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.Article Citation - WoS: 4Citation - Scopus: 4Tailored Bodipy-Based Fluorogenic Probes for Phosgene Detection: a Comparative Evaluation of Recognition Sites(Royal Soc Chemistry, 2024) Dartar, Suay; Kaya, Beraat Umur; Yayak, Yanki Oncu; Vural, Ezgi; Emrullahoglu, MustafaWe constructed two novel boron-dipyrromethene (BODIPY)-based fluorescent probes, BOPD and BOBA, each equipped with the phosgene specific recognition units o-phenylenediamine (OPD) and o-aminobenzylamine (OBA) at the 2-position of the BODIPY core. BOPD and BOBA represent rare examples of BODIPY-based probes that operate by modulating an intramolecular charge transfer process (ICT), as validated by computational studies. We systematically compared the analytic performance of those recognition units while focusing on selectivity, fluorescence turn-on ratios and response times. Probe BOBA, equipped with OBA as the recognition unit, demonstrated a remarkably low detection limit (i.e., 1.40 nM) and a rapid response time (<10 s) for triphosgene. By comparison, BOPD, featuring an OPD unit, showed superior selectivity towards triphosgene, with a detection limit of 93 nM and a response time of up to 30 s. A portable sensing platform was developed by loading BOPD onto test strips made of TLC plates, nonwoven materials and small-headed cotton swabs, which were assessed for their effectiveness in detecting phosgene. We additionally performed the first successful application of a fluorescent probe, namely BOPD, for monitoring the accumulation of phosgene in plants.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: 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: 10Citation - Scopus: 9Exploring Neuronal Differentiation Profiles in Sh-Sy5y Cells Through Magnetic Levitation Analysis(Amer Chemical Soc, 2024) Kartal, Rumeysa Bilginer; Yildiz, Ahu ArslanMagnetic levitation (MagLev) is a powerful and versatile technique that can sort objects based on their density differences. This paper reports the sorting of SH-SY5Y cells for neuronal differentiation by the MagLev technique. Herein, SH-SY5Y cells were differentiated with retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). Neuronal differentiation was confirmed by neurite extension measurement and the immunostaining assay. Neurites reached the maximum length on day 9 after sequential treatment with RA-BDNF. Neuronal marker expression of un-/differentiated cells was investigated by beta-III tubulin and neuronal nuclei (NeuN) and differentiated cells exhibited a higher fluorescence intensity compared to un-/differentiated cells. MagLev results revealed that the density of differentiated SH-SY5Y cells gradually increased from 1.04 to 1.06 g/mL, while it remained stable at 1.05 g/mL for un-/differentiated cells. These findings signified that cell density would be a potent indicator of neuronal differentiation. Overall, it was shown that MagLev methodology can provide rapid, label-free, and easy sorting to analyze the differentiation of cells at a single-cell level.Article Citation - WoS: 1Citation - Scopus: 1Experimental and Theoretical Investigation of Synthesis and Properties of Dodecanethiol-Functionalized Mos<sub>2</Sub>(Royal Soc Chemistry, 2023) Duran, Tuna A.; Şahin, Hasan; Sabani, Denis; Milosevic, Milorad V.; Sahin, HasanHerein, we investigate the DDT (1-dodecanethiol) functionalization of exfoliated MoS2 by using experimental and theoretical tools. For the functionalization of MoS2, DDT treatment was incorporated into the conventional NMP (N-methyl pyrrolidone) exfoliation procedure. Afterward, it has been demonstrated that the functionalization process is successful through optical, morphological and theoretical analysis. The D, G and 2LA peaks seen in the Raman spectrum of exfoliated NMP-MoS2 particles, indicate the formation of graphitic species on MoS2 sheets. In addition, as the DDT ratio increases, the vacant sites on MoS2 sheets diminish. Moreover, at an optimized ratio of DDT-NMP, the maximum number of graphitic quantum dots (GQDs) is observed on MoS2 nanosheets. Specifically, the STEM and AFM data confirm that GQDs reside on the MoS2 nano-sheets and also that the particle size of the DDT-MoS2 is mostly fixed, while the NMP-MoS2 show many smaller and distributed sizes. The comparison of PL intensities of the NMP-MoS2 and DDT-MoS2 samples states a 10-fold increment is visible, and a 60-fold increment in NIR region photoluminescent properties. Moreover, our results lay out understanding and perceptions on the surface and edge chemistry of exfoliated MoS2 and open up more opportunities for MoS2 and GQD particles with broader applications.Article Citation - WoS: 41Citation - Scopus: 45Measurements of P P → Z Z Production Cross Sections and Constraints on Anomalous Triple Gauge Couplings at √s=13tev(Springer Science and Business Media Deutschland GmbH, 2021) Sirunyan,A.M.; Tumasyan,A.; Adam,W.; Ambrogi,F.; Bergauer,T.; Dragicevic,M.; Bychkova,O.The production of Z boson pairs in proton–proton (p p) collisions, p p → (Z / γ∗) (Z / γ∗) → 2 ℓ2 ℓ′, where ℓ, ℓ′= e or μ , is studied at a center-of-mass energy of 13TeV with the CMS detector at the CERN LHC. The data sample corresponds to an integrated luminosity of 137fb-1, collected during 2016–2018. The Z Z production cross section, σtot(pp→ZZ)=17.4±0.3(stat)±0.5(syst)±0.4(theo)±0.3(lumi) pb, measured for events with two pairs of opposite-sign, same-flavor leptons produced in the mass region 60<mℓ+ℓ-<120GeV is consistent with standard model predictions. Differential cross sections are also measured and agree with theoretical predictions. The invariant mass distribution of the four-lepton system is used to set limits on anomalous Z Z Z and Z Z γ couplings. © 2021, CERN for the benefit of the CMS collaboration.
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