated a specific cell population in the IBP2 hydrogel. The cells in the IBP1 and IBP2 hydrogels with enhanced cell-cell interactions demonstrated higher resistance to docetaxel (DTX). Thus, our results indicate that these bioactive hydrogels can serve as a promising platform for in vitro assessment of cancer mechanisms and drug screening. © 2026 Wiley-VCH GmbH.Article Epigallocatechin Gallate and Punicalagin Combination Reduces Aβ Aggregation and Promotes Neurogenesis in Adult Zebrafish Brain(John Wiley and Sons Inc, 2026) Nazli, D.; Ipekgil, D.; Poyraz, Y.K.; Can, K.; Okmen, I.; Turhanlar-Sahin, E.; Ozhan, G.Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory impairment, and behavioral alterations. The pathogenesis of AD involves the accumulation of amyloid-beta (Aβ) plaques and the hyperphosphorylated tau proteins, which disrupt neuronal function and trigger neuroinflammation. This study explores the therapeutic potential of epigallocatechin gallate (EGCG) and punicalagin (PU) in mitigating Aβ-induced toxicity using an adult zebrafish model of AD. Our results demonstrate that the EGCG + PU combination significantly reduces Aβ accumulation, protects against cellular damage, suppresses acetylcholinesterase (AChE) activity, and normalizes the expression of amyloidogenic and AD-related genes. Additionally, EGCG + PU treatment alleviates neuroinflammation by suppressing glial activation, including reductions in L-plastin and proinflammatory cytokine expression, while promoting neuronal recovery through mechanisms of neurogenesis and neuroprotection. Notably, the combination treatment restored neuronal density and improved behavioral outcomes by alleviating anxiety- and aggression-like behaviors associated with Aβ toxicity. These results underscore the synergistic neuroprotective effects of EGCG + PU, highlighting their potential as a novel therapeutic approach for mitigating the pathological, behavioral, and inflammatory aspects of AD. © 2026 Wiley Periodicals LLC.Article Robust CVD Polymer Encapsulation for Thermally and Chemically Resistant Fluorescent Sensor Nanoprobes(Elsevier Ltd, 2026) Karabıyık, M.; Cihanoğlu, G.; Ebil, Ö.Semiconductor quantum dots (QDs) are attractive fluorophores for sensor applications due to their narrow emission bandwidths and high photostability; however, their performance is often limited by insufficient chemical and thermal durability under operating conditions. In this study, a solvent-free encapsulation strategy based on initiated chemical vapor deposition (iCVD) is proposed to enhance the stability of QD-based sensor nanoprobes. Cross-linked poly (glycidyl methacrylate-co-ethylene glycol dimethacrylate) (ECOP) thin films were conformally deposited as encapsulation layers onto CdTe QD-functionalized poly(GMA) sensor surfaces. The encapsulated nanoprobes were evaluated under chemically aggressive environments (water, salt water, toluene, and sulfuric acid) and elevated temperatures. Following exposure to aggressive solvents, both the polymer film thickness variation and QD fluorescence intensity change remained below 10 %, confirming the robustness of the cross-linked network. Also, thermal durability tests showed stable fluorescence performance after annealing at 250 °C, with structural and optical changes remaining within the accepted 10 % threshold. The results demonstrate that coatings deposited using iCVD exhibit conformal coverage and enhanced stability. This enables reliable protection of QD-based sensor nanoprobes without compromising optical performance. This study presents a promising method to extend the operational lifetime and environmental durability of QD-integrated sensor platforms by using chemically and thermally stable polymer encapsulation. © 2026 Elsevier LtdArticle On Group Connected Transmissive Beyond Diagonal RIS for MIMO Systems(Institute of Electrical and Electronics Engineers Inc., 2026) Ilguy, M.; Özbek, B.; Le Ruyet, D.Reconfigurable intelligent surfaces (RIS) have emerged as an important technology for next-generation wireless networks by intelligently manipulating the wireless propagation environment. Beyond Diagonal RIS (BD-RIS) extends the traditional RIS architecture by allowing non-diagonal reflection matrices, enabling more flexible signal manipulation. Transmissive RIS (T-RIS), on the other hand, facilitates the transmission of signals through the metasurfaces. In this paper, we propose a novel design called transmissive BD-RIS (T-BD-RIS), which integrates the functionalities of BD-RIS and T-RIS to enhance the user data rate. We design an algorithm for the group connected (GC) configuration, which jointly optimizes the beamforming at the base station, the T-BD-RIS transmission matrix, and the receive combiner at the user side. The fully connected (FC) and single connected (SC) cases are special instances of the proposed generic GC design, obtained by an appropriate choice of the number of groups. We evaluate the performance of various schemes, demonstrating the potential of the proposed approach. © 1997-2012 IEEE.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 Robust Scheduling of Crude Oil Farming and Processing Under Uncertainty(Elsevier, 2026) Yalcin, Damla; Sildir, HasanThe sulphur content in crude oil has a significant impact on refinery operations, influencing the feasibility of crude blending, the distribution of product yields, and overall economic performance. Variations in sulphur content introduce uncertainty in the short-term scheduling of crude oil loading, blending, and distillation processes. This study introduces a scenario-based stochastic optimization framework in which sulphur uncertainty is treated as a central modeling element, represented through a regression-based relationship with specific gravity (SG). The approach systematically propagates uncertainty through blending decisions, crude distillation unit (CDU) feed composition, and product yields. The problem is modeled as a mixed-integer quadratically constrained programming (MIQCP) formulation within a continuous-time scheduling framework, enabling the simultaneous optimization of timing, blending, and processing strategies. The results indicate that increased sulphur uncertainty adversely affects the distribution of yields for nine end-products, resulting in profit losses. These findings underscore the importance of explicitly managing compositional uncertainty and provide insights into cost-performance trade-offs in refinery scheduling.Article Rice-Like, Hollow, and Rhombohedral Nano-Calcite Synthesis by Carbonization(Elsevier, 2026) Kilic, Sevgi; Toprak, Gorkem; Ozdemir, EkremControlling the morphology and size of calcium carbonate (CaCO3) remains an essential challenge in the production of high-performance fillers and advanced functional materials. Here, we report a continuous carbonization strategy that enables the synthesis of monodisperse nano-calcite particles with tunable rice-like, hollow, and rhombohedral morphologies through precise control of CO2 dissolution into a flowing Ca(OH)2 solution under diffusion-limited conditions. A two-stage reactor was designed to decouple nucleation and growth by separating the gas-liquid interaction zone from a stabilization tank. pH and conductivity analyses revealed that crystallization is primarily governed by the CO2 dissolution kinetics rather than mixing intensity in the stabilization tank. SEM and XRD analyses demonstrate a distinct crystallization sequence such that initial formation of rice-like calcite, subsequent development of hollow nanoparticles through selective tip dissolution, and final transformation into rhombohedral calcite via dissolution-reprecipitation mechanism. The method provides a reproducible, template-free route for fabricating hollow CaCO3 nanoparticles, overcoming limitations of bubbletemplating and additive-mediated techniques. This scalable process provides a robust foundation for producing high-surface-area CaCO3 nanomaterials which have potential applications in thin films, ceramics, protective coatings, lightweight composites, thermal/acoustic insulation, adsorption, and catalysis, where tailored particle morphology and size can significantly enhance performance.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 Damage Assessment of Structures Following the February 6, 2023 Kahramanmaraş Earthquakes: A Dataset-Based Case Study in Gaziantep, Türkiye(Springer Heidelberg, 2025) Atasever, Kurtulus; Aydogdu, Hasan Huseyin; Narlitepe, Furkan; Goksu, Caglar; Demir, Ugur; Demir, Cem; Ilki, AlperFollowing the 2023 Kahramanmara & scedil; Earthquakes (Mw 7.7 and 7.6) that struck T & uuml;rkiye on February 6, 2023, the Ministry of Environment, Urbanization, and Climate Change (MoEUCC) initiated a large-scale post-earthquake damage assessment campaign, targeting more than 2,3 million structures within the affected region. A comprehensive field survey was carried out in and around Gaziantep, one of the most severely affected cities. The authors assessed more than 1700 structures representing a wide range of occupancy types, including residential, educational, healthcare, religious, administrative, industrial, and lodging structures. In this paper, the methodological process of post-earthquake data collection in and around Gaziantep is presented, together with the data on the distribution of damage with respect to construction period, number of stories, and building occupancy type, to ensure a complete understanding of the extent and characteristics of structural damage. The damage assessment employed two data sources: (i) the data gathered through the authors' newly developed, novel damage-assessment software, presented here for the first time, and (ii) the official post-earthquake damage database of the MoEUCC. A further novelty of this study is the presentation of the largest dataset to date for the investigated earthquake doublet, encompassing approximately 1700 buildings. Additionally, the relationship between damage states, peak ground accelerations, and fault distances is thoroughly investigated. The detailed earthquake-hit site investigations revealed that the examined structures displayed structural inadequacies akin to those witnessed in previous seismic events, with a notable focus on the arrangement of the structural system, the quality of construction materials and reinforcement detailing.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.