Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Comparative Stability of Synthetic and Natural Polymeric Micelles in Physiological Environments: Implications for Drug Delivery(MDPI, 2025) Polat, Hurriyet; Eren, Merve Cevik; Polat, Mehmet; Koss, Kyle M.; Polat, Onur K.Polymeric micelles are widely studied as nanocarriers for hydrophobic drugs, yet their structural stability under physiological conditions remains a major limitation. This review provides a comparative evaluation of synthetic and natural polymeric micelles with a focus on their stability under dilution and in protein-rich environments. The discussion integrates thermodynamic and kinetic factors governing micelle integrity and examines how molecular composition, hydrophobic segment length, and core-shell modifications influence disintegration behavior. While synthetic micelles commonly collapse below their critical micelle concentration during intravenous administration, natural polymeric micelles, such as those derived from chitosan, alginate, or heparin, exhibit improved resistance to dilution but remain vulnerable to protein-induced destabilization. Strategies such as core or shell cross-linking, surface functionalization, and natural polymer coatings are reviewed as promising approaches to enhance circulation stability and controlled drug release. The work provides a framework for designing micellar systems with balanced biocompatibility, biodegradability, and robustness suitable for clinical drug-delivery applications.Article Subinjectivity Relative To Cotorsion Pairs(MDPI, 2025) Alagoz, Yusuf; Alizade, Rafail; Buyukasik, Engin; Rozas, Juan Ramon Garcia; Oyonarte, LuisIn this paper, we define and study the X-subinjectivity domain of a module M where X=(A,B) is a complete cotorsion pair, which consists of those modules N such that, for every extension K of N with K/N in A, any homomorphism f:N -> M can be extended to a homomorphism g:K -> M. This approach allows us to characterize some classical rings in terms of these domains and generalize some known results. In particular, we classify the rings with X-indigent modules-that is, the modules whose X-subinjectivity domains are as small as possible-for the cotorsion pair X=(FC,FI), where FI is the class of FP-injective modules. Additionally, we determine the rings for which all (simple) right modules are either X-indigent or FP-injective. We further investigate X-indigent Abelian groups in the category of torsion Abelian groups for the well-known example of the flat cotorsion pair X=(FL,EC), where FL is the class of flat modules.Article Citation - WoS: 1Citation - Scopus: 1Calcium Indicators With Fluorescence Lifetime-Based Signal Readout: a Structure-Function Study(MDPI, 2024) Simonyan, Tatiana R.; Varfolomeeva, Larisa A.; Mamontova, Anastasia V.; Kotlobay, Alexey A.; Gorokhovatsky, Andrey Y.; Bogdanov, Alexey M.; Boyko, Konstantin M.The calcium cation is a crucial signaling molecule involved in numerous cellular pathways. Beyond its role as a messenger or modulator in intracellular cascades, calcium's function in excitable cells, including nerve impulse transmission, is remarkable. The central role of calcium in nervous activity has driven the rapid development of fluorescent techniques for monitoring this cation in living cells. Specifically, genetically encoded calcium indicators (GECIs) are the most in-demand molecular tools in their class. In this work, we address two issues of calcium imaging by designing indicators based on the successful GCaMP6 backbone and the fluorescent protein BrUSLEE. The first indicator variant (GCaMP6s-BrUS), with a reduced, calcium-insensitive fluorescence lifetime, has potential in monitoring calcium dynamics with a high temporal resolution in combination with advanced microscopy techniques, such as light beads microscopy, where the fluorescence lifetime limits acquisition speed. Conversely, the second variant (GCaMP6s-BrUS-145), with a flexible, calcium-sensitive fluorescence lifetime, is relevant for static measurements, particularly for determining absolute calcium concentration values using fluorescence lifetime imaging microscopy (FLIM). To identify the structural determinants of calcium sensitivity in these indicator variants, we determine their spatial structures. A comparative structural analysis allowed the optimization of the GCaMP6s-BrUS construct, resulting in an indicator variant combining calcium-sensitive behavior in the time domain and enhanced molecular brightness. Our data may serve as a starting point for further engineering efforts towards improved GECI variants with fine-tuned fluorescence lifetimes.Article Citation - WoS: 5Citation - Scopus: 6A Comparative Study of Metaheuristic Feature Selection Algorithms for Respiratory Disease Classification(MDPI, 2024) Gürkan Kuntalp, D.; Özcan, N.; Düzyel, Okan; Kababulut, F.Y.; Kuntalp, M.The correct diagnosis and early treatment of respiratory diseases can significantly improve the health status of patients, reduce healthcare expenses, and enhance quality of life. Therefore, there has been extensive interest in developing automatic respiratory disease detection systems. Most recent methods for detecting respiratory disease use machine and deep learning algorithms. The success of these machine learning methods depends heavily on the selection of proper features to be used in the classifier. Although metaheuristic-based feature selection methods have been successful in addressing difficulties presented by high-dimensional medical data in various biomedical classification tasks, there is not much research on the utilization of metaheuristic methods in respiratory disease classification. This paper aims to conduct a detailed and comparative analysis of six widely used metaheuristic optimization methods using eight different transfer functions in respiratory disease classification. For this purpose, two different classification cases were examined: binary and multi-class. The findings demonstrate that metaheuristic algorithms using correct transfer functions could effectively reduce data dimensionality while enhancing classification accuracy. © 2024 by the authors.Article Citation - WoS: 4Citation - Scopus: 4A New Shapley-Based Feature Selection Method in a Clinical Decision Support System for the Identification of Lung Diseases(MDPI, 2023) Kababulut, Fevzi Yasin; Kuntalp, Damla Gurkan; Düzyel, Okan; Özcan, Nermin; Kuntalp, MehmetThe aim of this study is to propose a new feature selection method based on the class-based contribution of Shapley values. For this purpose, a clinical decision support system was developed to assist doctors in their diagnosis of lung diseases from lung sounds. The developed systems, which are based on the Decision Tree Algorithm (DTA), create a classification for five different cases: healthy and disease (URTI, COPD, Pneumonia, and Bronchiolitis) states. The most important reason for using a Decision Tree Classifier instead of other high-performance classifiers such as CNN and RNN is that the class contributions of Shapley values can be seen with this classifier. The systems developed consist of either a single DTA classifier or five parallel DTA classifiers each of which is optimized to make a binary classification such as healthy vs. others, COPD vs. Others, etc. Feature sets based on Power Spectral Density (PSD), Mel Frequency Cepstral Coefficients (MFCC), and statistical characteristics extracted from lung sound recordings were used in these classifications. The results indicate that employing features selected based on the class-based contribution of Shapley values, along with utilizing an ensemble (parallel) system, leads to improved classification performance compared to performances using either raw features alone or traditional use of Shapley values.Article Citation - WoS: 15Citation - Scopus: 16Formulation of Gluten-Free Cookies Utilizing Chickpea, Carob, and Hazelnut Flours Through Mixture Design(MDPI, 2023) Doğruer, Ilgın; Başer, Filiz; Güleç, Şükrü; Tokatlı, Figen; Özen, BanuLegume flours, which offer high nutritional quality, present viable options for gluten-free bakery products. However, they may have an objectionable flavor and taste for some consumers. In this study, it was aimed to improve the gluten-free cookie formulation by incorporating carob and hazelnut flours to pre-cooked chickpea flour and to investigate the techno-functional properties of the formulated cookies. The flours used in the formulations were assessed for their chemical and physical properties. This study employed a mixture design (simplex-centroid) to obtain the proportions of the flours to be used in the cookie formulations. The rheological characteristics of the doughs and the technological attributes of the baked cookies were determined. The addition of the hazelnut and carob flours had the overall effect of reducing the rheological characteristics of the cookie doughs. Furthermore, the textural attribute of the hardness of the baked cookies decreased as the ratio of hazelnut flour in the formulations was raised. The analysed results and sensory evaluation pointed to a formulation consisting of 30% pre-cooked chickpea/30% carob/30% hazelnut flours, which exhibited improved taste and overall acceptability scores. A total of 16.82 g/100 g of rapidly digestible starch, 5.36 g/100 g of slowly digestible starch, and 8.30 g/100 g of resistant starch exist in this particular cookie. As a result, combinations of chickpea, hazelnut, and carob flours hold promise as good alternatives for gluten-free cookie ingredients and warrant further exploration in the development of similar products.Article Citation - WoS: 16Citation - Scopus: 17Techno-Functional and in Vitro Digestibility Properties of Gluten-Free Cookies Made From Raw, Pre-Cooked, and Germinated Chickpea Flours(MDPI, 2023) Doğruer, Ilgın; Çoban, Başak; Başer, Filiz; Güleç, Şükrü; Özen, BanuChickpea flour, which is produced in various forms, has high protein and fiber content; therefore, it can be a good ingredient for gluten-free cookies. The objective of this study was to investigate and compare the properties of cookies formulated using raw (RCF), cooked (CCF), and germinated (GCF) chickpea flours. The techno-functional properties of these flours were determined, and scanning electron microscope images and mid-infrared spectra were obtained. The rheological properties of cookie doughs were measured along with their mid-infrared spectra. Baked cookies were analyzed for their technological properties as well as their in vitro digestion properties. Sensory analysis was also performed for all the cookies. The most significant difference among the flours was observed in their water retention capacity, and CCF had 119.7% higher water retention capacity compared to RCF. The dough made with CCF had quite different rheological properties from the others. The cookies baked with GCF had the highest baking loss and spread ratio. The CCF-containing cookies had the hardest structure. The cookies made from RCF had a higher resistant starch content followed by the cookies with GCF. All the cookies had similar scores in all aspects tested in the sensory analysis. The use of three different forms of chickpea flour in cookie formulations resulted in products with very different properties; however, their overall acceptability levels were close.Article Citation - WoS: 2Citation - Scopus: 3High-Pressure Processing of Traditional Hardaliye Drink: Effect on Quality and Shelf-Life Extension(MDPI, 2023) Atmaca, Bahar; Demiray, Merve; Akdemir Evrendilek, Gülsün; Bulut, Nurullah; Uzuner, SibelHardaliye, as one of the oldest and lesser known traditional beverages, is produced using red grape pomace from wine production. This drink production is achieved through lactic acid fermentation, with the addition of sour cherry leaves and mustard seeds-either heat-treated, grinded, or whole-in various concentrations. Hardaliye has a very short shelf life; thus, efforts have recently been made to process hardaliye with novel processing technologies in order to achieve shelf-life extension. Therefore, the high-hydrostatic-pressure (HHP) processing of hardaliye was performed to determine its impact on important properties, including in microbial inactivation and shelf-life extension, with respect to a Box-Behnken experimental design. Maximum log reductions of 5.38 & PLUSMN; 0.6, 5.10 & PLUSMN; 0.0, 5.05 & PLUSMN; 0.2, and 4.21 & PLUSMN; 0.0 with HHP were obtained for Brettanomyces bruxellensis, total mesophilic aerobic bacteria, Lactobacillus brevis, and total mold and yeast, respectively. The processing parameters of 490 MPa and 29 & DEG;C for 15 min were found as the optimal conditions, with the response variables of an optical density at 520 nm and the inactivation of L. brevis. The samples processed at the optimal conditions were stored at both 4 and 22 & DEG;C for 228 d. While the non-treated control samples at 4 and 22 & DEG;C were spoiled at 15 and 3 d, the HHP-treated samples were spoiled after 228 and 108 d at 4 and 22 & DEG;C, respectively.Article Citation - WoS: 7Citation - Scopus: 11Applications of Uv–visible, Fluorescence and Mid-Infrared Spectroscopic Methods Combined With Chemometrics for the Authentication of Apple Vinegar(MDPI, 2023) Çavdaroğlu, C.; Özen, B.Spectroscopic techniques as untargeted methods have great potential in food authentication studies, and the evaluation of spectroscopic data with chemometric methods can provide accurate predictions of adulteration even for hard-to-identify cases such as the mixing of vinegar with adulterants having a very similar chemical nature. In this study, we aimed to compare the performances of three spectroscopic methods (fluorescence, UV–visible, mid-infrared) in the detection of acetic-acid/apple-vinegar and spirit-vinegar/apple-vinegar mixtures (1–50%). Data obtained with the three spectroscopic techniques were used in the generation of classification models with partial least square discriminant analysis (PLS-DA) and orthogonal partial least square discriminant analysis (OPLS-DA) to differentiate authentic and mixed samples. An improved classification approach was used in choosing the best models through a number of calibration and validation sets. Only the mid-infrared data provided robust and accurate classification models with a high classification rate (up to 96%), sensitivity (1) and specificity (up to 0.96) for the differentiation of the adulterated samples from authentic apple vinegars. Therefore, it was concluded that mid-infrared spectroscopy is a useful tool for the rapid authentication of apple vinegars and it is essential to test classification models with different datasets to obtain a robust model. © 2023 by the authors.Article Citation - WoS: 3Citation - Scopus: 3Her2-Specific Peptide (ltvspwy) and Antibody (herceptin) Targeted Core Cross-Linked Micelles for Breast Cancer: a Comparative Study(MDPI, 2023) Bayram, N.N.; Ulu, G.T.; Abdulhadi, N.A.; Gürdap, S.; İşoğlu, İ.A.; Baran, Yusuf; İşoğlu, S.D.This study aims to prepare a novel breast cancer-targeted micelle-based nanocarrier, which is stable in circulation, allowing intracellular drug release, and to investigate its cytotoxicity, apoptosis, and cytostatic effects, in vitro. The shell part of the micelle is composed of zwitterionic sulfobetaine ((N-3-sulfopropyl-N,N-dimethylamonium)ethyl methacrylate), while the core part is formed by another block, consisting of AEMA (2-aminoethyl methacrylamide), DEGMA (di(ethylene glycol) methyl ether methacrylate), and a vinyl-functionalized, acid-sensitive cross-linker. Following this, a targeting agent (peptide (LTVSPWY) and antibody (Herceptin®)), in varying amounts, were coupled to the micelles, and they were characterized by 1H NMR, FTIR (Fourier-transform infrared spectroscopy), Zetasizer, BCA protein assay, and fluorescence spectrophotometer. The cytotoxic, cytostatic, apoptotic, and genotoxic effects of doxorubicin-loaded micelles were investigated on SKBR-3 (human epidermal growth factor receptor 2 (HER2)-positive) and MCF10-A (HER2-negative). According to the results, peptide-carrying micelles showed a higher targeting efficiency and better cytostatic, apoptotic, and genotoxic activities than antibody-carrying and non-targeted micelles. Also, micelles masked the toxicity of naked DOX on healthy cells. In conclusion, this nanocarrier system has great potential to be used in different drug-targeting strategies, by changing targeting agents and drugs. © 2023 by the authors.
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