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 Classification of Colon Cancer Patients Into Consensus Molecular Subtypes Using Support Vector Machines(2023-12-28) Koçhan, Necla; Dayanç, Barış EmreBackground/aim: The molecular heterogeneity of colon cancer has made classification of tumors a requirement for effective treatment. One of the approaches for molecular subtyping of colon cancer patients is the consensus molecular subtypes (CMS), developed by the Colorectal Cancer Subtyping Consortium. CMS-specific RNA-Seq-dependent classification approaches are recent, with relatively low sensitivity and specificity. In this study, we aimed to classify patients into CMS groups using their RNA-seq profiles. Materials and methods: We first identified subtype-specific and survival-associated genes using the Fuzzy C-Means algorithm and log- rank test. We then classified patients using support vector machines with backward elimination methodology. Results: We optimized RNA-seq-based classification using 25 genes with a minimum classification error rate. In this study, we reported the classification performance using precision, sensitivity, specificity, false discovery rate, and balanced accuracy metrics. Conclusion: We present a gene list for colon cancer classification with minimum classification error rates and observed the lowest sensitivity but the highest specificity with CMS3-associated genes, which significantly differed due to the low number of patients in the clinic for this group.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: 9Citation - Scopus: 9Classical Heart Rate Variability and Non-Linear Heart Rate Analysis in Mice Under Na-Pentobarbital and Ketamine/Xylazine Anesthesia(Tubitak Scientific & Technical Research Council Turkey, 2022-01-01) Kazdagli, Hasan; Ozel, Hasan Fehmi; Ozbek, Mustafa; Alpay, Suheda; Alenbey, MuruvvetBackground/aim: Anesthetics are often used in animal experiments to achieve immobilization and relieve pain. However, many anesthetics can alter the dynamics of cardiovascular systems. We aimed to compare the effects of two frequently used anesthetics agents on heart rate variability (HRV) parameters in mice. Materials and methods: This observational study was performed between May and June 2014 in 21 male BALB/c mice aged 16-20 weeks. The animals were divided into three groups: pentobarbital (P), (n = 7); pentobarbital+fentanyl (P+ F), (n = 7); and ketamine+xylazine (K+X), (n = 7). Surface electrocardiography (ECG) electrodes were placed in lead II configuration. 'the tachogram of RR intervals was obtained after R waves were detected using the Pan-Tompkins real-time QRS recognition algorithm. Frequency-domain, time-domain, and nonlinear HRV analyses were performed. Results: The bradycardia effect was higher in the K+X group (p < 0.01). Time-domain indices were higher in group K+X compared to group P (p < 0.01) and group P+F (p < 0.001). Very low frequency (VLF) power was significantly lower in group K+X compared to group P and group P+F (p < 0.01). Low frequency (LF) power, low frequency/high frequency (LF/HF) ratio, and total power (TP) were higher in group K+X compared to group P (p < 0.01) and group P+F (p < 0.001). The detrended fluctuation analysis short-term parameter (DFA alpha(1)) was significantly higher in group K+X compared to group P+F (p < 0.05) and the long-term parameter (DFA alpha(2)) was lower in group K+X compared to group P (p < 0.05). Standard deviations SD1 and SD2 were higher in group K+X compared to group P (p < 0.001) and group P+F (p < 0.001), SD2/SD1 ratio was lower in group K+X compared to group P (p < 0.05) and group P+F (p < 0.05). Entropy measures did not differ between groups. Conclusion: HRV analyses, including nonlinear methods, indicated that a K+X combination reduces imbalance and disorder in the regulation of the autonomic nervous system (ANS) in comparison to both P and the P+F combination.Article Citation - Scopus: 1Effects of 1-(2 (trim) on Receptor-Independent And-Dependent Contractile Responses in Rat Aorta(Tubitak Scientific & Technical Research Council Turkey, 2016) Selli, Cigdem; Erac, Yasemin; Tosun, MetinerBackground/aim: This study investigates whether 1-(2-trifluoromethylphenyl)-imidazole (TRIM), originally proposed as a nitric oxide synthase inhibitor and also suggested to be an inhibitor of store-operated calcium entry in mouse anococcygeal muscle, inhibits receptor-independent and -dependent responses in rat thoracic aorta. Materials and methods: Cyclopiazonic acid-and serotonin-induced vascular responses were investigated in aortic segments isolated from male Sprague Dawley rats using isolated tissue experiments. Changes in intracellular calcium levels were also monitored via front surface fluorescence measurements in fura-2-loaded embryonic rat vascular smooth muscle cell line A7r5. Results: TRIM inhibited serotonin-mediated vascular contractions without affecting cyclopiazonic acid-induced responses. In addition, TRIM caused a nonlinear rightward shift in the serotonin concentration-response curve, possibly via serotonin receptor modulation. Conclusion: TRIM may have an impact on investigation of tissue-specific receptor-independent and -dependent vascular responses. It may also be used as a lead compound in the development of selective serotonin receptor modulators.Article Citation - WoS: 1G-Quadruplex Enrichment Analysis Reveals Their Role as Intronic Regulatory Elements in Plants(Tubitak Scientific & Technical Research Council Turkey, 2019-03-07) Doluca, OsmanG-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of the regulatory mechanism of cells. They can form in the genome where the double-stranded helix is unwound to facilitate formation of a G-quadruplex. The biological significance of these structures is yet to be understood entirely. This work presents a novel approach and investigates common characteristics in the distribution of G-quadruplexes relative to genes in plants through analysis of genomes and gene expressions. The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higher plants and, for the first tune, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.Article Citation - WoS: 3Citation - Scopus: 3A Minimally Invasive Transfer Method of Mesenchymal Stem Cells To the Intact Periodontal Ligament of Rat Teeth: a Preliminary Study(Tubitak Scientific & Technical Research Council Turkey, 2018-10-25) Gul Amuk, Nisa; Kurt, Gokmen; Kartal Yandim, Melis; Adan, Aysun; Baran, Yusuf; Amuk, Nisa Gul; Yandım, Melis KartalThe aim of this study was to introduce a minimally invasive procedure for mesenchymal stem cell (MSC) transfer into the intact periodontal ligament (PDL) of the molar teeth in rats. Ten 12-week-old Wistar albino rats were used for this preliminary study. MSCs were obtained from bones of two animals and were labeled with green fluorescent protein (GFP). Four animals were randomly selected for MSC injection, while 4 animals served as a control group. Samples were prepared for histological analysis, Cox-2 mRNA expression polymerase chain reaction analysis, and fluorescent microscopy evaluation. The number of total cells, number of osteoclastic cells, and Cox-2 mRNA expression levels of the periodontal tissue of teeth were calculated. The number of total cells was increased with MSC injections in PDL significantly (P < 0.001). The number of osteoclastic cells and Cox-2 mRNA expression were found to be similar for the two groups. GFP-labeled MSCs were observed with an expected luminescence on the smear samples of the PDL with transferred MSCs. The results of this preliminary study demonstrate successful evidence of transferring MSCs to intact FIX in a nonsurgical way and offer a minimally invasive procedure for transfer of MSCs to periodontal tissues.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.