Aptamer probes for specific recognition of glioblastoma multiforme were generated using a repetitive and broad cell-SELEX-based procedure without negative selection. The 454 sequencing technology was used to monitor SELEX, and bioinformatics tools were used to identify aptamers from high throughput data. A group of aptamers were generated that can bind to target cells specifically with dissociation constants (K d ) in the nanomolar range. Selected aptamers showed high affinity to different types of glioblastoma cell lines, while showing little or no affinity to other cancer cell lines. The aptamers generated in this study have potential use in different applications, such as probes for diagnosis and devices for targeted drug delivery, as well as tools for molecular marker discovery for glioblastomas.

Iron and steel production is one of the most resource and energy demanding industries around the world. Throughout the life cycle of iron and steel products, the intensive use of raw materials and energy results in contributions to a wide range of environmental impacts. This study conducts a life cycle assessment (LCA) for iron and steel production in Turkey using SimaPro software and IMPACT 2002+ impact assessment method with the purpose of comparing the impacts of life cycle stage (coke making, sintering, iron making, steel making) and final products (billet, slab, hot rolled wire rod, hot rolled coil). The system boundary was set as cradle-to-gate, the functional unit was selected as 1 ton of product, and the study was conducted using the inventory data collected from one of the three integrated iron and steel facilities representing the majority of the industry in Turkey. Different production scenarios for the final products were also evaluated to see the variation in the total impacts. The results indicated that, liquid steel production process exhibited the highest total environmental impact, which was followed by sinter production. Coke production process showed the highest impact on depletion of non-renewable energy sources. The comparison of the impacts for different final products revealed that hot rolled coil causes the highest total environmental impact. Moreover, the environmental impact of mechanical workshop of the facility was found negligible when compared to the production processes.

Cruise missile mission planning is a key activity of cruise missile operations. Ground planning activities aim at low observable missions that have high probability of success. These activities include end game planning, route planning and launch planning. While end game planning tries to optimize end game parameters for maximum effectiveness, route planning tries to maximize survivability and enable navigational supports by determining the waypoints to from launch zone to target through a defended area. And lastly, planner tries to find the appropriate launch parameters that will prohibit platform to contact enemy agents. Mission rehearsal is the execution of the planned mission in a virtual environment that will be constructed with the data that drives the planning process. Mission rehearsal will support planners by providing possible results of the planned mission. Stochastic processes of the execution of the planned mission will be incorporated in the simulation of the combat. Along with platform, cruise missile and target, other players like SAM Sites or Search Radars (Early Warning Radars) will be incorporated in the rehearsal process.

In order to overcome the various disadvantages of standalone INS and GPS, these systems are integrated using nonlinear estimation techniques and benefits of the two complementary systems are obtained at the same time. The standard and most widely used estimation algorithm in the INS/GPS integrated systems is Extended Kalman Filter (EKF). Linearization step involved in the EKF algorithm can lead to second order errors in the mean and covariance of the state estimate. Another nonlinear estimator, Unscented Kalman Filter (UKF) approaches this problem by carefully selecting deterministic sigma points from the Gaussian distribution and propagating these points through the nonlinear function itself leading third order errors for any nonlinearity. Scaled Unscented Transformation (SUT) is one of the sigma point selection methods which gives the opportunity to adjust the spread of sigma points and control the higher order errors by some design parameters. Determination of these parameters is problem specific. In this thesis, effects of the SUT parameters on integrated navigation solution are investigated and an &ldquo / Adaptive UKF&rdquo / is designed for a tightly-coupled INS/GPS integrated system. Besides adapting process and v measurement noises, SUT parameters are adaptively tuned. A realistic fighter flight trajectory is used to simulate IMU and GPS data within Monte Carlo analysis. Results of the proposed method are compared with standard EKF and UKF integration. It is observed that the adaptive scheme used in the sigma point selection improves the performance of the integrated navigation system especially at the end of GPS outage periods.

Properly preparing the drilling fluid is an essential part of any successful drilling operation, especially in complex operations like deviated and horizontal drilling. Understanding the flow behavior of the polymers used in the drilling fluids under different conditions takes a key part in this preparation. In this study, shear rheology of some traditionally used water soluble polymers in drilling and completion fluids / namely PAC (polyanionic cellulose) and xanthan gum, were investigated experimentally. Instead of an oilfield standard Fann Model 35 Viscometer, an Ofite Model 900 Viscometer was used because of its capability to measure at ultra-low shear rates. Effects of the concentration of the polymer, time of shear applied, test temperature and effects of aging were examined. Rheological measurements were conducted between the shear rate ranges of 0.01 to 1000s-1 with concentrations changing from 0.25 to 1.5 grams of polymer per 350 milliliters of water (equivalent to 0.25 to 1.5 lb/bbl). Rheograms were constructed to identify the effect the polymers in question have on the flow characteristics of the drilling fluid. An appropriate constitutive model was used to define the flow behavior of the polymer in question mathematically. It was observed from the constructed rheograms that increase in polymer concentration results in consistent increase of apparent viscosity. Amount of time of shear does not affect the selected polymers if they are dynamically aged at least for two hours. Also as expected increasing temperature of the sample lowers the apparent viscosity considerably.

The use of lime mortars with pozzolanic additives is of special importance for the repair of historic masonry. In this study, the effect of pozzolanic materials on the final characteristics of mortars was investigated. Metakaolin, fly ash and historic brick powder were used as pozzolanic materials in mortar mixes with varying binder:pozzolan:aggregate ratios. Historic mortar samples from rubble stone masonry of Kahta Castle, a medieval structure in close vicinity of the Nemrut Dag Monument, were also investigated to serve as a starting point for the preparation of repair mortars. Physical and physicomechanical tests, optical microscopy, chemical tests, SEM-EDX and XRD analyses were used to assess the properties of the historic mortars and repair mortars. Fat lime was found to be used in historic mortars with a high binder/aggregate ratio. They were observed to have relatively low density and high porosity with an average compressive strength of 7.4 MPa. Historic mortars were determined to have relatively high water vapour permeability and low water impermeability characteristics. In repair mortars setting was found to be predominantly due to carbonation along with pozzolanic reactions. However, abundant presence of stratlingite in mortars with added metakaolin indicated that the pozzolanic reactions preceded carbonation in those mortars. Use of pozzolanic materials increased the uniaxial compressive strength and modulus of elasticity of mortars compared with control samples. Using the same binder:pozzolan:aggregate ratio, highest increase was observed on mortars prepared with added fly ash at the end of 90 days. Durability parameters of repair mortars defined as wet to dry compressive strength were in the very good to excellent range according to Winkler&rsquo / s classification. By using fly ash, design of lime mortars with high water impermeability and high water vapour permeability characteristics was accomplished.

The aim of this study is planning the locations of emergency centers (ECs) as well as the number of vehicles in each EC of Corporation, Man Truck and Bus Group, to respond to the calls (arrival of the mobile/24 emergency service vehicle to the broken vehicle) within the desired time. The company aims to respondto the calls within 90 minutes. If the EC cannot respond to the calls within 90 minutes, they should be satisfiedwithin 180 minutes. We propose a probabilistic programming approach to maximize the number of responded calls in 90 minutes while responding to all the calls in 180 minutes. The model determines the locations of the new ECs addition to the existing ones and also the number of vehicles assigned to those centers. The data source to this study is the emergency service calls of the company within February 2008 and December 2010. There are 30 ECs of the company distributed all over Turkey. By using the data, it is examined if the company can get closer to its target in responding to the calls with the current ECs. Necessary changes are proposed in the number and the locations of emergency centers for the desired target. Furthermore, several scenarios for targets with different quality service levels are generated and the effects of these parameters on the objective are observed.

In this study, recombinant human growth hormone (rhGH) production by Pichia pastoris-Mut+ strain was improved by designing feeding strategies which were applied in the production phase of the bioreactor operations. During the bio-reactor experiments the cell growth, sorbitol and methanol consumptions, recom-binant hGH production, alcohol oxidase (AOX) activity, the by-products protease and organic acid concentrations were followed and analyzed. In this context, in the first part of the study, three bioreactor operations were designed and per-formed. In general, the designed strategies are fundamentally based on simulta-neous feeding of the two substrates starting at t=0 h of the production phase, i.e., batch-wise 50 gL-1sorbitol feeding, together with fed-batch methanol feeding with a specific growth rate of &mu / 0=0.03 h-1 or &mu / 0=0.04 h-1, and fed-batch sorbitol feeding with a specific growth rate of &mu / 0=0.025h-1 which was calculated based on the specific consumption rate qS=0.152 g g-1h-1 of sorbitol. Consequently, sorbitol concentration was kept constant at 50 gL-1 within t=0-15h of the production phase / where, sorbitol feeding was terminated at t=15h. Amongst, in the first strategy (SSM1), methanol was fed to the system with the specific growth rate of &mu / 0=0.03 h-1, and the H+ concentration (pH) in the bioreactor was kept constant at pH=5.0. In the second strategy (SSM2), pH was kept constant at 5.5 until t=24h of the induction phase (production phase), thereafter, was reduced to pH= 5.0 / where methanol was fed to the bioreactor with the specific growth rate of &mu / 0=0.03 h-1. In the third strategy (SSM3), methanol was fed with the specific growth rate of &mu / 0=0.04 h-1, and the pH in the bioreactor was kept constant at pH 5.0. The highest rhGH production and cell concentration were achieved in the first strategy SSM1 as CrhGH=640 mg L-1 and CX=105.3 g L-1, and the overall cell and product yields on total substrate were calculated as YX/S =0.21 g g-1 and YCrhGH/S =1.83 mg g-1. In the second part of this study the two-substrates sorbitol and methanol were fed simultaneously in a solution compose of 1.37 mol sorbitol and 6.21 mol methanol in 13.88 mol water, which is named as SM. In this strategy (SM), the two-substrate solution was fed to the medium with the specific growth rate of &mu / 0=0.03 h-1 on sorbitol until t=30h / thereafter, only methanol was fed to the bio-reactor with the specific growth rate of &mu / 0=0.03 h-1. The highest cell and rhGH concentrations obtained in SM were, respectively, Cx=104.7 g L-1 and CrhGH=124 mg L-1 / and the overall cell and product yields on the total substrate were calcu-lated as YX/S=0.21 g g-1 and YCrhGH/S=0.39 mg g-1. Although the highest cell con-centration obtained at SM is close to that of the SSM1, the rhGH concentration obtained at SM is 5.2-fold lower than that of the strategy SSM1.

In this study first time, we have cloned and sequenced the citrate synthase gene from a thermoacidophilic archaeon Thermoplasma (Tp.) volcanium (Optimum growth temperature of Tp.volcanium is 60oC and optimum pH is 2.0.). For cloning we have followed a PCR based approach. Amplification of citrate synthase gene from chromosomal DNA of Tp.volcanium yielded a product of 1476 bp containing an open reading frame of 1161 bp comprising the structural gene. After ligation of the PCR amplicon to pDrive vector through AU complementation, recombinant plasmids were transferred into E.coli TG-1 competent cells. Out of three recombinants, E.coli pDriveCS-31 was selected for further characterization by restriction mapping and DNA sequencing. Southern Blotting and Hybridization using the membrane blot of pDriveCS-31 plasmid and DIG-labeled PCR amplified citrate synthase gene probe, also confirmed the cloning of Tp.volcanium citrate synthase gene in E.coli. Clustal W Version 1.82 was used for alignment of aminoacid sequence of Tp.volcanium citrate synthase with that of other archaeal, bacterial and eukaryotic citrate synthases. The highest sequence similarity (87%) was found between Tp.volcanium and Tp.acidophilum enzymes. Despite low sequence homology (18%) with the pig enzyme, of the 11 residues implicated in catalytic activity of the pig citrate synthase 9 were conserved in the Tp.volcanium enzyme. Heterologous expression of this citrate synthase gene in E.coli has been achieved under the control of its promoter sequences. The recombinant enzyme (386 aa) has been purified to homogeneity by affinity chromatography on Reactive Red 120 column. The subunit molecular size was estimated as 43 kDa. The purified enzyme followed classical Michaelis-Menten kinetics. The Km values of 5.15 &amp / #956 / M and 5.60 &amp / #956 / M, and Vmax values of 1.74 &amp / #956 / moles/ml/min and 1.60 &amp / #956 / moles/ml/min were calculated from Lineweaver-Burk plots for acetyl-CoA and oxaloacetate, respectively. The recombinant enzyme was thermostable and retained about 80% of the activity at 85oC after 1 hour.

ABSTRACT EVALUATION OF COASTAL SCENIC ASSESMENT PARAMETERS / PILOT STUDY FOR SELECTED AREA &ldquo / ANTALYA/KONYAALTI BEACH&rdquo / &Ccedil / akir, Deniz M.S., Department of Civil Engineering Supervisor : Prof. Dr. AySen Ergin Co-Supervisor: Dr. Engin Karaesmen July 2004, 75 pages The present scenic assessment study has a checklist that itemizes 26 parameters (comprising physical and human parameters), as a first step in quantifying scenery. Each parameter was rated on a five-point score, essentially covering presence/absence or poor quality (1), to excellence/outstanding (5). The ratings were subjected to fuzzy logic matrices and weights to reflect importance of the various parameters, which produced histograms of weighted averages for the various attributes. Based on this methodology coastal scenery evaluation was carried out and coastal areas were grouped into 5 five classes from Class 1 = Top Natural Sites to Class 5 = Very Unattractive Urban. The present work focuses on human parameters from the perspective of people with mobility handicaps. Public surveys were carried out for the necessary arrangements in coastal areas for accessibility of these people. Selected site (Antalya/Konyaalti Beach) is reviewed to bring some recommendations from the point of view of people with mobility handicaps.