Research
The projects listed below are conducted by our team.
Classification and Segmentation of Nasopharyngeal Carcinoma Using Machine Learning Models from Head and Neck Computer Tomography Images (Acibadem University General Research Projects Support Program)
Project Leaders: Bora Güvendiren
Consultant: Lect. PhD Seda Nilgün Dumlu, Prof. Ata Akın, Prof. Dr. Enis Özyar, Assoc. Prof. Bükem Tanören
In this work, a machine learning algorithm is created from radiomics features with the intent of classifying and segmenting NPC tumor from computer tomography (CT) images. CT images of 73 patients were preprocessed and prepared before tumor classification and segmentation, then the performance of the model was evaluated by comparing the results with those identified by radiation oncologists. After obtaining the results, on average, 95$\%$ accuracy score was obtained for the NPC classification and a 0.75 Jaccard score was obtained for the segmentation parts of the algorithm. The algorithm was concluded to be capable of classifying the NPC tumor from the CT images, but lacked performance when it came to segmentation.
Investigation of Antimicrobial Effects of Different Quantum Dots on Standard Microorganism Strains Alongside Laboratory Collection Strains and Imaging of Them with Fluorescent Microscope (TUSEB-B)
Project Leaders: Beste Dipçin, Bora Güvendiren
Consultant: Assoc. Prof. Bükem Tanören, Prof. Dr. Zühtü Tanıl Kocagöz, Assoc. Prof. Kadriye Kızılbey, Asst. Prof. Özgül Gök Özatay
In this project it is aimed to synthesize doped, and sustainable carbon quantum dots (from coffee and tea wastes) and silver indium sulfate quantum dots to test their potential as antimicrobial agents in both standard bacteria strains and multidrug-resistant bacteria strains (ESKAPE microorganisms) alongside standard and multidrug-resistant fungi. Also, to understand how quantum dots present antimicrobial effects, molecular dynamic (MD) simulation of the microorganism membrane and their interaction with the quantum dots will be done.
Carbon Quantum Dot Synthesis With Hot Bubble Synthesis (HBBBS) Method and Its Characterization (Acibadem University General Research Projects Support Program)
Project Leaders: Beste Dipçin, Bora Güvendiren
Consultant: Assoc. Prof. Bükem Tanören, Assoc. Prof. Kadriye Kızılbey, Dr. Selçuk Birdoğan
This project is about synthesizing carbon quantum dots (C-dots) from 98% sulfuric acid, pure acetone, and sodium hydroxide with a newly developed method, hot bubble synthesis (HBBBS) method, and understanding the chemical and physical properties of C-dots alongside characterizing them by UV-Vis Spectrophotometry, Fourier Transform Infrared Spectroscopy (FT-IR), Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Dynamic Light Scattering (DLS), Zeta Potential analysis, and fluorescence microscopy.
Formation of TTR Gene Targeted Nanoparticles Investigating the Effect of Them on Transthyretin Protein Production and Cell Viability Alongside Observation of Their Cell Localization Utilizing Confocal Microscope (TUSEB-A)
Project Leader: Beste Dipçin
Consultant: Assoc. Prof. Bükem Tanören, Assist. Prof. Özgül Gök Özatay
Genetic transthyretin amyloidosis (hATTR) is a genetic rare disease that occurs because of mutation(s) in the TTR gene that has become endemic in a few countries and causes the protein structure of transthyretin to deteriorate. This disease causes a complex, multifunctional system disorder that affects many systems, especially the nervous and cardiovascular systems. In the treatment of the disease, liver transplantation, transthyretin protein stabilizing drugs, and gene-targeted drugs are used. Gene silencing using the RNA interference (RNAi) mechanism is one of the most preferred methods in gene-targeted drug delivery systems. Gene therapies based on gene silencing by RNA interference hold great potential for the treatment of hATTR. Within the scope of this project, conjugation of PEG, HIV-1 Tat peptide, and carbon quantum dot to chitosan polymer, physical encapsulation of the obtained coating to the TTR gene-targeted siRNA molecules into the formed chitosan complex, characterization and optimization of the nanoparticle, measurement of cytotoxicity of the resulting nanoparticle in cell lines are aimed. It is planned to observe the cell localization utilizing a confocal microscope and to investigate the changing transthyretin (TTR) protein levels in the cells with Protein Immunoblot (Western Blot). In addition, stabilization and drug release analyzes of the nanoparticle will be performed. Obtained nanoparticles’ analysis and characterization will be done with Fourier Transform Infrared Spectrophotometer (FT-IR), Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Zeta analysis, Nanodrop, agarose gel electrophoresis Dynamic Light Scattering Spectrometer (DLS) and Liquid Chromatography - Mass Spectrometry - Mass Spectrometry (LC-MSMS) instrument. With the findings obtained in the project, it is aimed to produce a gene therapy that can be used in the treatment of hATTR.
Investigation of the Effects of the PEGylation of Carbon Quantum Dots and Peptide Interactions on the
Cell Viability, Apoptosis, and Cellular Localization (Acibadem University General Research Projects Support Program)
Project Leader: Beste Dipçin
Consultant: Assoc. Prof. Bükem Tanören, Assoc. Prof. Kadriye Kızılbey, Assist. Prof. Nazlı Keskin Toklu, Assist. Prof. Özgül Gök Özatay
The goal of this project is to synthesize biocompatible bioimaging agents (carbon quantum dots) and to observe how PEGylation and peptide interactions effect the cell toxicity, cellular localization of the carbon quantum dots, and their effects on apoptosis which is a programmed cell process. The theranostic potential of bare and PEGylated/peptide physically absorbed carbon quantum dots will be tested in breast cancer and human embryonic kidney cells.
Development of a C-Shaped Transcranial Magnetic Stimulation Device and Magnetic Targeted Drug Delivery Combined Therapy in Animal Models of Neurophysiological Disorders
Project Leaders: Şevval Yıldız, Mert Parmaksızoğlu, Batuhan Güneş
Consultants: Prof. Dr. Jakub Antczak, Assoc. Prof. Bükem Tanören, Assist. Prof. Melis Yavuz, Dr. Ferit Tiryaki
Epilepsy significantly diminishes patients' quality of life, and preventing seizures remains challenging. This project aims to enhance antiepileptic drug delivery systems and Transcranial Magnetic Stimulation (TMS), both of which show promise but face clinical challenges. Antiepileptic drugs can prevent seizures by regulating neurons, but conventional delivery methods often lack efficiency, fail to target specific areas, and can accumulate in the blood-brain barrier, causing toxicity. TMS, which uses magnetic fields to prevent seizures, also faces issues with precise targeting and efficacy, and lacks standardized methodologies for in vivo and in vitro experiments.
The main objective of this project is to develop three types of drug-based nanoparticles for in vitro testing. These nanoparticles will be evaluated with a C-coil-based TMS device developed during the project. The goal is to increase the efficacy of TMS treatment and establish a novel therapeutic approach that reduces the effects of epileptic seizures. The effectiveness of the new TMS device and antiepileptic drug therapy will be tested through cell migration experiments, ensuring their potential for future research and clinical applications.
Investigation of The Effects of L-Arginine on Atherosclerotic Plaque Patients' Saphenous Vein and IMA Grafts
Project Leaders: Beste Dipçin, Ahmet Turan Keskintaş
Consultants: Assoc. Prof. Bükem Tanören, Prof. Dr. Murat Uğurlucan
In this project, it is aimed to investigate the effects of L-arginine on the morphology and the collagen content of the internal mammarian artery (IMA) and saphenous vein grafts that were collected from atherosclerotic plaque patients utilizing a cryostat microtome and a fluorescence microscope. Also, it is aimed to check how L-arginine affects the elemental composition of the grafts utilizing the EDS analysis. It is believed that with the outcomes of this project, L-arginine's potential as a new treatment option for the disease can be enlightened and can lead to further scientific research.