Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Development of Visual Analysis Interfaces for Large Biological Data and Characterization of Immunomodulatory Noncoding Rna Networks Cancer(01. Izmir Institute of Technology, 2023) Kuş, Muhammet Emre; Ekiz, Hüseyin Atakan; Ekiz, Hüseyin AtakanThese days we are collecting data in higher and higher dimensions, processing it, and developing tools that have strong descriptive and predictive powers. Especially in the field of cancer, the processing of data collected from patients has substantial potential in terms of discovering new biomarkers, developing personalized treatment methods, and better prognosticators. However, there are significant difficulties in utilizing and analyzing high-dimensional data. A good level of coding skills is required to bring the data together and apply different analysis methods. With the visual interfaces created in this study, we offer the opportunity to examine and analyze the high-dimensional data of thousands of cancer patients, which are open to the public through The Cancer Genome Atlas initiative, especially for bench scientists who has no prior coding expertise. The Cancer Genome Explorer, shortly TCGEx, is a robust bioinformatic tool that we developed to facilitate high-throughput cancer data analysis through several sophisticated algorithms. With special features like subset-specific analysis and comparative analysis by using multiple cancer data, TCGEx can contribute to the literature by accelerating the studies, especially in hypothesis-driven research. This study also describes a use-case scenario that demonstrates how hypothesis-driven research can be performed using TCGExplorer for melanoma. In melanoma, elucidating the interactions between the tumor and the immune system at the miRNA level is crucial for developing new therapeutics. In this study, we characterize the properties of potential therapeutic targets that act on tumor and immune cells, which we have identified using various statistical analysis methods including machine learning, dimensionality reduction, and survival modeling using the TCGEx portal.Master Thesis Optimization of a Liver Organ on Chip System for the Investigation of Breast Cancer Cell Invasion(01. Izmir Institute of Technology, 2023) Tosunoğlu, Perge Bilgesu; Yalçın Özuysal, ÖzdenThere are many challenges in creating an accurate and physiologically relevant three-dimensional (3D) model of the liver such as finding the suitable liver extracellular matrix (ECM) components and cell types for the development of cell-laden liver-on-a-chip systems. In recent years, precision tissue slice-based methods are used to reduce the problems caused by the cell-laden liver-on-a-chip system complexity. However, these methods require sophisticated tools which are not easily accessible. This study focuses on the development of a 3D liver model using simple and cost-effective methods. To achieve this, we aimed to optimize liver tissue size, maintenance and culture medium, scaffold gel, and viability assay. The needle method was found to be the easiest, most efficient, and cheap method for tissue processing as the equipment used was easily accessible and evaded enzymatic steps. Moreover, consistent samples that were all similar and in the desired size were easy to obtain. In addition to these, functionality and viability were analysed for 72 hours to assess the physiological state of the liver after tissue processing. Based on these findings a novel liver-on-a-chip system was successfully developed and as the next step, the invasion of the MDA-MB-231 breast cancer cell line towards the liver was investigated with and without the presence of C-X-C chemokine receptor type 4 (CXCR4) antagonists AMD3100 and AMD3465. In conclusion, this study demonstrated the development of a novel 3D model for the liver and provided a platform for studying breast cancer invasion with its potential implications for cancer therapy research.Master Thesis Deep Learning Based Real-Time Sequential Facial Expression Analysisusing Geometric Features(01. Izmir Institute of Technology, 2023) Köksal, Talha Enes; Gümüş, AbdurrahmanIn this thesis, macro and micro facial expression sequences from various datasets are trained using neural networks to classify them in one of the basic emotions. In macro expression experiments, for each frame of the sequences facial landmarks are extracted using MediaPipe FaceMesh solution and geometric features using both spatial and temporal information based on these landmarks are created. To classify the features, ConvLSTM2D followed by multilayer perceptron blocks are used. In order to achieve real time classification performance, all algorithms are implemented compatible to run on GPU. The proposed method for macro expressions is tested with CK+, Oulu-CASIA VIS, Oulu-CASIA NIR and MMI datasets. In micro expression experiments, apart from geometric features also blendshape features provided by MediaPipe are used. In order to improve classification performance, Phase-Based Video Motion Processing technique is used to magnify subtle facial movements of micro expressions. Experiments are conducted separately on same classification layers that consist of ConvLSTM1D followed by multilayer perceptron blocks. The proposed method for micro expressions is tested with SAMM and CASME II datasets. The datasets utilized in this study were accessed upon signing corresponding license agreements. Each dataset is specifically designated for academic purposes and is made available under these agreements. Only data from subjects who provided consent for their information to be used in publications was included in the thesis. The license agreements for each dataset can be found in the appendices section.Master Thesis Entanglement and Topological Phenomena in Quantum Walks(01. Izmir Institute of Technology, 2023) Gökalp, Harun; Çakır, ÖzgürQuantum walk, a counterpart of classical random walk, is widely used in the development of quantum algorithms and the modelling of physical systems. Since it has a simple and powerful mathematical structure, its implementation in physical systems serves to solve complex problems. In one-dimensional space, we investigated the topological properties of the simple quantum walk, and under which conditions the simple quantum walk possesses winding numbers. Then, we introduced the split-step quantum walk in a twodimensional space and numerically obtained Chern number phase diagram of each band as a function of rotation parameters. Subsequently, we introduced and studied the quantum walk protocols governed by two coins in a two-dimensional space. We first explored the entanglement and topological properties of a quantum walk protocol governed by a single non-local two-coin operator followed by translations along two spatial directions each governed by a different coin. We deduced that the motion reduces to one-dimensional motion in two spatial directions in decoupled coin subspaces. Then, we studied the split-step quantum walk protocols, where each step is comprised of local coin operations, followed by translations, non-local coin operations, and translations again. In these protocols, each step involves two translations along two spatial directions, and translations along a given spatial direction were either governed by the same coin or alternating coins. We also explored three different non-local coin operations, where a collective rotation takes place in a coin space conditioned on the state of the other coin's state along the same direction or perpendicular direction. We identified the effective Hamiltonian of the system and determined its eigenstates which are comprised of four bands in the Brillouin zone. For all the protocols we have introduced, we studied the coin-coin entanglement and topological properties as a function of coin rotation parameters.Master Thesis Topology Optimization of Non-Linear Elastic Microstructures(01. Izmir Institute of Technology, 2023) Güven, Murat; Özdemir, İzzetTopology optimization (TO) is used in a broad spectrum of engineering disciplines ranging from aerospace to civil engineering. A particular sub-field where topology optimization has been very instrumental is the design of microstructures that yield specific macroscopic properties, such as negative Poisson's ratio and negative magnetic permeability. In this thesis, based on a recently proposed method for nonlinear homogenization, a framework for topology optimization of nonlinear elastic microstructures is developed and implemented as a computer program using the Julia programming language. Following a plane strain formulation, a two-dimensional unit cell with periodic boundary conditions is used in combination with a neo-Hookean elastic material response. By exploiting the symmetry properties of the resulting orthotropic microstructure, it is shown that the computational domain can be reduced, and half of the original discretization is sufficient to carry out the optimization task. The obtained topologies from the developed computer program, the linear and nonlinear response comparison, and the computational gain achieved through domain reduction are presented along with the experiments on proof-of-concept type uni-axial tests.Master Thesis Development of Polymeric Carriers for Mrna Delivery(01. Izmir Institute of Technology, 2023) Savaş, Müge; Bulmuş Zareie, Esma VolgaDevelopment of efficient delivery systems is a constraint on the delivery of messenger RNA (mRNA). In gene therapy, it is crucial that mRNA molecules are efficiently delivered into cells. The thesis study has focused on the development of a relatively new polymer, P(OEGMA)-b-P(AEAEMA) as a new mRNA delivery system. P(OEGMA)-b-P(AEAEMA) block copolymers with changing block lengths (P(OEGMA)42-b-P(AEAEMA)48 and P(OEGMA)42-b-P(AEAEMA)71) were first synthesized via RAFT polymerization. The synthesized block copolymers efficiently complexed with eGFP encoded mRNA as shown by gel electrophoresis. The hydrodynamic size of polyplexes was less than 150 nm, as determined by dynamic light scattering measurements. Zeta potential measurements showed that the surface charge of the polymer-mRNA complexes was slightly negative. The eGFP-encoding mRNA transfection ability of the copolymers was investigated via fluorescence microscopy and Image J analyses. The block copolymers showed mRNA transfection efficiency on human embryonic kidney (HEK293T) and mouse fibroblast (L929) cell lines higher than the golden standard polymer, branched PEI. P(OEGMA)42-b-P(AEAEMA)48 and P(OEGMA)42-b-P(AEAEMA)71 showed a transfection efficiency of 54 and 64% of the positive control (cells transfected with Lipofectamine-mRNA complexes), respectively, on human embryonic kidney (HEK293T) cell line. On mouse fibroblast (L929) cell line, P(OEGMA)42-b-P(AEAEMA)48 and P(OEGMA)42-b-P(AEAEMA)71 block copolymers showed a transfection efficiency of 61 and 56% of the positive control, respectively. The polymer complexes showed tolerable (>70%) or no cytotoxicity on the cells in the tested range. In summary, P(OEGMA)-b-P(AEAEMA) block copolymers have shown promising mRNA transfection ability on both HEK293T and L929 cell lines.Master Thesis Lyotropic Liquid Crystal Templated Synthesis of Single-Crystalline Gold Microplates and Transparent Conductive Reduced Graphene Oxide Thin Films(01. Izmir Institute of Technology, 2023) Akkuş, Betül; Mert Balcı, FadimeSurfactants organize to form various mesophases of lyotropic liquid crystal (LLC) in the presence of water. In the literature, some acids, salts, and ionic liquids have also been used to form ordered LLC mesophases. In this thesis, two dimensional (2D) single-crystalline gold (Au) nano- and microplates and reduced graphene oxide (RGO) thin films have been synthesized using LLC mesophases. Stable LLC mesophases have been formed using 10-lauryl ether (C12EO10), an oligo-type surfactant, and sulfuric acid (H2SO4), a strong acid. Au plates with various anisotropic structures, such as triangular, truncated triangular, hexagonal, and gear-like, have been synthesized by a photochemical method in the presence of LLC mesophase. Most importantly, Au plates up to 39 µm in width have been obtained in the confined space of the LLC medium. The thickness of the obtained Au plates varies from 50 nm to 150 nm. The size and/or morphology of Au products synthesized in LLC medium depends on the power of the light source, the irradiation time, the amount of Au precursor added, the addition of different capping agents, and various inorganic salts. Additionally, spin-coated RGO thin films have been synthesized using the LLC mesophase for use as a transparent and conductive electrode in various electrochemical devices. The LLC mesophase has improved the sheet resistance values of RGO thin films. RGO thin films with a sheet resistance of 31 kΩ/sq and an optical transmittance of 92% at 550 nm have been achieved at the high thermal annealing temperature under an inert atmosphere.Master Thesis Recovery of Lithium From Aqueous System Using Manganese Oxide Adsorbent With Developed Electrospun Mat Substrate(01. Izmir Institute of Technology, 2023) Akgün, Berk; Ebil, Özgenç; Demir, Mustafa MuammerLithium is used in many fields due to its high energy density and unique electrochemical properties. Recently, there has been a strong increase in demand for lithium, so the extraction of lithium from natural water resources has become a remarkable research topic. One of the most effective methods of separating lithium from natural water sources is adsorption using lithium ion-sieve adsorbents. However, the powdered nature of the adsorbents makes them challenging to process and less recyclable. Recent studies have focused on developing adsorbents using different polymeric materials as substrates or binders. In the thesis, as a new approach, flexible and free-standing polyurethane electrospun mat substrates were produced and combined with λ-MnO2 to extract lithium from aqueous systems, and their lithium removal performance was investigated. After the fabricated mats and λ-MnO2 powder were characterized, the deposition process was performed, and filtration studies were carried out in synthetic lithium solution. Optimum conditions for lithium removal were found as an adsorbent amount of 200 mg, and 200 ppm initial [Li+], and pH 12. In addition, lithium removal performances have been improved by stacking mats and multi-stage filtration processes. Lithium removal reached 76.6% when a 400 ppm lithium solution and an 8-step filtration were used. Lithium removal experiments were performed with salt-lake brine containing high concentrations of various ions and showed that these ions reduced the lithium removal. In the study, PU electrospun mats for λ-MnO2 powder were found to be a promising substrate for lithium removal from aqueous systems.Master Thesis Valorization of Biomass for Fuel and Chemicals Production(01. Izmir Institute of Technology, 2023) Öcal, Bulutcem; Yüksel Özşen, AslıRapidly increasing global energy demand resulting from the growing population and worldwide development increased consumption of limited fossil fuel usage that causes severe environmental deterioration by CO2 emission have sparked interest in finding green, renewable, and sustainable alternative sources for energy. Bio-oil, derived by several biomass via liquefaction, is a promising candidate to replace fossil fuels. Turkey is a country, 27% of which is covered with forests (mostly oak trees). Therefore, it has great potential for cheap lignocellulosic feedstock forest residues from industrial applications and harvesting. In the present study, the thermal liquefaction of oak wood particles (OWP) was performed using various solvents besides water, such as ethanol, 1-butanol, and 1,4-dioxane. The experiments were carried out in a batch reactor for 1 and 2 h residence time at different temperatures (210oC, 240oC, and 270oC). Bio-oil samples obtained at best reaction temperature, 270oC, optimum residence time, 1 h, were analyzed with TGA, CHNS elemental analyzer, FTIR, and GC-MS. Based on energy recovery calculations, the enhancement of pristine OWP's energy efficiency depends on bio-oil yield, and quality was confirmed for all solvent types. 1,4-dioxane showed the best performance in yielding the maximum bio-oil with 51.8%. The higher heating values of the bio-oils ranged from 22.1 to 35 MJ/kg. Phenolic groups were the predominant components of bio-oil produced from OWP, while intensity of alcohols, ketones, and acids varied based on using solvents.Master Thesis Catalytic Pyrolysis of Virgin and Waste Polyolefins(01. Izmir Institute of Technology, 2023) Çalık, Fatma Defne; Yıldız, Günay; Şeker, ErolThe fact that increasing plastic production and the mismanaged waste released to the environment put the ecosystem at risk. One of the most promising recycling methods developed within this framework has been pyrolysis. In this thesis, a model feedstock mi (No: 119N302). Thermal (batch and continuous) and catalytic pyrolysis (in-situ and ex-situ) techniques were applied to the polyolefins. Silica-alumina-based solid acid catalysts were produced with the simple sol-gel method to compete with commercial ZSM-5 (30) and ZSM-5 (50). Catalyst-to-plastic ratios between 1/100 and 1/1000 were used for in-situ, and 200 h-1 and 500 h-1 WHSVs were used for ex-situ mode. 57 wt.% pyrolysis oil was produced from the thermal pyrolysis of the virgin PO mixture in the batch system. In the ex-situ catalytic pyrolysis experiments by 500 h-1 WHSV and by ZSM-5, silica-alumina, and ZSM-5 supported silica-alumina, 36 wt.%, 56.6% wt.% and 45.2 wt.% liquid, and by 200 h-1 WHSV, 29.9 wt.%, 54.1 wt.%, and 57.9 wt.% pyrolysis oils were collected, respectively. The most successful test in terms of product composition was ES2 with 82.9% gasoline (8.8% BTEX), and 16.7% diesel-range hydrocarbons. The motivation was investigating whether it was suitable to produce liquid hydrocarbons, in the range of C5-C20, as a feedstock in the petrochemical industry. As a result, it has been proven that energy recovery was possible and sustainable by plastics recycling instead of using fossil fuels.