Search for: models--biological
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    Global analysis of an SAIS model

    , Article Journal of Biological Dynamics ; Volume 6, Issue 2 , 2012 , Pages 457-474 ; 17513758 (ISSN) Razvan, M. R ; Yasaman, S ; Sharif University of Technology
    This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system  

    Real time simulation of grasping procedure of large internal organs during laparoscopic surgery

    , Article Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS ; Volume 2012 , 2012 , Pages 924-927 ; 1557170X (ISSN) Dehghani Ashkezari, H ; Mirbagheri, A ; Farahmand, F ; Behzadipour, S ; Firoozbakhsh, K ; Sharif University of Technology
    Surgical simulation systems facilitate safe and efficient training processes of surgical trainees by providing a virtual environment in which the surgical procedure can be repeated unlimitedly in a wide variety of situations. The present study attempted to develop a real time simulation system for the grasping procedure of large internal organs during laparoscopic surgery. A mass-spring-damper model was developed to simulate the nonlinear viscoelastic large deformations of the spleen tissue while interacting with a triple-jaw grasper. A novel collision detection algorithm was designed and implemented to determine the contact points between the tissue and the grasper jaws. Force or... 

    A meshless EFG-based algorithm for 3D deformable modeling of soft tissue in real-time

    , Article Studies in Health Technology and Informatics, 9 February 2012 through 11 February 2012 ; Volume 173 , February , 2012 , Pages 1-7 ; 09269630 (ISSN) ; 9781614990215 (ISBN) Abdi, E ; Farahmand, F ; Durali, M ; Sharif University of Technology
    The meshless element-free Galerkin method was generalized and an algorithm was developed for 3D dynamic modeling of deformable bodies in real time. The efficacy of the algorithm was investigated in a 3D linear viscoelastic model of human spleen subjected to a time-varying compressive force exerted by a surgical grasper. The model remained stable in spite of the considerably large deformations occurred. There was a good agreement between the results and those of an equivalent finite element model. The computational cost, however, was much lower, enabling the proposed algorithm to be effectively used in real-time applications  

    Quantitative determination of optical trapping strength and viscoelastic moduli inside living cells

    , Article Physical Biology ; Volume 10, Issue 4 , 2013 ; 14783967 (ISSN) Mas, J ; Richardson, A. C ; Reihani, S. N. S ; Oddershede, L. B ; Berg Sorensen, K ; Sharif University of Technology
    With the success of in vitro single-molecule force measurements obtained in recent years, the next step is to perform quantitative force measurements inside a living cell. Optical traps have proven excellent tools for manipulation, also in vivo, where they can be essentially non-invasive under correct wavelength and exposure conditions. It is a pre-requisite for in vivo quantitative force measurements that a precise and reliable force calibration of the tweezers is performed. There are well-established calibration protocols in purely viscous environments; however, as the cellular cytoplasm is viscoelastic, it would be incorrect to use a calibration procedure relying on a viscous environment.... 

    Self-organization of developing embryo using scale-invariant approach

    , Article Theoretical Biology and Medical Modelling ; Volume 8, Issue 1 , 2011 ; 17424682 (ISSN) Tiraihi, A ; Tiraihi, M ; Tiraihi, T ; Sharif University of Technology
    Background: Self-organization is a fundamental feature of living organisms at all hierarchical levels from molecule to organ. It has also been documented in developing embryos. Methods. In this study, a scale-invariant power law (SIPL) method has been used to study self-organization in developing embryos. The SIPL coefficient was calculated using a centro-axial skew symmetrical matrix (CSSM) generated by entering the components of the Cartesian coordinates; for each component, one CSSM was generated. A basic square matrix (BSM) was constructed and the determinant was calculated in order to estimate the SIPL coefficient. This was applied to developing C. elegans during early stages of... 

    Effect of input voltage frequency on the distribution of electrical stresses on the cell surface based on single-cell dielectrophoresis analysis

    , Article Scientific Reports ; Volume 10, Issue 1 , 2020 Dastani, K ; Moghimi Zand, M ; Kavand, H ; Javidi, R ; Hadi, A ; Valadkhani, Z ; Renaud, P ; Sharif University of Technology
    Nature Research  2020
    Electroporation is defined as cell membrane permeabilization under the application of electric fields. The mechanism of hydrophilic pore formation is not yet well understood. When cells are exposed to electric fields, electrical stresses act on their surfaces. These electrical stresses play a crucial role in cell membrane structural changes, which lead to cell permeabilization. These electrical stresses depend on the dielectric properties of the cell, buffer solution, and the applied electric field characteristics. In the current study, the effect of electric field frequency on the electrical stresses distribution on the cell surface and cell deformation is numerically and experimentally... 

    Relative efficiency of abdominal muscles in spine stability

    , Article Computer Methods in Biomechanics and Biomedical Engineering ; Volume 11, Issue 3 , 2008 , Pages 291-299 ; 10255842 (ISSN) Arjmand, N ; Shirazi Adl, A ; Parnianpour, M ; Sharif University of Technology
    Using an iterative kinematics-driven nonlinear finite element model, relative efficiency of individual abdominal muscles in spinal stability in upright standing posture was investigated. Effect of load height on stability and muscle activities was also computed under different coactivity levels in abdominal muscles. The internal oblique was the most efficient muscle (compared with the external oblique and rectus abdominus) in providing stability while generating smaller spinal loads with lower fatigue rate of muscles. As the weight was held higher, stability deteriorated requiring additional flexor-extensor activities. The stabilising efficacy of abdominal muscles diminished at higher... 

    Trunk biomechanical models based on equilibrium at a single-level violate equilibrium at other levels

    , Article European Spine Journal ; Volume 16, Issue 5 , 2007 , Pages 701-709 ; 09406719 (ISSN) Arjmand, N ; Shirazi Adl, A ; Parnianpour, M ; Sharif University of Technology
    Accurate estimation of muscle forces in various occupational tasks is critical for a reliable evaluation of spinal loads and subsequent assessment of risk of injury and management of back disorders. The majority of biomechanical models of multi-segmental spine estimate muscle forces and spinal loads based on the balance of net moments at a single level with no consideration for the equilibrium at remaining levels. This work aimed to quantify the extent of equilibrium violation and alterations in estimations when such models are performed at different levels. Results are compared with those of kinematics-driven model that satisfies equilibrium at all levels and EMG data. Regardless of the... 

    Tool-tissue force estimation in laparoscopic surgery using geometric features

    , Article Studies in Health Technology and Informatics ; Volume 184 , 2013 , Pages 225-229 ; 09269630 (ISSN) Kohani, M ; Behzadipour, S ; Farahmand, F ; Sharif University of Technology
    IOS Press  2013
    This paper introduces three geometric features, from deformed shape of a soft tissue, which demonstrate good correlation with probing force and maximum local stress. Using FEM simulation, 2D and 3D model of an in vivo porcine liver was built for different probing tasks. Maximum deformation angle, maximum deformation depth and width of displacement constraint of the reconstructed shape of the deformed body were calculated. Two neural networks were trained from these features and the calculated interaction forces. The features are shown to have high potential to provide force estimation either for haptic devices or to assess the damage to the tissue in large deformations of up to 40%  

    Retina-choroid-sclera permeability for ophthalmic drugs in the vitreous to blood direction: quantitative assessment

    , Article Pharmaceutical research ; Volume 30, Issue 1 , January , 2013 , Pages 41-59 ; 1573904X (ISSN) Haghjou, N ; Abdekhodaie, M. J ; Cheng, Y. L ; Sharif University of Technology
    To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

    An ellipsoidal model for studying response of head impacts

    , Article Acta of Bioengineering and Biomechanics ; Volume 12, Issue 1 , 2010 , Pages 47-53 ; 1509409X (ISSN) Heydari, M ; Jani, S ; Sharif University of Technology
    The objective of this study was to propose a new analytical model for studying response of head impacts. Head is modeled by fluidfilled ellipsoidal shell of inconstant thickness impacted by a solid elastic sphere. Modeling the head as an ellipsoid is more realistic than modeling it as a sphere, the previous model existing in the literature [3]-[8]. In this model, the effect of Hertzian contact stiffness and local shell stiffness are combined to derive explicit equations for impact duration, the peak force transmitted to head, and the head injury criterion. One of the advantages of the model presented is sensitivity to the site of impact. A comparison between the present analytical results... 

    Synchronizing hindmarsh-rose neurons over newman-watts networks

    , Article Chaos ; Volume 19, Issue 3 , 2009 ; 10541500 (ISSN) Jalili, M ; Sharif University of Technology
    American Institute of Physics Inc  2009
    In this paper, the synchronization behavior of the Hindmarsh-Rose neuron model over Newman-Watts networks is investigated. The uniform synchronizing coupling strength is determined through both numerically solving the network's differential equations and the master-stability-function method. As the average degree is increased, the gap between the global synchronizing coupling strength, i.e., the one obtained through the numerical analysis, and the strength necessary for the local stability of the synchronization manifold, i.e., the one obtained through the master-stability-function approach, increases. We also find that this gap is independent of network size, at least in a class of networks... 

    Dynamics of a magnetically rotated micro swimmer inspired by paramecium metachronal wave

    , Article Progress in Biophysics and Molecular Biology ; Volume 142 , 2019 , Pages 32-42 ; 00796107 (ISSN) Nematollahisarvestani, A ; Shamloo, A ; Sharif University of Technology
    Elsevier Ltd  2019
    In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple... 

    ECG denoising using parameters of ECG dynamical model as the states of an extended Kalman filter

    , Article 29th Annual International Conference of IEEE-EMBS, Engineering in Medicine and Biology Society, EMBC'07, Lyon, 23 August 2007 through 26 August 2007 ; 2007 , Pages 2548-2551 ; 05891019 (ISSN) ; 1424407885 (ISBN); 9781424407880 (ISBN) Sayadi, O ; Sameni, R ; Shamsollahi, M. B ; Sharif University of Technology
    In this paper an efficient Altering procedure based on the Extended Kalman Filter (EKF) has been proposed. The method is based on a modified nonlinear dynamic model, previously introduced for the generation of synthetic ECG signals. We have suggested simple dynamics as the governing equations for the model parameters. Since we have not any observation for these new state variables, they are considered as hidden states. Quantitative evaluation of the proposed algorithm on the MIT-BIH signals shows that an average SNR improvement of 12 dB is achieved for a signal of -5 dB. The results show improved output SNRs compared to the EKF outputs in the absence of these new dynamics. © 2007 IEEE  

    A correlative model to predict in vivo AUC for nanosystem drug delivery with release rate-limited absorption

    , Article Journal of Pharmacy and Pharmaceutical Sciences ; Volume 15, Issue 4 , 2012 , Pages 583-591 ; 14821826 (ISSN) Barzegar Jalali, M ; Mohammadi, K ; Mohammadi, G ; Valizadeh, H ; Barzegar Jalali, A ; Adibkia, K ; Nokhodchi, A ; Sharif University of Technology
    Purpose. Drug release from nanosystems at the sites of either absorption or effect biophase is a major determinant of its biological action. Thus, in vitro drug release is of paramount importance in gaining insight for the systems performance in vivo. Methods. A novel in vitro in vivo correlation, IVIVC, model denoted as double reciprocal area method was presented and applied to 19 drugs from 55 nano formulations with total 336 data, gathered from literature. Results. The proposed model correlated the in vitro with in vivo parameters with overall error of 12.4 ± 3.9%. Also the trained version of the model predicted the test formulations with overall error of 15.8 ± 3.7% indicating the... 

    Inferring causal molecular networks: Empirical assessment through a community-based effort

    , Article Nature Methods ; Volume 13, Issue 4 , 2016 , Pages 310-322 ; 15487091 (ISSN) Hill, S. M ; Heiser, L.M ; Cokelaer, T ; Linger, M ; Nesser, N. K ; Carlin, D. E ; Zhang, Y ; Sokolov, A ; Paull, E. O ; Wong, C. K ; Graim, K ; Bivol, A ; Wang, H ; Zhu, F ; Afsari, B ; Danilova, L. V ; Favorov, A. V ; Lee, W. S ; Taylor, D ; Hu, C. W ; Long, B. L ; Noren, D. P ; Bisberg, A. J ; Mills, G. B ; Gray, J. W ; Kellen, M ; Norman, T ; Friend, S ; Qutub, A. A ; Fertig, E. J ; Guan, Y ; Song, M ; Stuart, J. M ; Spellman, P. T ; Koeppl, H ; Stolovitzky, G ; Saez Rodriguez, J ; Mukherjee, S ; Afsari, B ; Al-Ouran, R ; Anton, B ; Arodz, T ; Askari Sichani, O ; Bagheri, N ; Berlow, N ; Bisberg, A. J ; Bivol, A ; Bohler, A ; Bonet, J ; Bonneau, R ; Budak, G ; Bunescu, R ; Caglar, M ; Cai, B ; Cai, C ; Carlin, D. E ; Carlon, A ; Chen, L ; Ciaccio, M. F ; Cokelaer, T ; Cooper, G ; Coort, S ; Creighton, C. J ; Daneshmand, S. M. H ; De La Fuente, A ; Di Camillo, B ; Danilova, L. V ; Dutta-Moscato, J ; Emmett, K ; Evelo, C ; Fassia, M. K. H ; Favorov, A. V ; Fertig, E. J ; Finkle, J. D ; Finotello, F ; Friend, S ; Gao, X ; Gao, J ; Garcia Garcia, J ; Ghosh, S ; Giaretta, A ; Graim, K ; Gray, J. W ; Großeholz, R ; Guan, Y ; Guinney, J ; Hafemeister, C ; Hahn, O ; Haider, S ; Hase, T ; Heiser, L. M ; Hill, S. M ; Hodgson, J ; Hoff, B ; Hsu, C. H ; Hu, C. W ; Hu, Y ; Huang, X ; Jalili, M ; Jiang, X ; Kacprowski, T ; Kaderali, L ; Kang, M ; Kannan, V ; Kellen, M ; Kikuchi, K ; Kim, D. C ; Kitano, H ; Knapp, B ; Komatsoulis, G ; Koeppl, H ; Krämer, A ; Kursa, M. B ; Kutmon, M ; Lee, W. S ; Li, Y ; Liang, X ; Liu, Z ; Liu, Y ; Long, B. L ; Lu, S ; Lu, X ; Manfrini, M ; Matos, M. R. A ; Meerzaman, D ; Mills, G. B ; Min, W ; Mukherjee, S ; Müller, C. L ; Neapolitan, R. E ; Nesser, N. K ; Noren, D. P ; Norman, T ; Oliva, B ; Opiyo, S. O ; Pal, R ; Palinkas, A ; Paull, E. O ; Planas Iglesias, J ; Poglayen, D ; Qutub, A. A ; Saez Rodriguez, J ; Sambo, F ; Sanavia, T ; Sharifi-Zarchi, A ; Slawek, J ; Sokolov, A ; Song, M ; Spellman, P. T ; Streck, A ; Stolovitzky, G ; Strunz, S ; Stuart, J. M ; Taylor, D ; Tegnér, J ; Thobe, K ; Toffolo, G. M ; Trifoglio, E ; Unger, M ; Wan, Q ; Wang, H ; Welch, L ; Wong, C. K ; Wu, J. J ; Xue, A. Y ; Yamanaka, R ; Yan, C ; Zairis, S ; Zengerling, M ; Zenil, H ; Zhang, S ; Zhang, Y ; Zhu, F ; Zi, Z ; Sharif University of Technology
    Nature Publishing Group  2016
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was... 

    A study of hyperelastic models for predicting the mechanical behavior of extensor apparatus

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 16, Issue 3 , 2017 , Pages 1077-1093 ; 16177959 (ISSN) Elyasi, N ; Karimi Taheri, K ; Narooei, K ; Karimi Taheri, A ; Sharif University of Technology
    Springer Verlag  2017
    In this research, the nonlinear elastic behavior of human extensor apparatus was investigated. To this goal, firstly the best material parameters of hyperelastic strain energy density functions consisting of the Mooney–Rivlin, Ogden, invariants, and general exponential models were derived for the simple tension experimental data. Due to the significance of stress response in other deformation modes of nonlinear models, the calculated parameters were used to study the pure shear and balance biaxial tension behavior of the extensor apparatus. The results indicated that the Mooney–Rivlin model predicts an unstable behavior in the balance biaxial deformation of the extensor apparatus, while the... 

    Digital implementation of a biological astrocyte model and its application

    , Article IEEE Transactions on Neural Networks and Learning Systems ; Volume 26, Issue 1 , 2014 , Pages 127-139 ; 2162237X (ISSN) Soleimani, H ; Bavandpour, M ; Ahmadi, A ; Abbott, D ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2014
    This paper presents a modified astrocyte model that allows a convenient digital implementation. This model is aimed at reproducing relevant biological astrocyte behaviors, which provide appropriate feedback control in regulating neuronal activities in the central nervous system. Accordingly, we investigate the feasibility of a digital implementation for a single astrocyte and a biological neuronal network model constructed by connecting two limit-cycle Hopf oscillators to an implementation of the proposed astrocyte model using oscillator-astrocyte interactions with weak coupling. Hardware synthesis, physical implementation on field-programmable gate array, and theoretical analysis confirm... 

    A stability-based model of a growing spine with adolescent idiopathic scoliosis: A combination of musculoskeletal and finite element approaches

    , Article Medical Engineering and Physics ; Volume 64 , 2019 , Pages 46-55 ; 13504533 (ISSN) Kamal, Z ; Rouhi, G ; Arjmand, N ; Adeeb, S ; Sharif University of Technology
    Elsevier Ltd  2019
    Using a combined musculoskeletal and finite element (FE) approach, this study aimed to evaluate stability-based muscle forces in a spine with adolescent idiopathic scoliosis (AIS) as compared to a normal spine; and subsequently, determine the effects of stress distribution on the growth plates (GPs) of the growing spine. For this purpose a nonlinear 3D FE model of one normal and one scoliotic thoracolumbar spine, consisting of GPs attached to rigid L1 to L4 vertebrae, were developed using computed tomography images coupled with a growth modulation using the Stokes’ model. Corresponding well with recent in-vivo and in-vitro studies, results of the models predicted intradiscal pressures at the... 

    1H NMR based metabolic profiling in Crohn's disease by random forest methodology

    , Article Magnetic Resonance in Chemistry ; Vol. 52, issue. 7 , July , 2014 , p. 370-376 Fathi, F ; Majari-Kasmaee, L ; Mani-Varnosfaderani, A ; Kyani, A ; Rostami-Nejad, M ; Sohrabzadeh, K ; Naderi, N ; Zali, M. R ; Rezaei-Tavirani, M ; Tafazzoli, M ; Arefi-Oskouie, A ; Sharif University of Technology
    The present study was designed to search for metabolic biomarkers and their correlation with serum zinc in Crohn's disease patients. Crohn's disease (CD) is a form of inflammatory bowel disease that may affect any part of the gastrointestinal tract and can be difficult to diagnose using the clinical tests. Thus, introduction of a novel diagnostic method would be a major step towards CD treatment.Proton nuclear magnetic resonance spectroscopy ( 1H NMR) was employed for metabolic profiling to find out which metabolites in the serum have meaningful significance in the diagnosis of CD. CD and healthy subjects were correctly classified using random forest methodology. The classification model for...