WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7150

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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
    Gypsophila Eriocalyx Roots Inhibit Proliferation, Migration, and Tgf-Β Signaling in Melanoma Cells
    (Walter de Gruyter GmbH, 2025) Azbazdar, Yagmur; Ozhan, Gunes; Helvacioglu, Selin
    Objectives: 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 progression
  • 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, Özden
    Objectives: 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: 14
    Citation - Scopus: 13
    Investigations 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, Ümit
    Polyamide 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: 1
    Citation - Scopus: 1
    The 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, Hakan
    Background 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.
  • Article
    Citation - WoS: 2
    Catalytic Activity of Heteropolytungstic Acid Encapsulated Into Mesoporous Material Structure
    (Walter de Gruyter GmbH, 2007) Gündüz, Gönül; Dimitrova, Rayna P.; Yılmaz, Selahattin
    The paper presents a spectroscopic and catalytic study of encapsulated Keggin type heteropoly acid (12-tungstophosphoric acid, HPW) in the mesopores of MCM-41 molecular sieves. Nitrogen physisorption, FTIR, SEM, XRD and catalytic methods have been used to characterize and compare the properties of the samples. Methanol conversion, alpha-pinene isomerization and ethyl acetate oxidation have been applied as model reactions for the evaluation of acid site activity. The combined physicochemical and catalytic investigations clearly show that the introduction of 12-tungstophosphoric acid into MCM-41 causes significant changes in the properties of the sample.
  • Article
    Citation - WoS: 8
    Citation - Scopus: 10
    Auditory Event-Related Potentials Demonstrate Early Cognitive Impairment in Children With Subclinical Hypothyroidism
    (Walter de Gruyter GmbH, 2019) Çatlı, Gönül; Kocaaslan Atlı, Sibel; Olgaç Dündar, Nihal; Bayazıt, Onur; Evirgen Esin, Nur; Erdoğan, Uğraş; Dündar, Bumin Nuri
    Background: The aim of this study was to examine the cognitive functions of children with subclinical hypothyroidism (SH) and healthy children with the use of auditory event-related potentials (AERPs) and neuropsychological tests. Methods: Twenty children aged between 8 and 17 wars, diagnosed with SH, and 20 age-matched healthy controls were included in this study. A classical auditory oddball paradigm was applied during the electroencephalography (EEG) recordings, and event-related potentials (ERPs) were evaluated between the 0.5- and 20-Hz frequency intervals. P1, N1, P2, N2 and P3 amplitudes and latencies were measured in Fz, FCz, Cz, CPz, Pz and Oz electrodes. Additionally, a number of neuropsychological tests evaluating the reaction time and various cognitive functions were carried out. Results: In children with SH, P3 amplitudes in FCz, Cz and CPz electrodes were significantly lower than those in controls (p <0.05). In addition to this, the P1N1 and N1P2 peak-to-peak amplitude values were also found to be smaller for children with SH than controls (p <0.05). With regard to the neuropsychological tests, no significant difference was observed between the SH and control groups on any of the cognitive test parameters, reaction time or correct response rates. Conclusions: In the present study, while children with SI I did not differ from controls with respect to their cognitive functions evaluated via neuropsychological tests, cognitive differences were detected via electrophysiological investigations. This result implies that implicit changes in cognition which are not yet overtly reflected on neuropsychological tests may be detected at an early stage in children with SH.
  • Article
    Citation - WoS: 14
    Visualization and Analysis of Micrornas Within Kegg Pathways Using Vanesa
    (Walter de Gruyter GmbH, 2017) Hamzeiy, Hamid; Suluyayla, Rabia; Brinkrolf, Christoph; Janowski, Sebastian Jan; Hofestaedt, Ralf; Allmer, Jens
    MicroRNAs (miRNAs) are small RNA molecules which are known to take part in post-transcriptional regulation of gene expression. Here, VANESA, an existing platform for reconstructing, visualizing, and analysis of large biological networks, has been further expanded to include all experimentally validated human miRNAs available within miRBase, TarBase and miRTarBase. This is done by integrating a custom hybrid miRNA database to DAWIS-M.D., VANESA's main data source, enabling the visualization and analysis of miRNAs within large biological pathways such as those found within the Kyoto Encyclopedia of Genes and Genomes (KEGG). Interestingly, 99.15 % of human KEGG pathways either contain genes which are targeted by miRNAs or harbor them. This is mainly due to the high number of interaction partners that each miRNA could have (e.g.: hsa-miR-335-5p targets 2544 genes and 71 miRNAs target NUFIP2). We demonstrate the usability of our system by analyzing the measles virus KEGG pathway as a proof-of-principle model and further highlight the importance of integrating miRNAs (both experimentally validated and predicted) into biological networks for the elucidation of novel miRNA-mRNA interactions of biological importance.
  • Article
    Citation - WoS: 16
    Citation - Scopus: 24
    Developing Polymer Composite-Based Leaf Spring Systems for Automotive Industry
    (Walter de Gruyter GmbH, 2018) Öztoprak, Nahit; Güneş, Mehmet Deniz; Tanoğlu, Metin; Aktaş, Engin; Eğilmez, Oğuz Özgür; Şenocak, Çiler; Kulaç, Gediz
    Composite-based mono-leaf spring systems were designed and manufactured to replace existing mono-leaf metal leaf spring in a light commercial vehicle. In this study, experimentally obtained mechanical properties of different fiber-reinforced polymer materials are presented first, followed by the description of the finite element analytical model created in Abaqus 6.12-1 (Dassault Systemes Simulia Corp., RI, US) using the obtained properties. The results from the finite element analysis are presented next and compared with actual size experimental tests conducted on manufactured prototypes. The results demonstrated that the reinforcement type and orientation dramatically influenced the spring rate. The prototypes showed significant weight reduction of about 80% with improved mechanical properties. The hybrid composite systems can be utilized for composite-based leaf springs with considerable mechanical performance.
  • Article
    Traveling Waves of Ddes With Rational Nonlinearity
    (Walter de Gruyter GmbH, 2016) Aslan, İsmail
    It has been found that the dynamical behavior of many complex physical systems can be properly described by nonlinear DDEs. However, in the related literature, research focusing on such equations with rational nonlinearity is rare. Hence, the present study makes an attempt to fill the existing gap. To this end, we consider two distinct DDEs with rational nonlinearity. We observed that the model equations assume three kinds of traveling wave solutions; hyperbolic, trigonometric and rational including kink-type solitary waves and singular periodic solutions. Our discussion is based on the auxiliary equation method.