Theses supervised by Prof. Dr. Mustafa Özilgen
11 theses · Yeditepe University
Assessment of the error involved in the PCR tests
PCR tests are the diagnostic method that is accepted as the gold standard in the diagnosis of COVID-19 disease. There are many different kits with differences such as targeted gene regions and kit content used in performing these tests around the world. There are many factors that affect the accuracy of PCR test results. In general, some of these may be caused by the suspected patient, the laboratory environment, the specialist, or the diagnostic kit used. These factors cause false positive and false negative results to occur. In this study, data from thirty-one articles related to the polymerase chain reaction (PCR) method used in the diagnosis of SARS-COV-2 were used. In total, approximately 188,201 disease test data were obtained. Of these tests, 1472 were identified as discordant test results (false positive/false negative). Of these results, 1025 were accepted as false negative and 447 as false positive. The approximate false positive rate (FPR) calculated according to these data is 0.56%, and the false negative rate (FNR) is 0.95%. This study was carried out by making calculations and researches on approximate data in order to obtain a general result. As a result of the research, it is thought that false positive results are caused by pipetting errors, contamination and false negative results are caused by improper sampling and sampling in the early stages of the disease.
Thermodynamic aspects of age-dependent deterioration of myometrium and detrusor muscles
Problems in labor and delivery effects millions of people every year and are the reason for a high number of mortality around the world. Due to the changing social increased age when giving birth is observed which has made treating older females that have difficulty when conceiving and giving birth an important part of today's medicine. In pregnancy, the myometrium turns from silent to and actively contracting organ to provide a decent delivery of the baby. Oxytocin is produced in the uterus and its application can be used to induce uterine contractions when giving birth. It is an effective stimulator and it can increase the frequency, force and the duration of the contractions. Due to the increase of the population of elderly people in developed countries will result in higher number of people dealing with problems related to bladder dysfunctions. Due to aging, micturition dynamics in vivo and contractile strength in vitro can have different responses to neurotransmitters. Isolated tissue baths are a classic apparatus that helps in determining the concentration-response relations in various tissues. It has been around over 150 years and due to its versatility and simplicity, it has been an important device for the scientists. In this study, organ bath method was used to measure the effects of aging on myometrium and detrusor tissues.
Exergy destruction and entropy generation in the skeletal and cardiac muscles, lifespan entropy generation by the masseter muscles during chewing and its use as an indicator of the life expectancy
The lifespan entropy concept suggests that the organisms may have a limited capacity of lifespan entropy generation when they reach to that limit they die. The masseter muscles of a subject who is consuming food along the guide lines of Institute of Medicine (USA) may generate almost 1 x 105 J/K of entropy while chewing his food during his 76 years of expected life time. The masseter muscles of an obese person, who uptakes 10 per cent more nutrients generates the same entropy about five years earlier. The cumulative entropy generation decreases as the second law efficiency of the muscle work rises. The results of this study imply that the concept of the lifespan entropy may be correct even at the individual muscle level, and may be employed to estimate the life expectancy of a person. Experimental data from the literature are employed to carry out thermodynamic analyses of the skeletal and cardiac muscle work performance to obtain additional information beyond what the classical medical studies may offer in description of the health problems. The muscle work efficiency decreases as a result of the reduction of the metabolic energy conversion in the mitochondria with metabolic or structural failure or aging. The reduction of the mitochondrial energy generation causes further deterioration of the muscle structure, which causes in turn further decline in the muscle work efficiency. Exergy loss and entropy generation in the muscles increase as a response to the attempts to higher work production. From the thermodynamic perspective, heart can be regarded as a machine that converts part of the consumed power in external power when it pumps blood. In the course of the contraction of the heart muscle, most of the utilized chemical energy transforms into heat and a much lesser portion turns out to be work. The ratio of the work and the chemical energy expenditure is called efficiency of the cardiac contraction, or basically heart efficiency.
Sustainable operation of the network of chicken meat and egg producing and consuming industries via manure management
Thermodynamic analyses of a model network of chicken meat and eggs producing and consuming businesses was carried out to assess the sustainability of the production network under different manure management practices. The model network included a chicken farm, a restaurant, a pet food manufacturing plant, a vegetable garden, an olive garden, a grain field and a manure gasifier. Cumulative degree of perfection (CDP) was referred to as the numerical indicator of the sustainability. When chemical fertilizers were used in the system alone and the poultry manure was discarded, the CDP of the system was 0.66, when poultry manure was used alone to substitute the chemical fertilizers the CDP was 0.67. In the case when poultry manure was used together with bio-fertilizers, the CDP was 0.68. Gasification of the poultry manure increased the CDP to 0.98, and the highest CDP (1.01) was obtained when the poultry manure was gasified and microbial fertilizers were employed in the agriculture.
Assessment of the renewability of black, instant and ice tea production and waste valorization processes
Energy and exergy utilization, carbon dioxide (CO2) emission and exergy destruction were calculated for the "orchard to the retail market" industrial production of the black tea in Turkey and pilot scale production of the instant and ice tea. Energy and exergy utilization was 12,748 and 45,532 MJ/t of black tea produced, being consistent with the results given in the literature. The total amount of the CO2 emission in the entire process was 1,732 kg/t of black tea. In the entire black tea process, 70 per cent of the total energy and 86 per cent of the total exergy utilization was allocated to the processing of the tea, which also accounted for 72 per cent of the total amount of the carbon dioxide emission. The largest amounts of energy and exergy were used in the drying, withering and packaging stages of the processes, respectively. The total exergy utilized in drying process was 22,424 MJ/t, corresponding to 52 per cent of the total exergy utilization. HVAC units employed in withering were causing the largest exergy destruction, 2,542 MJ/t of black tea, followed by 318 MJ/t of black tea of exergy destruction during drying. Energy and exergy utilization from agriculture to packaging were 1,431 MJ/kg and 3,987 MJ/kg of instant tea and 3,571 MJ/kg and 4,464 MJ/kg of ice tea, respectively. The total amount of the CO2 emission in the entire process was 140 kg/ kg of instant tea and 267 kg/ kg of ice tea. Waste from the extraction step was analyzed further for potential conversion into value added products - activated carbon, hydrogen and adsorbent. Energy and exergy requirement for the activated carbon production from tea waste was 59.8 MJ/kg and 249.5 MJ/kg of waste tea and for the adsorbent production 3.7 MJ/kg and 15.2 MJ/kg of waste tea, respectively. Instant tea production was the most and the brewed tea was the least energy and exergy utilizing process among all the cases studied. The cumulative degree of perfection (CDP) and renewability indicator of the products showed that all of these processes were nonrenewable.
Formation of nanoemulsion - based delivery systems for liposoluble vitamins: stability assessment and digestion studies
Liposoluble vitamins are the biological active micronutrients which have health promoting effects. They may possess poor chemical stability, poor water solubility and low bioavailability. Therefore it is required to design effective delivery systems to incorporate these bioactives into functional food and beverage products. Nanoemulsion-based vitamin delivery systems were aimed to be produced using natural emulsifiers: lecithin, quillaja saponin, whey protein isolate (WPI) and gum arabic (GA) in a high pressure homogenizer. The effect of nanoemulsion composition and environmental stresses (pH, ionic strength and temperature) on the mean particle diameter and zeta-potential of the delivery systems were investigated and the stability was assessed by referring to theoretical phenomena. Simulated gastrointesinal system was used to evaluate the influence of carrier oil type on the digestion and bioaccessability of the vitamin D3. The mean particle diameter had a minimum value at an intermediate vitamin E-to-orange oil ratio in the oil phase: d32= 0.13µm for lecithin and 0.12µm for quillaja saponin at 50% vitamin E. WPI (d32 = 0.11 μm, 1% emulsifier) was better than GA (d32 = 0.38 μm, 10% emulsifier) at producing small droplets at low emulsifier concentrations. Quillaja saponin and lecithin formed stable nanoemulsions at pH 3-8, however the loss of electrostatic repulsion caused instability at pH 2. Higher salt concentrations >100 mM NaCl for lecithin and ≥ 400 mM NaCl for quillaja saponin caused instability due to the electrostatic screening. All the sytems were stable at temperatures from 30 to 90 °C. WPI-stabilized nanoemulsions were unstable to flocculation at pH 5, at high ionic strength (>100 mM), and at elevated temperatures (>60 °C), whereas GA-stabilized emulsions were stable. The rate of free fatty acid release during lipid digestion decreased in the following order: medium chain triglycerides (MCT) > corn oil ≈ fish oil > orange oil > mineral oil. Long chain triglycerides were the most effective at increasing vitamin D3 bioaccessibility. These results provide useful information about the emulsifying and stabilizing capacities of natural emulsifiers for forming food-grade vitamin-enriched delivery systems.
Thermodynamic assessment of the impact of the climate change on honeybees
Honeybees are among the most sensitive biological species to the changes in environmental conditions. Since pollination is necessary for the cultivation of more than 75 per cent of the crops used directly by the people worldwide, any injury to the honeybee population due to the climate change may jeopardize the food security. Therefore, thermodynamic parameters which are implemented on the honeybees under the prevailing environmental conditions and which may be implemented in the case of an anticipated temperature change are assessed. Work performance and entropy generation by the honeybees while resting, foraging for nutrients outside of the hive and fanning the hive are assessed based on sucrose metabolism. The minimum entropy generation accounted was 1.2 x10-7 W/g honeybee K while the 1-7 h old young honeybees were resting under atmospheric pressure with 0.5 M of sucrose supply at 15 μl/min flow rate in the hive. The maximum entropy generation, 7.2 x10-5 W/g honeybee K, was accounted during foraging at 35oC at shade with 0.5 M of unlimited sucrose supply. With 3,000 honeybees, work performance was 3.17 kJ/kg dry air, heat generation was 4.44 kJ/kg dry air and the entropy generation is 161.6 W/g honeybee K while raising the temperature of the hive by 1oC. On the other hand, they have to perform 4.5 kJ/kg dry air of work, generate 7.27 kJ/kg dry air of heat and 308.9 W/g honeybee K of entropy to reduce the temperature of the hive by 1oC. The results show that during cooling by 1oC the honey bees performed 1.4 folds of work and generated 1.9 folds of entropy when compared to that of heating by 1oC, implying that global warming may create 90 per cent more entropy stress on the honeybees, when compared to that of a potential global cooling.
Thermodynamic analysis on energy-exergy requirement and efficiency of serogroup C antigen production, farm to fork bread production and sourdough leavening
Efficient use of food and energy sources has gained great importance with increasing population, the increase of greenhouse gases and global warming. Hence, the yield of food and chemical processes with low energy consumption is intended to provide the energy efficient production systems. In context of this thesis; three biochemical processes were studied by kinetic and thermodynamic models. Thermodynamic models are investigated by first and second laws of thermodynamics. In the first study; kinetic and thermodynamic models are developed to relate substrate consumption, serogroup C antigen production and growth rate of Neisseria meningitidis, a meningitides causing bacterium for three cases: the uncontrolled; pH controlled and dissolved oxygen controlled cultivation. The model shows that maximum antigen production, minimum energy consumption, minimum entropy generation and exergy loss are obtained under stress conditions that N. meningitidis are exposed to. As the second study; energy and exergy efficiencies of the wheat and rye bread and hamburger bun making processes are assessed based on data from Turkey and Germany. Energy and exergy consumption, the cumulative degree of perfection (CDP) and CExC in each step in production of these various breads were calculated. Agriculture is the most significant step in bread production affecting all following steps. Hamburger bun production requires the maximum energy utilization due to the higher weight loss in baking. The rye bread production process requires the minimum energy utilization due to the lower energy input in the agriculture and higher efficiency in the flour production. The maximum exergy destructions occur during the milling and the baking steps. In the third study; the leavening process in sourdough is investigated in presence of various ratios of Saccharomyces cerevisiae and Lactobacillus plantarum in different temperatures in order to find out the maximum carbon dioxide production, expansion work and dough volume increase with optimum energy and exergy utilization.
Thermodynamic assessment of nutrition with laboratory animals
The significance of this research is gathering three different approaches under a single concept and investigation of how different parameters may affect the cellular metabolism entropy generation profiles of rodents. The first assessment includes the obese and lean rats fed with butter fat (BF) and soybean oil (SO)-based diets and the results show that obese and lean rats fed with BF diet have higher average entropy generation values than the groups fed with SO diet. Besides, the obese rats may generate 1.75 times higher lifespan entropy when fed with BF diet than fed with SO diet. On the other hand, lean rats may generate 3 times higher lifespan entropy when they fed with BF diet than fed with SO diet. The second assessment of this study considers the pregnant mouse and thermodynamic analyses show that calculated energy consumption for internal work for cellular metabolism subsystem is substantially higher than the muscle work during pregnancy. Besides that, daily entropy generation and internal work fluxes follow a highly similar phasic behaviour. Towards to end of the pregnancy external work performance decreases, and with the progress of the pregnancy second law efficiency, which follows a phasic path, increases significantly. The third system assessment in this study considers the mice under calorie (CR) and protein (PR) restriction and thermodynamic analyses show that the average daily entropy generation of cellular metabolism of CR groups increases with the increasing work output and decreases with increasing level of CR, but for the PR group, there are not any meaningful relationships for these results. Estimations show that the lifespan of the mice may increase 56-13 percent with CR and 21-7 percent with PR when compared to 24 hours ad libitum (AL) control group. The calculated cellular metabolism subsystem second law efficiency of 24 hours AL group is around 36 percent. This average value is higher than the average value of pregnant mice (21 percent). This may be related to special circumstances (being pregnant). By this study, some computational techniques are introduced where the second law concept is used for "lifespan entropy generation", "entropy generation assessment during pregnancy" and "lifespan expectancy predictions".
Investigation of energy consumption and co2 emmission for hamburger menu production
Energy utilization and CO2 emission assessed during farm-to fork fast food production by referring to hamburger menu production with the data collected from the Turkish manufacturers. Energy intensity associated with the production of the ingredients were found consistently in the lower end of the international range, implying that machinery was at least partially substituted with labor in some production lines. Meanwhile, CO2 emission was at the higher end of the international range, emphasizing the use of relatively inefficient technology and pointing the need for improvement of mechanization and the level of the technology employed. Energy utilization for the entire menu in Turkey was 40,844 MJ/t accompanied with 15,399 kg/t of CO2 emission. The waste from the fast food industry was assessed for possible electric generation via combustion in Rankine cycle with regeneration and found to have a potential for generation of 3.5 GW/t of waste. Big Mac®, signature hamburger of the international fast food chain McDonald's, establishes a "basket" for the practical economic indicator "Big Mac index". This concept has been improved and a "basket", was defined by extending the coverage to the entire hamburger menu. The energy indicator of the proposed index when calculated with the data collected from the Turkish manufacturers was 40,884±3,126 MJ/t accompanied with 15,399±858 kg /t of CO2 emission. When the waste from the menu is combusted for electric power production in Rankine cycle, 17,472 MJ/t hamburger menu of energy may be recovered. The proposed index has been tested for the variations in the amounts of the constituents of the menu and found sensitive enough for practical use.
Exergy requirement and efficiency of biological activities of chlamydomonas reinhardtii
Chlamydomonas reinhardtii is considered as a potential lipid producer for industrial biodiesel manufacture. The thermodynamic aspects of the lipid production process is important, since the non-lipid producing biological activities of the algal cultivation consume part of the solar energy captured with photosynthesis, in expense of the exergetic efficiency of the lipid production process. The cultivation of Chlamydomonas reinhardtii is modeled as a three-step chemical mechanism, which represents growth, respiration and lipid production and a thermodynamic analysis is performed. The results have indicated that the cumulative degrees of perfections of the biomass production processes are high when those of lipid production are low, and vice versa. The exergy destruction per unit biomass production are accountable under the favorable biological growth conditions, whereas the highest exergetic efficiency of the lipid production is accountable under the least favorable growth conditions, reconfirming the results of the previous studies that the lipid production takes place under the stress conditions.