Sustainable Development Goal "Goal 3: Good Health and Well-being" ile 'a göz atma
  • Öge
    A dynamical systems approach to the interplay between tobacco smokers, electronic-cigarette smokers and smoking quitters
    ( 2020-07) Yıldız, Esmanur ; Özer, Saadet Seher ; Şengül, Mustafa Taylan ; 641335 ; Department of Mathematical Engineering
    In this thesis, the effect of e-cigarettes on smoking cessation is studied using the tools of dynamical systems theory. The purpose here is to examine this efficacy by representing and analysing a non-linear ODE system modelling potential smokers, tobacco smokers, e-cigarette smokers and quitters. Fundamental theories required for the interpretation of the behaviour of dynamical systems are given and some epidemiological models are analyzed. The natural behaviour of some linear physical systems is quite predictable. Contrary to that, many natural phenomena are unpredictable. So, we employ non-linear systems which are more complex and are not exactly suitable for the solution to the problem at hand as opposed to linear systems. Non-linear systems are ubiquitous throughout the natural world. As presented in this work, biological systems can be represented by non-linear systems. For instance, several disease models are generally investigated by using non-linear mathematical models. From a wider perspective, mathematical modelling is significant in describing the smoking cessation models. These models have been examined using ODE systems in view of the fact that we can analyse the spread and control of smoking with these systems. It is well known that smoking is a common social phenomenon in today's world. Since smoking is an addiction, some individuals see the use of electronic cigarette as a way of quitting tobacco smoking. We also know that the prevalence of smoking extremely affects the social behaviour of people in a population.
  • Öge
    Açık bilim üniversitelerde neleri değiştirecek?
    (İTÜ, 2022-02-03) Tonta, Yaşar ; 0000-0003-0285-1338 ; Hacettepe Üniversitesi Bilgi ve Belge Yönetimi Bölümü
    Açık Bilim Üniversitelerde Neleri Değiştirecek? adlı sunumunda akademik iletişim kültüründeki değişimin zorunluluğuna dikkat çekmiştir.
  • Öge
    An assessment of building information modeling (BIM) implementation for the Turkish transportation infrastructure industry
    (Institute of Science and Technology, 2020-07) Yiğiter, Feyza ; Atahan, Ali Osman ; 633458 ; Ulaştırma Mühendisliği
    Transportation infrastructure, which includes highways, railways, bridges, airports, and tunnels, is an integral part of the socio-economic development of a country. There is a great need for innovative techniques and technologies that increase productivity and efficiency in terms of time, cost, and quality for the design, construction, operation, and maintenance of transportation structures due to the growing population and the increasing demand for transportation. Building Information Modeling (BIM), an innovative technology widely adopted in the construction industry, has the potential to revolutionize the transportation infrastructure industry due to the knowledge-based nature of transportation infrastructure projects. BIM enables the creation of a 3D object-based and parametric model of a structure, and the BIM model supports collaborative working and interoperability among all disciplines via a digital information-sharing platform. It aims to ensure that all the information generated through the lifecycle of a project is accurately and efficiently stored, shared and used, thereby to make the decision-making and problem-solving processes easier, quicker and more accurate based on the information, and ultimately to minimize the possible time, cost and quality losses of the project. While the initiatives and investments are increasing in Turkey, as with the other countries in the world, BIM is not widely implemented in the Turkish transportation infrastructure industry.
  • Öge
    Composite nanofiber patches for topical drug delivery systems
    (Graduate School, 2021-04-19) Barbak, Zarife ; Karakaş, Hale ; 503122805 ; Textile Engineering ; Tekstil Mühendisliği
    Nanofibers are ultrafine, continuous, solid state textile fibers that have diameters less than 1 micrometre. Nanofibers possess remarkable properties such as high interconnected porosity, specific surface area, ability to imitate the Extra Cellular Matrix (ECM) and potential carrier for drug delivery. Due to these fascinating properties, nanofibers are attractive candidates for medical applications for instance wound dressings, tissue scaffolds and artificial blood vessels. Electrospinning is the simplest and most practical among all methods to produce fine fibers with diameters ranging from micrometres to nanometres. Basic electrospinning equipment includes a high voltage source, a solution feeding unit, a syringe with a tip and a collector. At first, high voltage is applied to the polymer solution to produce an electrical field between the tip and the collector to shape the droplet on the tip as Taylor Cone. When the electrostatic force is higher than the surface tension of the polymer solution, polymer jet is ejected from the tip to the collector. Then, polymer jet reaches to collector following a spiral way by getting longer and thinner. Finally, nanoscale fibers are obtained on the collector. Topical drug delivery systems are composed of a formulation that applied to the skin directly to heal disorders or disease of the skin which guide/target pharmacological effect of the drug to the skin surface. Different pharmaceutical dosage forms can be used in topical drug delivery such as gels, creams, ointment, liquid preparation, sprays and solid powders. Electrospun nanofibers are excellent materials for drug delivery systems due to high interconnected porosity, high surface area, ability to imitate the Extra Cellular Matrix (ECM), potential carrier for drug delivery. Utilization of nanofibers in drug delivery systems is based on the principle that the high surface area of the nanofibrous formulation increases the dissolution rate of the drug. Compared with other dosage forms such as; liposomes, micelles and hydrogels, major advantages of nanofibers are increment in drug loading efficiency and loading capacity, low systemic toxicity and excellent stability. Furthermore, several drugs can be carried within nanofibers with high local drug concentration due to their excellent targeting and drug transportation ability in a safe way. Electrospinning offers the opportunity for direct loading of drugs or biological agents for instance antibacterial molecules, antibiotics, enzymes, growth factors, proteins, peptides, vitamins, DNA into the electrospun nanofibers. Poly (ε-caprolactone) (PCL), Poly Lactic Acid (PLA) and Poly (ethylene oxide) (PEO) were used as carrier polymers for drug delivery. PEO is a highly aqueous soluble polymer, that interacts with the body fluid quickly due to its hydrophilicity resulting in dissolution. PEO is widely used in the polymer matrix to enhance bioavailability and solubility of drugs because of its high aqueous solubility and unique properties in drug delivery applications. The compatibility of PCL and PLA with different types of drugs enables uniform drug distribution in the polymer matrix and the slow degradation rate makes them favourable for prolonged drug delivery systems. In recent years, various studies were reported on the fabrication of drug delivery systems, generated by electrospinning of PCL, PEO, PLA and their blends. PCL, PEO, PLA nanofibers or their blends were loaded with different drugs and biological agents such as; Niclosamide, Silver nanoparticles, Vitamin B12, Curcumin, Lysozyme, AgNO3, Metronidazole (MNA). Polymer blending is an effective approach to prepare functional nanofibers by incorporating the favourable properties of the component polymers. Furthermore, polymer blending facilitates the manipulation of physical, mechanical or biochemical properties of nanofibers. Hydrophilic/hydrophobic polymer blends have been electrospun into nanofibers to fabricate controlled DDS. The hydrophobic polymer forms the backbone structure and it degrades slowly, creating a long term but steady-state drug release. On the other hand, the hydrophilic polymer degrades with a more rapid process, faster than hydrophobic, which accelerates the drug release. In this study, hydrophilic water-soluble PEO was selected for the polymer matrix to enhance the solubility and bioavailability of insoluble SSD. The hydrophobic character of PCL and PLA offers a long period SSD release therefore hydrophilic PEO was blended with hydrophobic PCL and PLA. Thus, PCL/ PEO and PLA/PEO composite polymer matrix was used to provide both increased solubility and controlled release of SSD. Silver sulfadiazine (SSD) is a non-ionized, water-insoluble, topical agent with a wide range of antimicrobial activity that is affected both on bacteria and fungi. SSD is a sulfonamide based drug that is formed by the reaction of sulfadiazine with silver nitrate to form complex silver salt. SSD is used extensively in the topical treatment of infected burns. Silver sulfadiazine provides a long-term release of silver ions, whereas in the case of other silver salts, such as silver nitrate, large amounts of silver ions are released all at once. Thus, the use of SSD decreases the need for frequent application. This makes SSD a desirable and favourable agent since the frequent application is not always practical or possible for patients. However, the low aqueous solubility (3.4 mg/l at pH = 6.8) restricts the drug efficiency, bioavailability and potential antimicrobial activity of SSD thus its applications are limited. Drug solubility is an important issue since efficient drug release and antimicrobial efficiency is contributed just by decomposition of SSD to sulfadiazine and silver ions. Also, the solubility problem of SSD makes it difficult to be stabilized and incorporated into the polymer matrix. The aim of the thesis is to produce a novel SSD loaded topical drug delivery system by using advantages of electrospun nanofibers. Also, a new buffer, Water/Propylene Glycol/ Phosphoric Acid (82:16:2) was utilized to investigate the dissolution and release behaviour of SSD. Thereby SSD containing PCL/PEO and PLA/PEO composite nanofiber carriers were electrospun to achieve the enhancement in solubility, effective drug release and efficient drug loading of SSD. For this purpose, initially, the water-insoluble SSD was incorporated into highly aqueous soluble PEO to increase the solubility. Afterwards, the PEO+SSD solution was blended with PCL and PLA solution to produce composite PCL/(PEO+SSD) and PLA/(PEO+SSD) nanofibers and PCL/(PEO+SSD) casting films for topical drug delivery. SEM method was used to enable the observations of fiber defects and irregularities in the nanofibers structures and to measure the average fiber diameters of the nanofibers. The morphological characterization of the casting films was carried out by SEM and Optical Profilometer. Energy dispersive spectra (EDS) analysis was performed to confirm that the composite nanofibers and casting film which contain SSD, by detecting the Silver (Ag), Nitrogen (N), Sulphur (S) content of the nanofibers. Moreover, EDS-Mapping was carried out to show the distributions of these elements in the composite nanofibers and casting films. The stability of SSD in the fiber structure and the molecular interactions in the drug-free and drug loaded nanofibers were examined by Attenuated Total Reflectance Infrared (FTIR-ATR) Spectroscopy. The crystalline structure of the SSD loaded composite electrospun nanofibers were investigated with X-ray diffraction (XRD) analysis. Atomic Force Microscopy (AFM) was used to determine the surface roughness of the composite nanofibers. 3D AFM Images show the roughness structure of nanofibers. Water contact angle measurements were performed to evaluate the wettability properties of the fabricated nanofibers and casting films surfaces. In vitro drug release media and release conditions were optimized and the controlled drug release profile was obtained for 24 hours. Drug loading efficiency of the nanofiber formulations and casting film were calculated. To understand the SSD drug release mechanisms from SSD loaded formulations; Zero Order, First Order, Higuchi, Hixon Crowell and Korsmeyer-Peppas kinetics models were applied in the drug release profiles of the formulations. Drug release studies were also verified with conductivity measurement due to the conductive nature of SSD. Antibacterial activities of the composite nanofibers against gram-positive Staphylococcus aureus (S. aureus) and gram negative Pseudomonas Aeruginosa (P. aeruginosa) Escherichia coli (E. Coli) bacteria were performed for the period of 24, 48 and 72 hours according to disc diffusion test method. Also, the antibacterial activity of commercial SSD cream was tested for comparison with nanofiber formulations. Furthermore, antibacterial activity of the SSD loaded PCL/PEO and PLA/PEO nanofibers were examined with determining MIC and MBC values. Stability studies of the composite nanofibers were done for 3 and 6 months periods. Nanofiber samples were kept both at refrigerator conditions (+4ºC) and room conditions (25ºC ±2 and 65 % ±2ºC relative humidity) to evaluate stability of nanofiber patches. Stability tests were performed with calculating drug loading amount, cumulative drug release by UV absorption measurements and analysing surface morphology by SEM analysis. Finally, the cytotoxicity studies of the drug loaded and drug-free PCL/PEO and PLA/PEO nanofiber patches were done with using the cell viability assay (MTT assay).
  • Öge
    Design of seafarer-centric safety system; mental workload (MWL) prediction
    (Graduate School, 2022-01-06) Özsever, Barış ; Tavacıoğlu, Leyla ; 512152011 ; Deniz Ulaştırma Mühendisliği
    It is known that the human factor has a major effect on maritime casualties that cause great harm to the environment, economy, and maritime sector. It was stated that while human error is the primary contributor to accidents, a good part of collisions and groundings were related to the mental workload (MWL) of watchkeeping officers. Automation, mechanization, and the introduction of new technologies have changed the working conditions together with reducing the number of crew and increasing the MWL of operators. This indicates that human element-related issues will continue to be one of the major issues in marine transportation assets. In maritime-related studies, it has been analyzed mostly how the ship's environment, working period, and other factors affect the seafarers. Almost all maritime-related studies couldn't have the potential to develop an MWL prediction system for maritime operations aspect. However, lots of studies on drivers and pilots, have produced successful results for MWL prediction. Taking into consideration the fact that MWL has a major contribution to maritime casualties, the development of a real-time MWL prediction system is vitally essential for ships. By implementing the similar measurement techniques used in the studies on drivers and pilots, to maritime transportation, this study aims to classify the physiological responses of the operators that can produce an output for the state of the officer on duty as "Safe" or "Risky" from the collected physiological data and task load data during the seaborn operations. This study predicates the theories which are the statement "minimum performance requires sufficient behavioral activity" of Sheridan and Simpson (1979) together with the inverted U function of Yerkes and Dodson (1908) which presents the relationship between arousal and performance. Moreover, the theory of Young et al. (2015) which presents the relationship among mental workload, performance, task demand, and resource supply and indicates the overload region, guides this study in terms of building the structure of the experimental research. By being predicated on the above-mentioned theories, this study aimed to design a Cognitive Seafarer-Ship Interface (CSSI) which is a main part of the Seafarer-Centric Safety System. The physiological data of the 17 junior deck officers (12 subjects performed navigation scenario, 5 subjects performed cargo operation scenario) was recorded according to the design. By being correlated with the performance of the officer, the change of physiological responses of the subjects were analyzed in low and high task load levels. The medical decision-making process, which deduced "Safe" or "Risky", was run for this change. For performance measurement which is a part of a triangulated measurement strategy (Wierwille and Eggemeier, 1993), Officer Performance Model which is used for MWL classification, was developed for navigation and cargo operation tasks. Additionally, the inputs of the Task Load Estimator were defined as data transcription from navigational aids according to the results of classification. In summary, the following process was done and results were found.
  • Öge
    Evaluation of edible films with palmarosa oil as active food packaging for kashar cheese
    (Institute of Science and Technology, 2020) Kırcı, Nefise Begüm ; Yeşilbuçuk Şahin, Neşe ; 630636 ; Department of Food Engineering
    Many materials are used to pack the food and food products in order to maintain the quality and freshness of food products. The most common materials are plastic, aluminium, paper and glass. In addition, in cases where packaging with these materials is insufficient to extend the shelf life and maintain the quality standards of food, chemical preservatives are added to the packaging or to the packaging material. However, inevitable loss of quality features and the components important for human health of foods have been observed as a result of these packagings. Furthermore, the use of chemical preservatives, plastic and aluminium wrappers have detrimental effects both on environment and living being. The disposal of most of plastic and aluminium materials used once and take a large space brought environmental pollution. The plastic wastes that are discarded randomly are easily spread to the nature with the effect of the wind. This situation both creates a bad appearance in nature and dissolves these plastics, which take a long time to cause pollution. On the other hand, plastic pollution is observed in our rivers, lakes and seas, and this pollution damages the living creatures living in lakes and seas. It has been proven that some chemical preservatives are harmful for human health and can cause cardiovascular diseases and even cancer in prolonged exposure. For these reasons, consumers do not approve the use of chemical preservatives and do not prefer to buy foods that use environmentally hazardous packaging material, so packaging and preservation methods that have been widely used have been insufficient recently. On the other hand, innovative food preservation methods have not been widely disseminated as they are expensive for producers. When considering all these reasons, manufacturers have turned to new types of packaging systems that are healthier, safer and more cost-effective to protect food products.
  • Öge
    Fabrication of multi-component superparamagnetic nanoparticles and magnetic heating performance for hyperthermia cancer therapy
    (Graduate School, 2021-02-16) Çetin, Ayşesimay ; Kılıç, Ali ; 513171012 ; Nanoscience and Nanoengineering
    Nowadays, cancer has become a major public health problem worldwide. It is known that 19.3 million new cancer cases and approximately 10 million cancer deaths occurred worldwide in 2020 alone. The TUIK 2020 report, the cancer is in second place with 80,186 people in Turkey ranking of causes of death. Traditional methods such as chemotherapy, radiotherapy and surgery do not give highly successful results in cancer stages that have spread in the body. These treatment methods carry fatal risks by damaging healthy tissues depending on the treatment method in the patient. For this reason, various treatment methods have been developed that are expected to affect only damaged tissue. Hyperthermia is one of the methods developed for this purpose. Multilayer functional superparamagnetic nanoparticles (NPs) are used in the method, which can be used in medical imaging and treatment applications. With these NPs, it is tried to develop the use of optical and magnetic methods for both diagnosis and treatment of cancer. Thanks to a dielectric shell coated on the NPs, its agglomeration can be prevented, and thanks to an organic shell coated on it, its properties such as biocompatibility and stability can be increased, as well as various molecule adhesion capabilities for treatment purposes can be given to the surfaces of the NPs. In addition to the magnetic properties of these NPs, it will be possible to heat them with the near infrared (NIR) laser to be applied due to their surface plasmon resonance properties. Basically in this method; It is aimed to; (a) reach the denaturation temperature (42ºC) of the cancer cells by applying an alternative magnetic field that will affect only the tumor area, and (b) the malignant cells are destroyed by heating while the other healthy tissues remain stable. In this way, the side effects that occur in traditional methods are tried to be minimized. The two most important factors determining the use of magnetic NPs in hyperthermia therapy are; (a) the applied NPs must have a high ability to heat the cancerous tissue to the desired temperature and (b) heating should be limited only to the cancerous tissue. These two factors can be achieved by having excellent magnetic properties that can reach the target temperature by using a small amount of NPs in the target tissue. For this reason, the type of magnetic NPs used and their magnetic heating performance are of great importance. Studies on various NPs such as Fe3O4, MnFe2O4 are quite common, but it becomes impossible to compare the experimental results due to the different methods and different environmental conditions determined for NPs fabrication in the studies. Therefore, more research is needed to make hyperthermia treatment available. In the thesis, in the first part, Fe3O4, MgFe2O4, MnFe2O4 and SrFe12O19 NPs were synthesiszed as cores. Later, their outher surface was first coated with SiO2 layer, functionalized with amination, then decorated via Au NPs and consequently the outer surface of overall NPs will be coated via PEG. After each coating, the NPs have been characterized using FTIR, SEM and EDX. Heating process was carried out under AMF, using induction generator, in water and in agar according to the rate calculation of 0.1% (v/m) of the produced NPs. According to the results of the heating tests, among all samples, SrFe12O19 NPs showed the lowest and MgFe2O4 NPs showed the highest heating performance among all samples in the tests where different core types were compared. According to the heating results comparing the different coating stages, the aminated NPs gave the fastest warming result among the other coating stages. Comparing different coating steps, PEG coated samples gave the slowest heating result in the heating results. In addition, the heating performance of gold-coated samples, which is the previous coating step from PEG, is very close to that of PEG coated samples and gave the second lowest performance. As a result, our study has shown that different coating stages and NPs differences change the heating performance of superparamagnetic NPs. Although there are many studies of magnetic NPs in the literature, the effects of different types of magnetic NPs on the heating performance of different coating stages of these NPs were compared under standardized laboratory conditions. It is possible to say that this study, which is carried out with easily accessible and economical laboratory materials, is illuminating for future researches related to the subject.
  • Öge
    Fully supervised and semi-supervised semantic segmentation of cardiac MR using deep learning
    ( 2021-09-02) Bolhassani, Mahyar ; Öksüz, İlkay ; 504191413 ; Biomedical Engineering ; Biyomedikal Mühendisliği
    Heart diseases are one of the primary causes of death worldwide. A key factor to accurately and effectively treating heart diseases is to have quantified measures like high-quality images of the organ. When we provided physicians with medical scans, they can pinpoint the kind of abnormality in the heart. Cardiac Ultrasound, CT, and MRI scans are some of the modalities that we can leverage, while each modality has both advantages and disadvantages. Depending on the situation and the patients' condition, we can choose a preferred modality. We concentrate on cardiac MRI, which is a non-ionizing modality that constructs high-quality images. Segmentation of different heart areas in CMR scans such as myocardium mass, wall thickness, left ventricle (LV), right ventricle volume, and ejection fraction (EF) is a quantitative measure that assists cardiologists in diagnosing cardiac failures. Thanks to computer-aided detection (CAD) advancements, the automatic segmentation of the heart cavity for diagnosis purposes alleviates the burden of quantitative interpretation of large numbers of cardiac scans for cardiologists. The ultimate goal of training an automatic model is to predict correctly on unseen data. Therefore, we need a large number of labeled data which is a tedious and expensive task. However, the variation of CMR data acquisition from different centers or vendors demands us to have training data from almost all centers and vendors for a robust model, which is almost impossible. To address this issue, this thesis proposes a semi-supervised segmentation setup to leverage unlabeled data to segment the left ventricle, right ventricle, and myocardium regions. We utilize an enhanced version of residual U-Net architecture on a large-scale cardiac MRI dataset. Handling the class imbalanced data issue using dice loss, the improved supervised model can achieve better dice scores than a vanilla U-Net model. We applied standard augmentation techniques as well as histogram matching techniques to increase the performance of our model in the multi-domain setup. Also, we introduce a simple but efficient semi-supervised segmentation method to improve segmentation results without the need for extensive labeled data. Finally, we applied our approach to two benchmark datasets, STACOM LVQuan 18 and M\&Ms 2020 challenges, to show the potency of the proposed model. The quantitative results demonstrate the effectiveness of our proposed model. The model achieves average dice scores of 0.926, 0.933, and 0.892 for the left ventricle, right ventricle, and myocardium respectively.
  • Öge
    Gamification design principles in healthcare: A study on vital signs measurement in pediatrics at self-service health kiosk
    (Institute of Science and Technology, 2020-03) Gökgür, Eren ; Köse, Hatice ; 621226 ; Department of Game and Interaction Technologies ; Oyun Teknolojileri Ana Bilim Dalı
    Studies on improving user experience through gamification have gained importance. Different sectors have been practicing with game-like factors to be successful in their sectors for many years. With the aid of digitalization in recent years, new possibilities raised in terms of seeing examples of gamification in various industries that have no game-related origin. We may give an instance, where we are witnessing the practices of the gamification field in Healthcare. Even there are focused studies taking advantage of gamification in particular health fields. Specifically, medical examination for pediatrics is an open area that may yield promising outcomes once enhanced with gamification. Medical examination, which is not part of children's daily routine, may often be associated with uncertainties, and thus with worrying experiences, and is one of the areas which can be improved through a gamification design approach. This research examines the gamification design of a self-service health kiosk prototype to get vital signs measurements in pediatrics. Analysis of the effect of gamification design on the accuracy of the vital signs measurements while providing the child with a comfortable experience with playful design is the goal of the study. This thesis begins with the industrial origin of gamification, the theories that gamification is derived from, the disciplines that gamification taps into and its positive effect on children's health by promoting adherence, increasing the accuracy of the vital signs measurement and reducing stress. The methods regarding testing our hypothesis involve an application, vital sign measurement devices in a self-serving health kiosk, analyzing of the results, comparison of the results with normal values and our observation on the participants as well as the participants' remarks. As we are in pursuit of observing the positive effects of gamification of vital sign measurements on children's health, we would like to observe three things, those are, promoting adherence, increasing the accuracy of the vital signs measurement and reducing stress. With the data at hand and relying on our observations, we may come into some preliminary facts that in the healthcare domain, by using gamification design principles we can promote adherence, increase accuracy and reduce pediatric patience's stress. Exceeding the patient interests, healthcare providers can also gain from gamification technology through gathering insights into patients, pulled from usage data, a better comprehension of preventive care requirements.
  • Öge
    Göğüs kafesi röntgen görüntülerinde derin öğrenme metoduyla zatürre hastalığının tanısı
    (Fen Bilimleri Enstitüsü, 2020) Darıcı, Muazzez Buket ; Dokur, Zümray ; 637304 ; Elektronik Mühendisliği Bilim Dalı
    Bu çalışmada göğüs kafesi radyografik görüntüleri kullanılarak ilk olarak pnömoni (zatürre) ve sağlıklı olmak üzere ikili sınıflama yapılarak hastalığın varlığı tespit edilmeye çalışılmıştır. Buna ek olarak ise aynı veri kümesi üzerinden zatürrenin iki farklı çeşidi olan bakteriyel ve viral zatürre sınıfları da kullanılarak, sağlıklı, viral zatürre ve bakteriyel zatürre olmak üzere üçlü sınıflama yapılarak incelenen görüntünün hangi sınıfa ait olduğu tespit edilmeye çalışılmıştır. Her iki çalışmada da iki farklı derin öğrenme metodu kullanılmıştır. Bunlar Evrişimsel Sinir Ağları (ESA) ve Topluluk Öğrenimi modelidir. Bu çalışma için Topluluk Öğrenimi modeli üç farklı ağı içeren bir modeldir. Bu ağlar iki farklı ESA modeli ve öğrenme aktarımı yoluyla kullanılan Inception-V3’tür. Topluluk Öğrenimi modelinde her ağ ayrı ayrı eğitildikten sonra çoğunluk oylaması yöntemiyle incelenen görüntünün sınıfına karar verilir. İkili sınıflamada kullanılan veri kümesi normal ve zatürre olmak üzere iki ayrı sınıf etiketi içermektedir. Üçlü sınıflama için ise zatürre olarak etiketlenen görüntüler dikkatli incelendiğinde bu sınıfın da kendi içinde ikiye ayrıldığı görülmüştür. Bunlar virus zatürre ve bakteriyel zatürredir. Zatürre sınıfı da bunlar dikkate alınarak ikiye ayrılmış ve toplamda normal, virüs zatürre ve bakteriyel zatürre olmak üzere üç sınıf içeren bir veri kümesi elde edilmiştir. Kullanılan veri kümesi sınıflar üzerinde dengeli bir dağılıma sahip olmadığı için eğitilen modelin, görüntü sayısı fazla olan sınıfa doğru eğilimini engellemek amacıyla her iki sınıflama türü için de kullanılan sınıflar Smote metoduyla dengelenmiştir. Smote metodu bir aşırı örnekleme algoritmasıdır. Bu yöntemle görüntü sayıları, çoğunluğu içeren sınıf baz alınarak sentetik veriler üretimiyle dengelenir. Smote metodu uygulanmadan önce veri kümesi eğitim ve test kümelerine ayrılır.
  • Öge
    Imaging of multiple slices with single lateral scan
    (Graduate School of Science Engineering and Technology, 2020) Tekpınar, Miyase ; Fehanoğlu, Onur ; 633782 ; Department of Electronics and Communication Engineering
    Bessel beams or so-called non-diffracting beams have received great attention from the biomedical optics community, especially in 3D imaging researches, with its long propagation distance in diffractive mediums (see section 1.1). This work presents an architecture to create higher-order Bessel-like optical beams, through off-axis coupling of light into a multimode fiber. Utilizing the aberration that is inherent in spherical surfaces, through directing the Bessel-like beam comprising multiple concentric rings onto a low-cost lens, we created multiple foci at different depths. Moreover, scanning of the optical fiber with a piezoelectric actuator in the lateral direction, we were able to acquire data from different targets located at different lateral planes, therefore proposing a faster confocal system. After coupling back into the fiber, the reflected portions of light from different targets could be spatially differentiated and directed to different photo-detection units. The proposed architecture is particularly appealing for laser scanning endoscopy applications, as it does not require additional passive or active optical components for generating Bessel beams (axicons or spatial light modulators), therefore offering both miniaturized realization and high optical transmission. Secondly, a two-dimensional piezo-fiber actuator geometry is proposed to achieve three different scanning pattern with single device. Having multiple scan options, the operator of the actuator is free to choose between improved uniformity, high frame rate to image abrupt biological event, or circular field-of-view to better image cylindrical cavities (gastrointestinal tract, esophagus, etc.) that are cylindrical in nature. The capabilities of the device has been demonstrated through first presenting its mechanical frequency behavior, then offering an actuation scheme to achieve different scan patterns, and finally generating 256 pixel width or diameter raster, spiral, and Lissajous patterns at ≥ 20 frames per second. With further development, the presented actuator design and drive scheme could serve as a useful tool as part of a minimally invasive optomedical device in the clinic Finally, the compact 3D imaging system utilizing both proposed methods will allow addressing multiple slices at a single lateral scan, thus offering improved speed and different scanning pattern options for endoscopic applications.
  • Öge
    Investigation of familial multiple sclerosis genetics
    (Graduate School, 2022-05-16) Everest, Elif ; Turanlı Tahir, Eda ; 521152104 ; Molecular Biology-Genetics and Biotechnology
    Multiple sclerosis (MS) is a chronic, neuroinflammatory, neurodegenerative disease of the central nervous system. Several lines of evidence have shown that the primary pathophysiological mechanism of MS is the infiltration of autoreactive lymphocytes through the blood-brain barrier, attacking central nervous system components such as myelin and resulting in oligodendrocyte death. This process has been thought to be responsible for axonal pathology and neuronal loss, which result in progressive neuronal dysfunction in some patients. Over the recent years, the roles of astrocytes, microglia, and pericytes have also been increasingly shown in MS pathology. To date, several studies have revealed disease-related cellular pathways that emphasize the different pathological components of the disease; however, underlying mechanisms in MS development and progression are yet to be elucidated. Consistently with its heterogeneous clinical presentation and complex pathophysiology, MS also has a complex inheritance pattern and develops in genetically susceptible individuals under environmental influences. Many studies have been carried out using different approaches and methods to identify genomic regions and variants that cause genetic predisposition to MS, identifying hundreds of common variants as well as candidate rare variants that increase the risk of MS. Today, MS associations of 233 common variants, as well as hundreds of suggestive associations, have been identified. However, all significant common variants, together with the suggestive effects, can cumulatively explain approximately half of MS heritability. Meta-analyses have shown that rare variants can further explain up to 5% MS heritability, still leaving a large proportion of MS genetics unknown. In this thesis study, it was aimed to reveal novel information on MS genetics and pathogenesis. Multiplex MS families with more than two affected family members were collected to identify possible novel genes that contribute to the high MS aggregation in these families. Seven multiplex MS families with the highest number of affected individuals and parental consanguinities were selected, and SNP genotyping (710K or 2.5M, Illumina) was performed (N=41). Candidate MS-associated genomic regions were identified through linkage analysis and homozygosity mapping. Exome sequencing (N=56) revealed that there were no fully penetrant, homozygous, rare, exonic variants segregating within the families. However, two variants were found to be segregated with the disease with an autosomal dominant inheritance pattern in the LRRC6 gene (rs139131485) in family FMS01 and RNF217 (rs73580047) gene in family FMS05, which may increase the risk of MS in corresponding families. Additionally, many incompletely penetrant, rare and low-frequency variants were identified. Subsequently, a weighted sum score analysis including previously identified common MS-associated risk variants and polygenic risk score (PRS) analysis were conducted in MS families (24 affected, 17 unaffected), 23 sporadic MS cases, 63 individuals in 19 non-MS control families, and 1272 independent, ancestry-matched controls to determine whether an increased burden of known MS-associated common variants explain the increased MS risk in these families. Logistic regression analyses showed that familial MS cases had higher sum scores (OR=2.16, P=0.002; OR=2.4, P=0.014) and PRS (OR=1.84, P=0.0077; OR=2.27, P=0.049) compared with the population controls and control families, respectively. Moreover, affected individuals in the MS families had higher weighted sum score and PRS values compared with the unaffected family members; however, the differences were not significant after Bonferroni correction. When individual families were observed, it was seen that the higher sum score and PRS trends in MS cases were evident in only three of the families, and in others, there were no apparent differences in the sum score and PRS values between the affected and unaffected family members or the unaffected individuals had higher sum score and PRS values compared with their relatives with MS, further supporting the polygenic inheritance of MS. Sporadic MS cases had significantly higher PRS compared with both affected and unaffected individuals in MS families, control families, and population controls (P=0.02, P=0.0055, P=0.003, and P=0.0008, respectively), supporting the presence of higher rare risk variation loading in the familial cases. There was no significant difference in the sum scores of familial and sporadic MS cases, possibly due to the high degree of convergence between common and rare risk variation in significant loci for MS. As part of this thesis study, we also performed an integrated bioinformatic analysis using genomic and proteomic data of an unrelated MS group. For this, first, SNP genotyping (300K, Illumina) was performed for 11 unrelated MS cases selected from our MS family cohort whose cerebrospinal fluid samples had been previously included in our proteomic study, in which 2D-gel electrophoresis, mass spectrophotometry, and pathway analyses had been conducted, revealing 151 differentially expressed proteins between MS cases with different clinical MS phenotypes and non-MS controls. To integrate the genomic and proteomic datasets of this patient group to reveal the most relevant disease pathways, pathway enrichment analyses of MS-associated SNPs and differentially-expressed proteins were conducted using the functional enrichment tool, PANOGA. Nine shared pathways were detected between the genomic and proteomic datasets after merging and clustering the enriched pathways. Among those, complement and coagulation cascade was the most significantly associated pathway (hsa04610, P=6.96×10−30). Other pathways involved in neurological or immunological mechanisms included adherens junctions (hsa04520, P=6.64 × 10−25), pathogenic Escherichia coli infection (hsa05130, P=9.03×10−14), and prion diseases (hsa05020, P=5.13×10−13). We conclude that despite the overall increased genetic burden in familial MS cases, weighted sum score and PRS distributions among affected and unaffected family members within individual families revealed that known susceptibility alleles can explain disease development in some high-risk multiplex families, while in others, additional genetic factors remain to be identified through more detailed genomic analyses such as genome sequencing. Additionally, integrating multiple omics datasets of the same patients helps reduce false negative and positive results of genome-wide SNP associations and highlights the most prominent cellular players among the complex pathophysiological mechanisms in MS.
  • Öge
    İTÜ’de açık erişim çalışmaları ve hedefler
    (İTÜ, 2022-02-03) Kubat, Gülçin ; 0000-0001-9009-8758 ; Referans Birimi
    İTÜ Mustafa İnan Kütüphanesi 2013 yılından bugüne açık erişim alanında yürüttüğü çalışmaları anlatmıştır.
  • Öge
    Küçük hacimlerde durağan dalgaların (modların) oda geometrisi ve oda oranları ile ilişkisinin incelenmesi
    (Fen Bilimleri Enstitüsü, 2020) Sefer, İlkay ; Yılmaz, Sevtap ; 636920 ; Mimarlık Anabilim Dalı
    Mimari tasarımda oda oranları 20'inci yüzyılın ikinci yarısından itibaren tasarımın iyi ve kötü olarak nitelendirilmesine yönelik olarak tartışılmaya başlandı. Platon, Pisagor, Euclid gibi filozofların doğada bulunan oranlara ilişkin matematiksel yaklaşımları, bu tartışmanın epey öncesinde başlamıştır. Matematiksel oranların mimari tasarıma uygulanması bu düşünceler ışığında önemli bir konu haline geldi. Rönesans dönemi boyunca sanat üretiminde kullanılan altın oran, Fibonacci serisi ile tanımlanan matematiksel oranlar; doğanın düzeni ve kanunu olan karşılıklı anlaşma ve uyum olarak ifade edilir. Sanatta güzellik kavramı yalın olarak optik bir olayı değil, daha derin bir anlamı (karşılıklı anlaşma ve uyum) ifade eder. Modern mimari, Rönesans dönemi mimari anlayışından farklı olarak, mekânın sade, yalın ve net olarak üretir. Mekânın yüzeyleri, köşeleri, tavan, duvar, döşeme ve mobilya tasarımı net yüzeyler ile kurgulanır. Bu form değişimi sesin mekândaki davranışlarını da değiştirir. Sesin yayılmasını sağlayacak yüzeyler bu tasarım anlayışında yoktur. Bu durum özellikle küçük hacimlerde oda modlarını ortaya çıkarır. Bu çalışmada, küçük hacimlerde oldukça önemli bir olay olan oda modlarının, hacmin şekil ve boyut özellikleri ile ilişkisi ve oda oranlarının modlar üzerindeki etkisi incelenmiştir. Çalışmanın birinci bölümü, mimaride kullanılan oda oranlarını inceler. İkinci bölüm, küçük oda tanımını ve küçük odaların akustik parametrelerini ayrıntılı olarak ele alır. Üçüncü bölüm, literatür araştırması sonucunda belirlenen çalışma matrisinin bilgisayar ortamında benzetiminin yapılmasıdır. Elde edilen sonuçlar üzerinden, modal karakteristiği en kötü olan hacim çalışmanın ikinci aşamasında incelenir. İkinci aşamada hacmin köşe ve yüzeylerine farklı şekil değişiklikleri uygulanarak modal karakteristiğindeki değişimler incelenmiştir. Yedi elemanlı matris (eşit hacimde yedi adet oda) üzerinde yapılan çalışma, birbirinin tam sayı katlarına sahip oranlı hacimlerin modal davranışlarının ve ses yayılımının akustik kusurlar içerdiğini gösterir. En kötü sonucu 1:1:1 oranlı küp hacim verir. En iyi sonucu ise 1:0.57:1.28 oranlı hacim verir. İkinci aşamada küp hacim, birim olarak kabul edilir. Hacmin köşe ve yüzeylerine uygulanan değişiklikler sonucunda modal karakteristiğin nasıl etkilendiği incelenmiştir. Çalışmanın iki aşamasında da yüzeylere malzeme bilgisi girilmez. Çalışma, tasarım sürecinin malzeme kararlarının verilmediği ilk aşamasında, şekil ve boyut özelliklerinin akustik kaliteye etkisini incelemeyi amaçlar. Yapılan çalışma sonucunda, hacme uygulanan köşe değişiklikleri olay modun dalga boyu ile ilişkili olarak etki gösterdiği görülmüştür. En etkin akustik durum, hacimde yüzey paralelliklerinin bozulduğu örnekte görülmektedir. Paralelliğin bozulması hacmin modal karakteristiği üzerinde olumlu sonuçlar verir.
  • Öge
    Microwave spectroscopy based breast cancer diagnosis using support vector machines
    (Institute of Science and Technology, 2020-07-16) Önemli, Emre ; Akduman, İbrahim ; Abdolsaheb Yılmaz, Tuba ; 504171403 ; Biomedical Engineering ; Biyomedikal Mühendisliği
    Interactions of electromagnetic (EM) fields with materials relies on their intrinsic dielectric properties. Knowledge of the dielectric values of each material allows to develop electromagnetic technologies in many fields including medical technologies. There are a variety of electromagnetic medical technologies such as Microwave Imaging, Electrical Impedance Tomography and radiofrequency ablation and they promise faster, safer and low-cost applications. They rely on inherent differences among the dielectric properties of various biological tissue groups and health conditions. Hence, knowledge of the tissue dielectric properties of different biological tissues is crucial for developing EM healthcare technologies. Many works have been performed to investigate difference between dielectric properties of healthy and malignant tissues. It has been discovered that healthy and malignant tissues differ for the EM interactions because of the disperancies in their dielectrical properties. This contrast have been attributed to more water presence in malignant tumors. Breast carcinoma became one of the most researched cancer because of its high incidence and mortality rate. It is responsible for twenty three percent of new cancers and fourteen percent of cancer deaths in total. Thus, early diagnosis of the breast cancer is gaining more importance. Currently, there are some diagnostic methods such as mamography or MRI. However, they have some drawbacks such as harmful effects and low accuracy. Lately, microwave imaging (MWI) gained many interests. MWI fundamentally relies on the inherent dielectric contrast between healthy and malignant tissues. In cancer resection surgeries, determination of clear surgical margins is also possible using dielectric properties. Numerous studies were performed to expand the knowledge of the dielectric properties. However, existing dielectric datasets do not include every tissue type, frequency and temperature. Hence, more studies are needed. Open-ended coaxial probe has became the most preferred measurement method, because it is non-destructive, easy and suitable for biological materials. More dielectric data requires fast and accurate classification methods. For medical applications, most preferred one is Support Vector Machines (SVM). Being a supervised classification method, SVM is widely used because of its high classification performance on medical data. In this study, performance of SVM and infinite feature selection was investigated on the dielectric data of female rat normal breast tissues and malignant tumors in microwave frequencies. Measurements were conducted between 0.5 GHz and 6 GHz with 0.55 GHz intervals at 101 frequency points. Relative permittivity, conductivity and combination of them were tested separately. Firstly, they were tested without feature selection, raw dielectric data was also compared with normalization and logarithm of the dielectric data. Raw permittivity and combined data outperformed others resulting in 100% accuracy. Note that cross validation (CV) technique does not allow memorization of the learning model. Selecting top 100 features, the algorithm resulted in 100% accuracy with permittivity data whereas using top 50 features, it resulted in 99.23% accuracy with combined data. Using nested cross validation, features were selected as top 1 to top 100. Raw permittivity data gave more than 99% accuracy for more than sixty features. Using only one feature, 83.69% accuracy was obtained. Logarithm of the conductivity data resulted in 90.31% and 90% accuracy using one feature with linear and RBF kernels respectively. Best result of conductivity data is 98% using raw data and selecting top 70 features. With one feature, frequency of 5.505 GHz resulted in the best result. S11 response was also tested to avoid dielectric property calculation and to design narrow band devices. Note that this response indicates the energy transfer between probe and biological tissue related to tissue intrinsic electrical properties. Logarithm of the data outperformed with 93.85% accuracy using 10-fold linear SVM. Feature selection step was performed with 10-fold CV. With top 100 features, logarithm of data resulted in slightly higher performance as 91.85% accuracy with RBF kernel. With top 50 features, raw data was slightly better with 85.85% accuracy using linear SVM. Nested CV was applied to logarithm of S-parameter data. Selecting top 10 to 100, with decreasing number of features, accuracy dropped from 91.69% to 87.23% for RBF kernel and 91.38% to 87.08% for linear kernel. Besides, using top 1 to 10 features, accuracy dropped from 87.23% to 86.92% for RBF kernel and 87.08% to 83.08% for linear kernel. Best feature was corresponding to real part of S11 response at 610 MHz. The results show that dielectric measurement data can become acceptable diagnostic tool for breast cancer diagnosis. Thus, development of the EM medical technologies requires more tissue dielectric data. This study provides more dielectric data to the literature and it provides a perspective for analysing the dielectric data on the classification manner.
  • Öge
    Molecular docking study on the DNA binding domain of master regulator of the mammalian HSR protein
    (Institute of Science of Technology, 2020-07) Bozan, Gülbahar ; Tüzün, Nurcan ; Sungur, Fethiye Aylin ; 637082 ; Chemistry Programme
    Heat shock factor 1 (HSF1) is the primary regulator of heat shock response (HSR) in mammalian cancer cells and have been described as a family of transcription factors which are activated with stress conditions. Upon stress, HSF1 upregulates the heat shock proteins (HSP) that help misfolded proteins to refold for the cell functions. One of the heat shock proteins, HSP90, acts as chaperon in cancer cells as well and supports the proliferation and repair of cancer cells. For years, many efforts have been devoted to studies for finding molecules that inhibit these chaperon proteins but at the same time present drug properties, act compatibly with the physiological conditions with the lessened side effects. For this reason, in recent years, drug design studies have mainly concentrated on inhibiting proteins that trigger the process or production of HSP90. As a result of HSF1-HSE complex, formed by HSF1 and the promoter part of DNA, which is called Heat Shock Element, the unwanted heat-shock proteins are synthesized in the cancer cells. HSF1 protein has emerged as a potential target and in recent years shown as a target for specifically breast, pancreas and prostate cancers. In the last decade, in silico drug design has been an integral part of drug development processes. Likewise, in this project, it was planned to design molecules that inhibit HSF1 protein via in silico methods. Herein, our target was to search for inhibitors via in silico methods and bring forward candidate lead molecules to literature. The starting point for the determination of the docking protocol was to calculate the docking scores of the ligands with the most effective IC50 value and to ensure qualitative agreement by comparing the binding energies calculated with the experimental IC50 values. This also enabled us to recognize the residues involved in the binding. The candidate inhibitor structures of the library formed by virtual screening were studied by the receptor (selected flexible residues) - flexible ligand docking procedure. The candidate molecules with the best binding scores were refined by the MM-GBSA method. The molecular dynamic simulation was further performed for nine selected compounds. From the results, we propose candidate lead molecules that can effectively act in cancer cells, especially in breast, pancreas and prostate cancers.
  • Öge
    Pet karışımlı viskon örme kumaşlarda parça boyama sonrası ortaya çıkan boncuklanma probleminin araştırılması ve iyileştirilmesi
    (Fen Bilimleri Enstitüsü, 2020-07) Bekiroğlu, Erkan ; Özcan, Gülay ; 637255 ; Tekstil Mühendisliği Ana Bilim Dalı
    Parça boyama işlemi sonrası giysilerin görünümü (özellikle dikişlerdeki eskitme efekti) pazarda ciddi talep gören bir moda eğilimi haline gelmiştir. Bununla birlikte parça boyama işleminin modadaki anlık değişimlere hızlı cevap verebilmesi parça boyamaya olan ilginin daha da artmasına sebep olmuştur. Parça boyama işleminin en önemli ise boncuklanma problemidir. Özellikle sentetik lif karışımlı kumaşlarda boncuk oluşum hızının, koparak dökülme hızından daha yüksek olması, bu problemin daha fazla yaşanmasına sebep olmaktadır. Parça boyamada, genel olarak giysi ya da parçaların işleme girmeden önce hazırlıkları yapılmaktadır. Ham haldeki kumaştan dikilen ürünlerin parça boyama işlemi yapılacaksa bu durumda mutlaka iyi bir ön terbiye işleminden geçirilmesi gerekmektedir. Viskon /PET karışımlı ipliklerden elde edilen örme kumaşların parça boyama makinasında reaktif boyarmaddelerle boyanmasıyla tatmin edici melanj efektlerin alınabilmesi, pazar taleplerinin hızla karşılanmasını sağlarken melanj renk gamı ile ilgili yeterli renk çeşitliliği olmaması ve renk başına minimum üretim miktarının yüksek olması gibi sorunlara da önemli bir çözüm getirmiştir. Polyester (PET) ile viskon lifinin farklı oranlardaki karışımı, kumaşlarda farklı tonlarda melanj görüntüsü almaya imkan vermektedir. Fakat buradaki en büyük kısıt, istenen iplik numarasında ve karışımda ipliğin tedarik edilememesidir. Bu sorunu çözebilmek için pazarda yaygın olarak ring eğirme sistemiyle üretilmiş iplikler kullanılmaktır. Bununlabirlikte pazarda her iplik numarasında ve karışımda ipliği rahatlıkla bulabilme imkanı veren ring ipliklerinin boncuklanma açısından ciddi sıkıntıları söz konusudur. Özellikle yüksek kopma dayanımına sahip PET lifi karışıma dahil olması ve kullanılan ipliklerin ring eğirme sistemiyle üretilmiş olması, boncuklanma sorununu daha da arttırmaktadır. Tüm bu sorunlar dikkate alınarak tez çalışmasında; Viskon/PET karışımı ring ipliğin, karışım oranı, iplik büküm katsayısı, bu ipliklerle elde edilen örme kumaşların ön terbiye, boyama ve bitim işlemlerinin kumaşların boncuklanma eğilimi üzerine etkisi incelenmiştir. Bu tez çalışması için Viskon/PET'in 5 farklı karışım oranında kullanıldığı ve αe değerleri 3,00-3,54 arasında değişen toplam 5 farklı tipte ring iplikleri üretilmiştir. Üretilen ipliklerle, açık en yuvarlak örme makinasında her biri 10 kg olacak şekilde, % 80/20, 50/50, 33/67 Viskon/PET karışımı 3 tip kumaş ve kontrol amaçlı %100 Viskon ve %100 PET iplikten yapılan örme kumaşlar üretilmiştir. Farklı karışım oranlarındaki ipliklerden örülen süprem kumaşlara 20 farklı işlem uygulanarak toplamda 100 adet numune üretilmiştir. Kumaşlar, açık en olarak ön terbiye işlemlerinden geçirilmiştir. Ardından 1 er metre boyutlarında kesilerek parça boyama makinasında 3 farklı boya konsantrasyonunda hazırlanan boyama reçeteleriyle boyandıktan sonra biyo-parlatma işlemi ve son olarak 3 farklı reçete ile bitim işlemlerine tabi tutulmuştur. Tez kapsamında yapılan literatür araştırmaları ve deneysel çalışmalar sonucunda, Viskon/PET karışımlı kumaşlarda PET oranı arttıkça, literatüre paralel olarak termofikse adımının eklenmesi ve maliyet parametresi ile birlikte sürdürülebilirlik açısından bir işlem basamağının ve kimyasal kullanımının azaltılması göz önüne alındığında enzim uygulama basamağının çıkarılmasının boncuklanmayı tatmin edici düzeyde azaltabileceği gözlemlenmiştir.
  • Öge
    Stability analysis of a mathematical model of Crimean Congo haemorrhagic fever disease
    (Graduate School Of Science Engineering And Technology, 2020) Alın, Miray ; Özer, Saadet Seher ; 637195 ; Department of Mathematical Engineering
    Today, ticks are harmful parasitic creatures feared by humans. Ticks do not always carry dangerous diseases. However, we should not ignore the pathogens and viruses that may be carried because these creatures can carry various viruses and seriously threaten human health. If it is not diagnosed early, it can result in fatal consequences. Ticks can get viruses from their hosts at various stages of their lives. Ticks can transmit these viruses to humans in the adult tick stage. Here we can say that the animals that ticks use as hosts are only vectors. Cattle, bovine or chickens do not show symptoms of diseases which are caused by ticks. In this thesis, the spread of Crimean-Congo haemorrhagic fever disease is investigated by considering the problem as an epidemic model. Before stating the problem, in first chapter, some information about dynamic systems is given. The definition of systems of differential equations and their stability analysis are mentioned. Besides, the autonomous systems of equations are briefly explained. And how their stability can be analysed is mentioned. Then, to guide our own problem, information about the well-known SI, SIR, SIS epidemic models and Prey-Predator model and their stability is given in the second chapter. And finally in the third chapter the original problem of the thesis is examined. The system of equation of these models is non-linear. After writing system of equation we found the equilibrium points first. Then, we do linearisation by substituting the equilibrium point in to the Jacobian matrix. We investigated sign of the eigenvalues of these Jacobian matrices which are evaluated by equilibrium points of epidemic models. If all eigenvalues are negative the equilibrium point is stable. If at least one eigenvalue is positive, then the equilibrium point is called unstable. It is not always possible to determine the sign of eigenvalues. In such a case, we could talk about basic reproduction number. Basic reproduction number is represented by R0. If R0 < 1, all eigenvalues are negative and the equilibrium point is a stable equilibrium point. The disease disappear over time. Otherwise, if R0 > 1, at least one of the eigenvalues is positive. Also, the endemic equilibrium point exist when R0 > 1. In addition to, when R0 > 1 disease free equilibrium point is unstable and endemic equilibrium point is stable. And the disease becomes endemic. The problem is expressed as the combination of the variation of population dynamics of human, tick and birds(chicken). In all dynamics of human and tick we considered the in and outs to the compartments, outs as both in the meaning of transfers between compartments and removals such as death. The inputs to the system are either taken constants or logistic growth effects. In this thesis, we investigate the problem in three different ways. • The model which takes logistic growth both in tick and chicken populations, • The model which takes logistic growth only in chicken population, • The model which takes logistic growth only in tick population. We use a system of five ODEs to represent the interaction between chicken population, susceptible and infected populations of humans and ticks. It can be said that there is SI model between infected tick and susceptible tick, SIS model between infected human and susceptible human, and Prey-Predator model between tick and chicken. We have determined the equilibrium points for each model and investigate the stability of the equilibrium points. During the studies the reproduction numbers were found and the stability is investigated with respect to the reproduction numbers. The bifurcation analysis has also been done for tick logistic - chicken logistic model and tick logistic -chicken constant model. According to the results of the first and second models, it was observed that there was a decrease in the number of ticks when the chicken population in the environment was increased. In addition, if the frequency of unleashing of chickens into the environment is increased, then ticks can be more likely to increase among chickens is. Therefore, the number of ticks in the environment may decrease. Due to this decrease, it has mathematically shown that the Crimean Congo Haemorrhagic Fever disease decreases over time.
  • Öge
    Synthesis of folate receptor 1 targeted dye-conjugated peptides for use in positron emission tomography imaging systems
    (Graduate School, 2022-01-26) Cin, Derya ; Alptürk, Onur ; Yılmaz, Özgür ; 513191022 ; Nanoscience and Nanoengineering ; Nano Bilim ve Nano Mühendislik
    Nowadays, it is tried to find solutions for human beings to have a long and high-quality life, increase the number of studies in the field of health, and detect diseases that become difficult to treat with their progress. Cancer is one of the first causes of death statistics in official records in the world and Turkey. It is known that the diagnosis of cancer is difficult and takes time, and the number of cases continues to increase rapidly day by day. Because of the metabolism change in cancer cells, the cells continue to grow and divide instead of dying. Cancer factors; inherited mutations can be internal, such as hormones, or acquired environmental, such as carcinogens, radiation, infectious organisms, and lifestyle. By imaging the changes caused by cancer in cells, information about the stage of cancer can be obtained. Cancer researchers want to detect cells where cancers develop, identify biomarkers of cancers early, and create treatment plans for cancer. Proteins produced by tumor cells can be used as biomarkers to evaluate disease processes. Molecular imaging (MI) aims to combine patient and disease-specific molecular information and is an interdisciplinary area covering a wide range of sciences when is used in the diagnosis and treatment of diverse disease genres. For this purpose, targeted cell-specific chemical biomolecules are delivered to the organism by labeled radioactive isotopes. The imaging method to be utilized varies specifically according to the disease state. Positron emission tomography (PET), which has become more advanced with the integration of scanners such as computerized tomography (CT) used in the imaging of cancer, is one of the several imaging methods widely used in the diagnosis of cancer today. Since radioisotope imaging agents are required for imaging in PET devices, studies for their development are increasing day by day. Peptides are used as ligands/agents in imaging cancer imaging, thanks to their properties such as high selectivity and high affinity, ease of synthesis and chemical stability, quick removal from blood, and low immunogenicity/safety for cell surface proteins. Due to the metabolic rate of cancer cells, more folic acid is produced in these cells than in normal healthy body cells, and this uncontrolled increase has led to its use in cancer imaging studies. Peptide-based imaging agents are used for molecular imaging by binding to target cancer receptors such as Folate Receptor 1 (FOLR1) of tumor cells. Molecules that can bind to the FOLR1 receptor with high sensitivity and affinity were synthesized by the Solid Phase Peptide Synthesis (SPPS) method. The peptides KWGFR, KLWWN, KFLSW, KWIAG, KWSYW, KGWRN, and KSYFA were selected from the peptide library and successfully synthesized. Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) was used to purify the peptides and Liquid Chromatography-Mass Spectrometry (LC-MS) was utilized for peptide characterization. Finally, the imaging agent will be obtained by conjugating the peptide-based signaling agent labeled with the 68Ga isotope.
  • Öge
    Şehir hastanelerinde atık yönetimi ve COVİD-19'un hastanelerde atık miktarı ve dağılımına etkisinin incelenmesi
    (Lisansüstü Eğitim Enstitüsü, 2021-10-20) Koncagül, Merve ; Arıkan, Osman Atilla ; 501181723 ; Çevre Bilimleri Mühendisliği ve Yönetimi Programı ; Environmental Sciences Engineering and Management
    Artan nüfus ve kentleşme, toplumların refah seviyesinin yükselmesi, gelişen teknolojiler, satın alma gücündeki artış, artan tüketim alışkanlıkları, davranışları, hizmette lüks ve kalite arayışı atık miktarının artmasına sebep olmaktadır. Bu çalışmada şehir hastanelerindeki atıkların kaynağında ayrı toplanması ve azaltılması stratejilerine uygun olarak yapılan atık yönetimi ve Covid-19'un hastanelerde atık miktarı ve dağılımına etkisi incelenmiştir. Bu çalışmada bir adet şehir hastanesinde atık yönetiminin incelenmesi yapılmış, altı adet şehir hastanesinde Covid-19'un atık miktarlarına ve dağılımına etkisini incelmek için Covid-19'un ülkemizde ilk görüldüğü yıl olan 2020 yılı verileri ile önceki yıllara ait veriler karşılaştırılmıştır. Çalışma yapılan Tekirdağ İsmail Fehmi Cumalıoğlu Şehir Hastanesinde atıkların oluştuğu andan bertaraf edilmesine kadar hastanede izlediği süreç incelenmiştir. Hastanede evsel, ambalaj ve tıbbi atıklar 40 L ve 65 L'lik konteynerlerde, tehlikeli atıklar 30 L ve 60 L'lik mavi varillerde ayrı olarak toplanıp, katlardaki 240 L konteynerlerin yer aldığı atık odalarına taşınmaktadır. Atık taşıma asansörü ve koridorundan geçirilen atıkların tartımı yapılıp kayıt altına alınmaktadır. Tartım ve kayıt işlemi tamamlanan atıklar geçici depolama alanına götürülmekte ve uygun atık taşıma araçlarına verilmektedir. İncelenen hastanede atıkların kaynağında ayrıştırıldığı, toplandığı, depolandığı ve atık yönetiminin başarılı bir şekilde uygulandığı görülmüştür. Çalışma yapılan altı adet şehir hastanesinde (Isparta, Manisa, Yozgat, Elazığ Fethi Sekin, Kayseri, Ankara Bilkent) Covid-19 öncesi (2019 yılı) ve sonrası (2020 yılı) tıbbi atık miktarları incelenmiş, sadece üçünde (Isparta, Manisa, Yozgat) evsel, ambalaj ve tehlikeli atık miktarlarına da bakılmıştır. Evsel atık miktarları (ambalaj atığı hariç) Covid-19 öncesi (2019) 2,94-3,53 kg/yatak.gün arasında değişirken, Covid-19 sonrası (2020) 1,76-3,16 kg/yatak.gün değerlerine (Isparta'da %28,2, Manisa'da %1,6, Yozgat'ta %50,1) azalmıştır. Atık oluşumunun en fazla görüldüğü birim yemekhane olmuştur. Ambalaj atığı miktarları Covid-19 öncesi 0,63-0,72 kg/yatak.gün arasında değişirken, Covid-19 sonrası 0,44-0,67 kg/yatak.gün aralığında değişmiştir. Ambalaj atıkları, Covid-19 sonrası evsel atıklara benzer şekilde (Isparta'da %23,6, Yozgat'ta %30,2) azalmıştır. Sadece Manisa'da %3,1 artış olmuştur. Ambalaj atıklarının en fazla oluştuğu birim evsel atıklara benzer şekilde yemekhane olmuştur. Tehlikeli atıklar Covid-19 öncesi 0,05-0,21 kg/yatak.gün arasında değişirken, Covid-19 sonrası (2020) 0,16-0,21 kg/yatak.gün aralığında değişmiştir. Tehlikeli atıklar, Covid-19 sonrası (Isparta'da %50, Yozgat'ta %220, Manisa'da %1) artmıştır. Tehlikeli atıkların oluştuğu birimler açısından hastanelerde benzer bir eğilim bulunmamaktadır. Tehlikeli atıklar 2019 ve 2020'de ağırlıklı olarak teknik birim, laboratuvar ve yoğun bakımdan oluşmuş, bununla birlikte 2020 yılında Covid-19 ve göğüs hastalıkları servislerinden de ciddi oranda tehlikeli atık kaynaklandığı gözlenmiştir. Tıbbı atık miktarları Covid-19 öncesi 0,80-1,36 kg/yatak.gün arasında değişirken, Covid-19 sonrası 0,96-1,91 kg/yatak.gün değerlerine (Isparta'da %8,1, Yozgat'ta %31,1, Manisa'da %72,1, Elazığ'da %20 ve Kayseri'de %69,1) artmıştır. Tıbbi atıklar 2019 yılında ağırlıklı olarak yoğun bakımdan kaynaklanmış, ameliyathaneden de önemli oranda tıbbi atık oluşmuştur. 2020 yılında en fazla tıbbi atık 2019'a benzer şekilde yoğun bakımdan gözlenmiş, Covid-19 biriminden de ciddi oranda tıbbi atık kaynaklanmıştır. İncelenen şehir hastanelerindeki 2019 yılı tıbbi atık üretimi ortalaması 1,11 kg/yatak.gün olup, bu değer Türkiye'de Sağlık Bakanlığına bağlı hastanelerin ortalaması olan 1,73 kg/yatak.gün'den düşüktür. Bu çalışmada yatak başına atık verileri karşılaştırılmış olup, hastanelerdeki yatak doluluk oranları değişebildiğinden değerlendirmede hatalar olabilmektedir. Hasta başına atık verileri değerlendirme yapmak için daha uygun olup, bu çalışmada hasta sayıları bilgilerine ulaşılamamıştır. Sonraki çalışmalarda hasta başına atık verilerinin de hesaplanması önerilmektedir.