Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article 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 Future Circular Collider Feasibility Study Report: Volume 1 Physics, Experiments, Detectors(Springer Nature, 2025) Benedikt, M.; Zimmermann, F.; Auchmann, B.; Bartmann, W.; Burnet, J.P.; Carli, C.; Alonso, B.A.Volume 1 of the FCC Feasibility Report presents an overview of the physics case, experimental programme, and detector concepts for the Future Circular Collider (FCC). This volume outlines how FCC would address some of the most profound open questions in particle physics, from precision studies of the Higgs and EW bosons and of the top quark, to the exploration of physics beyond the Standard Model. The report reviews the experimental opportunities offered by the staged implementation of FCC, beginning with an electron-positron collider (FCC-ee), operating at several centre-of-mass energies, followed by a hadron collider (FCC-hh). Benchmark examples are given of the expected physics performance, in terms of precision and sensitivity to new phenomena, of each collider stage. Detector requirements and conceptual designs for FCC-ee experiments are discussed, as are the specific demands that the physics programme imposes on the accelerator in the domains of the calibration of the collision energy, and the interface region between the accelerator and the detector. The report also highlights advances in detector, software and computing technologies, as well as the theoretical tools/reconstruction techniques that will enable the precision measurements and discovery potential of the FCC experimental programme. The content and structure of this report are guided by the scope and priorities defined in the mandate of the FCC Feasibility Study. It is therefore not intended to serve as an exhaustive review of the full physics potential of FCC. Several topics, already covered in earlier reports such as the FCC CDR, are not reiterated here or are addressed only briefly, in alignment with the study’s focus. This volume reflects the outcome of a global collaborative effort involving hundreds of scientists and institutions, aided by a dedicated community-building coordination, and provides a targeted assessment of the scientific opportunities and experimental foundations of the FCC programme. © CERN for the benefit of the FCC collaboration 2025.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 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 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.Article Almond Cheese Analog Fortified with Microencapsulated Lactiplantibacillus Plantarum DSM 1954: Evaluation of Viability and Quality Parameters Using Different PlantBased Proteins(Springer India, 2025) Ozturk, Burcu; Elvan, Mensure; Harsa, Hayriye SebnemThe objective of this study was to evaluate the viability of Lactiplantibacillus plantarum DSM1954 encapsulated using plant-based proteins as novel coating materials, when supplemented into almond cheese-analog during storage. Freeze-dried Lb. plantarum strains that were both microencapsulated and non-microencapsulated were added to cheese-analog. A water-in-oil emulsion method was used with a variety of plant-based proteins, including soy, pea, and potato. Microbial analysis, chemical composition, color analysis were conducted on the cheese-analogs. Microencapsulation was successfully achieved with pea and soy proteins, demonstrating encapsulation efficiencies of 85.8% and 86.6%, respectively; however, potato protein concentrate failed to form microcapsules. The viability of microencapsulated cells was higher than 10 log CFU/g during storage. The survivability of Lb. plantarum under acidic conditions was observed to be 0.85 log reduced in microencapsulated cells, whereas 3 log reduction was determined in non-microencapsulated cells. According to the SEM analysis, the diameter of the microencapsulated cells was found to be 0.8-1.5 mu m. Both microencapsulated and non-microencapsulated probiotic cells maintained viability above the probiotic threshold (> 6 log CFU/g) in cheese-analogs during storage. Although plant-based microencapsulation slightly affected the appearance by causing a darker color in cheese-analogs, this novel approach provides a promising alternative for enhancing probiotic stability in plant-based dairy alternatives.