WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Conference Object Human Neu3 Sialidase Reduces GM2 Ganglioside Accumulation in Neuroglia Cells of Tay-Sachs Disease Mice Model(Springernature, 2024) Basirli, Hatice Hande; Ozgur, Melike Can; Seyrantepe, VolkanConference Object Enhancing Genomic Data Sharing With Blockchain-Enabled Dynamic Consent in Beacon V2(Springernature, 2024) Binokay, Leman; Celik, Hamit Mervan; Gurdal, Gultekin; Ayav, Tolga; Tuglular, Tugkan; Oktay, Yavuz; Karakulah, GokhanArticle Novel Strut-Based Mechanical Analysis: Flow Stress Determination of Electron Beam Melt (EBM) Lattice Structures(Springernature, 2025) Bin Riaz, Muhammad Arslan; Erten, Hacer Irem; Guden, MustafaIn modeling lattices, the material flow stress equation, such as the Johnson and Cook (JC) equation, is usually determined from the mechanical tests conducted on bulk, relatively large test size specimens which were manufactured using the same process parameters with the lattices. However, the flow stresses of struts were shown in several studies to be significantly lower than those of large size test specimens. To overcome this discrepancy, a novel approach that combined the strut compression test, the strut double shear test (DST) and the numerical model of the strut DST using the JC equation was proposed. The study confirmed that the flow stress determined from the machined bulk tension test specimens overestimated the experimental compression stress-strain behavior of a body centered cubic (BCC) Ti6Al4V lattice. The flow stress parameters determined from the compression stress-strain curves of the as-printed strut specimens, on the other side, showed the best match to the experimental compression stress-strain behavior of the BCC lattice. The fidelity of the determined parameters of the JC equation was further verified with the experimental and numerical DSTs. It was also shown that the numerical iterations of DST model could be used for the fine-tuning the flow stress parameters.Article A Comprehensive MicroRNA-Seq Transcriptomic Analysis of Tay-Sachs Disease Mice Revealed Distinct MiRNA Profiles in Neuroglial Cells(Springernature, 2025) Kaya, Beyza; Orhan, Mehmet Emin; Yanbul, Selman; Demirci, Muserref Duygu Sacar; Demir, Secil Akyildiz; Seyrantepe, VolkanTay-Sachs disease (TSD) is a rare lysosomal storage disorder marked by the progressive buildup of GM2 in the central nervous system (CNS). This condition arises from mutations in the HEXA gene, which encodes the alpha subunit of the enzyme beta-hexosaminidase A. A newly developed mouse model for early-onset TSD (Hexa-/-Neu3-/-) exhibited signs of neurodegeneration and neuroinflammation, evidenced by elevated levels of pro-inflammatory cytokines and chemokines, as well as significant astrogliosis and microgliosis. Identifying disease-specific microRNAs (miRNAs) may aid the development of targeted therapies. Although previous small-scale studies have investigated miRNA expression in some regions of GM2 gangliosidosis mouse models, thorough profiling of miRNAs in this innovative TSD model remains to be done. In this study, we employed next-generation sequencing to analyze the complete miRNA profile of neuroglial cells from Hexa-/-Neu3-/- mice. By comparing KEGG and Reactome pathways associated with neurodegeneration, neuroinflammation, and sphingolipid metabolism in Hexa-/-Neu3-/- neuroglial cells, we discovered new microRNAs and their targets related to the pathophysiology of GM2 gangliosidosis. For the first time, our findings showed that miR-708-5p, miR-672-5p, miR-204-5p, miR-335-5p, and miR-296-3p were upregulated, while miR-10 b-5p, miR-615-3p, miR-196a-5p, miR-214-5p, and miR-199a-5p were downregulated in Hexa-/-Neu3-/- neuroglial cells in comparison to age-matched wild-type (WT). These specific changes in miRNA expression deepen our understanding of the disease's neuropathological characteristics in Hexa-/-Neu3-/- mice. Our study suggests that miRNA-based therapeutic strategies may improve clinical outcomes for TSD patients.Article Citation - WoS: 1Citation - Scopus: 1The Role of Trna Fragments on Neurogenesis Alteration by H2o2-Induced Oxidative Stress(Springernature, 2025) Karacicek, Bilge; Katkat, Esra; Binokay, Leman; Ozhan, Gunes; Karakulah, Goekhan; Genc, SerminTransfer RNAs (tRNAs) are small non-coding RNA molecules transcribed from tRNA genes. tRNAs cleaved into a diverse population tRNA fragments (tRFs) ranging in length from 18 to 40 nucleotides, they interact with RNA binding proteins and influence the stability and translation. Stress is one of the reasons for tRFs cleavage. In our study, we modeled oxidative stress conditions with hydrogen peroxide (H2O2) exposure and dealt with one of the frequently expressed tRF in the hippocampus region of the brain, which is tRF-Glu-CTC. For this purpose, neural stem cells (NSCs) were exposed to H2O2, and tRF-Glu-CTC levels were increased in various H(2)O(2 )concentrations. A decrease was seen in microtubule-associated protein 2 (MAP2) marker expression. To understand the H(2)O(2)oxidative stress condition on the expression of tRNA fragments, 72 hpf zebrafish embryos exposed to different H(2)O(2 )concentrations, an increase in the level of tRF-Glu-CTC was observed in all concentrations of H(2)O(2 )compared to control. Subsequently, neurogenesis markers were figured out via Calb2a (calbindin 2a) in situ hybridization (ISH) and HuC/D immunofluorescence staining (IF) staining experiments. Under H(2)O(2 )exposure, a decline was observed in Calb2a and HuC/D markers. To understand the inhibitory role of tRF-Glu-CTC on neurogenesis, NSCs were transfected via tRF-Glu-CTC inhibitor, and neurogenesis markers (ss III-tubulin, MAP2, and GFAP) were determined with qRT-PCR and IF staining. tRF-Glu-CTC inhibitor reversed the diminished neuronal markers expression under the exposure of H2O2. Gene Ontology (GO) enrichment analysis showed us that targets of tRF-Glu-CTC are generally related to neuronal function and synaptic processes.Conference Object The Impact of Nutritional Ketosis on Autophagy in the Brain of Tay-Sachs Mouse Model(Springernature, 2024) Inci, Orhan Kerim; Seyrantepe, VolkanConference Object Investigation of the Regulatory Role of Lysosomal Cathepsin a in the Autophagy(Springernature, 2024) Yanbul, Selman; Seyrantepe, VolkanConference Object Therapeutic Efficacy of Intrathecal Administration of Aavrh10-Mhexa Vector in a Mouse Model of Tay-Sachs Disease(Springernature, 2024) Ozgur, Melike Can; Basirli, Hatice Hande; Ausseil, Jerome; Seyrantepe, VolkanArticle Citation - WoS: 1Citation - Scopus: 1Fractional Duals of the Poisson Process on Time Scales With Applications in Cryptography(Springernature, 2024) Gharari, Fatemeh; Hematpour, Nafiseh; Bakouch, Hassan S.; Popovic, Predrag M.A super-structure system for probability densities, covering not just typical types but also fractional ones, was developed using the time scale theory. From a mathematical point of view, we discover duals of the Poisson process on the time scale T=R\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {R}$$\end{document} for the time scales T=Z\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\mathbb {T}=\mathbb {Z}$$\end{document} and T=qZ,\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \mathbb {T}=q<^>{\mathbb {Z}},$$\end{document} evaluating del-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\nabla -$$\end{document}calculus and Delta-\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\Delta -$$\end{document}calculus. Also, we search the fractional extensions of the Poisson process on these time scales and detect duals of them. A simulation allows for comparing the nabla and delta types of the observed distributions, not just typical types but also fractional ones. As an application, we also propose new substitution boxes (S-boxes) using the proposed stochastic models and compare the performance of S-boxes created in this way. Given that the S-box is the core for confusion in Advanced Encryption Standard (AES), the formation of these new S-boxes represents an interesting application of these stochastic models.Article Citation - WoS: 2Citation - Scopus: 4A Study on a Computationally Efficient Controller Design for a Surgical Robotic System(Springernature, 2023) Ayit, Orhan; Dede, Mehmet Ismet CanThe control algorithms of the surgical robotic system using the robot's dynamics produce a relatively high computational load on the processor. This paper develops a computationally efficient computed torque controller by using a simplified dynamic modeling method and implemented in a novel surgical robot experimentally. In addition, an independent joint controller is designed and implemented to compare the results of the computed torque controller.