PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Epigallocatechin Gallate and Punicalagin Combination Reduces Aβ Aggregation and Promotes Neurogenesis in Adult Zebrafish Brain(John Wiley and Sons Inc, 2026) Nazli, D.; Ipekgil, D.; Poyraz, Y.K.; Can, K.; Okmen, I.; Turhanlar-Sahin, E.; Ozhan, G.Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory impairment, and behavioral alterations. The pathogenesis of AD involves the accumulation of amyloid-beta (Aβ) plaques and the hyperphosphorylated tau proteins, which disrupt neuronal function and trigger neuroinflammation. This study explores the therapeutic potential of epigallocatechin gallate (EGCG) and punicalagin (PU) in mitigating Aβ-induced toxicity using an adult zebrafish model of AD. Our results demonstrate that the EGCG + PU combination significantly reduces Aβ accumulation, protects against cellular damage, suppresses acetylcholinesterase (AChE) activity, and normalizes the expression of amyloidogenic and AD-related genes. Additionally, EGCG + PU treatment alleviates neuroinflammation by suppressing glial activation, including reductions in L-plastin and proinflammatory cytokine expression, while promoting neuronal recovery through mechanisms of neurogenesis and neuroprotection. Notably, the combination treatment restored neuronal density and improved behavioral outcomes by alleviating anxiety- and aggression-like behaviors associated with Aβ toxicity. These results underscore the synergistic neuroprotective effects of EGCG + PU, highlighting their potential as a novel therapeutic approach for mitigating the pathological, behavioral, and inflammatory aspects of AD. © 2026 Wiley Periodicals LLC.Article Valorization of Recycled Waste in Green/White Purification and LC-QTOF/MS Analysis of Beverages Adulterated with Incapacitating Drugs(Elsevier B.V., 2026) Anilanmert, Beril; Yonar, Fatma Cavus; Er, Elif Ozturk; Pekcaliskan, Elif Yılmaz; Cengiz, SalihIncapacitating drugs constitute a growing threat for the community, since victims may drink adulterated beverages without noticing. A validated eco-friendly/economical purification/analysis kit prototype, along with an LC-QToF/MS method has been developed in coke and mixed fruit-juice, for simultaneous determination of 10 drugs used for incapacitating victims (zaleplone, zolpidem, zopiclone, mephedrone, fentanyl, phenytoin, thiopental, sertraline, ketamine and GHB). A combination of two different waste nut-shells which yielded the highest recovery for these drugs were directly used as adsorbent after grinding and modification and a reusable separation apparatus recycled from waste were utilized for the first time in a toxicological analysis. In the method, after adding the adsorbent on to the sample, pH was adjusted. Following 25-min (min) automatic vortexing for adsorption, matrix was removed easily, using the separation apparatus. After 25-min desorption via cold ultrasonication using 500 μL methanol, a 9.5-min LC-QToF/MS analysis was performed. The validated method in fruit-juice and coke, extraordinarily gave successful results also in urine and saliva. Assessment tools for greenness/whiteness and pictograms confirmed the environmental friendliness of the method kit. © 2025 Elsevier B.V.Article A Simplified Molecular Imprinting Strategy Through Electrospinning of Polyacrylonitrile for Thin Film Microextraction of Selected Pesticides(Elsevier B.V., 2026) Şahin, A.; Akpinar, Y.; Yildirim, E.; Eroǧlu, A.E.; Boyaci, E.Molecularly imprinted polymers (MIPs) have been extensively used as selective extractive phases for sample preparation because of their analyte-selective binding sites. However, MIP preparation requires optimized monomer-template interactions and long polymerization reactions. In this study, a novel and simple method of MIP preparation was proposed based on electrospinning. Instead of preparing analyte-monomer complexes before polymerization, model analytes (trifluralin and carbaryl) were directly dissolved in a polyacrylonitrile (PAN) solution, then electrospun into nanofibrous mats. This allowed for a means of preparation of highly crystalline, template-imprinted nanostructures with minimal synthetic complexity. Following the characterization studies for the new material, the extraction properties of the imprinted and nonimprinted electrospun mats were investigated in thin film microextraction (TFME) studies by extracting trifluralin and carbaryl from water samples, followed by gas chromatography-mass spectrometry (GC–MS) analysis. The optimization results showed that samplers containing 10.0 mg of MIP sorbents made by electrospinning of a solution containing 5.0 mg of template in 1.0 mL of PAN solution resulted in approximately 4 and 7 times enhanced extraction recoveries for carbaryl and trifluralin compared to samplers made of non-imprinted bulk PAN. Moreover, the cross-reactivity testing performed with non-template analytes (malathion and diazinon) suggested a more specific extraction towards trifluralin compared to carbaryl. The proposed new technique was also validated using computational methodology, which supported the experimental finding about higher selectivity towards trifluralin. This may signify a probability for structural orientation of partially charged trifluralin under an electrical field in electrospun PAN creating favorable extraction sites. © 2025 Elsevier B.V.Conference Object Citation - WoS: 24Effect of pH and Hydration on the Normal and Lateral Interaction Forces Between Alumina Surfaces(2006) Polat, Mehmet; Sato, Kimiyasu; Nagaoka, Takaaki; Watari, KojiNormal and lateral interaction forces between alumina surfaces were measured using Atomic Force Microscopy-Colloid Probe Method at different pH. The normal force curves exhibit a well-defined repulsive barrier and an attractive minimum at acidic pH and the DLVO theory shows excellent agreement with the data. The normal forces are always repulsive at basic pH and the theory fails to represent the measurements. Lateral forces are almost an order of magnitude smaller in the basic solutions. These differences, which have important implications in the study of stability and rheology, are attributed to the hydration of the alumina surface at basic pH. © 2013 Elsevier B.V., All rights reserved.Article Vision Transformers-Based Deep Feature Generation Framework for Hydatid Cyst Classification in Computed Tomography Images(Springer, 2025) Sagik, Metin; Gumus, AbdurrahmanHydatid cysts, caused by Echinococcus granulosus, form progressively enlarging fluid-filled cysts in organs like the liver and lungs, posing significant public health risks through severe complications or death. This study presents a novel deep feature generation framework utilizing vision transformer models (ViT-DFG) to enhance the classification accuracy of hydatid cyst types. The proposed framework consists of four phases: image preprocessing, feature extraction using vision transformer models, feature selection through iterative neighborhood component analysis, and classification, where the performance of the ViT-DFG model was evaluated and compared across different classifiers such as k-nearest neighbor and multi-layer perceptron (MLP). Both methods were evaluated independently to assess classification performance from different approaches. The dataset, comprising five cyst types, was analyzed for both five-class and three-class classification by grouping the cyst types into active, transition, and inactive categories. Experimental results showed that the proposed VIT-DFG method achieves higher accuracy than existing methods. Specifically, the ViT-DFG framework attained an overall classification accuracy of 98.10% for the three-class and 95.12% for the five-class classifications using 5-fold cross-validation. Statistical analysis through one-way analysis of variance (ANOVA), conducted to evaluate significant differences between models, confirmed significant differences between the proposed framework and individual vision transformer models (p<0.05\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p < 0.05$$\end{document}). These results highlight the effectiveness of combining multiple vision transformer architectures with advanced feature selection techniques in improving classification performance. The findings underscore the ViT-DFG framework's potential to advance medical image analysis, particularly in hydatid cyst classification, while offering clinical promise through automated diagnostics and improved decision-making.Article Citation - WoS: 4Citation - Scopus: 4Novel Electrospun-Based Extractive Probes for Rapid Determination of Clinically Important Compounds in Human Plasma(Elsevier B.V., 2024) Temel,E.R.; Eroğlu,A.E.; Salih,B.; Boyaci,E.Background: Coated blade spray (CBS) represents an innovative approach that utilizes solid-phase microextraction principles for sampling and sample preparation. When combined with ambient mass spectrometry (MS), it can also serve as an electrospray ionization source. Therefore, it became a promising tool in analytical applications as it can significantly reduce the analysis time. However, the current CBS coatings are based on the immobilization of extractive particles in bulk polymeric glue, which constrains the diffusion of the analytes to reach the extractive phase; therefore, the full reward of the system cannot be taken at pre-equilibrium. This has sparked the notion of developing new CBS probes that exhibit enhanced kinetics. Results: With this aim, to generate a new extractive phase with improved extraction kinetics, poly(divinylbenzene) (PDVB) nanoparticles were synthesized by mini-emulsion polymerization and then immobilized into sub-micrometer (in diameter) sized polyacrylonitrile fibers which were obtained by electrospinning method. Following the optimization and characterization studies, the electrospun-coated blades were used to determine cholesterol, testosterone, and progesterone in plasma spots using the CBS-MS approach. For testosterone and progesterone, 10 ng mL−1 limits of quantification could be obtained, which was 200 ng mL−1 for cholesterol in spot-sized samples without including any pre-treatment steps to samples prior to extraction. Significance: The comparison of the initial kinetics for dip-coated and electrospun-coated CBS probes proved that the electrospinning process could enhance the extraction kinetics; therefore, it can be used for more sensitive analyses. The total analysis time with this method, from sample preparation to instrumental analysis, takes only 7 min, which suggests that the new probes are promising for fast diagnostic applications. © 2024 Elsevier B.V.Article Citation - Scopus: 5Risk Analysis for Groundwater Intakes Based on the Example of Neonicotinoids(Elsevier Ltd, 2024) Pietrzak,D.; Kania,J.; Kmiecik,E.; Baba,A.Neonicotinoids are a class of broad-spectrum insecticides that are dominant in the world market. They are widely distributed in the environment. Understanding the sources, distribution, and fate of these contaminants is critical to mitigating their effects and maintaining the health of aquatic ecosystems. Contamination of surface and groundwater by neonicotinoids has become a widespread problem worldwide, requiring comprehensive action to accurately determine the mechanisms behind the migration of these pesticides, their properties, and their adverse effects on the environment. A new approach to risk analysis for groundwater intake contamination with emerging contaminants was proposed. It was conducted on the example of four neonicotinoids (acetamiprid, clothianidin, thiamethoxam, and imidacloprid) in relation to groundwater accessed by a hypothetical groundwater intake, based on data obtained in laboratory tests using a dynamic method (column experiments). The results of the risk analysis conducted have shown that in this case study the use of acetamiprid and thiamethoxam for agricultural purposes poses an acceptable risk, and does not pose a risk to the quality of groundwater extracted from the intake for food purposes. Consequently, it does not pose a risk to the health and life of humans and other organisms depending on that water. The opposite situation is observed for clothianidin and imidacloprid, which pose a higher risk of groundwater contamination. For higher maximum concentration of neonicotinoids used in the risk analysis, the concentration of clothianidin and imidacloprid in the groundwater intake significantly (from several to several hundred thousand times) exceeds the maximum permissible levels for drinking water (<0.1 μg/L). This risk exists even if the insecticides containing these pesticides are used according to the information sheet provided by the manufacturer (lower maximum concentration), which results in exceeding the maximum permissible levels for drinking water from several to several hundred times. © 2024 Elsevier LtdArticle Citation - WoS: 10Citation - Scopus: 11Arabinoxylan-Based Psyllium Seed Hydrocolloid: Single-Step Aqueous Extraction and Use in Tissue Engineering(Elsevier B.V., 2024) Yildirim-Semerci,Ö.; Bilginer-Kartal,R.; Arslan-Yildiz,A.Biomacromolecules derived from natural sources offer superior biocompatibility, biodegradability, and water-holding capacity, which make them promising scaffolds for tissue engineering. Psyllium seed has gained attention in biomedical applications recently due to its gel-forming ability, which is provided by its polysaccharide-rich content consisting mostly of arabinoxylan. This study focuses on the extraction and gelation of Psyllium seed hydrocolloid (PSH) in a single-step water-based protocol, and scaffold fabrication using freeze-drying method. After characterization of the scaffold, including morphological, mechanical, swelling, and protein adsorption analyses, 3D cell culture studies were done using NIH-3 T3 fibroblast cells on PSH scaffold, and cell viability was assessed using Live/Dead and Alamar Blue assays. Starting from day 1, high cell viability was obtained, and it reached 90 % at the end of 15-day culture period. Cellular morphology on PSH scaffold was monitored via SEM analysis; cellular aggregates then spheroid formation were observed throughout the study. Collagen Type-I and F-actin expressions were followed by immunostaining revealing a 9- and 10-fold increase during long-term culture. Overall, a single-step and non-toxic protocol was developed for extraction and gelation of PSH. Obtained results unveiled that PSH scaffold provided a favorable 3D microenvironment for cells, holding promise for further tissue engineering applications. © 2024 Elsevier B.V.Article Citation - WoS: 9Citation - Scopus: 11Experimental Investigation of Spray Characteristics of Ethyl Esters in a Constant Volume Chamber(Springer, 2024) Ulu, A.; Yildiz, G.; Özkol, Ü.; Rodriguez, A.D.Abstract: Biodiesels are mainly produced via the utilization of methanol in transesterification, which is the widespread biodiesel production process. The majority of this methanol is currently obtained from fossil resources, i.e. coal and natural gas. However, in contrast with methanol, biomass-based ethanol can also be used to produce biodiesels; this could allow the production line to become fully renewable. This study aimed to investigate the spray characteristics of various ethyl ester type biodiesels derived from sunflower and corn oils in comparison to methyl esters based on the same feedstocks and reference petroleum-based diesel. Spray penetration length (SPL) and spray cone angle (SCA) were experimentally evaluated in a constant volume chamber allowing optical access, under chamber pressures of 0, 5, 10 and 15 bar and injection pressures of 600 and 800 bar. Sauter mean diameter (SMD) values were estimated by using an analytical correlation. Consequently, ethyl esters performed longer SPL (2.8–20%) and narrower SCA (5.1–19%) than diesel under ambient pressures of 5 and 10 bar. Although the SMD values of ethyl esters were 48% higher than diesel on average, their macroscopic spray characteristics were very similar to those of diesel under 15 bar chamber pressure. Moreover, ethyl esters were found to be very similar to methyl esters in terms of spray characteristics. The differences in SPL, SCA and SMD values for both types of biodiesels were lower than 4%. When considering the uncertainty (± 0.84%) and repeatability (±5%) ratios, the difference between the spray characteristics of methyl and ethyl esters was not major. Graphical abstract: [Figure not available: see fulltext.] © 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Article Citation - WoS: 6Citation - Scopus: 6Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models(Academic Press Inc., 2024) Güler,G.; Acikgoz,E.; Mukhtarova,G.; Oktem,G.Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc.