TR Dizin İndeksli Yayınlar Koleksiyonu / TR Dizin Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/4
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Article Bioinformatics Based Drug Repurposing Approach for Breast and Gynecological Cancers: RECQL4/FAM13C Genes Address Common Hub Genes and Drugs(Galenos Publ House, 2025-01-02) Duran, Gizem Ayna; Duran, Assist. Prof. Dr. Gizem AynaObjective: The prevalence of breast cancer and gynaecological cancers is high, and these cancer types can occur consecutively as secondary cancers. The aim of our study is to determine the genes commonly expressed in these cancers and to identify the common hub genes and drug components. Materials and Methods: Gene intensity values of breast cancer, gynaecological cancers such as cervical, ovarian and endometrial cancers were used from the Gene Expression Omnibus database Affymetrix Human Genome U133 Plus 2.0 Array project. Using the linear modelling method included in the R LIMMA package, genes that differ between healthy individuals and cancer patients were identified. Hub genes were determined using cytoHubba in Cytoscape program. “ShinyGo 0.80” tool was used to determine the disease-specific biological KEGG pathways. Drug.MATADOR from the ShinyGo 0.80 tool was used to predict drug-target relationships. Results: The RecQ Like Helicase 4 and Family with Sequence Similarity 13 Member C genes were found to be similarly expressed in breast cancer and gynaecological cancers. Upon KEGG pathway analyses with hub genes, Drug.MATADOR analysis with hub genes related to cancer related pathways was performed. We have determined these gene/drug interactions: NBN (targeted by Hydroxyurea), EP300 (targeted by Acetylcarnitine) and MAPK14 (targeted by Salicylate and Dibutyryl cyclic AMP). Conclusion: The drugs associated with hub genes determined in our study are not routinely used in cancer treatment. Our study offers the opportunity to identify the target genes of drugs used in breast and gynaecological cancers with the drug repurposing approach.Article Fluorescence Microscopy Denoizing Via Neighbor Linear Embedding(Istanbul University, 2024-01-31) Kırmızıay, Çağatay; Aydeniz, Burhan; Türkan, MehmetOne of the difficulties in studying fluorescence imaging of biological structures is the presence of noise corruption. Even though hardware- and software-related technologies have undergone continual improvement, the unavoidable effect of Poisson–Gaussian mixture type is generally encountered in fluorescence microscopy images. This noise should be mitigated to allow the extraction of valuable information from fluorescence images for various types of biological analysis. Thus, this study introduces a new and efficient learning-based denoizing approach for fluorescence microscopy. The proposed approach is based mainly on linear transformations between noise-free and noisy submanifold structures of patch spaces, benefiting from linear neighbor embeddings of local image patches. According to visual and statistical results, the developed algorithm called "neighbor linear-embedding denoizing" algorithm has a highly competitive and generally superior performance in comparison with the other algorithms used for fluorescence microscopy image denoizing in the literature. © 2024 Istanbul University. All rights reserved.Article Preantral Follicle Morphometry and Ultrastructure of Antral Follicles in Anatolian Water Buffalo(TUBITAK, 2023-10-17) Bakı, Acar, D.; Bırdane, M.K.; Tokyol, Ç.; Göçmen, Karabekır, N.N.; Hayran, Mürvet; Özenç, E.; Aktepe, F.; Uçar, Mehmet; Hayran, Hatice Mürvet; Göçmen Karabekır, Nermin Nüket; Bakı Acar, Duygu; Karabekir, Nermin Nuket Gocmen; Yağcı, İlknur Pir; Yazıcı, Ebubekir; Mas, Nuket Gocmen; Acar, Duygu BakiThis study aimed to evaluate quantitative and morphometric analyses of preantral follicles and the ultrastructural characteristics of antral follicles in different oestrous cycle stages in Anatolian water buffaloes. Twenty-four ovaries collected from twelve slaughtered Anatolian water buffaloes were classified macroscopically as luteal or follicular stages. The ovaries were prepared for histological examination (Hematoxylin-eosin staining), and primordial, primary, and secondary follicle numbers were calculated, and the diameters of oocytes, follicles, and nuclei were measured under a light microscope with a micrometre. The theca and granulosa cells of antral follicles were observed under a transmission electron microscope. The mean number of preantral follicles was 18584 ± 4855, and there was a significant difference in the number of primordial follicles (p < 0.0001) and primary follicles (p < 0.001) between buffaloes. The number of primordial follicles was 10,636, that of primary follicles was 6514, and that of secondary follicles was 1434; the statistical difference was found between primordial, primary, and secondary follicle and oocyte diameters (p < 0.001) in Anatolian water buffaloes. In this study, the ultrastructural evaluation of antral follicles showed that the theca cells were active in the luteal stage with their functional organelles and higher lipid droplets. The granulosa cells were still inactive in the luteal stage. In the follicular stage of the oestrous cycle, the theca cells were found inactive, although granulosa cells showed moderate or high activity. It was found that the serum progesterone concentration and cycle stage directly affected the theca and granulosa cell ultrastructural activity in Anatolian water buffalo. In this research, information from light and electron microscopic analyses of preantral and antral follicles has been obtained for the first time for Anatolian water buffaloes. The result of our study suggests that detailed molecular research is needed to evaluate the ultrastructural activity of antral follicles in different oestrous cycle stages and steroidogenic circumstances. © TÜBİTAK.Article Citation - WoS: 2Citation - Scopus: 4The Effects of Yoga Education on the Cognitive Functions of Children in Early Childhood(Turkish Education Assoc, 2020-12-30) Ozgun, Songul Yasemin; Özkul, Fatma Betül; Oral, Ezgi; Şemin, Makbule İlgi; Şemin, İlgi; Özkul, Betül; Cura, Fatma Betül OzkulThe aim of this research study is to analyze the effects of yoga education on the cognitive functions in early childhood. This study is a semi- experimental study with Pretest Posttest Control Group Experimental Design. The research sample comprises 28 children between the ages of 4-5 years, 10 in the experimental and 18 in the control group, who are currently enrolled in separate preschool programs in the city of Izmir. Application of Cognitive Functions Scale (ACFS) and Personal Information Form were used in the research in order to identify the children's cognitive functions. In the study, children in the experimental group were provided with 1 hour a week of yoga education given by a certified, expert yoga instructor for 12 weeks, while the control group children were left without intervention. Mann Whitney-U test and Wilcoxon Signed Rank Test were used for data analysis. The research findings showed that the experimental group's total ACFS scores and average posttest scores for the Tasks Section Subscales were significantly higher than their average total pretest scores. No significant difference was found between the pretest and posttest score averages of the control group. A comparison of the total posttest scores of experimental and control groups showed no statistically significant differentiation in the subscales of short term auditory memory, perspective-taking, and verbal planning; while the differentiation was statistically significant between the subscales of classification, sequential short term auditory memory, short term visual memory, and pattern completion, as well as the total ACFS posttest scores. The research findings are discussed in relation to the literature.