Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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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 A Small Indole Derivative Isolated From Caper (Capparis Ovata) as an Inducer of P53-Mediated Apoptosis in Prostate Cancer: Comprehensive In Vitro and In Silico Studies(Wiley, 2025-12-31) Acar, Ozden Ozgun; Gazioglu, Isil; Oruc, Hatice; Kale, Elif; Senol, Halil; Topcu, Gulacti; Sen, AlaattinNatural products with stunning chemical diversity have been extensively researched for their anticancer potential for more than fifty years. This study aimed to determine the effect of indole derivative 1H-indole-2-hydroxy-3-carboxylic acid (IHCA), isolated as a novel alkaloid from Capparis ovata, on selected tumor suppressor, apoptotic, and cell cycle regulatory genes, which are known to be important in cancer pathophysiology, on Caco-2 and LNCaP cells in comparison with Taxol. The molecular mechanism of IHCA's anticancer activity is essentially undefined. Different concentrations of IHCA increased the expression levels of apoptosis-related genes, including BCL-2 and TNF-alpha. In addition, the tumor suppressor genes PTEN, P53, and RB were increased in LNCaP and Caco-2 cells. KRAS, an oncogenic gene, was significantly downregulated by IHCA in LNCaP cells. Western blot results showed that the protein expression levels of P53 and PTEN in LNCaP cells were increased when treated with IHCA, whereas CDK4 and TNF-alpha were decreased. Finally, IHCA and doxorubicin significantly increased P53-driven luciferase activity compared to the control. The results strongly suggest that the novel natural compound IHCA has an anticancer effect involving the regulation of the P53 gene and its networks in vitro. The molecular docking and MD simulation analyses reveal that IHCA exhibits superior binding potential to the MDM2 protein compared to Nutlin-3a. MD simulations further confirm that IHCA maintains a more stable and consistent interaction with MDM2, as indicated by lower RMSD values and reduced ligand fluctuation. These results highlight IHCA's potential as a more effective MDM2 inhibitor, suggesting its promise as a lead compound for anticancer drug development.Clinical Trial Registration: Not applicable.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: 6Citation - Scopus: 6The Different Impacts of g-C3N4 Nanosheets on PVDF and PSF Ultrafiltration Membranes for Remazol Black 5 Dye Rejection(Wiley, 2023-08-02) Senol-Arslan, Dilek; Gul, Ayse; Dizge, Nadir; Ocakoglu, Kasim; Uzal, NigmetMembranes combined with nanoparticles are an excellent combination capable of successfully removing various contaminants, such as dyes from wastewater while using very little energy and decreasing pollution. The present study reports an efficient approach for Remazol Black 5 (RB5) dye removal using composite graphitic carbon nitride nanosheets (g-C3N4), polysulfone (PSF), and polyvinylidene fluoride (PVDF) membranes. The membranes were prepared using the phase inversion method, with varying quantities of g-C3N4 nanosheets ranging from 0.1%, 0.2% to 0.3%. The prepared g-C3N4 nanosheets were characterized by FTIR, SEM analyses, and zeta potential measurements. FTIR and SEM studies, contact angle, water permeability, COD, and dye rejection measurements were used to characterize the g-C3N4 nanosheets embedded in PSF and PVDF membranes. After the addition of 0.3 wt% g-C3N4, the water flux of the 0.3 wt% g-C3N4 embedded PSF membrane was the highest, whereas the water flux of the 0.3 wt% g-C3N4 embedded PVDF membrane was the lowest. The ultrafiltration (UF) membrane's performance with g-C3N4 embedded showed an RB5 rejection rate of more than 80% and a COD removal efficiency of more than 45%. The results of the experimental filtration showed that RB5 rejection reached maximum values of 91.3% for 0.1 wt% g-C3N4/PSF, and 85.6% for 0.3 wt% g-C3N4/PVDF.Article Citation - WoS: 28Citation - Scopus: 35Tactile Sensitivity and Capability of Soft-Solid Texture Discrimination(Wiley, 2015-08-09) Aktar, Tugba; Chen, Jianshe; Ettelaie, Rammile; Holmes, MelvinThe sensation and perception of food texture is regulated by tactile-dominated mechanisms and therefore, it is believed that one's capability in discriminating food textural properties could be related to one's tactile sensitivity. However, evidence to support this hypothesis is currently not available. This work aims to test this hypothesis by examining tactile sensitivity of individuals' (touch detection threshold and two-point discrimination threshold) and texture discrimination capability. A range of soft-solid food samples with controlled firmness and elastic moduli were designed for textural discrimination tests. A total of 32 healthy subjects threshold of touch detection was found to be 0.028 g for the fingertip and 0.013 g for the tongue. Similarly, the mean threshold of two-point discrimination was 1.42 mm and 0.62 mm for the fingertip and tongue, respectively. Threshold for firmness discrimination (compressing until yielding) of the gel samples was 13.3% for the fingertip and 11.1% for the tongue. However, the elasticity discrimination threshold (by gentle pressing) of the population was found to be much smaller at 2.3% and 1.2% for the fingertip and the tongue respectively. Results show that tongue is slightly more sensitive than the fingertip in discriminating food texture (P < 0.05). An expected correlation between individual's capability of texture discrimination and their tactile sensitivity was not observed. PRACTICAL APPLICATIONS Texture discrimination capability is a significant factor for food texture preference and appreciation. In order to understand texture perception, it is essential to identify the relevant factors and define characteristics that govern the processes involved. Having a meaningful and reliable texture discrimination indicator is critically important for the food industry in the development and optimization of new food products, and in particular for specific food design for individuals' with special needs, e.g., elderly, dysphagic patients, etc. With this study, we illustrate the differential threshold for soft-solid texture (firmness and elasticity) and also investigate the capabilities of tactile sensation (touch detection and two-point discrimination) and evaluate potential correlations. The results and correlations may provide information about texture sensitivity and also might provide useful information to R&D researchers. Methodologies could also be applied in general food sensory studies and also investigating relationships between sensory psychology and sensory physiology.Article Citation - WoS: 2Citation - Scopus: 2Rural Feet Voting of Leisure Explorers(Wiley, 2025-01) Turk, Umut; Toger, Marina; Osth, John; Kourtit, Karima; Nijkamp, PeterIn the COVID-19 period, spatial leisure behavior, often driven by the desire to escape urban life, reflected health and environmental concerns. This study examines how pandemic-induced spatial motives and changes impacted disparities in leisure mobility, specifically urban-to-rural tourism, in Sweden. Analyzing pre-pandemic, during pandemic, and post-pandemic periods, using anonymized mobile phone and socioeconomic data, the paper explores urban-rural leisure mobility variations. Despite a decline in professional geographical mobility, mainly of people in affluent urban areas, due to remote work, the spatial leisure activities remained rather stable? Our findings, based on a negative binomial regression analysis, reveal also exacerbated socioeconomic segregation in recreational trips. The disruption in mobility accessibility due to COVID-19 appears to amplify existing socioeconomic disparities, notably in urban-to-rural leisure travel. Our research sheds new light on the widening gap in geographical leisure activities, emphasizing the need for equitable access to nonurban destinations.Article Citation - WoS: 25Citation - Scopus: 27Progression of Irradiated Mesenchymal Stromal Cells From Early to Late Senescence: Changes in SASP Composition and Anti-Tumour Properties(Wiley, 2023-03-22) Alessio, Nicola; Acar, Mustafa Burak; Squillaro, Tiziana; Aprile, Domenico; Ayaz-Guner, Serife; Di Bernardo, Giovanni; Galderisi, UmbertoGenotoxic injuries converge on senescence-executive program that promotes production of a senescence-specific secretome (SASP). The study of SASP is particularly intriguing, since through it a senescence process, triggered in a few cells, can spread to many other cells and produce either beneficial or negative consequences for health. We analysed the SASP of quiescent mesenchymal stromal cells (MSCs) following stress induced premature senescence (SIPS) by ionizing radiation exposure. We performed a proteome analysis of SASP content obtained from early and late senescent cells. The bioinformatics studies evidenced that early and late SASPs, besides some common ontologies and signalling pathways, contain specific factors. In spite of these differences, we evidenced that SASPs can block in vitro proliferation of cancer cells and promote senescence/apoptosis. It is possible to imagine that SASP always contains core components that have an anti-tumour activity, the progression from early to late senescence enriches the SASP of factors that may promote SASP tumorigenic activity only by interacting and instructing cells of the immune system. Our results on Caco-2 cancer cells incubated with late SASP in presence of peripheral white blood cells strongly support this hypothesis. We evidenced that quiescent MSCs following SIPS produced SASP that, while progressively changed its composition, preserved the capacity to block cancer growth by inducing senescence and/or apoptosis only in an autonomous manner.Article Citation - WoS: 10Citation - Scopus: 12Production of Flower-Shaped Nanobiocatalysts From Green Tea and Investigation of Their Peroxidase Mimicking Activity on the Polymerization of Phenol Derivatives(Wiley, 2023-12-13) Kalayci, Berkant; Kaplan, Naime; Dadi, Seyma; Ocsoy, Ismail; Gokturk, ErsenEnzyme catalyzed reactions are known to be environmental friendly and easy method for many applications. However, utilization of enzymes in a variety of reactions is strictly limited due to their high cost, instability in aqueous solutions, denaturation in organic solvents and high temperatures. For this reason, it is important to discover new generation catalyst systems indicating enzyme-like catalytic activity. Here, we report hybrid organic-inorganic flower-shaped green tea-Cu2+ nanobiocatalyst synthesized from green tea extract as an organic component and copper (II) ions (Cu2+) as inorganic component. The effect of the peroxidase-mimicking activity of green tea-Cu2+ nanobiocatalyst was investigated on the polymerization of phenol and derivatives (guaiacol and salicylic acid) through Fenton-like reaction mechanism. Obtained successful outcomes showed that the synthesized nanobiocatalyst showed very high catalytic activity upon polymerization of phenol and guaiacol. The slight solubility of salicylic acid in water limited to achieve its polymerization under-performed reaction conditions. The yields and molecular weights of the obtained polymers were found to be quite high. While free peroxidase enzymes like horseradish peroxidase (HRP) enzyme loses its catalytic activity at 60 degrees C and above temperatures, green tea-Cu2+ nanobiocatalyst exhibited very high catalytic activity upon polymerization reactions even at 60 degrees C reaction temperature. This outcome provides significant advantages in some reactions requiring high temperatures. In order to understand the origin of the catalytic activity of the green tea-Cu2+ nanoflowers, similar biocatalysts were also synthesized from caffeine and catechin alkaloids which are the active components of green tea. Caffeine-Cu2+ and catechine-Cu2+ nanobiocatalysts also exhibited quite high catalytic activity toward polymerization of phenol and derivatives. We suggest that green tea-Cu2+ and similar types of nanobiocatalysts may expand their utilization in polymer chemistry as promising catalytic agents for radicalic polymerizations.