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 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 Turkish Adaptation and Validation of Behavioral Inhibition Questionnaire Parent Form(Aves, 2023-01-02) Kilinc, Saliha; Bilgiç, Ayhan; Gormez, VahdetBackground: Behavioral inhibition has been proposed as a temperamental risk factor for the development of childhood anxiety disorders universally; however, there is no validated instrument for, especially, its evaluation in Turkish children. This study aimed to examine reliability and validity of the Turkish version of Behavioral Inhibition Questionnaire parent form for children aged 3-7 years. Methods: Around 250 mothers or fathers of 3-7 years old children were recruited from non-clinical population to collect responses to the questionnaires. The sample was created by reaching 3 schools at preschool or elementary grade for the purpose of providing the questionnaires filled about the student and/or his/her little sisters and brothers by their parents; questionnaires were sent out to parents and then gathered. Parents were asked to fill sociodemographic data form, Behavioral Inhibition Questionnaire parent form, Children Behavior Questionnaire, and Strengths and Difficulties Questionaire parent form in order to perform convergent and divergent validity analyses. Results: As a result of reliability analysis, total Cronbach alpha coefficient for Behavioral Inhibition Questionnaire was determined as 0.92 with strong reliability. The internal consistency coefficients for Behavioral Inhibition Questionnaire subscales also showed strong reliability with alphas ranging between 0.81 and 0.87 except for the performance (a = 0.69) and physical challenges (a = 0.19) subscales of which some items were excluded due to item-total correlations and confirmatory factor analysis results. In the validity assessment analyses, confirmatory factor analysis demonstrated that Behavioral Inhibition Questionnaire has a construct validity with 5 factors loaded on the 2-second order main factors and one third-order final factor (root mean square error = 0.032, root mean square residual = 0.153, Comparative Fit Index = 0.978, Goodness of Fit Index = 0.915, and Turker-Lewis Index = 0.970). While the strongest correlations with the overall Behavioral Inhibition Questionnaire score were found for 2 main subscales, inhibition to social novelties (r = 0.926, P <.001) and situational novelties (r = 0.928, P <.001), similarly peers (r = 0.848, P <.001) and new situations (r = 0.898, P <.001) subscales, had strong correlations with the overall Behavioral Inhibition Questionnaire score. The weakest correlation with overall Behavioral Inhibition Questionnaire score was observed for physical challenges subscale even though this subscale displayed moderate association (r = 0.454, P <.001). A good convergent validity was determined accompanied by significant moderate positive correlations with Children Behavior Questionnaire shyness and Strengths and Difficulties Questionnaire internalizing scales. An adequate divergent validity was also demonstrated based on significant positive mild to moderate correlations with Children Behavior Questionnaire impulsivity, Children Behavior Questionnaire smiling/laugh, Strengths and Difficulties Questionnaire prosocial scales, and nonsignificant correlation with Strengths and Difficulties Questionnaire externalizing scale. Conclusion: The study demonstrated that the Turkish version of the Behavioral Inhibition Questionnaire parent form is an effective tool with good reliability and validity among 3-7 years old children.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: 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.