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 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 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 Investigation of Few-Layer Graphene-Ubiquitin Interactions with Optical Spectroscopy Techniques(MDPI, 2025) Gencay, Burcu; Guler, GunnurUnderstanding the molecular mechanisms of protein-nanoparticle interactions is crucial for enabling the development of new applications in biomedicine and nanotechnology. Ubiquitin, an important and structurally small functional protein, plays a central role in numerous cellular processes. Therefore, in the current study, we focused on the few-layer graphene (FLG)-Ubiquitin complexes formed by exfoliating FLG structures using only water. Optical spectroscopic techniques (Raman, FT-IR, UV-Vis and circular dichroism) were employed to investigate these complexes on the molecular level. Overall, both CD and FT-IR data reveal that the formation of the FLG-Ubiquitin complexes occurred without inducing disordered structures in the protein. Based on the existence of a blue shift (hypsochromic shift) in the UV-Vis data, the presence of a single tyrosine and two phenylalanine residues in ubiquitin enables the detection of FLG-induced micro-environmental changes, particularly influencing the protein's beta-sheet and alpha-helix structures. The CD spectral results and CDPro quantitative estimations are in line with ATR FT-IR results, confirming the absence of disordered structure formation while altering the protein's chirality. UV-Vis and CD spectroscopy results revealed concentration-dependent trends consistent with FLG-protein interactions that preserve the overall protein structure. This study has potential applications in both academic research and practical usage, particularly in biomedicine and nanotechnology specifically for FLG.Article CFD-DEM Investigation on Particle Separation from Fluid Flow Using Magnetic Fields(Elsevier, 2026) Morsali, Shaghayegh; Kazemi, Saman; Farahani, Farhang Jalali; Zarghami, RezaThis study presents a numerical simulation of magnetic particle separation from fluid flow using CFD-DEM modeling. Studies have shown that magnetic fields are an effective tool for particle separation, especially on small scales, and variables such as magnetic field intensity, fluid velocity, and particle size significantly impact separation efficiency. Other factors, such as the initial location of particles and their density, were also examined, and their effect on the attraction of particles was determined. The magnetic field was applied through a line dipole in the fluid channel. The simulation results show that particles accumulate in the channel area where the line dipole is located, with higher particle concentration at the beginning of the dipole compared to other sections. Additionally, the results indicate that increasing the magnetic field intensity significantly improves separation efficiency, while increasing fluid velocity can decrease this efficiency. At a velocity of 0.2 m per second, results showed that increasing the magnetic field intensity from 0.6 to 3 T improved the capture efficiency from 69 % to 91 %. Similarly, at a magnetic field intensity of 1 T, reducing the fluid velocity from 0.3 to 0.1 m per second doubled the capture efficiency. In the optimal state, combining maximum field intensity with minimum velocity can achieve an efficiency of 98 %. It was also observed that larger particle diameters and higher densities have a positive effect on particle attraction.Article Toward Reliable Annotation in Low-Resource NLP: A Mixture of Agents Framework and Multi-LLM Benchmarking(IEEE-Inst Electrical Electronics Engineers Inc, 2025) Onan, Aytug; Nasution, Arbi Haza; Celikten, TugbaThis paper introduces the Mixture-of-Agents (MoA) framework, a structured approach for improving the reliability of large language model (LLM)-based text annotation in low-resource NLP contexts. MoA employs coordinated agent interactions to enhance agreement, interpretability, and robustness without manual supervision. Evaluations on Turkish classification benchmarks demonstrate that MoA achieves up to 10-point improvements in macro-F1 over single-model baselines and significantly increases inter-agent consistency. Additionally, three novel reliability metrics-Conflict Rate (CR), Ambiguity Resolution Success Rate (ARSR), and Refinement Correction Rate (RCR)-are proposed to quantify annotation stability and correction dynamics. The results indicate that multi-agent coordination can substantially improve label quality, offering a scalable pathway toward trustworthy annotation in low-resource and cross-domain applications. The framework is language-agnostic and adaptable to other low-resource contexts beyond Turkish, including morphologically rich or typologically diverse languages such as Indonesian, Urdu, and Swahili. These findings highlight the scalability of MoA as a generalizable solution for multilingual and cross-domain annotation.Article Hydrological Insights From SWOT: Comparative Analysis of Water Surface Elevation and Area Time Series From Hydrocron API(Elsevier, 2025) Karahan, Sait Mutlu; Gunduz, OrhanThe Surface Water and Ocean Topography (SWOT) mission plays an essential role in enhancing the monitoring and management of inland water bodies by providing high-resolution global observations of surface water dynamics. A critical tool in leveraging SWOT data is the Hydrocron API (Application Programming Interface), which facilitates access to temporally consistent SWOT-derived hydrological datasets. In this study, SWOT's Lake data "L2_HR_LakeSP" time series data retrieved from Hydrocron was utilized to evaluate water surface elevation (WSE) and surface area dynamics across six distinct lake locations around the world. To quantify the accuracy of SWOT, error metrics including Symmetric Mean Absolute Percentage Error (SMAPE), Absolute Percentage Error (APE), and Normalized Root Mean Square Error as a percentage (NRMSE%) were computed for both WSE and surface area estimates. The results indicated that the highest WSE error, with a SMAPE of 3.83 %, was observed in the lake characterized by the smallest surface area, suggesting a sensitivity of SWOT measurements to spatial scale. Conversely, the greatest error in surface area estimation occurred in the shallowest lake with SMAPE and APE values of 19.56 % and 22.01 %, respectively, highlighting the influence of bathymetric complexity on SWOT's detection capabilities. Despite these localized variances, the overall performance of SWOT data was found to be highly promising, demonstrating strong potential for operational hydrological applications and long-term water resource monitoring. The integration of SWOT observations with hydrological models via platforms such as Hydrocron underscores the mission's potential in advancing the understanding of inland water dynamics at both regional and global scales.Article Lapatinib-Loaded ZIF-8 Nanoparticles: a Multifunctional Drug Delivery System With Anticancer, Antibacterial, and Antioxidant Properties(American Chemical Society, 2025) Aslan, Ezgi; Sanli-Mohamed, GulsahThe pitfalls of conventional chemotherapy, including poor solubility, off-target toxicity, and multidrug resistance, have driven the development of nanoparticle-based delivery systems. Here, we report the facile one-pot synthesis of lapatinib-encapsulated zeolitic imidazolate framework-8 (LAP@ZIF-8) nanoparticles. The formulation achieved an encapsulation efficiency of 72.4% and a drug loading capacity of 6.6%. Comprehensive physicochemical characterization confirmed uniform hexagonal morphology (SEM), favorable hydrodynamic size (236 +/- 2 nm; DLS), positive surface charge (+29 mV; zeta-potential), high crystallinity (XRD), and excellent thermal stability (TGA). LAP release was pH-responsive, with similar to 77% cumulative release at pH 5.5 (tumor-mimicking) versus 43% at pH 7.4 after 96 h. Serum-protein binding (<11%) and hemolysis (<2%) assays demonstrated good biocompatibility. In vitro, LAP@ZIF-8 exhibited potent, selective cytotoxicity toward HER2-positive SK-BR-3 breast-cancer cells (72 h IC50 = 1.2 mu g mL-1) while sparing HER2-negative MCF-7 cells. Importantly, both free LAP and LAP@ZIF-8 were well-tolerated by nontumorigenic MCF-10A mammary epithelial cells: viability remained >= 90% at <= 1 mu g mL-1 and exceeded 50% even at 100 mu g mL-1, indicating that the IC50 was not reached and providing a preliminary safety window for healthy tissues. Beyond its anticancer effects, the nanocarrier displayed broad-spectrum antibacterial activity (minimum bactericidal concentrations: 5 mg mL-1 for Staphylococcus aureus and 10 mg mL-1 for Escherichia coli) and moderate antioxidant capacity (DPPH IC50 = 666 mu g mL-1). Collectively, these results position LAP@ZIF-8 as a versatile, pH-sensitive platform that combines selective anticancer efficacy with low toxicity to healthy cells alongside ancillary antibacterial and antioxidant properties suitable for multimodal therapy.Article Nagaoka Ferromagnetism in Semiconductor Artificial Graphene(IOP Publishing Ltd, 2026) Oztarhan, Gokhan; Potasz, Pawel; Guclu, A. D.We present the emergence of Nagaoka ferromagnetism in semiconductor-based artificial graphene with realistic Coulomb interaction using high-precision variational and diffusion Monte Carlo methods, complemented by exact diagonalization calculations of the generalized Hubbard model. We analyze models of armchair hexagonal geometries nanopatterned on GaAs quantum wells. Our results reveal a distinct magnetic phase transition driven by the absence/addition of a single electron at half-filling. This form of itinerant magnetism, predicted rigorously for the Hubbard model, remained unascertained in large scale realistic systems. We demonstrate that Coulomb scattering terms play a crucial role in stabilizing Nagaoka ferromagnetism, enabling the observation of the phase transition for system parameters near U/t approximate to 60.Article Magnetic Levitation-Based Determination of Single-Nuclei Density(Elsevier, 2026) Anil-Inevi, Muge; Sarigil, Oyku; Unal, Yagmur Ceren; Tekin, H. Cumhur; Mese, Gulistan; Ozcivici, EnginThe biophysical properties of cells and intracellular compartments provide critical insights into their structural and functional states, holding significant potential for biological and medical applications. Single-cell density has recently emerged as a promising biomarker in various research areas, including disease detection, making its precise measurement in biological samples an important analytical objective. Magnetic levitation offers significant advantages over traditional density detection techniques by enabling single-cell analysis rather than bulk measurements, providing precise quantification while preserving natural sample properties and eliminating the need for complex and expensive equipment. While magnetic levitation has been successfully applied to singlecell and cell-aggregate analysis, its use for subcellular compartments remains unexplored. Here, we demonstrate the first application of magnetic levitation technology for the density-based analysis of cell nuclei, a critical organelle essential for genomic preservation and organization. To accommodate the unique size and density characteristics of nuclei compared to whole cells, we systematically investigated appropriate paramagnetic agents, sample loading concentrations, and nuclear equilibrium times required for optimal levitation. We mapped density distributions of nuclei from different cell lines and conducted parallel assessments of cellular and nuclear density changes following cell cycle perturbations and treatments inducing cell death through distinct mechanisms. Our findings establish magnetic levitation as a powerful tool for subcellular density analysis, with potential applications in cell biology research and clinical diagnostics through improved understanding of subcellular physical parameters.