Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Role of Long Non-Coding RNA X-Inactive Transcript (XIST) in Neuroinflammation and Myelination: Insights From Cerebral Organoids and Implications for Multiple Sclerosis(MDPI, 2025) Pepe, Nihan Aktas; Acar, Busra; Zararsiz, Gozde Erturk; Guner, Serife Ayaz; Sen, AlaattinBackground/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods: Human cerebral organoids with oligodendrocytes were produced from XIST-silenced H9 cells, and the mature organoids were subsequently treated with either FTY720 or DMF. Gene expression related to inflammation and myelination was subsequently analyzed via qRT-PCR. Immunofluorescence staining was used to assess the expression of proteins related to inflammation, myelination, and neuronal differentiation. Alpha-synuclein protein levels were also checked via ELISA. Finally, transcriptome analysis was conducted on the organoid samples. Results: XIST-silenced organoids presented a 2-fold increase in the expression of neuronal stem cells, excitatory neurons, microglia, and mature oligodendrocyte markers. In addition, XIST silencing increased IL-10 mRNA expression by 2-fold and MBP and PLP1 expression by 2.3- and 0.6-fold, respectively. Although XIST silencing tripled IBA1 protein expression, it did not affect organoid MBP expression. FTY720, but not DMF, distinguished MBP and IBA1 expression in XIST-silenced organoids. Furthermore, XIST silencing reduced the concentration of alpha-synuclein from 300 to 100 pg/mL, confirming its anti-inflammatory role. Transcriptomic and gene enrichment analyses revealed that the differentially expressed genes are involved in neural development and immune processes, suggesting the role of XIST in neuroinflammation. The silencing of XIST modified the expression of genes associated with inflammation, myelination, and neuronal growth in cerebral organoids, indicating a potential involvement in the pathogenesis of MS. Conclusions: XIST may contribute to the MS pathogenesis as well as neuroinflammatory diseases such as and Alzheimer's and Parkinson's diseases and may be a promising therapeutic target.Article Demystifying Power and Performance Variations in Gpu Systems Through Microarchitectural Analysis(Comsis Consortium, 2025) Topcu, Burak; Karabacak, Deniz; Oz, IsilGraphics Processing Units (GPUs) serve efficient parallel execution for general-purpose computations at high-performance computing and embedded systems. While performance concerns guide the main optimization efforts, power issues become significant for energy-efficient and sustainable GPU executions. Profilers and simulators report statistics about the target execution; however, they either present only performance metrics in a coarse kernel function level or lack visualization support that can enable microarchitectural performance analysis or performance-power consumption comparison. Evaluating runtime performance and power consumption dynamically across GPU components enables a comprehensive tradeoff analysis for GPU architects and software developers. In this work, we present a novel memory performance and power monitoring tool for GPU programs, GPPRMon, which performs a systematic metric collection and provides useful visualization views to guide power and performance analysis for target executions. Our simulation-based framework dynamically gathers SM and memory-related microarchitectural metrics by monitoring individual instructions and reports dynamic performance and power values. Our interface presents spatial and temporal views of the execution. While the first demonstrates the performance and power metrics across GPU memory components, the latter shows the corresponding information at the instruction granularity in a timeline. We demonstrate performance and power analysis for memory-bound graph applications and resource-critical embedded programs from GPU benchmark suites. Our case studies reveal potential usages of our tool in memory-bound kernel identification, performance bottleneck analysis of a memory-intensive workload, performance-power evaluation of an embedded application, and the impact of input size on the memory structures of an embedded system.Article Citation - WoS: 3Citation - Scopus: 3Numerical Assessment of Vertical Axis Hydrokinetic Turbine Efficiencies With Different Grate Protections(Inst Engineering Technology-IET, 2025) Karakaya, Derya; Elci, SebnemHydrokinetic turbines are crucial for sustainable power generation, but their performance is often impacted by floating debris and sediment transport, which can damage turbine blades. Sediment retention enhances the turbine's lifespan and reduces maintenance by preventing blade erosion, cavitation and clogging. Protective grates reduce abrasive particle entry, minimising blade wear. They also avoid buildup of sediment, lowering the risk of blockages and cavitation, which harm efficiency and accelerate degradation. This study presents the numerical performance of Darrieus-type vertical axis hydrokinetic turbines under the impact of straight and Coanda type grate protection structures. The effects of these two types of grate structures with different design angles on turbine power coefficient (CP) and torque coefficient (CT) were investigated using the ANSYS Fluent program. The dynamic mesh technique simulated the turbine rotation and the semi-implicit method for pressure-linked equations (SIMPLE) was applied with a shear stress transport (SST) k-omega turbulence model. The turbine's efficiency was compared and the results were evaluated for steady and unsteady flow conditions. The highest power coefficients were obtained as 0.230 and 0.264 for steady and unsteady flow, respectively, in the Coanda grate with a 30 degrees central angle. The highest power coefficients were obtained as 0.215 and 0.247 for steady and unsteady flow, respectively, in the straight grate design with a 60 degrees inclination angle. The sediment retention capacities of Coanda grates (30 degrees central angle) and straight grates (60 degrees inclination angle) with varying particle size distributions were further investigated using the discrete phase model (DPM) under steady flow conditions.Article Citation - WoS: 6Citation - Scopus: 7Physics-Based Machine Learning for Modeling of Laminated Composite Plates Based on Refined Zigzag Theory(Springer, 2025) Ermis, Merve; Dorduncu, Mehmet; Aydogan, GokayPhysics-based machine learning techniques have recently gained prominence for their ability to model complex material and structural behavior, particularly in laminated composite structures. This study introduces an innovative approach, being the first to employ physics-informed neural networks (PINNs) in conjunction with refined zigzag theory (RZT) for the stress analysis of laminated composite plates. A multi-objective loss function integrates governing partial differential equations (PDEs) and boundary conditions, embedding physical principles into the analysis. Using multiple fully connected artificial neural networks, called feedforward deep neural networks, tailored to handle PDEs, PINNs are trained using automatic differentiation. This training process minimizes a loss function that incorporates the PDEs governing the underlying physical laws. RZT, particularly suitable for the stress analysis of thick and moderately thick plates, simplifies the formulation by using only seven kinematic variables, eliminating the need for shear correction factors. The capability of the proposed method is validated through several benchmark cases in stress analysis, including 3D elasticity solutions, analytical solutions, and experimental results from a three-point bending test based on displacement measurements reported in the literature. These results show consistent agreement with the referenced solutions, confirming the accuracy and reliability of the proposed method. Comprehensive evaluations are conducted to examine the effects of softcore presence, elastic foundation, various lamination schemes, and differing loading and boundary conditions on the stress distribution in laminated plates.Article Citation - WoS: 1Citation - Scopus: 1Adaptive Reuse of Industrial Heritage in Crises Zones: the Soap Factories in the Levant(Taylor & Francis Ltd, 2025) Saifi, Yara; Zawawi, Zahraa; Yuceer, HulyaThis paper articulates critical considerations for policies related to the adaptive reuse of industrial heritage, particularly in contexts affected by crises, such as conflicts, wars, and natural disasters using the soap factories of the Levant as a case study. It critically investigates the role of adaptive reuse in conserving industrial heritage buildings impacted by crises. The Levant provides a unique context for examining the intersection of cultural heritage and resilience; soap factories, reflective of the region's olive-oil-rich history and industrial legacy dating back to the 18th century, symbolise the conservation challenges and opportunities posed by ongoing regional conflict. The study systematically analyses existing literature on adaptive reuse and questions conventional paradigms in crisis environments, particularly the suitability of standard transformations such as converting industrial heritage into museums or exhibition spaces. Instead, it aims to broaden the dialogue on adaptive reuse by offering context-sensitive policy recommendations. These strategies balance the imperatives of heritage conservation, sustainable development, and contemporary community demands, contributing to a nuanced understanding of industrial heritage preservation in crisis-affected regions.Article Ggnn: Group-Guided Nearest Neighbors for Efficient Image Matching(Springer, 2025) Cine, Ersin; Bastanlar, Yalin; Ozuysal, MustafaThe widely adopted image matching approach remains dependent on exhaustive matching of local features across images. Existing methods aiming to improve efficiency either approximate nearest neighbor (NN) search, compromising accuracy, or apply filtering only after establishing tentative matches, which restricts potential efficiency gains. We challenge the assumption that exhaustive NN search is necessary by proposing a more efficient hierarchical approach that maintains matching accuracy without relying on full-scale NN search. Our key insight is that efficiently identifying sufficiently similar, geometrically meaningful feature matches-rather than the most similar but geometrically random ones-can improve or maintain performance at a lower computational cost. We propose a novel method, Group-Guided Nearest Neighbors (GGNN), which matches groups of features first and then matches individual features only within these matched groups. This hierarchical pipeline reduces the computational complexity of feature matching from \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta (n<^>2)$$\end{document} to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\theta (n \sqrt{n})$$\end{document}, significantly improving efficiency. Experimental results on homography estimation demonstrate that GGNN outperforms standard NN search while achieving performance comparable to state-of-the-art methods. Additionally, we formulate GGNN as a general framework, where conventional NN search is a special case with a single global feature group. This formulation provides a continuum of feature matching methods with varying computational costs, enabling automatic selection based on a given time budget.Article Digital Transformation in Leather Color Fastness Evaluation: Computer-Assisted Grey Scale Analysis(Korean Fiber Soc, 2025) Efendioglu, Nilay Ork; Mutlu, Mehmet Mete; Inan, Emrah; Ozgunay, HasanLeather is a critical material in the fashion industry, where it is required to meet specific customer demands for color, specifications, and performance, especially regarding color fastness. Traditional methods for assessing color fastness rely on subjective evaluations conducted by professional experts using grey scale standards. However, human evaluation can be inconsistent due to various factors, such as lighting conditions and individual perception. In this study, leather samples were first subjected to expert evaluations and scored using the grey scale system. These evaluations were then compared with color measurement data obtained through a spectrophotometer, which was processed using custom-designed software (written in the Python programming language). This software provided precise grey scale values based on the color measurements, enabling accurate digital assessments. The results of the comparative analysis showed that the computer-assisted grey scale assessment could be completed in a significantly shorter time frame with a minimal margin of error, offering a more reliable and efficient alternative to traditional evaluation methods. This approach not only enhances the accuracy of color assessments but also streamlines the evaluation process in the leather industry.Article Citation - WoS: 1Citation - Scopus: 1Electrochemical Evaluation of Strontium-Doped Micro-Arc Oxidation Surfaces on Titanium(Mdpi, 2025) Alves, Alexandra C.; Duraes, Carolina; Toptan, FatihTitanium (Ti) alloys are widely used in biomedical applications but face challenges like poor biological activity and corrosion at modular interfaces. Strontium (Sr)-doped micro-arc oxidation (MAO) surfaces are proposed to improve biocompatibility and tribocorrosion resistance. This study examines the electrochemical behaviour of Ti surfaces treated with 0.0013 M and 0.13 M Sr-doped MAO via open circuit potential, potentiodynamic polarisation, and electrochemical impedance spectroscopy in a basic physiological solution at 37 degrees C. The results indicate that higher Sr concentrations led to lower passivation current densities (more than two times lower than at the lowest Sr concentration) and reduced barrier layer capacitance (more than one and a half times lower than at the lowest Sr concentration), suggesting improved corrosion resistance for Sr-enriched MAO treatments on Ti implants.Article Citation - WoS: 2Citation - Scopus: 2Impact of Green Wall and Roof Applications on Energy Consumption and Thermal Comfort for Climate Resilient Buildings(Mdpi, 2025) Turhan, Cihan; Carpino, Cristina; Austin, Miguel Chen; Ozbey, Mehmet Furkan; Akkurt, Gulden GokcenNowadays, reducing energy consumption and obtaining thermal comfort are significant for making educational buildings more climate resilient, more sustainable, and more comfortable. To achieve these goals, a sustainable passive method is that of applying green walls and roofs that provide extra thermal insulation, evaporative cooling, a shadowing effect, and the blockage of wind on buildings. Therefore, the objective of this study is to evaluate the impact of green wall and roof applications on energy consumption and thermal comfort in an educational building. For this purpose, a university building in the Csb climate zone is selected and monitored during one year, as a case study. Then, the case building is modelled in a well-calibrated dynamic building energy simulation tool and twenty-one different plant species, which are mostly used for green walls and roofs, are applied to the envelope of the building in order to determine a reduction in energy consumption and an increase in thermal comfort. The Hedera canariensis gomera (an ivy species) plant is used for green walls due to its aesthetic appeal, versatility, and functional benefits while twenty-one different plants including Ophiopogon japonicus (Mando-Grass), Phyllanthus bourgeoisii (Waterfall Plant), and Phoenix roebelenii (Phoenix Palm) are simulated for the green roof applications. The results show that deploying Hedera canariensis gomera to the walls and Phyllanthus bourgeoisii to the roof could simultaneously reduce the energy consumption by 9.31% and increase thermal comfort by 23.55% in the case building. The authors acknowledge that this study is solely based on simulations due to the high cost of all scenarios, and there are inherent differences between simulated and real-world conditions. Therefore, the future work will be analysing scenarios in real life. Considering the limited studies on the effect of different plant species on energy performance and comfort, this study also contributes to sustainable building design strategies.Article Citation - WoS: 1Citation - Scopus: 1Effect of Drying Method on Selected Physical and Functional Properties of Powdered Black Soldier Fly Larvae(Mdpi, 2025) Bogusz, Radoslaw; Nowacka, Malgorzata; Gondek, Ewa; Delman, Murat; Szulc, KarolinaThis research aimed to assay the impact of convective drying (CD) or infrared-convective (IR-CD) drying methods on the physical and techno-functional properties, FTIR spectra, and mathematical modeling of adsorption kinetics of black soldier fly larvae powders. By using convective drying, insect powder exhibited higher water content and water activity but lower hygroscopicity than powder dried with the infrared-convective method. After drying with the convective method, the powder exhibited a significantly lower loose and tapped bulk density and oil holding capacity (OHC). Furthermore, this powder was lighter and more yellow. The FTIR spectrum of the CD-dried powder showed lower absorption at key wavenumbers for the protein (1625 and 1350-1200 cm-1), indicating lower denaturation and less ability to bind water and water vapor. The mathematical modeling of the water vapor adsorption kinetics of insect powders via the second Fick's law for transient diffusion showed that this equation is suitable for adjusting the experimental data based on the high coefficient of determination (0.997-0.999) and the low root mean square (2.50-3.34%). This study revealed that the drying method influences insect powder properties, and the IR-CD method seems better in terms of obtaining better techno-functional properties.