Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Integrating QSAR Analysis and Machine Learning To Explore the Antidiabetic Potential of Natural Compounds(AMG Transcend Association, 2025) Sincar, B.; Yalcin, D.; Bayraktar, O.This study explores the antidiabetic potential of 72 natural compounds using molecular descriptors and QSAR modeling combined with machine learning techniques. The dataset includes 11 experimentally obtained compounds and 61 from the literature, characterized by their IC50 values indicating 50% inhibition of α-glucosidase enzyme activity. Molecular descriptors were generated using ChemAxon’s MarvinSketch and PADEL software, narrowing down over 3000 descriptors to 23 relevant features. Statistical analysis revealed significant multicollinearity among variables, necessitating the application of non-linear machine learning models, namely Random Forest and Gradient Boosting. These models demonstrated predictive capabilities with R² values of 0.7751 and 0.8066, respectively, and highlighted molecular weight and the number of heteroatoms in ring structures as critical features influencing IC50 values. Despite the dataset's variability and limited size, the study underscores the potential of integrating QSAR and machine learning approaches to effectively predict the antidiabetic activity of natural compounds. The findings provide valuable insights for advancing computational methods in drug discovery. © 2025 by the authors.Article Citation - Scopus: 1Recent Advances in Hydrogel-Based 3D Disease Modeling and Drug Screening Platforms(2025) Bilginer-Kartal, R.; Çoban, B.; Yildirim-Semerci, Ö.; Arslan-Yildiz, A.Three-dimensional (3D) disease modeling and drug screening systems have become important in tissue engineering, drug screening, and development. The newly developed systems support cell and extracellular matrix (ECM) interactions, which are necessary for the formation of the tissue or an accurate model of a disease. Hydrogels are favorable biomaterials due to their properties: biocompatibility, high swelling capacity, tunable viscosity, mechanical properties, and their ability to biomimic the structure and function of ECM. They have been used to model various diseases such as tumors, cancer diseases, neurodegenerative diseases, cardiac diseases, and cardiovascular diseases. Additive manufacturing approaches, such as 3D printing/bioprinting, stereolithography (SLA), selective laser sintering (SLS), and fused deposition modeling (FDM), enable the design of scaffolds with high precision; thus, increasing the accuracy of the disease models. In addition, the aforementioned methodologies improve the design of the hydrogel-based scaffolds, which resemble the complicated structure and intricate microenvironment of tissues or tumors, further advancing the development of therapeutic agents and strategies. Thus, 3D hydrogel-based disease models fabricated through additive manufacturing approaches provide an enhanced 3D microenvironment that empowers personalized medicine toward targeted therapeutics, in accordance with 3D drug screening platforms. © 2025. The Author(s), under exclusive license to Springer Nature Switzerland AG.Article Citation - Scopus: 1Assessing the Density of Wood in Heritage Buildings’ Elements Through Expedited Semi-Destructive Techniques(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Henriques, Dulce F.; Sen, Ali Umut; Gomes, Maria da GloriaFeatured Application The research presented and justified in this text aims to provide agents involved in the conservation and refurbishment of old timber elements in buildings with a correlation table for interpreting the readings obtained with penetration resistance testing equipment.Abstract Historically, wood has been among the main materials used in heritage buildings. However, the species and mechanical properties of these elements are often unknown. This uncertainty complicates safety assessment calculations, aggravated by the natural variability of the wood properties. The aim of this work is to assess the density of wooden elements in service using semi-destructive techniques that retain the integrity of structural elements. This research had two phases. First, penetration resistance tests were carried out on laboratory scale on Pinus sylvestris L. wood samples taken from 18th, 19th, and 20th century heritage buildings in Lisbon, Portugal. Later, a field study was carried out on wooden elements from the same buildings, involving needle penetration, core drilling, and moisture content determination tests. The laboratory test results showed a strong correlation between the needle penetration depth and wood density, with an R2 value of 0.76. The results of the field study indicated that the density estimated by the needle penetration test correlated effectively with the measured density of extracted cores after moisture correction, with an R2 of 0.99. In conclusion, the experimental results confirm that penetration resistance and moisture tests are reliable and practical for estimating wood density under in-service conditions.Article Citation - Scopus: 2Digital Sensing Technologies in Cancer Care: a New Era in Early Detection and Personalized Diagnosis(Elsevier Ltd, 2025) Yucel, M.; Önder, A.; Kurt, T.; Keles, B.; Beyaz, M.; Karadağ, Y.; Yildiz, U.H.Digital sensor platforms are systems that integrate sensors with digital technology, which revolutionize data collection, processing, and transmission for enabling real-time, high-precision and automated diagnostics. These platforms often serve as the backbone of modern monitoring systems, enabling real-time data acquisition and analysis for a wide range of applications. Recent advancements in digital sensor platforms have paved the way for transformative innovations in cancer diagnosis. These cutting-edge technologies offer unprecedented opportunities to facilitate early detection, improve diagnostic accuracy, and personalize treatment methods. This review explores the landscape of digital sensor platforms in the context of cancer diagnosis, providing an overview of their principles, functionalities, and clinical applications. The review further illustrates that biosensors, lab-on-a-chip (LOC) devices and wearable sensors have leveraged on nanotechnology, biorecognition materials and artificial intelligence (AI) for revolutionizing cancer diagnosis. It consolidates the recent advances in digital sensor platforms for cancer diagnosis and the associated critical challenges, such as regulatory concerns, standardization, and ethical considerations. Further, the review summarizes the feasibility for the integration of digital sensor platforms with routine clinical practices for the development of efficient cancer diagnosis and treatment methods. © 2025 The AuthorsArticle Citation - WoS: 4Citation - Scopus: 2CFD-DEM Investigation of the Effects of Particle Size and Fluidization Regime on Heat Transfer in Fluidized Beds(Springer int Publ Ag, 2025) Alipoor, Mahdi; Kazemi, Saman; Zarghami, Reza; Mostoufi, NavidThis paper presents an in-depth study of heat transfer in fluidized beds, employing the CFD-DEM technique. The primary focus is to examine the impacts of inlet gas velocity, fluidization regime, and particle size on the thermal behavior of fluidized beds. The results revealed that thermal convection predominantly governs heat transfer in fluidized beds, accounting for the largest fraction of the overall heat transfer process. Particle-fluid-particle thermal conduction was found to contribute approximately 10-20% of the heat transfer, whereas particle-particle conduction exhibits a minor role. Upon increasing the inlet gas velocity, the convection rate intensifies, whereas the particle-fluid-particle conduction rate decreases. Furthermore, the study highlights the differences in temperature distribution between turbulent and bubbling fluidized beds. Turbulent bed demonstrated a more uniform and homogenous particle temperature compared to bubbling. At similar fluidization numbers in bubbling beds, increasing particle diameter enhances thermal convection while reducing particle-fluid-particle conduction. In contrast, the turbulent regime shows minimal differences in heat transfer mechanisms when particle size varies. Additionally, smaller particles are found to significantly improve temperature uniformity in fluidized beds. A comprehensive comparison of simulation results with experimental data validates the accuracy of the employed model, reinforcing its ability to predict heat transfer in fluidized beds reliably. This research provides valuable insights into the complex interplay of various mechanisms of heat transfer within fluidized beds, enabling engineers and researchers to optimize bed performance and enhance temperature control in various industrial applications.Article Citation - WoS: 1Citation - Scopus: 1Exploring Sainfoin (Onobrychis Viciifolia) Seed Flour as a Sustainable Plant-Based Food: Germination-Induced Changes in Nutritional Quality, Anti-Nutritional Factors, Phenolic Content, Bioaccessibility, and in Vitro Toxicity(Wiley, 2025) Kaya, Havva Polat; Gungor, Sevde Nur; Tuncel, Nese Yilmaz; Sakarya, Fatma Betul; Andac, Ali Emre; Ozkan, Gulay; Tuncel, Necati BarisBackground and Objectives: Sainfoin is a drought-resistant perennial plant mainly used as animal feed, but its seeds remain underexplored as a food source. This study investigates the effects of germination on the nutritional quality of dehulled sainfoin seeds. Specifically, it examines changes in proximate composition, antinutrients (hydrocyanic acid, tannins, phytates, saponins, and trypsin inhibitors), in vitro starch digestibility, phenolic content, antioxidant capacity, and cytotoxicity. Findings: Germination significantly increased crude protein (up to 45%) and fat (up to 10%) contents. Despite low total starch (similar to 7%), 45-h germination reduced total digestible starch while increasing rapidly digestible starch. Antinutrient levels decreased significantly-tannins by 57%, phytates by 30%, saponins by 40%, and trypsin inhibitors by 29%-with the exception of hydrocyanic acid. Although total phenolics, flavonoids, and antioxidant capacity declined, their bioaccessibility improved. No cytotoxic effects were observed in either raw or germinated seeds. Conclusions: Germination improved the nutritional profile of sainfoin seeds by increasing protein and fat contents, while reducing most antinutrients. Despite a decrease in antioxidant levels, their bioaccessibility was enhanched. The absence of cytotoxic effects further supports the potential application of germinated sainfoin seeds in human nutrition. Significance and Novelty: Although few studies have focused on the green form of sainfoin, which is commonly used as livestock feed, this study reveals that sainfoin seeds offer substantial potential as food, with germination emerging as a simple and effective approach to improving their nutritional properties.Article Nanostructured Ox-MWCNT-Ppy-Au Electrochemical Sensor for Ultralow Detection of Retrorsine and Evaluation of Its Cytotoxic Effects on Liver Cells(Taylor & Francis Ltd, 2025) Akturk, Ezgi Zekiye; Njjar, Muath; Ata, Melek Tunc; Kaya, Ahmet; Akdogan, Abdullah; Onac, CananThis study presents the development of a novel retrorsine (RTS)-imprinted sensor utilizing oxidized multi-walled carbon nanotubes (Ox-MWCNTs), polypyrrole (PPy), and gold nanoparticles (AuNPs), employing square wave voltammetry for the sensitive and selective detection of RTS which causes oxidative-stress and DNA damage. The fabricated Ox-MWCNT-PPy-AuNP sensor demonstrated a surface-area of (0.218 cm2) is 4.25 times larger than a bare glassy carbon electrode, with a low charge transfer resistance (10.9 Omega), enhancing electron transfer kinetics. The sensor showed excellent sensitivity in detecting retrorsine, with a limit of detection of 0.035 nM in synthetic matrices and -0.030 nM in HepaRG cell culture medium. Toxicity assays in HepaRG cells revealed dose-dependent oxidative-stress, with glutathione levels decreasing from 23.08 +/- 0.21 mu mol/109 to 21.21 +/- 0.02 mu mol/109 at 35 mu M retrorsine. Concurrently, GSSG levels increased from 1.32 +/- 0.26 mu mol/109 to 2.22 +/- 0.02 mu mol/109. DNA-damage assessed via comet assay, showed significant increases in tail-moment (2.53 mu m) and tail-migration (16.13 mu m). Oxidative DNA-damage, indicated by 8-OHdG levels, increased significantly from 0.29 +/- 0.02 ng.mL- (control) to 0.47 +/- 0.07 ng.mL- at 35 mu M retrorsine. These findings demonstrate the sensor's effectiveness for retrorsine detection and its applicability in toxicological studies. The integration of nanomaterial engineering and molecular imprinting provides a highly sensitive, selective, and eco-friendly solution for monitoring toxic agents and assessing their biological impacts.Article In-Depth Analysis of Drought Trend in Semiarid Saïs Plateau and Middle Atlas Region in Morocco(Springer int Publ Ag, 2025) Qadem, Zohair; Tayfur, Gokmen; Kankal, MuratThis study explores the spatiotemporal properties of droughts and their evolution in the semiarid Sa & iuml;s Plateau and the Middle Atlas regions in Morocco. The methodology includes the analysis of 36 years of precipitation data recorded at 16 meteorological stations, the use of the standardized precipitation index (SPI) at different temporal scales of short term (1 and 3 months), medium term (6 months), and long term (12 and 24 months) to capture historical droughts, and the application of the Mann-Kendall test to assess the drought trends. The wet and dry periods in the Sa & iuml;s Plateau and Middle Atlas regions are almost evenly distributed, with 65% in the "near-normal" condition. The "extremely dry" period, with a value of 1%, was lower than the "extremely humid" period (1.65%). There is no topographically and climatically significant difference between the Sa & iuml;s Plateau and the Middle Atlas in terms of droughts, which are found to decrease over time in both regions. The results of Mann-Kendall test reveal that the short-term trends are generally positive, except at the Boulemane station (- 0.06 for SPI-1, - 0.13 for SPI-3). The long-term precipitation increases in the Middle Atlas region, particularly at the Ait Khabach (0.33 for SPI-24) and the Imouzzer (0.36 for SPI-24) stations. On the Sa & iuml;s Plateau, the trends are positive at the stations of Fez City (0.16 for SPI-24) and Dar Elarsa (0.27 for SPI-24). Significant trends are more pronounced at longer time scales.Article Citation - WoS: 2Citation - Scopus: 2Charting the Landscape of Design Cognition: Bridging the Gap Between Design Cognition and Cognitive Science(Taylor & Francis Ltd, 2025) Ata, F. Zeynep; Dogan, FehmiThis study examines the trajectory of cognitive studies on design processes (DesCog), charting its scientific landscape and interactions with cognitive science (CogSci). First, the study delineates the boundaries of DesCog within all published scholarly works. The analysis indicates that DesCog is a focused field with lesser impact on other fields, showing divergent bibliographic positions and connections for 'design cognition' and 'design thinking'. Second, the longitudinal evolution of DesCog is identified as gradually becoming more diverse and more connected. Third, DesCog's foundational connections to CogSci demonstrate that the relationship is spontaneous rather than following 'generalising interdisciplinarity' aims. The analysis indicates a unidirectional flow from CogSci to DesCog, with occasional reciprocal interactions. The volume and diversity of CogSci literature cited by DesCog appear narrow, and most cited publications are based on the information-processing theory of cognition. Fourth, the study identifies common themes at the intersection of two fields, demonstrating that creativity has been a focal theme for both since earlier studies. Finally, the individual impact of CogSci researchers on DesCog highlights the significance of Simon and Newell's influence. The study contributes to reflections on DesCog's knowledge production, underlining unidirectional knowledge flows from CogSci to DesCog and partial theoretical connections within the field.Article Citation - WoS: 7Citation - Scopus: 9A Holistic Overview of the Applications of Grace-Observed Terrestrial Water Storage in Hydrology and Climate Science(Springer, 2025) Khorrami, Behnam; Gunduz, OrhanTerrestrial Water Storage (TWS) represents a vital element of the hydrological cycle, with its fluctuations significantly impacting the climate of the Earth and its ecological balance. Since its launch in 2002, the Gravity Recovery and Climate Experiment (GRACE) satellite mission has revolutionized the ability to observe and analyze large-scale mass changes within Earth's system components. This paper offers a comprehensive and current overview of GRACE satellite gravimetry, highlighting its relevance to hydrological and climate-related studies. It outlines the fundamental measurement principles of the GRACE mission, provides an in-depth explanation of GRACE data products (including spherical harmonic and mascon solutions), examines emerging trends in GRACE-based research, and reviews key applications in hydrology and climate science. Additionally, it addresses the major challenges in utilizing GRACE data and explores promising avenues for future research and applications.