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 Expressions of the Satellite Repeat Hsat5 and Transposable Elements Are Implicated in Disease Progression and Survival in Glioma(Tubitak Scientific & Technological Research Council Turkey, 2024-08-23) Köse, Sıla Naz; Yaraş, Tutku; Bursalı, Ahmet; Oktay, Yavuz; Yandım, Cihangir; Karakulah, GökhanThe glioma genome encompasses a complex array of dysregulatory events, presenting a formidable challenge in managing this devastating disease. Despite the widespread distribution of repeat and transposable elements across the human genome, their involvement in glioma's molecular pathology and patient survival remains largely unexplored. In this study, we aimed to characterize the links between the expressions of repeat/transposable elements with disease progression and survival in glioma patients. Hence, we analyzed the expression levels of satellite repeats and transposons along with genes in low-grade glioma (LGG) and high-grade glioma (HGG). Endogenous transposable elements LTR5 and HERV_a-int exhibited higher expression in HGG patients, along with immune response-related genes. Altogether, 16 transposable elements were associated with slower progression of disease in LGG patients. Conversely, 22 transposons and the HSAT5 satellite repeat were linked to a shorter event-free survival in HGG patients. Intriguingly, our weighted gene coexpression network analysis (WGCNA) disclosed that the HSAT5 satellite repeat resided in the same module network with genes implicated in chromosome segregation and nuclear division; potentially hinting at its contribution to disease pathogenesis. Collectively, we report for the first time that repeat and/or transposon expression could be related to disease progression and survival in glioma. The expressions of these elements seem to exert a protective effect during LGG-to-HGG progression, whereas they could have a detrimental impact once HGG is established. The results presented herein could serve as a foundation for further experimental work aimed at elucidating the molecular regulation of glioma genome.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 - WoS: 1Psychometric Evaluation of the Implicit Positive and Negative Affect Test in Turkish Samples(Turkiye Sinir Ve Ruh Sagligi Dernegi, 2019) Peker, Mehmet; Mese, Gulgun; Ersoy, Nevra CemObjective: Implicit affect is a concept distinct from explicit affect as it describes the affect processed by the individual at a preconscious level. The aim of this research is to evaluate the psychometric properties of the Turkish form of the Implicit Positive and Negative Affect Test (IPANAT-TR), originally developed by Quirin et al. (2009a) to measure affect indirectly. Method: The study data comprised of psychology and sociology students from Ege University, and full-time and part-time employees from public and private organizations in Izmir. A pilot study was carried out with a group of 57 undergraduate students in order to select the artificial words to be used in the scale. Subsequently the scale was sent to a total of 938 participants, comprising 569 students and 369 employees. Test-retest reliability was assessed with 46 participants after a one-week interval and with 55 participants after a four-week interval. Results: The principal components analysis showed a clear two-factor structure for the IPANAT-TR. The internal consistency scores were 0.92 for Implicit Positive Affect (IPA) and 0.85 for Implicit Negative Affect (INA). The one-week and four-week test retest reliability estimates varied between 0.51 and 0.75. The construct validity assessments showed that the expected relationships between the IPANAT-TR and tested constructs were mostly confirmed. The results of measurement invariance analysis showed that the IPANAT-TR has full measurement invariance across employee and student samples. Conclusion: The results of the reliability, validity and measurement invariance analyses carried out in the current study demonstrated that the IPANAT-TR is a reliable and valid measurement instrument to assess implicit affect.Article Citation - WoS: 15Citation - Scopus: 17Identification of the Nucleotide Substitutions in 62 Sars-Cov Sequences From Turkey(Tubitak Scientific & Technical Research Council Turkey, 2020-06-21) Demir, Ayse Banu; Benvenuto, Domenico; Abacioglu, Hakan; Angeletti, Silvia; Ciccozzi, MassimoA previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been shown to cause coronavirus disease 2019 (COVID-19) pandemic. The first case of COVID-19 in Turkey has been declared in March 11th, 2020 and from there on, more than 150,000 people in the country have been diagnosed with the disease. In this study, 62 viral sequences from Turkey, which have been uploaded to GISAID database, were analyzed by means of their nucleotide substitutions in comparison to the reference SARS-CoV-2 genome from Wuhan. Our results indicate that the viral isolates from Turkey harbor some common mutations with the viral strains from Europe, Oceania, North America and Asia. When the mutations were evaluated, C3037T, C14408T and A23403G were found to be the most common nucleotide substitutions among the viral isolates in Turkey, which are mostly seen as linked mutations and are part of a haplotype observed high in Europe.