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Item Open Access Item Open Access Advanced numerical techniques for the scattering of waves by dielectric scatterers(2012) Gürel, LeventItem Open Access Amateur video and Apollo 18(2012-06) Künüçen, H. H.; Olguntürk, KağanItem Open Access Analysis of composite objects involving multiple dielectric and metallic partswith the parallel multilevel fast multipole algorithm(Applied Computational Electromagnetics Society, 2012-04) Ergül, Özgür; Gürel, LeventItem Open Access An analysis of manipulated information and respective alternative costs in information systems and in decision making structures(International Institute of Informatics and Systemics, IIIS, 2006) Güvenen O.; Öztürk, M.H.Today Information Technologies create base for the most important decision support systems for the practices in academia, business and politics. The effectiveness and success of operations that are supported by information systems are directly correlated with the quantity, accuracy, timing, credibility and the quality of the information that prevails in the system. Rapid development of these technologies in recent decades allows high level of information transaction and communication through the whole world. The quantity of information that flows through information systems has increased tremendously. New researches and technological applications in this area aim to improve the systems quantitatively. However, despite a huge and continuous increase in information flow, the quality and reliability of the information in the systems are doubtful from many perspectives. We believe that quality and reliability considerations in information technologies are not handled by researchers and users adequately. So in this research we decided to discuss about quality and reliability aspects of the information flow. To be able to evaluate the information from qualitative perspectives, we believe that it is crucial to handle the problem in science and especially in social sciences by endogenising socio-economic phenomena and science methodology approaches. We hope this work will create a stimulus for researchers of Information Technologies and Systems to give importance to the reliability and quality of information issues.Item Open Access Application of fast methods to large scale rough surface scattering and propagation problems(2006) Altıntaş, Ayhan; Ertürk, Vakur B.; Tunç, Celal; Topçu, SatılmışItem Open Access Application of modified particle swarm optimization method for parameter extraction of 2-D TEC mapping(EGU, 2012-04) Toker, C.; Gökdağ, Y. E.; Arıkan, F.; Arıkan, OrhanIonosphere is a very important part of Space Weather. Modeling and monitoring of ionospheric variability is a major part of satellite communication, navigation and positioning systems. Total Electron Content (TEC), which is defined as the line integral of the electron density along a ray path, is one of the parameters to investigate the ionospheric variability. Dual-frequency GPS receivers, with their world wide availability and efficiency in TEC estimation, have become a major source of global and regional TEC modeling. When Global Ionospheric Maps (GIM) of International GPS Service (IGS) centers (http://iono.jpl.nasa.gov/gim.html) are investigated, it can be observed that regional ionosphere along the midlatitude regions can be modeled as a constant, linear or a quadratic surface. Globally, especially around the magnetic equator, the TEC surfaces resemble twisted and dispersed single centered or double centered Gaussian functions. Particle Swarm Optimization (PSO) proved itself as a fast converging and an effective optimization tool in various diverse fields. Yet, in order to apply this optimization technique into TEC modeling, the method has to be modified for higher efficiency and accuracy in extraction of geophysical parameters such as model parameters of TEC surfaces. In this study, a modified PSO (mPSO) method is applied to regional and global synthetic TEC surfaces. The synthetic surfaces that represent the trend and small scale variability of various ionospheric states are necessary to compare the performance of mPSO over number of iterations, accuracy in parameter estimation and overall surface reconstruction. The Cramer-Rao bounds for each surface type and model are also investigated and performance of mPSO are tested with respect to these bounds. For global models, the sample points that are used in optimization are obtained using IGS receiver network. For regional TEC models, regional networks such as Turkish National Permanent GPS Network (TNPGN-Active) receiver sites are used. The regional TEC models are grouped into constant (one parameter), linear (two parameters), and quadratic (six parameters) surfaces which are functions of latitude and longitude. Global models require seven parameters for single centered Gaussian and 13 parameters for double centered Gaussian function. The error criterion is the normalized percentage error for both the surface and the parameters. It is observed that mPSO is very successful in parameter extraction of various regional and global models. The normalized reconstruction error varies from 10-4 for constant surfaces to 10-3 for quadratic surfaces in regional models, sampled with regional networks. Even for the cases of a severe geomagnetic storm that affects measurements globally, with IGS network, the reconstruction error is on the order of 10-1 even though individual parameters have higher normalized errors. The modified PSO technique proved itself to be a useful tool for parameter extraction of more complicated TEC models.Item Open Access Armed forces and society in Turkey: An empirical approach(International Political Science Association (IPSA), 2012-07) Sarıgil, ZekiItem Open Access Atomic layer deposition of functional III-Nitride thin films & nano-structures(2012) Bıyıklı, N.; Ozgit-Akgun, C.; Dönmez, İ.; Kayacı, F.; Uyar, TamerItem Open Access Augmented reality based continuous onboarding framework(CEUR-WS, 2018) Ohri, İ.; Öge, İ.; Orkun, B.; Yılmaz, M.; Tüzün, E.Having an efficient and effective onboarding process for a newcoing employee is a very important factor for the following work performance. For this reason, the orientation process is a process that should be well assessed both in terms of company and employees. Based on the fact that using virtual objects in the real environment enhances the efficiency in learning new things, in this project, the onboarding process is managed by augmented reality (AR) technology. One of the main objectives of the project is guiding the software engineers effectively with the help of augmented reality by providing them interactive communication between their colleagues and the projects.Item Open Access Autofocused sparse SAR image reconstruction by EMMP algorithm(IEEE, 2012-05) Uğur, Salih; Gürbüz, A. C.; Arıkan, OrhanItem Open Access Bilateral trade in discrete type spaces by linear and convex optimization with application to supply chain coordination(INSA Lyon, 2018) Pinar, M. C.We consider the bilateral trade of an object between a seller and a buyer through an intermediary who aims to maximize his expected gains as in Myerson and Satterthwaite [1], in a Bayes-Nash equilibrium framework where the seller and buyer have private, discrete valuations for the object. Using duality of linear network optimization, the intermediary's initial problem is transformed into an equivalent linear programming problem with explicit formulae of expected revenues of the seller and the expected payments of the buyer, from which the optimal mechanism is immediately obtained. Then, an extension due to Spulber [2] is considered where the seller is also a producer with a cost parameter that is private information. Assuming suitable utility and production functions for the respective parties, the resulting non-convex mechanism design problem of a utility maximizing broker is revealed to have hidden convexity and transformed into an equivalent (almost) unconstrained convex optimization problem over output variables, which, in many cases, can be solved easily by calculus. A contracting game under asymmetric information specific to two-echelon supply chain coordination between a retailer of unknown type and a supplier, akin to the bilateral trade game of the paper, is also studied. Special cases leading to closed-form solution with increasing information rent for higher types are identified along with the requisite conditions for their validity.Item Open Access Bioremediation of 2, 4, 6 trinitrotoluene contaminated soil using in vessel composting method(2012) Gümüşçü, B.; Tekinay, T.; Çekmecelioğlu, D.Item Open Access Causal mutation discovery using next generation sequencing data: development and application of a pipeline to reduce false positive calls and to map regions of shared homozygosity and IBD(American Society of Human Genetics, 2012-11) Gülsüner, Süleyman; Walsh, T.; Watts, A. C.; Lee, M. K.; Özçelik, Tayfun; King, M. C.Next generation sequencing technologies have brought enormous successes for disease gene discovery but also challenges for data analysis, particularly in genomic regions with low or low quality sequence coverage. Errors in variant calling may lead to missing true variants or to calling many false positives. The false discovery rate can be reduced by optimizing variant calling thresholds such as quality of base pair identification, mapping, and alignment. However, such optimization strategies are often associated with the loss of true variants. We present and apply a pipeline for variant identification and verification using aligned sequences of related individuals. It is comprised of three modules: (1) an identification pipeline for de novo variants where data of parents and siblings are aligned in order to rule out false positive calls in children, false negative calls in parents, and indel artifacts; (2) a homozygosity mapping and IBD analysis module; and (3) a variant read depth module that reveals variants that may have been missed due to sequence coverage and quality issues. We applied module (1) to a large trio-based gene discovery project and reduced the number of variant calling errors by 74%, thereby significantly streamlining the experimental validation protocol for potential de novo variants. We also applied the pipeline to the discovery of the gene responsible for mega corpus callosum and microcephaly with developmental delay, and epilepsy in a brother and sister whose unaffected parents were first cousins. Our error correction pipeline significantly improved homozygosity mapping and IBD analysis and facilitated the rapid identification of the causal allele in this family.Item Open Access The cBioPortal for cancer genomics and its application in precision oncology(American Association for Cancer Research, 2016) Gao, J.; Lindsay, J.; Watt, S.; Doğrusöz, Uğur; Lukasse, P.; Abeshouse, A.; Chen, H.; Bruijn, I.; Gross, B.; Li, D.; Kundra, R.; Heins, Z.; Reis-Filho, J.; Sumer, O.; Sun, Y.; Wang, J.; Wang, Q.; Zhang, H.; Kumari, P.; Şahin, Mehmet Furkan; Ridder, S.; Schaeffer, F.; Bochove, K.; Pugh, T.; Sander, C.; Cerami, E.; Schultz, N.; Bahçeci, İstemiAbstract The cBioPortal for Cancer Genomics provides intuitive visualization and analysis of complex cancer genomics data. The public site (http://cbioportal.org/) is accessed by more than 1,500 researchers per day, and there are now dozens of local instances of the software that host private data sets at cancer centers around the globe. We have recently released the software under an open source license, making it free to use and modify by anybody. The software and detailed documentation are available at https://github.com/cBioPortal/cbioportal. We are now establishing a multi-institutional software development network, which will coordinate and drive the future development of the software and associated data pipelines. This group will focus on four main areas: 1. New analysis and visualization features, including: a. Improved support for cross-cancer queries and cohort comparisons. b. Enhanced clinical decision support for precision oncology, including an improved patient view with knowledge base integration, patient timelines and improved tools for visualizing tumor evolution. 2. New data pipelines, including support for new genomic data types and streamlined pipelines for TCGA and the International Cancer Genome Consortium (ICGC). 3. Software architecture and performance improvements. 4. Community engagement: Documentation, user support, and training. This coordinated effort will help to further establish the cBioPortal as the software of choice in cancer genomics research, both in academia and the pharmaceutical industry. Furthermore, as the sequencing of tumor samples has entered clinical practice, we are expanding the features of the software so that it can be used for precision medicine at cancer centers. In particular, clean, web-accessible, interactive clinical reports integrating multiple sources of genome variation and clinical annotation over time has potential to improve clinical action beyond current text-based molecular reports. By making complex genomic data easily interpretable and linking it to information about drugs and clinical trials, the cBioPortal software has the potential to facilitate the use of genomic data in clinical decision making. Citation Format: Jianjiong Gao, James Lindsay, Stuart Watt, Istemi Bahceci, Pieter Lukasse, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Dong Li, Ritika Kundra, Zachary Heins, Jorge Reis-Filho, Onur Sumer, Yichao Sun, Jiaojiao Wang, Qingguo Wang, Hongxin Zhang, Priti Kumari, M. Furkan Sahin, Sander de Ridder, Fedde Schaeffer, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for cancer genomics and its application in precision oncology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5277.Item Open Access Ceza hukukunda yoruma ilişkin bazı gözlemler: hukuk ve yorum(Ankara Barosu, 2010-01) Katoğlu, TuğrulItem Open Access Characterization of fruit juice processing wastes as biosorbent for heavy metal removal(2012) Akgül, G.; Tekinay, T.Item Open Access Co-encapsulating nucleic acid based TLR ligands in nanoliposomes induce potent antiviral immune activation(European Molecular Biology Organization, 2012-05) Bayyurt, Banu; Erikçi, Erdem; Gürsel, İhsanItem Open Access Coaching engineering freshmen at Bilkent University(Middle East Technical University, Faculty of Engineering, 2005) Özdemir, B. U.; Verhoeven, J. M.; Çelik, B. K.In September 2003, the Faculty of Engineering at Bilkent University created an office to help first year students adapt to university life and start their academic studies effectively. For each of the three Departments of the Faculty, an 'academic student coordinator' offers personal coaching and consulting services for each individual student; the coordinator follows the progress of the students and contacts and advises them if necessary. The office offers an Engineering Orientation course that covers time management, study skills, problem solving and critical thinking. Besides this, the office offers tutorial sessions for physics courses, and organizes social activities.Item Open Access