Master Tezleri

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Analysing Pakistani architecture in the context of critical regionalism
(Izmir Institute of Technology, 2022-06) Bahadur, Aujala Naveed; Yılmaz, Ebru
Pakistani architectural practise is adopting global trends and universal ideals without regard to its traditional roots, meanwhile critical regionalism has emerged as a significant global strategy for delivering a blend of legitimacy and contemporary architecture, particularly in developing nations. In addition, it promotes the production of architecture directly related to their surroundings and communities while being a component of the contemporary world. Therefore, using critical regionalism as a tool, this study will examine Pakistani architecture to understand the linkage between its tradition and modern technology. Within the scope of this thesis, theoretical studies on Critical Regionalism are first explored, concluded by eight aspects that, according to this research, go beyond what Kenneth Frampton and others had established. Then, an examination of the persisting problems in Pakistani architectural practises is performed. The following chapter examines critical regionalism in Pakistani architecture using the same eight factors. The examination includes the ideologies, works, and interviews with Pakistan's three most prominent architects: Nayyar Ali Dada, Kamil Khan Mumtaz, and Naeem Pasha. The research concludes by determining, via observations and deductions, the viability of critical regionalism as a tool. Due to a lack of publications on Pakistani architects and architecture, this study attempts to develop a framework for future studies on awareness and inspiration from selected architects' work.
Bioinformatic approaches to investigate HIV capsid-nanobody interaction
(01. Izmir Institute of Technology, 2023-07) Atik, Şeref Berk; Taşkent Sezgin, Hümeyra
Infection with HIV is still a global pandemic. Since the discovery of this highly mutagenic virus, nearly 40 million people have passed away as a result of HIV-related health problems. Currently, 38.4 million people are HIV-positive. Following infection, the viral genome gets integrated into the host cell genome. The infected person carries the virus for the rest of their life and can spread it to others through bodily fluids. Because there is no treatment for HIV, the World Health Organization recommends that infected people be diagnosed early through comprehensive screening to restrict the virus's spread. As a result, there is still a need to create practical, sensitive diagnostic tools, particularly for use in the field of HIV infection testing. In this study, the interaction between HIV-1 capsid protein, the first antigen found in the blood during the acute phase of HIV infection, and a nanobody (Nb, a single domain antibody) known to bind to capsid is investigated at the molecular level through computational methods. Because the structure of HIV-1 CA binding-Nb is unknown, all-atom models of the Nb structure were constructed using comparative methods, deep-learning-based methods, and hybrid methods (SwissModel, trRosetta, Robetta, AlphaFold2), and promising models were chosen. In the second stage, molecular docking was used to produce HIV-1 capsid- nanobody complex structures, which were then tested for stability and native-likeness using standard molecular dynamics simulations. Understanding the molecular details of the HIV-1 capsid-nanobody complex, we believe, will provide essential data for using this antigen-antibody pair inan immunosensor system for HIV-1 infection diagnosis.
Catalytic pyrolysis of virgin and waste polyolefins
(01. Izmir Institute of Technology, 2023-06) Çalık, Fatma Defne; Yıldız, Günay; Şeker, Erol
The 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.
Cell separation in microfluidic devices
(01. Izmir Institute of Technology, 2022-07) Öksüz, Cemre; Tekin, Hüseyin Cumhur
Cell separation is used to separate homogeneous and individual cell classes from a heterogeneous cell population. The efficiency and purity of these separated cells are of great importance in personalized medicine, regenerative medicine, disease monitoring and drug testing as well as in the therapeutic and diagnostic research. In this thesis, different microfluidic approaches were presented for cell separation. With this regard, a closed channel vacuum-integrated microfluidic chip was developed using an air permeability of a Polydimethylsiloxane and density-based separation of microparticles was performed. Besides, a centrifugal microfluidic system, Spinochip, was developed with one reservoir as inlet and outlet for the first time and different fluid manipulations were shown in the system. The system was applied to clinical tests of hematocrit measurements and white blood cell estimation using real patient samples. The developed system offered correlated results with clinical results. In addition to closed channel microfluidics, negative-magnetophoresis microfluidic chip was demonstrated for the size-based separation of microparticles and cells. In this regard, capturing rate of breast cancer cells (MCF-7) and human monocyte cells (U937) was investigated. The results showed that the approaches presented here could promote to the microfluidic studies for size-based cell separation.
Characteristic properties and recyclability of aluminium beverage cans and coffee capsules
(Izmir Institute of Technology, 2022-06) Önen, Rabia; Genç, Aziz; Gökelma, Mertol
Recycling is an effective way to reduce environmental pollution. Recycled aluminium uses 95% less energy than primary production. Therefore, there is a high demand for more efficient recovery technologies. Aluminium is used in transportation, consumer products, and electronics. Short life cycles, thin walls, and surface coatings make aluminium recycling difficult. This study focuses on UBCs and coffee capsules' properties and recyclability (CCs). A lab-scale electrical resistance heating chamber furnace was used for the de-coating and remelting experiments. The coatings were characterized using Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM/EDS). As a result of the study, it was found that thermal pre-treatment temperature is more critical for alloys that have high Mg content due to their oxidation tendency. Suitable thermal pre-treatment temperature was observed between 520 to 550 °C for the samples. On the other hand, when the volatile organic content of the scraps was analyzed, it was observed that clean UBCs and CCs contain 2.2% and 9% volatile organic content, respectively, but it can be increased with increasing drink rest inside of it. A result of these experiments shows that the metal yield can differ up to 3.5% due to the drink residues (sugar). Also, it was observed that high-density pressing of the samples prior to the de-coating process increases the amount of the entrapped carbonaceous materials and decreases the de-coating efficiency. Finally, it was observed that samples with low wall thicknesses should be remelted under a salt flux to prevent oxidation and allow coalescence.
Characteristics of Byzantine period building bricks used in St.Jean Basilica (Ayasuluk Hill) and Anaia Church (Kadıkalesi)
(Izmir Institute of Technology, 2022-07) Çam, Elif; Uğurlu Sağın, Elif
Fired bricks, one of the oldest man-made building materials, are historical documents that reflect the production technologies of their periods and the raw material characteristics of the geography they were located. Characterization of bricks is essential for revealing production techniques of their times and contributing to conservation works on monuments built with this material to pass through next generations. The fired bricks were frequently used as one of the important building materials in Byzantine Architecture. In this study, the fired bricks collected from the different construction periods of St. Jean Basilica, Ayasuluk Hill and Anaia Church, Kadıkalesi, which belong to the Byzantine Period, were investigated to determine material properties, periodical differences, and production technologies. The properties of Byzantine bricks were determined by standard test methods, compression tests, SEM-EDS, XRD, FTIR, and TGA analyses. According to the results, brick samples taken from both areas were highly porous and low-dense materials. Ca-poor clay source was used in producing St. Jean Basilica bricks, while Anaia Church bricks were produced with Ca-rich clay sources. This situation was decisive in the colour of bricks, and St. Jean Basilica bricks were in reddish colours, while Anaia Church bricks were in brown/beige colours. Also, raw material was extracted from a single source in the production of all St. Jean Basilica bricks, while two different sources were utilized for Anaia Church bricks throughout the three construction periods. Besides, the bricks of both churches were found to be fired at low temperatures (700–900°C) due to the technology of Byzantine kilns. Despite low firing temperatures, the majority of the bricks did not possess pozzolanic properties since they did not contain a sufficient amount of clay minerals. The highest mechanical strength was determined in the bricks with higher firing temperature and bricks with the higher calcium content. The properties of fired bricks were differentiated based on production technologies; contrary, a distinctive difference was not observed depending on their periods.
Cloning, expression and characterization of sericin like octamer-repeat protein
(01. Izmir Institute of Technology, 2021-12) Şahin, Alper; Sürmeli Eraltuğ, Nur Başak; 01. Izmir Institute of Technology
Silk proteins are natural polymers which are synthesized by insects like silkworms and spiders. There are two proteins in the silk obtained from the cocoon of B. mori, these are silk fibroin and silk sericin. While the silk fibroin is the main part of the cocoon with a high commercial importance, sericin is the "glue" protein that holds fibroins together. Sericin has wide variety of applications from cosmetics to biomaterial research. Because of its high fibrillar structure, it can be used in wound healing or drug delivery studies. It can be obtained from the degumming process of cocoons which includes chemical treatment like alkali treatment and boiling, or biological treatment like enzymatic digestion. However, sericin obtained by these processes are not consistent in structure, and the sequence of the protein obtained depends on the extraction methodology and conditions. However, proteins obtained by recombinant production can be standardized, and repeat-chain length can be adjusted as desired. In this thesis study, a sericin like protein which includes eight repeats of the 38 amino acid sequence of the natural sericin was cloned and expressed in E. coli. The resulting protein, Ser-8mer, was analyzed in terms of fibril structure and secondary structure. It was found out that the protein has beta sheet conformation in contrast to commercial sericin with random coils. And as a result of this conformation, it forms insoluble self-assembled fibril structures which shows a promising contribution to the biomaterial research.
Co-production of chitin nanofibers, proteins, and lipids in marine diatoms belonging to the Thalassiosira genus
(Izmir Institute of Technology, 2022-06) Sezgin, Tuğçe; Özkan, Altan
Chitin is a biopolymer used in various industries, including biomedical, pharmaceutical, medical, and food. Today, the vast majority of chitin is obtained from waste shellfish. Shellfish chitin has an inherent impurity problem because chitin in these organisms is embedded in other organics and inorganics. Thus, new sources have been investigated. Diatoms, particularly Thalassiosira and Cyclotella species, have the potential to be the providers for applications requiring high quality through their unique ability to biosynthesize and extrude chitin nanofibers. The primary aim of this study is to study this potential. This investigation entailed the cultivation of three Thalassiosira strains according to a standard cultivation protocol under photobioreactor conditions. The secondary aim was to assess the possibility of commercially valuable co-product generation. For this, biomass protein, lipid, and fatty acids contents were analyzed. Chitin productivity varied significantly between the strains. The peak productivities and final concentrations ranged from 4 to 25 mg/L-day and from 60 to 250 mg/L, respectively. Average fiber diameters ranged from 68.5 to 95.0 nm. Silicon limited growth increased the chitin biosynthesis in T.weissflogii 1336 and T.pseudonana 2135. Biomass lipid contents of over 45% were obtained with T.pseudonana 2135 under silicon depletion. The fatty acid profiles indicated the suitability for application as live aquaculture feed for T.weissflogii 1336, and biodiesel feedstock material for T.pseudonana 2135. The highest biomass protein contents were about 30%, which were obtained under silicon availability. This study, for the first time, assessed the chitin productivity of Thalassiosira strains and demonstrated unique multiproduct generation scenarios.
A computational chemistry study on the interactions between hydrogenated borophene and amino acids
(Izmir Institute of Technology, 2022-07) Bozkurt, Yağmur; Elmacı Irmak, Nuran
In this work, the adsorption behavior of hydrogenated borophene to amino acids was examined to provide its geometric and electronic structures information and to check whether hydrogenated borophenes’ potential can be used in new biosensor devices for amino acids or not. In the aspect of this thesis adsorption of 4 amino acids from different types of amino acid classes (acidic, basic, nonpolar, and polar) on hydrogenated borophene surfaces has been studied by computational chemistry methods. Electronic and geometric structures of B36H6 and its complexes with glycine, tyrosine, aspartic acid, and histidine were obtained by DFT calculations at B3LYP-D2 / 6-311G** level of theory. In the energetically most favorable configurations of complexes, amino acids approaching from the bottom of the B36H6 surface with a horizontal orientation (exception for histidine complexes) of amino acid was observed. The most reactive parts of the B36 structure (edges) have been stabilized with hydrogenation, the whole boron cluster became more stable and adsorption ability has fallen. It was found that hydrogenated borophene has indistinguishable electronic responses for each the amino acids studied in this thesis since the complexes exhibited nearly the same band gap. Thus, hydrogenated borophene shows no sensor ability to GLY, TYR, ASP, and HIS.
Coupled wake and blockage modelling for a wind farm
(Izmir Institute of Technology, 2022-10) Çam, Janset Betül; Bingöl, Ferhat
One of the significant reasons for the power loss in wind farms is the wake effect. Therefore, the wake effect is crucial for designing a wind farm. However, only wake modeling is not sufficient to explain power losses. Wake is the turbulent, complex, and relatively weak flow behind the wind turbine. The wake effect is not required for the front row turbines in wind farms, and the wake model cannot be applied. It is assumed that the wind farm directly encounters the free stream wind speed. However, the blockage effect, also known as the induction zone effect, is observed at the front of the wind turbines. Due to this effect, the wind farm encounters a lower wind speed than the free-stream wind speed. This situation reduces the accuracy of the Annual Energy Production (AEP) calculation in wind farms. The motivation of this study is to obtain an improved coupled wake and blockage model that converges to the accurate SCADA data of a wind farm more than the wakeonly or blockage-only models. This study applies seven wake and six blockage models to the wind farm. The similarities and differences between the coupled models and the wind farm SCADA data and their reasons are discussed.
Crude pectinolytic enzymes production in fed-batch shake flask cultivation
(01. Izmir Institute of Technology, 2023-05) Esen, Büşra Nur; Uzuner, Sibel; Taşkent Sezgin, Hümeyra
The use of waste in the production of enzymes, which is one of the products with high added value, is one of the right strategies to reduce the production cost of the product and sustainability movement. In this study, the production of polygalacturonase (PGase) and pectin lyase (PLase) enzymes from Bacillus subtilis ATCC 6633 in fed batch submerged fermentation, the conditions and composition of the fermentation medium and the effects of pretreatment methods (thermal, thermo-chemical, microwave assisted dilute acid (MW- DA)) on the conversion of fermentable sugar from black carrot pulp were investigated. The MW-DA was chosen the best with higher fermentable sugar content (FSC). The three different powers (300, 600, 850 W) and 3 different treatment time (30, 60, 90 s) were examined by Taguchi design. The highest FSC was found at 300 Watt for 30 seconds. MW-DA followed by ES produced the most fermentable sugar (0.493 g/g, 87.3% conversion). The amount of fermentable sugar was enhanced from 15.8% to 87.3% when MW-DA treatment is combined with enzymatic saccharification (ES). Yeast extract, whey and pea protein were examined as nitrogen sources. According to the enzyme activity results obtained, the fermentation medium was modified with pea protein. Certain concentrations (2.5%, 5%, 10%, 15%) were fed to the fermentation medium. The highest PGase activity was determined at the 15% feed concentration and 72th hours (164.34±2.26 U/L) whereas the highest PLase activity was obtained at 72th hours (188.22±1.72 U/L) at 5% feed concentration.
Crystal plasticity inspired modelling of fibre reinforced composites
(Izmir Institute of Technology, 2022-07) Dizman, Emir Aybars; Özdemir, İzzet
There is an increasing demand in carbon fibre reinforced (CFR) composites primarily due to their high strength-to-weight ratio. Although their single-ply behaviour is rather brittle (as compared to metals), by reducing the ply thickness and stacking differently oriented plies, brittleness is suppressed, and a ductile behaviour similar to metals is achieved. In this thesis, a recently proposed material model inspired by crystal plasticity is reconsidered and implemented in an implicit finite element solution framework. To this end, a user-defined element is developed in a geometrically non-linear continuum setting and implemented in commercial finite element software Abaqus through UEL (Userdefined ELement) subroutine. The model is validated by analytical solutions derived for simple shear cases and two experiments for different loading cases from the literature. The model is capable of predicting stress-strain response well in cases where matrix plasticity is dominant. Moreover, a parametric study on the cross-ply shear specimen is conducted to investigate the influence of different material parameters. In the last part, the model is extended by a continuum scale damage in the matrix and degradation in elastic material properties. The predictive capabilities of the damage extended model are assessed by re-analyzing the cross-ply shear test.
Design and synthesis of a BODIPY based probe for cadmium ions
(01. Izmir Institute of Technology, 2021-12) Cebeci, Miray; Emrullahoğlu, Mustafa; 01. Izmir Institute of Technology
Given the severely toxic effects of heavy metals on living systems and the environment in general, identifying and quantifying heavy metal ions in synthetic samples and in vivo are highly significant activities. One such heavy metal, cadmium, allows only a low level of tolerable exposure and can thus have fatal consequences or cause critical health problems such as ostial disorders, nephrotic syndromes, various types of cancer even in extremely low concentrations. Although several standard techniques for detecting cadmium have been used, including atomic absorption and emission spectroscopy and inductively coupled plasma mass spectrometry, all of them require complex instruments that are also expensive, time-consuming to use, and hardly portable. For that reason, sensitive, selective, less labour-intensive methods of detecting cadmium ions are greatly needed. In response, fluorogenic or chromogenic methods afford high analyte sensitivity and selectivity, easy sample preparation, and easy monitoring, all with affordable instrumentation. Against that background, this thesis reports the design, synthesis, and development of a fluorescent molecular sensor that can detect Cd2+ ions within spectroscopic behavior and living cells. In the design, based on the mechanism of intramolecular charge transfer (ICT), borondipyrromethene (BODIPY) dye was used as a signal reporter due to its unique properties, and di-(2-picolyl)amine (DPA) was chosen to represent the recognition unit. Altogether, the sensor offers rapid response, high selectivity, and high sensitivity in detecting Cd ions is reversible with the aid of CN- and can be used to efficiently image Cd2+ species in vitro.
Design and synthesis of a BODIPY based probe for mercury ions
(01. Izmir Institute of Technology, 2021-12) Tütüncü, Büşra Buse; Emrullahoğlu, Mustafa; 01. Izmir Institute of Technology
The detection of heavy metal ions in living systems and aqueous environments has attracted significant attention in recent years, especially the detection of mercury, one of the most toxic heavy metals on Earth. To reduce mercury's lethal effects on the human body, animals, and marine life trace amounts of mercury species can be detected by using classical spectroscopic techniques for example atomic absorption and emission spectroscopy, high-performance liquid chromatography, and inductively coupled plasma mass spectrometry. However, because those techniques are time-consuming and expensive, fluorescence analysis, which offers high selectivity and sensitivity, has emerged as a suitable alternative for detecting mercury species. In the work presented here, a new BODIPY -based fluorescent probe functionalised with a phenylhydrazine unit was designed and synthesised for the selective and sensitive detection of mercury species. The probe's detection limit was determined to be 29 nM, and the probe could detect mercury species in living cells without any changes in cell morphology.
Design of a physical human-robot interface for lifting operations
(Izmir Institute of Technology, 2022-07) Nalbant, Uğur; Dede, Mehmet İsmet Can
In this thesis, the design of a physical human-robot interface for lifting operations which controls the vertical movement of the payload is studied. The new design uses a low stiffness type of admittance control method that is aimed at reducing the surface impact force of the payload and providing better control for the operator while having the option of high stiffness admittance control. To reduce impact forces by using low stiffness admittance control, a sliding handle mechanism is introduced into the system. This type of design includes springs and bearings to create a low stiffness admittance-type user interface. Mathematical models are developed to calculate spring forces and mechanical strength. According to design requirements and mathematical calculations, the prototype is designed and manufactured. In the tests, it is seen that the spring forces are low, and the sliding motion of the handle is not consistent over different displacements. According to the test results, revisions are done, and the final design of the system is developed. In the final tests, it is seen that the new design of the physical human-robot interface performance is improved and the problem of the sliding motion of the handle is solved. Also, the surface impact forces are reduced with low stiffness admittance control. Another improvement of the new design is the ability to control the payload with high stiffness admittance control if the user chooses it. With this option, users can control the payload by touching the payload. Having both types of control methods, the user can choose which type of control method to use to handle payload in the factory.
Design of stacker crane for mini-load automated storage and retrieval systems
(Izmir Institute of Technology, 2022-07) Bekleviç, Mustafa; Mihçin, Şenay
The objection of the thesis is to design and analyze a 3 degree of freedom stacker crane mechanism for Mini Load Automated Storage and Retrieval Systems. Automated Storage and Retrieval System (AS/RS) is an automated system in which the product of a company to be stored is placed in or retrieved from specified location on a rack system by means of computer aided mechanism which is nothing but a stacker crane. This study first introduces an inclusive literature review on AS/RSs. Several types of AS/RSs are examined and the differences between them are introduced. Additionally, several types of stacker cranes in the literature are also presented. Moreover, the linear motion systems used in similar mechanism are explained briefly in the chapter. In the design chapter of the thesis, theory of the stacker crane mechanism is introduced. A conceptual design is created and, elements and sub-sections of the desired mechanism are presented with the conceptual design of the mechanism. After the conceptual design, critical design calculations are performed approximately before the detailed design of the mechanism. Afterwards, the detailed design of the mechanism is created and calculations are verified due to detailed design. The detailed design of the mechanism is analyzed using Finite Element Analysis methods in the analysis chapter of the thesis. Analysis of critical components and critical sub-sections of the stacker crane mechanism are analyzed using Computer Aided Engineering program. Revises are made according to the results of the FEA and design is validated at the end. At the prototyping chapter of the thesis, the manufacturing studies of the mechanism are presented. Manufacturing stages are introduced and experiments of the sub-section of the mechanism are done.
Developing a LAMP PCR based diagnostic test for Crimean Congo hemorrhagic fever virus
(Izmir Institute of Technology, 2022-07) Üstün, Selcen; Taşkent Sezgin, Hümeyra
Crimean-Congo hemorrhagic fever infection is one of the most common tickborne viral infections, non-infectious in animals and fatal to humans with a mortality rate around 40%. The high mortality rate and lack of vaccines or drug treatment point to the potential danger of infection. The aim of this thesis was to detect 21 complete S-segment Crimean-Congo hemorrhagic fever virus strains originating in Turkey using Fluorimetric Loop Mediated Isothermal Amplification (LAMP) method, which is one of the PCRbased isothermal amplification methods for detecting viral infections. Conserved regions of the 21 strains of the CCHFV observed in Turkey were determined by sequence alignment and LAMP primers for these conserved regions were designed. DNA of CCHFV Ank-2 (GeneBank accession number: MK309333) strain was used and optimum LAMP reaction conditions were determined by changing the temperature, primer amount and MgSO4 concentration. LAMP results were compared with qPCR, which is considered the gold standard. The detection limit for LAMP and qPCR was 2x106 copies/µl. In the study, the CCHFV LAMP primer set-1 gave similar results to the qPCR primer set. The CCHFV LAMP primer set-4 performed better by turning positive 9 minutes earlier than the qPCR primer set. This results indicate LAMP is an alternative method for detecting CCHFV but reveals the necessity of improving the sensitivity of the test.
Development of co-evolution tracker tool for software with acceptance criteria
(Izmir Institute of Technology, 2022-07) Yalçın, Ali Görkem; Tuğlular, Tuğkan; Tuğlular, Tuğkan
Testing is a vital part of achieving good-quality software. Deploying untested code can cause system crashes and unexpected behavior. In order to reduce these problems, testing must be prioritized. However, once test suites are created, they should not remain static throughout the software updates. Since whenever software gets updated, new functionalities are added or existing functionalities are changed, so whenever the application is updated, test suites must be updated along with the software. If the old test suites are used with the new updates, unexpected testing results can occur. In order to repair test cases in the process of software evolution, analyzing real-world projects’ software and test case evolution is an important prerequisite. Software repositories contain valuable information about the software systems. Having access to older versions and by differentiating adjacent versions’ test and production code changes can provide information about the evolution process of the software. This thesis concentrates on the development of a tool that is used for the analysis of 21 real-world projects in the terms of co-evolution of both software and its test suites. Related projects are retrieved from repositories and filtered according to this study’s needs, then for each project's every update is analyzed, and graphs and analysis related to the co-evolution process are created.
Development of high stability antioxidant emulsions based on citrus and fig pectins
(Izmir Institute of Technology, 2022-07) Büyük, Miray; Yemenicioğlu, Ahmet
In this thesis, stability and antioxidant activity of olive oil-in-water emulsions prepared with citrus pectin (CPEC) and pectins extracted from two fig cultivars (Sarılop: FPECn and Siyah Orak: FPECc) were evaluated in the presence of green tea (GTE) and grape seed extracts (GSE), and a basic monomeric flavonoid, (+) catechin (CAT). The emulsion stabilities of FPECn and FPECc between 0.125 and 1% (w/v) were comparable to those of CPEC. Control olive oil-in-water emulsions with 0.5% CPEC, FPECn or FPECc prepared without the addition of polyphenols lost 29 to 36% of their initial emulsion stability only within 1 day. The addition of GSE at 0.25 or 0.5% caused a considerable increase in the stability of emulsions prepared with CPEC at 0.5% (less than 10% loss in emulsion stability within 14 days) while GTE caused only a limited increase in the stability of CPEC emulsions. The CAT is the only polyphenol that caused significant increases in the stability of all pectin emulsions. In contrast, both GTE and GSE showed almost no effect in stability of FPECn and FPECc emulsions. The polyphenol added emulsions were characterized for their droplet size, zeta potential and viscosities. The CAT and GSE added emulsions showed significantly higher total phenolic content and antioxidant activity than GTE added emulsions during 14 days of storage. This thesis clearly showed that GSE and CAT stabilized CPEC emulsions, and CAT stabilized FPECn or FPECc emulsions have a great potential to develop novel antioxidant olive oil based functional foods.
Development of keratin based hydrogel systems
(Izmir Institute of Technology, 2022-07) Yalçın Göl, Damla; Top, Ayben
In this study, keratin proteins from Merino sheep wool were obtained via oxidative extraction (Chapter 2), sulfitolysis extraction (Chapter 3) and sulfitolysis with reductive extraction methods (Chapter 4). Keratin proteins were characterized XRD and FTIR spectroscopy and thermal analysis. In the SDS-PAGE gel results of the keratins diffusive protein bands between ~23 kDa and >170 kDa and a discrete band at about 12 kDa were observed confirming highly polydisperse nature of the protein samples. Then, keratin-based hydrogel systems were obtained via different methodologies. In Chapter 2, oxidized keratins (keratoses) were crosslinked with THPC to form keratose hydrogels. Effect of the amount of the crosslinking agent on the viscoelastic, swelling, and morphological properties of hydrogels was investigated. In Chapter 3, the keratin hydrogels were obtained via reformation of disulfide bridge and self-assembly of the keratin chains. In Chapter 4, keratins reduced with DTT were crosslinked with 2000 Da PEG-(C2H4-mal)2 and 6000 Da PEG-(C2H4-mal)2 to prepare PEG-hydrogels. Storage moduli of the hydrogels were obtained in the range of 63 ± 22 and 2613 ± 254 Pa and were shown to be tuned by the amount and chain length of the crosslinker. The highest swelling ratios were obtained for the THPC crosslinked hydrogels whereas the highest pore size was observed in PEG-keratin hydrogels. Cytocompatibility of the keratin based hydrogel systems was confirmed using L929 mouse fibroblast cells by applying CCK-8 tests. Of these hydrogels, PEG-keratin hydrogels were found to support cell proliferation with a higher rate than empty TCPS wells up to 4 days. These results demonstrate that low-cost keratin-based hydrogels can be used in a variety of biomedical applications, such as drug delivery systems for cancer therapy, and scaffolds in wound healing and soft tissue engineering.

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