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 Identification of the Role of Tg2 on the Expression of Tgf-Β, Timp-1 and Timp-2 in Aged Skin(Walter De Gruyter Gmbh, 2024-02-12) Ergülen, Elvan; Akdoğan, Gül; Guner, Gul AkdoganObjectives Transglutaminase 2 (TG2) is a unique protein having enzymatic and nonenzymatic functions that have been implicated in various biological and pathological processes such as cell survival and apoptosis, cell signaling, differentiation, adhesion and migration, wound healing and inflammation. As reported in previous studies, TG2 expression and activity increase by age suggesting that TG2 possibly has roles in cellular aging process. In this study, we aimed to explore the role of TG2 in chronological skin aging through its impact on the expression of some important extracellular matrix (ECM) proteins including TGF-beta, TIMP-1 and TIMP-2. Methods We have compared TG2 expression and activity in young and in vitro chronologically aged human dermal fibroblasts via Western blot and in situ TG2 activity assays. Afterwards, we inhibited TG2 expression via siRNA transfection and activity via active site inhibitor of TG2 separately in aged dermal fibroblasts and monitored the expression levels of TGF-beta, TIMP-1 and TIMP-2 in these cells by Western blot and compared to that of untreated control cells. Results We obtained evidence that both TG2 expression and activity increase in aged cells. However, protein levels of TGF-beta, TIMP-1 and TIMP-2 do not exhibit any significant difference in TG2 downregulated or TG2 activity inhibited aged cells compared to control cells. Conclusions Our results indicate that changes in the expression and activity of TG2 in (in vitro) chronologically aged human dermal fibroblasts do not impact the expression patterns of TGF-beta, TIMP-1 and TIMP-2 proteins.Article Citation - WoS: 2Differences in the Differential Expression of Micrornas Between Patients With Familial Multiple Sclerosis and Those With Sporadic Multiple Sclerosis(Galenos Publ House, 2023-12-28) Güllüoğlu, Halil; Uysal, Hasan Armağan; Poyraz, Turan; Altun, Zekiye; Kaya, Derya; Özcelik, Pınar; İdiman, Egemen; Poyraz, TuranObjective: Multiple sclerosis (MS) is a heterogeneous disease with clinical and immunological features. Most MS cases occur sporadically, but a considerable proportion of patients have a family history of MS. The etiology and pathophysiology of MS remain unclear. Recent epidemiological and gene expression studies have indicated that dysregulation of microRNAs (miRNAs) may play a role in MS pathogenesis. This study aimed to evaluate the differential expression of miRNAs in sporadic MS (sMS) and familial MS Materials and Methods: This cross-section, single-center study was conducted in 20 FMS and 10 sMS patients and 8 healthy controls. The patients were in the remission. In total, 2,549 miRNA genes were screened in the blood mononuclear cells from the whole blood samples of MS patients depending on miRBase 21. Differential expression of miRNAs in MS patients was identified compared with the control group, and miRNAs with a fold change >= 2 were validated using reverse transcription-polymerase chain reaction. Differentially expressed miRNAs were then compared between FMS and sMS patients. Results: Initial findings showed that miR-5100 and hsa-miR-16-2-3p were increased and miR-432-3p was decreased in FMS compared with sMS, whereas miR-548-aa, hsa-miR-142-3p, and miR-451-b were increased in both sMS and FMS, but miR-548-v was increased only in sMS. Some miRNAs showed the same expression patterns in both groups. Conclusion: Differential expression of certain miRNAs may be a useful biomarker in the diagnosis of MS. This study showed that miRNAs may discriminate between FMS and sMS cases and MS subtypes, as indicated in earlier studies.Article New Lymph Node Parameters and a Comparison With the American Joint Committee on Cancer N-Stages in Breast Cancer(Galenos Publ House, 2023-08-01) Eliyatkin, Nuket Ozkavruk; Başkır, İnci; İşlek, Akif; Zengel, BahaBACKGROUND/AIMS: The N-stage of TNM systems considers only the number of metastatic lymph nodes (NMLN) in breast cancer (BC). However, new lymph node parameters refer to the number of harvested lymph nodes (NHLN) and negative lymph nodes (NNLN), which have had an increasing significance in the current literature. This study aimed to compare NHLN, NNLN, lymph node ratio (LNR), modified lymph node ratio (mLNR), and log odds of positive lymph nodes (LODDS) against the standard American Joint Committee on Cancer (AJCC) N-stage for the prognosis of BC patients. MATERIALS AND METHODS: This study was designed retrospectively. The socio-demographic data, clinical features, histopathological factors, treatment modalities, receptor status of BC, and lymph node related parameters (AJCC N, LNR, mLNR, LODDS) were identified. Then, lymph node related parameters were compared for cancer-related mortality (CRM), cancer recurrence, disease-free survival (DFS), and overall survival (OS). RESULTS: Eight hundred seven women who underwent surgery for BC were included in this study according to its eligibility criteria. The mean follow-up period was 113.34±74.85 (range: 6-378) months. The NHLN was 21.24±9.22, the NMLN was 4.85±7.38, the NNLN was 16.39±9.48, the LNR was 0.23±0.29, the mLNR was 5.38±7.38 and the LODDS was -0.74±0.80 on average. During the follow-up period, 42 (5.2%) patients had local recurrence, 188 (23.3%) had distant metastases, and 252 (31.2%) patients died due to BC. NMLN, LNR, mLNR, and LODDS were found to be significantly higher, and NNLN was significantly lower in those patients with cancer recurrence and CRM (p<0.001). AJCC N-stages, and also LNR, mLNR, and LODDS groups according to the calculated cut-off values, were significant for DFS and OS according to survival analysis. In Cox regression analysis, only LODDS was a significant independent risk factor for OS [p=0.014, heart rate (HR)=3.78, 95% confidence interval (CI) for HR: 1.30-10.94)]. CONCLUSION: The results indicated that LODDS was more successful compared to other lymph node staging systems, especially for OS. However, randomized prospective controlled studies with larger samples and homogeneous study groups are needed to create standard classification systems as alternatives to AJCC N.Article Citation - WoS: 3Metal Nanopartiküllerin Mikroalgler Aracılığı ile Yeşil Sentezi(Ege Univ, FAC Fisheries, 2023-03-15) Mutaf, Tuğçe; Çalışkan Bilgin, Gülizar; Öncel, Suphi; Elibol, Murat; Caliskan, GulizarYeşil sentez olarak adlandırılan, nanopartiküllerin biyolojik kaynaklar aracılığı ile sentezlenmesine olan ilgi son yıllarda artış göstermiştir. Bunun temel nedeni geleneksel yöntemler olan fiziksel ve kimyasal yöntemlerde indirgeyici ve stabilize edici ajanlar olarak yüksek miktarlarda toksik kimyasala ihtiyaç duyuluyor olmasıdır. Daha çevre dostu ve insan sağlığı için tehdit oluşturmayan bitki, fungus, bakteri, alg gibi organizmalar yeşil nanopartikül sentezi için alternatif kaynaklardır. Sucul mikroorganizmalar olan mikroalgler üretmiş oldukları proteinler, vitaminler, pigmentler, yağ asitleri, hücre içi- hücre dışı polisakkaritler gibi fonksiyonel özelliğe sahip metabolitler sayesinde uzun yıllardır gıda, kozmetik ve ilaç endüstrilerinde formülasyonlara eklenmektedir. Bunların yanı sıra, son yıllarda yapılan çalışmalarla nanopartikül sentezinde de yüksek potansiyele sahip oldukları görülmüştür. Özellikle metal iyonlarının depolanmasını ve detoksifikasyonunu yapabildiklerinden ve metal iyonlarını elementel hale indirgeyen hücre içi ve hücre dışı metabolitlerce zengin olduklarından, metal nanopartiküllerin sentezi için yüksek potansiyele sahiptirler. Son yıllarda mikroalglerden nanopartikül sentezine odaklanmış olan yayın sayısı artmış ve pek çok mikroalg türünün gümüş, altın, titanyum, çinko, demir vb. metal nanopartikülleri hücre içi ve hücre dışı yollarla sentezleme potansiyeli araştırılmıştır. Bu derleme makale kapsamında, nanopartikül sentezi için çalışılmış olan mikroalg ve siyanobakteri türleri, kullanılan farklı sentez yöntemleri, nanopartiküllerin sentez mekanizması, temel karakterizasyon yöntemleri ve yeşil sentezle üretilen nanopartiküllerin antimikrobiyal aktivitelerine odaklanılmıştırArticle Citation - WoS: 2Citation - Scopus: 2Testing the Concealed Ovulation Hypothesis in the Framework of Facial Symmetry Fluctuations Moderated by Menstrual Cycle in Women(Turkish Psychologists Assoc, 2010) Çeti̇nkaya, Hakan; Dural, Seda; Gulbetekin, Evrim; Çetinkaya, Seda DuralWith three studies, a long lived position that women have concealed ovulation, and its possible adaptive value were investigated. In the first study, systematic changes in women across the menstural cycle were elaborated and of those, cyclic changes in the facial symmetry in regularly ovulating women were investigated. The findings showed predictable fluctuations on females' facial symmetry throughout their menstural phases. In order to determine whether the differences among the deviation from the symmetry scores of the facial pictures obtained from four menstural phases (namely, menstural, proliferative, ovulatory, and secretory phases) were detectable by males, in the second experiment, males evaluated the facial-menstural pictures for their attractiveness. The male participants rated the pictures obtained from ovulatory phases as the most attractive of all. Also they found the pictures obtained from the menstural phases to be least attractive. In the third study, half of the male participants (familiar males) rated four menstural pictures obtained from the same females, the other half of them (unfamiliar males) rated four menstural pictures, but this time each of which obtained from different females. The males in the latter group were not able to distinguish attractiveness of the facial pictures of different females. The results indicate that although there is some extent of concealment of ovulation in women as an adaptation, it is not completely concealed, especially from the familiar (or pair-bonded) males. Thus, men might have equipped with a counter-adapt, a mental device, through their evolutionary history to cope with the problem of concealment of ovulation in women by staying with her and observing the cyclic changes on her facial attractiveness.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 - WoS: 7Citation - Scopus: 11The Effect of Virtual Laboratory Simulations on Medical Laboratory Techniques Students' Knowledge and Vocational Laboratory Education(Walter De Gruyter Gmbh, 2022-08-01) Keles, Didem; Bulgurcu, Alihan; Demir, Esra Feyzioglu; Şemin, Makbule İlgi; Feyzioğlu Demir, Esra; Şemin, Ilgi Makbule; Feyzioğlu-demir, EsraObjectives Virtual laboratory simulations (VLSs) are computer-based tools that offer unlimited application options in scientific, medical, and engineering fields. The aim of this study was to evaluate whether VLSs are efficient learning tools and how these simulations can be integrated into laboratory practice in medical laboratory education. Methods In this pre-test/post-test control group study, 32 volunteers were randomly assigned to either experimental or control groups. The experimental group performed laboratory simulations based on biochemistry and microbiology and then completed a self-report survey to evaluate their satisfaction and beliefs about simulations. Results In the experimental group, post-test scores of each simulation were significantly elevated compared to pre-test scores; however, pre- and post-test scores of control group were statistically the same. The experimental group agreed that these simulations should be applied before theoretical lectures and laboratory practices. They also highlighted that translating from English to their native language creates difficulties in applying and understanding the simulation. Conclusions We emphasized that VLSs are excellent learning tools that increase not only the knowledge but also the self-motivation and focus of the students. Based on feedbacks, native language options are necessary to enable the students to achieve equality of opportunity in education.