WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Tooth Decay Promotes Senescence in Dental Pulp Stem Cells, Modifying Their Biological and Proteomic Profiles(Wiley, 2026) Durukan, Sebahat Melike; Tez, Banu Cicek; Ozcan, Servet; Simsek, Ahmet; Al-Sammarrie, Sura Hilal Ahmed; Gunaydin, Zeynep; Acar, Mustafa BurakDental caries is a prevalent oral health problem that significantly reduces an individual's quality of life; although, it can be effectively managed through restorative treatments. Even in cases where the caries does not reach the pulp, released microbial products from the lesion can still penetrate the pulp chamber, potentially inducing stress on pulp cells. In this study, we conducted a comparative analysis of the biological and proteomic profiles of dental pulp stem cells (DPSCs) isolated from clinically asymptomatic teeth with dentinal caries that had not reached the pulp and isolated from healthy teeth. Following biological evaluations, we examined proteomes of these DPSCs by conducting a shotgun proteomics approach. Our findings show that DPSCs from decayed teeth exhibit a significantly higher proportion of senescent cells. Proteomic profiling revealed upregulation of inflammatory signaling, extracellular matrix remodeling, and senescence-associated secretory phenotype (SASP) related proteins. Additionally, we observed an upregulation in the expression of proteins associated with extracellular matrix (ECM) remodeling and components of the SASP, which are hallmarks of the senescence process. The study reveals that DPSCs can be affected by stress from carious lesions, even when the pulp appears clinically intact. Senescence and inflammatory response in these affected cells may have deleterious effects on other tissues within the organism. Consequently, restorative treatments should consider targeting not only the decayed tissue but also the senescent cells within the pulp that may have been affected by the stress induced by caries.Article Optimizing Nanoclay-Enhanced Membranes for Oil Rejection Using Response Surface Methodology(Wiley, 2026) Gul, Ayse; Baris, Mesut; Boyraz, Pınar; Senol-Arslan, Dilek; Alibaz, Name NurThe efficient separation of waste oil from contaminated water is critical due to its challenges in environmental and industrial applications. This study investigated the production and optimization of polysulphone (PSF) membranes using two different types of clay (nanomer clay/CN and commercial nanoclay/NC). Response Surface Methodology (RSM) was applied to optimize the basic production parameters and nanoclay concentrations systematically to maximize oil rejection and permeability flow. The experimental results showed that NC and CN significantly increased the hydrophilicity, permeability, and fouling resistance of the membrane compared to pure PSF membranes. The contact angle significantly decreased from 64.34 degrees (pristine PSF) to 36.23 degrees (2% NC), indicating highly improved hydrophilicity. Consequently, the pure water flux increased from 177.2 L/m2 h to a maximum of 248.6 L/m2 h (1% NC). Furthermore, the modified membranes exhibited outstanding anti-fouling properties; the flux recovery ratio (FRR) improved from 88.09% to 96.20% (1% CN), while the decline ratio (DR) drastically dropped from 60.89% to 32.14%. The optimized condition for maximum removal efficiency using a modified quadratic model revealed that 2572 mg/L oil can be treated with a PSF membrane containing 2.0% CN to remove 98.271% of the oil. The model also suggests superiority of CN over NC with desirability factors of 0.978 and 0.900, respectively, while both demonstrated high efficiency. This theoretically modeled experimental comparative study highlights the importance of PSF membrane technology for efficient and sustainable oil-water separation and demonstrates the promising potential of nanoclay modifications.Article BrAIn: A Comprehensive Artificial Intelligence-Based Morphology Analysis System for Brain Organoids and Neuroscience(Wiley, 2026-03-12) Polatli, Elifsu; Guner, Huseyin; Bastanlar, Yalin; Karakulah, Gokhan; Evranos, Ali Eren; Kahveci, Burak; Guven, SinanHuman-induced pluripotent stem cells (iPSCs) offer transformative potential for biomedical research, with iPSC-derived organoids providing more physiologically relevant models than traditional 2D cell cultures. Among these, brain organoids (BO) are particularly valuable for drug screening, disease modeling, and investigations into molecular pathways. Accurate representation of brain morphology is critical, as more complex organoid structures better mimic the human brain. Deep learning (DL) and machine learning (ML) approaches have become integral to analyzing organoid morphology, yet tools for comprehensive, time-resolved assessments are scarce. Here, we introduce BrAIn, a DL-based application for analyzing the developmental progression of BOs. BrAIn tracks their evolution from embryoid bodies (EBs) and quantifies parameters including area, Feret diameter, perimeter, roundness, and circularity. It also classifies budding and abnormal morphologies of 3D organoids and detects monolayer neural rosette structures, key features of neuronal differentiation. Designed with accessibility in mind, BrAIn provides a no-code interface, enabling researchers of all technical backgrounds to conduct advanced morphological analyses with ease. Our study demonstrates the application of BrAIn to evaluate the effects of different growth conditions-static, orbital shaker, and microfluidic chip-based-on BO development. Orbital shaker cultures resulted in the largest organoids, while chip-based systems achieved more homogeneous growth. Both conditions produced organoids with greater morphological complexity compared to static culture. BrAIn emerges as a robust, user-friendly tool to quantify BO development and explore how versatile growth conditions influence their morphology and maturation.Article An Adaptation Mechanism of Model Reference Adaptive System Based on Variable Structure Control for Online Parameter Estimation of IPMSM(Wiley, 2026-01) Tekgun, Burak; Barut, Murat; Ates, ErtugrulThis study introduces stator currents-based model reference adaptive system (MRAS) estimators that employ variable structured control (VSC) in the adaptation mechanism to enable the online estimation of stator resistance and permanent magnet (PM) flux in interior permanent magnet synchronous motors (IPMSMs). These MRAS estimators estimate stator resistance and PM flux by analysing the error between the stator currents measured as the reference model and the stator currents generated by the adaptive model. The performance of the proposed estimators is assessed through simulation studies. Furthermore, the proposed approach is compared to a conventional MRAS employing a fixed-gain proportional-integral (PI) controller. Simulation results and error analyses indicate that the VSC-based MRAS algorithms outperform traditional PI-based MRAS in terms of accuracy and reliability. Additionally, the proposed method eliminates the reliance on a fixed-gain PI controller, a common component in conventional MRAS systems.Article Comparative Analysis of Modulation Shapes on Laser Diode Performance with a High-Efficiency LLC Resonant Converter Driver(Wiley, 2026-02-06) Yigit, Hayri; Rifat boynuegri, Ali; Tekgun, Burak; Rifat Boynuegri, AliHigh-power laser diodes (LDs) are key components in laser-based wireless power transfer (WPT) systems, where end-to-end efficiency is one of the most critical performance metrics. This study investigates the driving performance of an LD powered by a high-efficiency LLC resonant converter under three distinct excitation waveforms-sinusoidal, triangular, and rectified-sine-using a MATLAB/SIMULINK model and an experimental setup designed to reproduce real-world operating conditions. Each waveform is synthesized through frequency modulation of a full-bridge inverter stage and filtered at the output. The analysis examines the impact of modulation shape on output current ripple, converter efficiency, and overall LD efficiency. Experimental validation confirms the simulation trends, underscoring the trade-offs between waveform smoothness, implementation complexity, and efficiency. Beyond confirming that constant-current operation yields the highest LD efficiency, this study explicitly quantifies how low-frequency current ripple induced by different modulation waveforms propagates through the LLC resonant converter, alters RMS current stress, and translates into measurable efficiency degradation at both the driver and LD levels. By experimentally correlating waveform symmetry, ripple magnitude, and loss mechanisms, the work establishes practical design boundaries for waveform-modulated laser drivers in WPT systems.Article Zinc Chalcogenide Based Shell Layers for Colloidal Quantum Wells(Wiley, 2025-04-27) Aldemir, Cagatay Han; Yazici, Ahmet Faruk; Ergezer, Nehir; Korkmaz, Taha Can; Mutlugun, Evren; Kelestemur, YusufColloidal quantum wells, also known as colloidal nanoplatelets (NPLs), have emerged as a promising class of materials for light-emitting devices (LEDs). However, the most widely studied core/shell NPLs, which rely on cadmium-based shell layers, face challenges due to toxicity concerns and improper charge confinement. To address these limitations, a new synthetic approach is presented that enables the controlled growth of zinc chalcogenide-based shell layers on NPLs. The synthesized CdSe/ZnSe core/shell NPLs exhibit emission between 615 and 630 nm, with a moderate photoluminescence quantum yield (PL-QY) of 40-50%. It is also demonstrated that the lateral dimensions of the CdSe core NPLs significantly affect the optical properties of the core/shell heterostructures, with smaller lateral dimensions resulting in narrower emission linewidths as low as 20 nm. Further passivation of these core/shell NPLs with an additional ZnS shell layer significantly increases the PL-QY up to 80-90%. Finally, the device performance of these two core/shell NPLs is investigated by fabricating solution-processed LEDs. With LEDs incorporating CdSe/ZnSe/ZnS core/multi-shell NPLs as the active light-emitting layer, an external quantum efficiency (EQE) of 3.82% and a maximum brightness of 6477 cd m-2 is obtained. These findings underscore the significant potential of zinc chalcogenide-based shell layers in advancing colloidal NPLs toward high-performance light-emitting devices.Article Citation - WoS: 7Citation - Scopus: 7Villages in the City - Urban Planning for Neighbourhood Love(Wiley, 2024-03-17) Kourtit, Karima; Nijkamp, Peter; Turk, Umut; Wahlstrom, MiaThe city comprises of a wide variety of heterogeneous territorial units (e.g. districts or neighbourhoods). In many - especially larger - cities, social capital assets (like community bonds) are mirrored at the level of neighbourhoods which form the home for many sociocultural communities or distinct socio-economic classes. We postulate in this study that the big city is essentially an 'archipelago' made up of 'urban villages'. We analyse the residents' perceived attractiveness regarding their daily local neighbourhood by introducing the concept of 'village love' (or 'neighbourhood love'), inspired by the recent literature on 'city love' (comprising 'body', 'soul' and 'community' constituents of urban life). Based on an extensive and detailed multi-annual database for all neighbourhoods in Rotterdam, the present paper seeks to identify the background factors shaping 'village love' in the city, with particular attention to the citizens' subjective appreciation for and access to a great variety of (physical and immaterial) urban amenities shaping the place-based satisfaction of residents. The theoretical framing of our research resembles the basics of traditional central place theory here transmitted to the urban space in which local proximity to amenities plays a key role. A wide array of relevant amenities impacting on the place-specific well-being feelings ('village love') of residents in various neighbourhoods in the city of Rotterdam is distinguished using inter alia-rich multi-annual survey data. This approach is empirically tested and verified by means of LISA statistics and advanced spatial econometric dependence models ('urbanometrics'). The findings confirm the usefulness of a central place interpretation of 'urban village love' in the city. 'Villages in the City - Urban Planning for Neighbourhood Love': This study advocates that cities are composed of interconnected 'urban villages', each with its own social capital and community bonds. Using extensive data from Rotterdam, we investigate the factors influencing residents' perceived attractiveness and satisfaction with their local neighbourhoods. Our analysis highlights the importance of access to diverse amenities in shaping residents' sense of 'village love'. Through spatial econometric models, the study confirms the central place interpretation of 'urban village love' in the city, shaping future urban planning strategies for fostering vibrant and cohesive communities.imageArticle Citation - WoS: 1Citation - Scopus: 1Unhappiness Among the Unemployed: The Roles of Descriptive Norms, Injunctive Norms and Personal Beliefs(Wiley, 2025-05-19) Ugur, Zeynep B.; Durak, AysenurThis study explores the influence of social norms and individual beliefs on the well-being of unemployed individuals in Turkey, a context marked by both chronic unemployment and a high societal valuation of employment. Using province-level representative data from the 2013 Life Satisfaction Survey, encompassing 196,203 observations, we analyse how descriptive norms (prevalence of unemployment) and injunctive norms (social pressures due to unemployment) at the province level affect the happiness of the unemployed. We utilized people's perception of employment for being respected in social life and personally feeling social pressure as a measure of individual beliefs. Multilevel regression results reveal that descriptive norms can modestly alleviate the adverse impact of unemployment, particularly for the short-term unemployed, while injunctive norms slightly intensify the unhappiness of being unemployed, especially in the short term. The unemployed's personal beliefs about the value of employment matter for their happiness. These findings underscore the theoretical implications of social norms in shaping the well-being of the unemployed and highlight the importance of individual beliefs in moderating these effects.Article Citation - WoS: 6Citation - Scopus: 6Uncovering Nanoclusters in Amorphous AlN: An Ab Initio Study(Wiley, 2014-12-22) Durandurdu, MuratAmorphous AlN (a-AlN) is modeled by melt-and-quench technique using ab initio molecular dynamic simulations. For the first time, three-dimensional hexagonal-like nanoclusters embedded in amorphous matrix are proposed for a-AlN. The model is chemically ordered and dominantly fourfold coordinated, but its short-range order is partially different from the crystalline morphology due to the nanoclusters. The model is semiconducting with a theoretical band gap of 1.7eV.Article Citation - WoS: 6Citation - Scopus: 6Two Successive Amorphous-to Phase Transformations in TiO2(Wiley, 2017-05-22) Durandurdu, MuratBased on constant pressure ab initio simulations, we propose, for the first time, two successive amorphous-to-amorphous phase transformations for TiO2. The first one is a gradual phase transformation from a low-density amorphous phase to a high-density amorphous phase, whereas the second one is a first-order phase transformation from the high-density amorphous phase to a very high-density amorphous phase. The low-density amorphous to high-density amorphous phase change is irreversible, whereas the high-density amorphous to very high-density amorphous phase transformation is reversible. The high-density amorphous and very high-density amorphous phases consist of differently coordinated configurations. The sevenfold and ninefold-coordinated arrangements formed in amorphous TiO2 under pressure are similar to the main building motif of the baddeleyite and cotunnite polymorphs of TiO2, respectively, while the eightfold-coordinated configuration is different from the local structure of the cubic TiO2 phase. The electronic structure calculations suggest that both dense amorphous phases present a semiconducting character with a band gap energy less than that of the original low-density amorphous phase.