PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article A Novel Technique Using Integral Transforms and Residual Functions for Nonlinear Partial Fractional Differential Equations Involving Caputo Derivatives(Public Library of Science, 2024) Khan, Z.A.; Riaz, M.B.; Liaqat, M.I.; Akgül, A.Fractional nonlinear partial differential equations are used in many scientific fields to model various processes, although most of these equations lack closed-form solutions. For this reason, methods for approximating solutions that occasionally yield closed-form solutions are crucial for solving these equations. This study introduces a novel technique that combines the residual function and a modified fractional power series with the Elzaki transform to solve various nonlinear problems within the Caputo derivative framework. The accuracy and effectiveness of our approach are validated through analyses of absolute, relative, and residual errors. We utilize the limit principle at zero to identify the coefficients of the series solution terms, while other methods, including variational iteration, homotopy perturbation, and Adomian, depend on integration. In contrast, the residual power series method uses differentiation, and both approaches encounter difficulties in fractional contexts. Furthermore, the effectiveness of our approach in addressing nonlinear problems without relying on Adomian and He polynomials enhances its superiority over various approximate series solution techniques. © 2024 Khan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Article Citation - WoS: 2Citation - Scopus: 2Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration(Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, FundaIn recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.Article Citation - WoS: 1Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems(Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide AlsoyIn this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.Correction Diaph1-Deficiency Is Associated With Major T, Nk and Ilc Defects in Humans (vol 44, 175, 2024)(Springer/plenum Publishers, 2025) Azizoglu, Zehra Busra; Babayeva, Royala; Haskologlu, Zehra Sule; Acar, Mustafa Burak; Ayaz-Guner, Serife; Okus, Fatma Zehra; Eken, Ahmet[No Abstract Available]Article Citation - WoS: 2Citation - Scopus: 2Invasion/Chemotaxis- and Extravasation-Chip Models for Breast Cancer Bone Metastasis(Public Library Science, 2024) Firatligil-Yildirir, Burcu; Bati-Ayaz, Gizem; Nonappa, Devrim; Pesen-Okvur, Devrim; Yalcin-Ozuysal, OzdenBone is one of the most frequently targeted organs in metastatic cancers including the breast. Breast cancer bone metastasis often results in devastating outcomes as limited treatment options are currently available. Therefore, innovative methods are needed to provide earlier detection and thus better treatment and prognosis. Here, we present a new approach to model bone-like microenvironments to detect invasion and extravasation of breast cancer cells using invasion/chemotaxis (IC-) and extravasation (EX-) chips, respectively. Our results show that the behaviors of MDA-MB-231 breast cancer cells on IC- and EX-chip models correlate with their in vivo metastatic potential. Our culture model constitutes cell lines representing osteoblasts, bone marrow stromal cells, and monocytes embedded in three-dimensional (3D) collagen I-based extracellular matrices of varying composition and stiffness. We show that collagen I offers a better bone-like environment for bone cells and matrix composition and stiffness regulate the invasion of breast cancer cells. Using in situ contactless rheological measurements under cell culture conditions, we show that the presence of cells increased the stiffness values of the matrices up to 1200 Pa when monitored for five days. This suggests that the cellular composition has a significant effect on regulating matrix mechanical properties, which in turn contribute to the invasiveness. The platforms we present here enable the investigation of the underlying molecular mechanisms in breast cancer bone metastasis and provide the groundwork of developing preclinical tools for the prediction of bone metastasis risk.Article Citation - WoS: 2Citation - Scopus: 2Investigation of the Biocompatibility of Various Pulp Capping Materials on Zebrafish Model(Public Library Science, 2024) Karahan, Meltem; Eliacik, Bahar Basak Kiziltan; Cagiral, Umut; Iscan, Evin; Ozhan, GunesTesting the biocompatibility of commercially available dental materials is a major challenge in dental material science. In the present study, the biocompatibility of four commercially available dental materials Mineral Trioxide Aggregate, Biodentine, Harvard BioCal-CAP and Oxford ActiveCal PC was investigated. The biocompatibility analysis was performed on zebrafish embryos and larvae using standard toxicity tests such as survivability and hatching rates. Comparative toxicity analysis of toxicity was performed by measuring apoptosis using acridine orange dye and whole mount immunofluorescence methods on zebrafish larvae exposed to the dental materials at different dilutions. Toxicity analysis showed a significant decrease in survival and hatching rates with increasing concentration of exposed materials. The results of the apoptosis assay with acridine orange showed greater biocompatibility of Biodentine, Oxford ActiveCal PC, Harvard BioCal-CAP and Biodentine compared to MTA, which was concentration dependent. Consequently, this study has shown that showed resin-modified calcium silicates are more biocompatible than traditional calcium silicates.Article Citation - WoS: 9Citation - Scopus: 6Fluorescence Lifetime Multiplexing With Fluorogen Activating Protein Fast Variants(Nature Portfolio, 2024) Bogdanova, Yulia A.; Solovyev, Ilya D.; Baleeva, Nadezhda S.; Myasnyanko, Ivan N.; Gorshkova, Anastasia A.; Gorbachev, Dmitriy A.; Baranov, Mikhail S.In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling. A genetically encoded labeling system uses smallest-in-class fluorogen-activating protein tags for time-resolved fluorescence multiplexed cellular imaging, offering monoexponential decay and potential for sophisticated fluorescence lifetime analysis.Article Citation - WoS: 25Citation - Scopus: 25Topology Degree Results on a G-Abc Implicit Fractional Differential Equation Under Three-Point Boundary Conditions(Public Library Science, 2024) Rezapour, Shahram; Thabet, Sabri T. M.; Rafeeq, Ava Sh.; Kedim, Imed; Vivas-Cortez, Miguel; Aghazadeh, NasserThis research manuscript aims to study a novel implicit differential equation in the non-singular fractional derivatives sense, namely Atangana-Baleanu-Caputo (A B C) of arbitrary orders belonging to the interval (2, 3] with respect to another positive and increasing function. The major results of the existence and uniqueness are investigated by utilizing the Banach and topology degree theorems. The stability of the Ulam-Hyers (U H) type is analyzed by employing the topics of nonlinear analysis. Finally, two examples are constructed and enhanced with some special cases as well as illustrative graphics for checking the influence of major outcomes.Article Citation - WoS: 6Citation - Scopus: 6Tumour-Intrinsic Endomembrane Trafficking by Arf6 Shapes an Immunosuppressive Microenvironment That Drives Melanomagenesis and Response To Checkpoint Blockade Therapy(Nature Portfolio, 2024) Wee, Yinshen; Wang, Junhua; Wilson, Emily C.; Rich, Coulson P.; Rogers, Aaron; Tong, Zongzhong; Grossmann, Allie H.Tumour-host immune interactions lead to complex changes in the tumour microenvironment (TME), impacting progression, metastasis and response to therapy. While it is clear that cancer cells can have the capacity to alter immune landscapes, our understanding of this process is incomplete. Herein we show that endocytic trafficking at the plasma membrane, mediated by the small GTPase ARF6, enables melanoma cells to impose an immunosuppressive TME that accelerates tumour development. This ARF6-dependent TME is vulnerable to immune checkpoint blockade therapy (ICB) but in murine melanoma, loss of Arf6 causes resistance to ICB. Likewise, downregulation of ARF6 in patient tumours correlates with inferior overall survival after ICB. Mechanistically, these phenotypes are at least partially explained by ARF6-dependent recycling, which controls plasma membrane density of the interferon-gamma receptor. Collectively, our findings reveal the importance of endomembrane trafficking in outfitting tumour cells with the ability to shape their immune microenvironment and respond to immunotherapy. The small GTPase ARF6 is known to regulate endocytosis and recycling of plasma membrane proteins. Here the authors show that tumourintrinsic ARF6 promotes an immunosuppressive microenvironment that accelerates melanoma progression but that is vulnerable to immune checkpoint blockade, mechanistically linked to ARF6-dependent recycling of interferon-gamma receptors in tumour cells.Review Citation - WoS: 10Citation - Scopus: 12Trends in Authentication of Edible Oils Using Vibrational Spectroscopic Techniques(Royal Soc Chemistry, 2024) Ozen, Banu; Cavdaroglu, Cagri; Tokatli, FigenThe authentication of edible oils has become increasingly important for ensuring product quality, safety, and compliance with regulatory standards. Some prevalent authenticity issues found in edible oils include blending expensive oils with cheaper substitutes or lower-grade oils, incorrect labeling regarding the oil's source or type, and falsely stating the oil's origin. Vibrational spectroscopy techniques, such as infrared (IR) and Raman spectroscopy, have emerged as effective tools for rapidly and non-destructively analyzing edible oils. This review paper offers a comprehensive overview of recent advancements in using vibrational spectroscopy for authenticating edible oils. The fundamental principles underlying vibrational spectroscopy are introduced and chemometric approaches that enhance the accuracy and reliability of edible oil authentication are summarized. Recent research trends highlighted in the review include authenticating newly introduced oils, identifying oils based on their specific origins, adopting handheld/portable spectrometers and hyperspectral imaging, and integrating modern data handling techniques into the use of vibrational spectroscopic techniques for edible oil authentication. Overall, this review provides insights into the current state-of-the-art techniques and prospects for utilizing vibrational spectroscopy in the authentication of edible oils, thereby facilitating quality control and consumer protection in the food industry. The authentication of edible oils has become increasingly important for ensuring product quality, safety, and compliance with regulatory standards.