WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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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 An Effective Legendre Wavelet Technique for the Time-Fractional Fisher Equation(Univ Tabriz, 2026) Idiz, Fatih; Tanoglu, Gamze; Aghazadeh, Nasser; Mohammadi, AmirThis study modifies the time-fractional Fisher equation by adding a source term and generalizing the non-linear power to an arbitrary order. A numerical technique is proposed for the modified time-fractional Fisher equation using Legendre wavelets and the quasilinearization technique. The non-linear term is iteratively linearized using the quasilinearization technique. The convergence analysis and error estimates of the proposed method are studied. Several test problems are solved using the proposed technique, and numerical outcomes are contrasted with those obtained using some other approaches existing in the literature.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 Linking RNA Methylation to Structure: A Biophysical Perspective(Wiley, 2026) Akgul, Bunyamin; Guler, Gunnur; Saglam, Buket; Akkus, Onur; Akcaoz-Alasar, AzimeRecent epitranscriptomic studies show that ribonucleic acids (RNAs) are coated with an array of chemical modifications that dictate their cellular fate. Genetic, biochemical, and genomic approaches have been employed to elucidate the molecular details of RNA methylation, one of the most prevalent types of RNA modifications with significant implications for health and disease. Various biochemical approaches have been developed to identify RNA methylations both at the global and nucleotide resolution levels. However, simpler detection methods are needed to assess the global methylation status of synthetic or cellular RNAs. Although significant progress has been made in elucidating the factors involved in writing, erasing, or reading methylated epitopes or structures, the impact of these methyl moieties on the secondary structure of RNAs or macromolecular interactions remains to be fully understood. Typically, biophysical approaches, such as Fourier transformed-infrared (FT-IR) spectroscopy, circular dichroism (CD), and Raman spectroscopy, have been used to study the structures and interactions of macromolecules, including DNA and proteins. Although RNAs harbor similar chemical modifications or structure-mediated functions, the number of RNA studies that employ biophysical approaches is scarce. In this viewpoint article, we present a biophysical perspective that links RNA methylation to structure and propose that FT-IR analyses can be employed to examine global changes in the abundance of cellular RNA m(6)A marks. Additionally, we discuss the potential applications of biophysical approaches that may be employed to gain insight into methylation-mediated changes in RNA structures.Article Development of Self-Assembled Peptide Hydrogels Containing Matrix-Metalloproteinase Degradable Motifs for 3D Lung Cancer Models(Royal Society of Chemistry, 2026) Tarim, Burcu Sirma; Tamburaci, Sedef; Top, AybenHydrogel-forming peptides, including matrix metalloproteinase (MMP)-degradable motifs, have been employed to investigate cell-extracellular matrix interactions in vitro. However, their potential in 3D cancer models has been explored only in a few studies. In this study, we used modified MMP-2 degradable motifs (VSLRA or ASLRA) in the design of EDP1 (RVSLRADARVSLRADA) and EDP2 (RASLRADARASLRADA) peptide hydrogelators. The peptides self-assembled into nanofibrillar hydrogels with storage moduli between similar to 300 and similar to 400 Pa. MMP-2 degradation properties of the peptides were confirmed, and a slightly higher MMP-2 responsiveness of the EDP1 hydrogel was observed. The hydrogels were used in the encapsulation of A549 lung adenocarcinoma cancer cells and MRC-5 human lung fibroblast cells. The designed hydrogels supported the proliferation of these cells with high viability and induced cluster formation of encapsulated A549 cells similar to that observed with the RADA hydrogel. However, the hydrogel network structure affected the morphology of the migrated cells in the absence of curcumin. The addition of curcumin decreased the migration and invasion of A549 cells, resulting in a round cell morphology independent of the hydrogel matrices. Anticancer drug tests indicated that cell viability after drug treatment was higher in the 3D hydrogels than in 2D cultures. It was also confirmed that the combinational therapy of doxorubicin and curcumin decreased the cell proliferation and colonization to a greater extent compared to doxorubicin monotherapy. Thus, the hydrogels developed in this study can be used for 3D cancer models or other tissue engineering applications as an alternative to the RADA hydrogel by exploiting the MMP-2 degradation properties.Article Enhanced Osteoconductive Properties of Quince Seed Hydrocolloid-Based Composite Scaffolds Enriched With Bioactive Glass for Bone Tissue Engineering(Wiley-VCH Verlag GmbH, 2025) Yilmaz-Dagdeviren, Hilal Deniz; Zheng, Kai; Boccaccini, Aldo Roberto; Arslan Yildiz, AhuBioactive composite scaffolds enhance osteoconduction and mineralization, offering potential for bone regeneration. In this study, polysaccharide-based Quince Seed Hydrocolloid (QSH) was combined with Gelatin (Gel), mesoporous bioactive glass nanoparticles (MBGNs), and 45S5 bioactive glass (BG) to fabricate osteoconductive scaffolds. QSH/Gel/BG and QSH/Gel/MBGN composites were characterized for chemical composition, mechanical behavior, and in vitro bioactivity. FTIR and SEM-elemental mapping confirmed homogeneous bioactive glass incorporation. BET analysis revealed a >3-fold increase in surface area for MBGN-containing scaffolds compared to BG and pristine QSH/Gel samples, attributed to the nanoscale mesoporous structure of MBGNs. Swelling tests showed a hydrophilic nature in all scaffolds, with MBGN composites exhibiting the highest swelling ratio (2094 +/- 571%), nearly twice that of BG composites (1105 +/- 56%). Compression tests indicated similar elastic moduli for MBGN and BG containing scaffolds (2330 and 2140 Pa). Human osteosarcoma cell cultures (28 days) demonstrated high viability (>70%) and osteoconductive response in all composites. Alizarin Red staining and SEM mapping revealed greater mineral accumulation in MBGN-containing scaffolds (Ca/P: 2.53). Overall, both composites supported a 3D osteoconductive microenvironment, while MBGN scaffolds exhibited superior long-term cell viability and mineralization potential, emphasizing their suitability for bone tissue engineering applications.