Browsing by Subject "Models"

Now showing 1 - 20 of 20

Open Access
Algebraic reconstraction for 3D magnetic resonance-electrical impedance tomography (MREIT) using one component of magnetic flux density
(Institute of Physics and Engineering in Medicine, 2004) Ider, Y. Z.; Onart, S.
Magnetic resonance-electrical impedance tomography (MREIT) algorithms fall into two categories: those utilizing internal current density and those utilizing only one component of measured magnetic flux density. The latter group of algorithms have the advantage that the object does not have to be rotated in the magnetic resonance imaging (MRI) system. A new algorithm which uses only one component of measured magnetic flux density is developed. In this method, the imaging problem is formulated as the solution of a non-linear matrix equation which is solved iteratively to reconstruct resistivity. Numerical simulations are performed to test the algorithm both for noise-free and noisy cases. The uniqueness of the solution is monitored by looking at the singular value behavior of the matrix and it is shown that at least two current injection profiles are necessary. The method is also modified to handle region-of-interest reconstructions. In particular it is shown that, if the image of a certain xy-slice is sought for, then it suffices to measure the z-component of magnetic flux density up to a distance above and below that slice. The method is robust and has good convergence behavior for the simulation phantoms used.
Open Access
Analysis of blood cell production under growth factors switching
(Elsevier B.V., 2017) Djema, W.; Özbay, Hitay; Bonnet, C.; Fridman, E.; Mazenc, F.; Clairambault, J.
Hematopoiesis is a highly complicated biological phenomenon. Improving its mathematical modeling and analysis are essential steps towards consolidating the common knowledge about mechanisms behind blood cells production. On the other hand, trying to deepen the mathematical modeling of this process has a cost and may be highly demanding in terms of mathematical analysis. In this paper, we propose to describe hematopoiesis under growth factor-dependent parameters as a switching system. Thus, we consider that different biological functions involved in hematopoiesis, including aging velocities, are controlled through multiple growth factors. Then we attempt a new approach in the framework of time-delay switching systems, in order to interpret the behavior of the system around its possible positive steady states. We start here with the study of a specific case in which switching is assumed to result from drug infusions. In a broader context, we expect that interpreting cell dynamics using switching systems leads to a good compromise between complexity of realistic models and their mathematical analysis. © 2017
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.
Open Access
Analytical model of asynchronous shared-per-wavelength multi-fiber optical switch
(IEEE, 2011) Akar, Nail; Raffaelli, C.; Savi, M.
In this paper, a buffer-less shared-per-wavelength optical switch is equipped with multi-fiber interfaces and operated in asynchronous context. An analytical model to evaluate loss performance is proposed using an approximate Markov-chain based approach and the model is validated by simulations. The model is demonstrated to be quite accurate in spite of the difficulty in capturing correlation effects especially for small switch sizes. The model is also applied to calculate the number of optical components needed to design the optical switch according to packet loss requirements. The impact of the adoption of multiple fiber interfaces is outlined in terms of the remarkable saving in the number of wavelength converters employed, while increasing at the same time the number of optical gates needed by the space switching subsystem. The numerical results produced are a valuable basis to optimize overall switch cost. © 2011 IEEE.
Open Access
Architecture framework for mapping parallel algorithms to parallel computing platforms
(CEUR-WS, 2013) Tekinerdogan, Bedir; Arkin, E.
Mapping parallel algorithms to parallel computing platforms requires several activities such as the analysis of the parallel algorithm, the definition of the logical configuration of the platform, and the mapping of the algorithm to the logical configuration platform. Unfortunately, in current parallel computing approaches there does not seem to be precise modeling approaches for supporting the mapping process. The lack of a clear and precise modeling approach for parallel computing impedes the communication and analysis of the decisions for supporting the mapping of parallel algorithms to parallel computing platforms. In this paper we present an architecture framework for modeling the various views that are related to the mapping process. An architectural framework organizes and structures the proposed architectural viewpoints. We propose five coherent set of viewpoints for supporting the mapping of parallel algorithms to parallel computing platforms. We illustrate the architecture framework for the mapping of array increment algorithm to the parallel computing platform. Copyright © 2013 for the individual papers by the papers' authors.
Open Access
Effects of daylight saving time changes on stock market volatility: a reply
(Sage Publications, Inc., 2011) Berument, Hakan; Dogan, N.
There is a rich array of evidence that suggests that changes in sleeping patterns affect an individual's decision-making processes. A nationwide sleeping-pattern change happens twice a year when the Daylight Saving Time (DST) change occurs. Kamstra, Kramer, and Levi argued in 2000 that a DST change lowers stock market returns. This study presents evidence that DST changes affect the relationship between stock market return and volatility. Empirical evidence suggests that the positive relationship between return and volatility becomes negative on the Mondays following DST changes.
Open Access
How the ocean personality model affects the perception of crowds
(Institute of Electrical and Electronics Engineers, 2011) Durupınar, F.; Pelechano, N.; Allbeck, J. M.; Güdükbay, Uğur; Badler, N. I.
A personality model named High-Density Autonomous Crowds (HiDAC) simulation system provides individual differences by assigning each person different psychological and physiological traits. Users normally set these parameters to model a crowd's nonuniformity and diversity. The approach creates plausible variations in the crowd and enables novice users to dictate these variations by combining a standard personality model with a high-density crowd simulation. HiDAC addresses the simulation of local behaviors and the global wayfinding of crowds in a dynamically changing environment. It directs autonomous agents' behavior by combining geometric and psychological rules. HiDAC handles collisions through avoidance and response forces. Over long distances, the system applies collision avoidance so that agents can steer around obstacles. HiDAC assigns people specific behaviors. The number of actions they complete depends on their curiosity.
Open Access
Location and logistics
(Springer, 2014) Alumur, Sibel A.; Kara, Bahar Y.; Melo, M. T.; Laporte, G.; Nickel, S.; Saldanha da Gama, F.
Facility location decisions play a critical role in designing logistics networks. This chapter provides some guidelines on how location decisions and logistics functions can be integrated into a single mathematical model to optimize the configuration of a logistics network. This will be illustrated by two generic models, one supporting the design of a forward logistics network and the other addressing the specific requirements of a reverse logistics network. Several special cases and extensions of the two models are discussed and their relation with the scientific literature is described. In addition, some interesting applications are outlined that demonstrate the interaction of location and logistics decisions. Finally, new research directions and emerging trends in logistics network design are provided.
Open Access
Model-driven approach for supporting the mapping of parallel algorithms to parallel computing platforms
(Springer, Berlin, Heidelberg, 2013) Arkin, E.; Tekinerdogan, Bedir; Imre, K.M.
The trend from single processor to parallel computer architectures has increased the importance of parallel computing. To support parallel computing it is important to map parallel algorithms to a computing platform that consists of multiple parallel processing nodes. In general different alternative mappings can be defined that perform differently with respect to the quality requirements for power consumption, efficiency and memory usage. The mapping process can be carried out manually for platforms with a limited number of processing nodes. However, for exascale computing in which hundreds of thousands of processing nodes are applied, the mapping process soon becomes intractable. To assist the parallel computing engineer we provide a model-driven approach to analyze, model, and select feasible mappings. We describe the developed toolset that implements the corresponding approach together with the required metamodels and model transformations. We illustrate our approach for the well-known complete exchange algorithm in parallel computing. © 2013 Springer-Verlag.
Open Access
A new model of cell dynamics in Acute Myeloid Leukemia involving distributed delays
(2012) Avila, J. L.; Bonnet, C.; Clairambault, J.; Özbay, Hitay; Niculescu, S. I.; Merhi, F.; Tang, R.; Marie, J. P.
In this paper we propose a refined model for the dynamical cell behavior in Acute Myeloid Leukemia (AML) compared to (Özbay et al, 2012) and (Adimy et al, 2008).We separate the cell growth phase into a sequence of several sub-compartments. Then, with the help of the method of characteristics, we show that the overall dynamical system of equations can be reduced to two coupled nonlinear equations with four internal sub-systems involving distributed delays. © 2012 IFAC.
Open Access
An ontology for collaborative construction and analysis of cellular pathways
(Oxford University Press, 2004-02-12) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül
Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology. © Oxford University Press 2004; All rights reserved.
Open Access
Operational research: methods and applications
(Taylor and Francis Ltd., 2023-12-27) Petropoulos, F.; Laporte, G.; Aktas, E.; Alumur, S.; Archetti, C.; Ayhan, H.; Battarra, M.; Bennell, J.; Bourjolly, J.; Boylan, J. E.; Breton, M.; Canca, D.; Charlin, L.; Chen, B.; Cicek, C.; Cox, L.; Currie, C. S.M.; Demeulemeester, E.; Ding, L.; Disney, S. M.; Ehrgott, M.; Eppler, M. J.; Erdoğan, G.; Fortz, B.; Franco, L. A.; Frische, J.; Greco, S.; Gregory, A. J.; Hämäläinen, R. P.; Herroelen, W.; Hewitt, M.; Holmström, J.; Hooker, J. N.; Işık, T.; Johnes, J.; Kara, B. Y.; Karsu, Özlem; Kent, K.; Köhler, C.; Kunc, M.; Kuo, Y.; Letchford, A. N.; Leung, J.; Li, D.; Li, H.; Lienert, J.; Ljubić, I.; Lodi, A.; Lozano, S.; Lurkin, V.; Martello, S.; McHale, I. G.; Midgley, G.; Morecroft, J. D.W.; Mutha, A.; Oğuz, C.; Petrovic, S.; Pferschy, U.; Psaraftis, H. N.; Rose, S.
Throughout its history, Operational Research has evolved to include methods, models and algorithms that have been applied to a wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first summarises the up-to-date knowledge and provides an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion and used as a point of reference by a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes.
Open Access
PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization
(Oxford University Press, 2006-02-01) Doğrusöz, Uğur; Erson, E. Zeynep; Giral, Erhan; Demir, Emek; Babur, Özgün; Çetintaş, Ahmet; Çolak, Recep
Summary: PATIKAweb provides a Web interface for retrieving and analyzing biological pathways in the PATIKA database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats. © The Author 2005. Published by Oxford University Press. All rights reserved.
Open Access
Physical optics modeling of 2D dielectric lenses
(Optical Society of America, 2009-01-27) Yurchenko, V. B.; Altintas, A.
We propose an advanced physical optics formulation for the accurate modeling of dielectric lenses used in quasi-optical systems of millimeter, submillimeter, and infrared wave applications. For comparison, we obtain an exact full-wave solution of a two-dimensional lens problem and use it as a benchmark for testing and validation of asymptotic models being considered.
Open Access
Privacy-preserving genomic testing in the clinic: a model using HIV treatment
(Nature Publishing Group, 2016) Mclaren, P. J.; Raisaro, J. L.; Aouri, M.; Rotger, M.; Ayday, E.; Bartha, I.; Delgado, M. B.; Vallet, Y.; Günthard, H. F.; Cavassini, M.; Furrer, H.; Doco-Lecompte, T.; Marzolini, C.; Schmid, P.; Di Benedetto, C.; Decosterd, L. A.; Fellay, J.; Hubaux, Jean-Pierre; Telenti A.
Purpose:The implementation of genomic-based medicine is hindered by unresolved questions regarding data privacy and delivery of interpreted results to health-care practitioners. We used DNA-based prediction of HIV-related outcomes as a model to explore critical issues in clinical genomics.Methods:We genotyped 4,149 markers in HIV-positive individuals. Variants allowed for prediction of 17 traits relevant to HIV medical care, inference of patient ancestry, and imputation of human leukocyte antigen (HLA) types. Genetic data were processed under a privacy-preserving framework using homomorphic encryption, and clinical reports describing potentially actionable results were delivered to health-care providers.Results:A total of 230 patients were included in the study. We demonstrated the feasibility of encrypting a large number of genetic markers, inferring patient ancestry, computing monogenic and polygenic trait risks, and reporting results under privacy-preserving conditions. The average execution time of a multimarker test on encrypted data was 865 ms on a standard computer. The proportion of tests returning potentially actionable genetic results ranged from 0 to 54%.Conclusions:The model of implementation presented herein informs on strategies to deliver genomic test results for clinical care. Data encryption to ensure privacy helps to build patient trust, a key requirement on the road to genomic-based medicine.
Open Access
Quercetin/β-cyclodextrin inclusion complex embedded nanofibres: slow release and high solubility
(Elsevier, 2016-04) Aytac Z.; Kusku, S. I.; Durgun, Engin; Uyar, Tamer
Electrospinning of polyacrylic acid (PAA) nanofibres (NF) incorporating β-cyclodextrin inclusion complex (β-CD-IC) of quercetin (QU) was performed. Here, β-CD was used as not only the crosslinking agent for PAA nanofibres but also as a host molecule for inclusion of QU. The phase solubility test showed enhanced solubility of QU due to the inclusion complexation; in addition, the stoichiometry of QU/β-CD-IC was determined to be 1:1. Computational modelling studies confirmed that 1:1 and 1:2 complex formation are desirable; 1:1 complex formation was chosen to have higher weight loading of QU. SEM images showed that PAA/QU/β-CD-IC-NF were bead-free and uniform. XRD indicated that PAA/QU/β-CD-IC-NF were amorphous in nature without the crystalline peaks of QU. Comparative results revealed that the release profile of QU from PAA/QU/β-CD-IC-NF was much slower but greater in total than from PAA/QU/β-CD-IC-film. Moreover, high antioxidant activity and photostability of QU was achieved in PAA/QU/β-CD-IC-NF.
Open Access
State aggregation-based model of asynchronous multi-fiber optical switching with shared wavelength converters
(Elsevier, 2013) Akar, N.; Raffaelli, C.; Savi, M.
This paper proposes new analytical models to study optical packet switching architectures with multi-fiber interfaces and shared wavelength converters. The multi-fiber extension of the recently proposed Shared-Per-Input-Wavelength (SPIW) scheme is compared against the multi-fiber Shared-Per-Node (SPN) scheme in terms of cost and performance for asynchronous traffic. In addition to using Markov chains and fixed-point iterations for modeling the mono-fiber case, a novel state aggregation technique is proposed to evaluate the packet loss in asynchronous multi-fiber scenario. The accuracy of the performance models is validated by comparison with simulations in a wide variety of scenarios with both balanced and imbalanced input traffic. The proposed analytical models are shown to remarkably capture the actual system behavior in all scenarios we tested. The adoption of multi-fiber interfaces is shown to achieve remarkable savings in the number of wavelength converters employed and their range. In addition, the SPIW solution allows to save, in particular conditions, a significant number of optical gates compared to the SPN solution. Indeed, SPIW allows, if properly dimensioned, potential complexity and cost reduction compared to SPN, while providing similar performance.
Open Access
The substrate temperature dependent electrical properties of titanium dioxide thin films
(2010) Yildiz, A.; Lisesivdin, S.B.; Kasap, M.; Mardare, D.
Titanium dioxide thin films were obtained by a dc sputtering technique onto heated glass substrates. The relationship between the substrate temperature and the electrical properties of the films was investigated. Electrical resistivity measurements showed that three types of conduction channels contribute to conduction mechanism in the temperature range of 13-320 K. The temperature dependence of electrical resistivity between 150 and 320 K indicated that electrical conductioninthe films was controlled by potential barriers caused by depletion of carriers at grain boundaries. The conduction mechanism of the films was shifted from grain boundary scattering dominated band conduction to the nearest neighbor hopping conduction at temperatures between 55 and 150 K. Below 55 K, the temperature dependence of electrical resistivity shows variable range hopping conduction. The correlation between the substrate temperature and resistivity behaviorisdiscussed by analyzing the physical plausibility of the hopping parameters and material properties derived by applying different conduction models. With these analyses, various electrical parameters of the present samples such as barrier height, donor concentration, density of states at the Fermi level, acceptor concentration and compensation ratio were determined. Their values as a function of substrate temperature were compared. © Springer Science+Business Media, LLC 2009.
Open Access
The two cultures and the crisis in the humanities
(Forum on Public Policy, 2007) Arndt, D.
The debate over the crisis in the humanities has focused on several disparate problems but failed to illuminate their underlying ground. To understand the crisis we have to understand the genealogy of the university and the origin of the humanities as a distinct set of disciplines. The university has been governed by four distinct models of higher education: the Christian university; the liberal arts college; the research university; and the commercial university. The more recent models have not simply replaced the older models; instead older institutions have been incorporated into more recent institutions and reinterpreted in light of their basic assumptions. “The humanities” first appeared as such within the liberal arts model, and the original aims of humanistic education were grounded in that model’s basic assumptions about the nature of truth, language, and tradition. The humanities were thrown into crisis when the liberal arts college was incorporated into the modern research university, and when the umanistic disciplines were detached from the assumptions that supported their original aims, reinterpreted in light of the assumptions about truth, language, and tradition underlying the research university, and recast in the mold of the modern sciences. To begin to respond to the crisis in the humanities we have to both recover and reinvent the idea of the liberal arts.
Open Access
VISIBIOweb: visualization and layout services for BioPAX pathway models
(Oxford University Press, 2010-06-01) Dilek, Alptuğ; Belviranlı, Mehmet E.; Doğrusöz, Uğur
With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within onés web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. © The Author(s) 2010. Published by Oxford University Press.