Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Dissecting the Metabolic Landscape of Breast Cancer Subtypes via Elastic Net Modeling and Examining Its Immune Correlates(Walter de Gruyter GmbH, 2026) Kus, M.E.; Ekiz, H.A.Objectives: Breast cancer is a heterogeneous disease, and the estrogen receptor (ER) status is a key factor in disease classification and treatment planning. While metabolomic profiling has revealed subtype-specific differences, cross-study comparisons have been limited, posing challenges for data extrapolation. This study aims to investigate metabolites that differentiate ER-positive and ER-negative tumors via integrative analyses of multi-omics data. Methods: We jointly analyzed two untargeted metabolomics datasets via elastic net modeling using consistent analysis pipelines tuned for low sample sizes, namely multiple bootstrapping and stability selection. Significant metabolite predictors from two studies were cross-examined to reveal distinctions and commonalities. We also performed differential gene expression analysis using RNA sequencing data from matching samples to link metabolic patterns with transcriptomic signatures and intratumoral immune cell signatures. Results: This study identified unique metabolite signatures in distinct datasets and a limited overlap of discriminating metabolites that can be broadly generalizable for subtyping. Nevertheless, several glycolysis and fatty acid metabolism intermediates exhibited variation depending on the tumor ER status. Consistently, genes related to fatty acid metabolism and glycolysis were enriched in ER-positive and ER-negative tumors respectively. Furthermore, we used multiple immune cell deconvolution algorithms to correlate various immune cell types with the metabolite levels within the tumor microenvironment. Conclusions: Together, these findings highlight the metabolic and immunological diversity of breast cancer and establish a reproducible machine-learning framework for integrating multi-omics data to interrogate tumor complexity. © 2025 the author(s), published by De Gruyter, Berlin/Boston.Article Development and Evaluation of 177Lu-Imatinib: Radiolabeling and Cell Culture Studies(Walter de Gruyter GmbH, 2025) Ozgenc, E.; Karpuz, M.; Guler, G.; Burak, Z.; Başpainar, Y.; Gundogdu, E.A.Targeted radiopharmaceuticals offer promising approaches for cancer diagnosis and therapy. This study developed freeze-dried kit formulations of 177Lu-Imatinib (IMT) and evaluated their potential efficacy through in vitro studies. Four formulations (F1-F4) containing IMT and chelating agents were prepared and characterized via Fourier transform infrared (FTIR), ultraviolet spectrum (UV), and thermogravimetric analysis (TGA) to confirm complex formation. Biocompatibility was assessed in NIH-3T3 cells using the MTT assay. Radiolabeling with 177Lu was optimized by varying pH, incubation time, and reactant ratios. Radiochemical purity and stability were analyzed over 7 days using HPLC. Binding affinity and cytotoxicity were evaluated in MCF-7 and NIH-3T3 cells. Spectroscopic analyses confirm successful complex formation. All formulations exhibited >90% viability in NIH-3T3 cells. Optimal radiolabeling conditions (45mg IMT-chelator, pH 5, 60min incubation) yielded >90% efficiency, with stable radiolabeling for 7 days. The 177Lu-IMT-DOTA (F3) formulation showed significantly higher binding and cytotoxic effects in MCF-7 cells compared to controls. The 177Lu-IMT-DOTA (F3) kit demonstrates high radiolabeling efficiency, stability, and selective in vitro cytotoxicity toward breast cancer cells, supporting its potential as a targeted radiopharmaceutical. © 2025 Walter de Gruyter GmbH, Berlin/Boston 2025.Article Gypsophila Eriocalyx Roots Inhibit Proliferation, Migration, and Tgf-Β Signaling in Melanoma Cells(Walter de Gruyter GmbH, 2025) Azbazdar, Yagmur; Ozhan, Gunes; Helvacioglu, SelinObjectives: Melanoma is a highly malignant and serious form of skin cancer. In addition to the standard treatments, complementary approaches, including phytotherapy, are also used to alleviate symptoms and improve patient well- being. This study aims to investigate the anticancer effects of Gypsophila eriocalyx (GE), an endemic species from Türkiye, on melanoma cells. We set out to determine the efficacy of GE in inhibiting melanoma cell proliferation, migration, and growth, and to explore its underlying mechanisms. Methods: We examined the impact of GE on the prolifera- tion of two melanoma cell lines, Malme-3M and SK-MEL-28, and assessed its developmental toxicity in zebrafish em- bryos. Next, we evaluated GE’s influence on colony forma- tion and wound healing in melanoma cells, as well as its ability to induce apoptosis and affect the TGF-β/Smad signaling pathway, by measuring pathway reporter activity and target gene expression. Results: GE inhibited cell proliferation in melanoma cell lines at concentrations 104 to 488 times lower than those required for normal non-malignant L929 fibroblast cells. In zebrafish embryos, GE demonstrated developmental toxicity only at concentrations above 50 μg/mL. GE treatment significantly impaired the colony formation and wound healing abilities of melanoma cells, indicating reduced pro- liferation and migration. Moreover, GE induced apoptosis in melanoma cells and inhibited the TGF-β/Smad signaling pathway, as evidenced by decreased pathway reporter activity and target gene expression. Conclusions: This study highlights the potential of GE as a novel therapeutic agent in melanoma treatment by demon- strating its ability to inhibit tumor growth and progressionArticle Citation - WoS: 1Citation - Scopus: 1Assessment of the Validity and Reliability of Edinburgh Postpartum Depression Scale in Turkish Men(Walter de Gruyter GmbH, 2024) Alkan, C.; Didikoǧlu, A.; Çöme, O.; Yllmaz, B.; Mevsim, V.Objectives: Perinatal depression (PD) affects individuals during pregnancy and early parenthood, resembling major depression. Recent research highlights paternal perinatal depression (PPD) in fathers. PPD has adverse effects on fathers and their children. This study assesses the Turkish version of the Edinburgh Postnatal Depression Scale (EPDS) for Turkish fathers, aiming to provide a tool for PPD identification. Methods: This methodological study validates the EPDS for Turkish fathers and explores associations with demographic and psychosocial factors. The study involved 295 fathers with infants aged 2 weeks to 12 months. The EPDS, originally designed for perinatal depression and validated in Turkish women, was used. Fathers completed a participant information questionnaire, the EPDS, and the Beck Depression Inventory (BDI) during clinic visits. Data on sociodemographic factors, paternal roles, and pregnancy and postpartum support were collected. Mothers also completed the EPDS. Descriptive statistics, exploratory factor analysis, confirmatory factor analysis, and correlation tests were used. Results: The study included fathers with an average age of 30.5 years, mostly with a high school education or higher. The EPDS had a mean total score of 3.1. Factor analysis suggested a three-factor structure for the EPDS in Turkish fathers, including anhedonia, anxiety, and depression. Confirmatory factor analysis validated the three-factor structure, with acceptable model fit indices. Positive correlations were found between fathers' EPDS scores, maternal EPDS scores, and paternal BDI scores. The EPDS effectively discriminated between different levels of depression severity. Various factors, such as education level and lack of support during pregnancy and after childbirth, were associated with higher EPDS scores. Conclusions: These findings emphasize the significance of assessing and addressing PPD in fathers, supporting the use of the EPDS as a valid tool in the Turkish context. The three-factor structure aligns with international research, highlighting the importance of a multi-dimensional approach to PPD assessment. Early intervention can mitigate PPD's impact on fathers, mothers, and children, benefiting mental health and well-being. © 2024 Walter de Gruyter GmbH, Berlin/Boston.Book Part Citation - Scopus: 1A Recycling Route of Plastics Via Electrospinning: From Daily Wastes To Functional Fibers(Walter de Gruyter GmbH, 2019) Isık, Tuğba; Horzum,N.; Demir, Mustafa MuammerSince large-scale plastic production has begun in the 1940s, plastics have been produced and used globally, bringing many advantages to modern life. The consumption of plastics has increased exponentially due to their low cost, chemical resistance, lightness, durability and ability to combine with other materials. However, plastic materials represent high tonnage in urban wastes, and it is known that these plastics discarded at the end of their useful life by filling the landfill sites. Electrospinning is a well-established and versatile technique for the fabrication of submicron fibers. In addition, it is a promising approach for the recycling of waste polymers without using complex methodologies. In this chapter, utilization of electrospinning approach for the recycling of daily wastes will be discussed. The literature about the daily wastes of both synthetic materials and natural/agricultural materials will be analyzed, and the applications of these materials will be given in detail. © 2019 Walter de Gruyter GmbH, Berlin/Boston. All rights reserved.Article Citation - WoS: 5Citation - Scopus: 4Influence of Partitioning Treatment on Microstructure and Mechanical Properties of an Alloyed Ductile Iron Austempered at Different Temperatures(Walter de Gruyter GmbH, 2023) Neite, Maximilian; Münstermann, Sebastian; Nalçacı, Burak; Davut, Kemal; Erdoğan, MehmetThe present study was conducted to uncover effects of partitioning treatment on Cu-Ni-Mo alloyed ductile iron (DI) austempered at different temperatures. For this purpose, the DI samples, produced via sand casting, were austenitized at 900 °C for 60 min, followed by austempering at the temperatures of 275-325-375 °C for 120 min and afterwards a partitioning treatment was applied at 200 °C for 15 min. In the characterization studies, dilatometer, image analysis, JMat-Pro, mechanical tests, XRD, optical microscope, and scanning electron microscope (SEM) equipped with EBSD detector were utilized. Characterization studies showed that the effects of partitioning treatment were directly correlated with austempering temperature and high carbon austenite volume fraction changed in the range of 19.48-35.45%. That redistribution of carbon (C) between bainitic ferrite and high carbon austenite occurred, in turn, the carbon content of high carbon austenite increased with the partitioning treatment irrespective of austempering temperature were uncovered. Furthermore, the partitioning treatment considerably changed the grain morphologies of both high carbon austenite and banitic ferrite. As a consequence of these microstructural differences, the highest tensile strength of 1489.2 MPa was established in the sample austempered at 275 °C and partitioned at 200 °C, whereas the highest ductility of 5.61% acquired at the austempering temperature of 375 °C. © 2023 Walter de Gruyter GmbH, Berlin/Boston.Article Citation - WoS: 3Citation - Scopus: 3Nondestructive Microstructural Characterization of Austempered Ductile Iron(Walter de Gruyter GmbH, 2023) Tüzün, Mert Yağız; Yalçın, Mustafa Alp; Davut, Kemal; Kılıçlı, VolkanAustempered ductile iron (ADI) has been preferred in a wide range of applications due its unique combination of high strength, good ductility, wear resistance and fracture toughness together with lower cost and lower density compared to steels. Magnetic Barkhausen noise (MBN) measurement offers a better alternative to traditional characterization techniques by being fast and non-destructive. A simple linear regression using only one single independent variable cannot correlate the MBN with the microstructure of ADI, since its microstructure is multi component. Multiple linear regression analysis (MLRA) was used to build a model that uses the characteristic features of microstructural constituents as input parameters to predict the MBN. For that purpose, Cu-Ni-Mo alloyed ductile iron samples austempered between 325 and 400 degrees C and for 45-180 min duration were used. The results show that MBN is most sensitive to the size and shape of acicular ferrite and retained austenite. Moreover, MBN is almost insensitive to the size, morphology and volume fraction of graphite particles. This indicates that retained austenite pins the domain walls more effectively than the graphite particles. Considering the results MLRA, MBN technique can be used to characterize the ausferritic microstructure of ADI.Article Epithelial-Mesenchymal Transition as a Potential Route for Dapt Resistance in Breast Cancer Cells(Walter de Gruyter GmbH, 2023) Tellı, Kubra; Ozuysal, Ozden Yalcın; Telli, Kübra; Yalçın Özuysal, ÖzdenObjectives: Notch is a conserved pathway involved in cell- fate determination and homeostasis. Its dysregulation plays a role in poor prognosis and drug resistance in breast cancer. Targeting Notch signaling via inhibition of the gamma- secretase complex is in the spotlight of modern cancer treat- ments. Gamma-secretase inhibitors (GSI) have shown suc- cessful clinical activity in treating cancers, yet the possible resistance mechanism remains unstudied. Modeling the resistance and understanding culprit molecular mechanisms can improve GSI therapies. Accordingly, the aim of this study is to generate and analyze GSI-resistant breast cancer cells. Methods: Gradually increasing doses of DAPT, a well-known GSI, were applied to MCF-7 breast cancer cell lines to generate resistance. Cell viability, migration and gene expressions were assessed by MTT, wound healing and qRT-PCR analyses. Results: DAPT-resistant MCF-7 cells exhibited abnormal expression of Notch receptors, Notch targets (HES1, HES5, HEY1), and epithelial-mesenchymal transition (EMT) markers (E-cadherin, ZO-1, SNAIL2, N-cadherin) to overcome the continuous increase in DAPT toxicity by increased migration through mesenchymal transition. Conclusions: This study prospects into the role of EMT in the potential resistance mechanism against DAPT treatment for breast cancer cells. Complementary targeting of EMT should be investigated further for a possible effect to potentiate DAPT’s anti-cancer effects.Article Citation - WoS: 14Citation - Scopus: 13Investigations of Polyamide Nano-Composites Containing Bentonite and Organo-Modified Clays: Mechanical, Thermal, Structural and Processing Performances(Walter de Gruyter GmbH, 2021) Akar, Alinda Öykü; Yıldız, Ümit Hakan; Tayfun, ÜmitPolyamide 6 (PA) matrix was reinforced with Na-activated bentonite, amino functional silane treated bentonite and organo-modified clays at different concentrations. The preparation of composites was carried out using melt-blending method and the test samples were prepared by injection-molding process. Mechanical, thermal, structural and processing investigations of PA based composites were reported performing via tensile, hardness, and impact tests, differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), scanning electron microscopy (SEM), X-ray diffraction analysis (XRD) and force measurements, respectively. According to mechanical test results, additions of fillers to PA matrix caused slight improvements for tensile strength and modulus parameters. Silane treated BNT exhibited improvement in mechanical results compared to Na-activated bentonite additions. Thermal studies revealed that decomposition and melting temperatures of PA shifted to higher values after inclusion of clay into polymer matrix. Results confirmed that organo-clay and bentonite additions with their lower filling ratios yielded enhancements for the mechanical and thermal performance of polyamide.Article Citation - WoS: 1Citation - Scopus: 1The Impact of Visual Thinking in Medical Education(Walter de Gruyter GmbH, 2022) Demir, Ayşe Banu; Okuyan, Zuhal; van Eck, Alexander; Mura, Gökhan; Gönlügür, Emre; Karaca, Can; Abacıoğlu, HakanBackground Considering medical humanities, medicine and art are two areas that resemble each other at several features. Clinical diagnosis involves the observation, description and interpretation of information of which visual ones take an important one. The skills described are important skills in the field of visual arts, as well. Underlying a good clinical practice; clinical examination and observation skills constitute an important place. Although in several studies, these skills are shown to be improved by analyzing visual art pieces, courses intended to improve visual thinking skills are not that much common in medical faculty curriculums. Materials and methods In this article, we share our opinion about the use of visual thinking in medical education by providing preliminary reflection results of learners from the second year of medical education about the visual thinking course that we have recently started to apply in Faculty of Medicine in collaboration with Faculty of Fine Arts in Izmir University of Economics in order to improve the observational skills of learners. Results Reflection results of the learners support the view that training art-viewing skill is helpful to improve observational and descriptive skills. Conclusions Increasing interdisciplinary programs on visual thinking in medical curriculums have the potential to overcome several professional development challenges in clinics.