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    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
    Abstract
    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... 

    Disc size markedly influences concentration profiles of intravenously administered solutes in the intervertebral disc: A computational study on glucosamine as a model solute

    , Article European Spine Journal ; Vol. 23, issue. 4 , April , 2014 , p. 715-723 Motaghinasab, S ; Shirazi-Adl, A ; Parnianpour, M ; Urban, J. P. G ; Sharif University of Technology
    Abstract
    Purpose: Tests on animals of different species with large differences in intervertebral disc size are commonly used to investigate the therapeutic efficacy of intravenously injected solutes in the disc. We hypothesize that disc size markedly affects outcome. Methods: Here, using a small non-metabolized molecule, glucosamine (GL) as a model solute, we calculate the influence of disc size on transport of GL into rat, rabbit, dog and human discs for 10 h post intravenous-injection. We used transient finite element models and considered an identical GL supply for all animals. Results: Huge effects of disc size on GL concentration profiles were found. Post-injection GL concentration in the rat... 

    Simulation of movement in three-dimensional musculoskeletal human lumbar spine using directional encoding-based neurocontrollers

    , Article Journal of Biomechanical Engineering ; Vol. 136, issue. 9 , 2014 Nasseroleslami, B ; Vossoughi, G ; Boroushaki, M ; Parnianpour, M ; Sharif University of Technology
    Abstract
    Despite development of accurate musculoskeletal models for human lumbar spine, the methods for prediction of muscle activity patterns in movements lack proper association with corresponding sensorimotor integrations. This paper uses the directional information of the Jacobian of the musculoskeletal system to orchestrate adaptive critic-based fuzzy neural controller modules for controlling a complex nonlinear redundant musculoskeletal system. The proposed controller is used to control a 3D 3-degree of freedom (DOF) musculoskeletal model of trunk, actuated by 18 muscles. The controller is capable of learning to control from sensory information, without relying on pre-assumed model parameters.... 

    Diagnosis of early Alzheimer's disease based on EEG source localization and a standardized realistic head model

    , Article IEEE Journal of Biomedical and Health Informatics ; Volume 17, Issue 6 , 2013 , Pages 1039-1045 ; 21682194 (ISSN) Aghajani, H ; Zahedi, E ; Jalili, M ; Keikhosravi, A ; Vahdat, B. V ; Sharif University of Technology
    2013
    Abstract
    In this paper, distributed electroencephalographic (EEG) sources in the brain have been mapped with the objective of early diagnosis of Alzheimer's disease (AD). To this end, records from a montage of a high-density EEG from 17 early AD patients and 17 matched healthy control subjects were considered. Subjects were in eyes-closed, resting-state condition. Cortical EEG sources were modeled by the standardized low-resolution brain electromagnetic tomography (sLORETA) method. Relative logarithmic power spectral density values were obtained in the four conventional frequency bands (alpha, beta, delta, and theta) and 12 cortical regions. Results show that in the left brain hemisphere, the theta... 

    Protein fibrillation and nanoparticle interactions: Opportunities and challenges

    , Article Nanoscale ; Volume 5, Issue 7 , Jan , 2013 , Pages 2570-2588 ; 20403364 (ISSN) Mahmoudi, M ; Kalhor, H. R ; Laurent, S ; Lynch, I ; Sharif University of Technology
    2013
    Abstract
    Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,... 

    Optimal robust control of drug delivery in cancer chemotherapy: A comparison between three control approaches

    , Article Computer Methods and Programs in Biomedicine ; Volume 112, Issue 1 , 2013 , Pages 69-83 ; 01692607 (ISSN) Moradi, H ; Vossoughi, G ; Salarieh, H ; Sharif University of Technology
    2013
    Abstract
    During the drug delivery process in chemotherapy, both of the cancer cells and normal healthy cells may be killed. In this paper, three mathematical cell-kill models including log-kill hypothesis, Norton-Simon hypothesis and Emax hypothesis are considered. Three control approaches including optimal linear regulation, nonlinear optimal control based on variation of extremals and H∞-robust control based on μ-synthesis are developed. An appropriate cost function is defined such that the amount of required drug is minimized while the tumor volume is reduced. For the first time, performance of the system is investigated and compared for three control strategies; applied on three nonlinear models... 

    Discovering dominant pathways and signal-response relationships in signaling networks through nonparametric approaches

    , Article Genomics ; Volume 102, Issue 4 , October , 2013 , Pages 195-201 ; 08887543 (ISSN) Nassiri, I ; Masoudi Nejad, A ; Jalili, M ; Moeini, A ; Sharif University of Technology
    2013
    Abstract
    A signaling pathway is a sequence of proteins and passenger molecules that transmits information from the cell surface to target molecules. Understanding signal transduction process requires detailed description of the involved pathways. Several methods and tools resolved this problem by incorporating genomic and proteomic data. However, the difficulty of obtaining prior knowledge of complex signaling networks limited the applicability of these tools. In this study, based on the simulation of signal flow in signaling network, we introduce a method for determining dominant pathways and signal response to stimulations. The model uses topology-weighted transit compartment approach and comprises... 

    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
    2013
    Abstract
    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.... 

    Trajectory of human movement during sit to stand: A new modeling approach based on movement decomposition and multi-phase cost function

    , Article Experimental Brain Research ; Volume 229, Issue 2 , 2013 , Pages 221-234 ; 00144819 (ISSN) Sadeghi, M ; Andani, M. E ; Bahrami, F ; Parnianpour, M ; Sharif University of Technology
    2013
    Abstract
    The purpose of this work is to develop a computational model to describe the task of sit to stand (STS). STS is an important movement skill which is frequently performed in human daily activities, but has rarely been studied from the perspective of optimization principles. In this study, we compared the recorded trajectories of STS with the trajectories generated by several conventional optimization-based models (i.e., minimum torque, minimum torque change and kinetic energy cost models) and also with the trajectories produced by a novel multi-phase cost model (MPCM). In the MPCM, we suggested that any complex task, such as STS, is decomposable into successive motion phases, so that each... 

    A meta-model analysis of a finite element simulation for defining poroelastic properties of intervertebral discs

    , Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 227, Issue 6 , 2013 , Pages 672-682 ; 09544119 (ISSN) Nikkhoo, M ; Hsu, Y. C ; Haghpanahi, M ; Parnianpour, M ; Wang, J. L ; Sharif University of Technology
    2013
    Abstract
    Finite element analysis is an effective tool to evaluate the material properties of living tissue. For an interactive optimization procedure, the finite element analysis usually needs many simulations to reach a reasonable solution. The metamodel analysis of finite element simulation can be used to reduce the computation of a structure with complex geometry or a material with composite constitutive equations. The intervertebral disc is a complex, heterogeneous, and hydrated porous structure. A poroelastic finite element model can be used to observe the fluid transferring, pressure deviation, and other properties within the disc. Defining reasonable poroelastic material properties of the... 

    How well do the muscular synergies extracted via non-negative matrix factorisation explain the variation of torque at shoulder joint?

    , Article Computer Methods in Biomechanics and Biomedical Engineering ; Volume 16, Issue 3 , 2013 , Pages 291-301 ; 10255842 (ISSN) Moghadam, M. N ; Aminian, K ; Asghari, M ; Parnianpour, M ; Sharif University of Technology
    2013
    Abstract
    The way central nervous system manages the excess degrees of freedom to solve kinetic redundancy of musculoskeletal system remains an open question. In this study, we utilise the concept of synergy formation as a simplifying control strategy to find the muscle recruitment based on summation of identified muscle synergies to balance the biomechanical demands (biaxial external torque) during an isometric shoulder task. A numerical optimisation-based shoulder model was used to obtain muscle activation levels when a biaxial external isometric torque is imposed at the shoulder glenohumeral joint. In the numerical simulations, 12 different shoulder torque vectors in the transverse plane are... 

    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
    Abstract
    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%  

    Model-based needle control in prostate percutaneous procedures

    , Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 227, Issue 1 , 2013 , Pages 58-71 ; 09544119 (ISSN) Maghsoudi, A ; Jahed, M ; Sharif University of Technology
    2013
    Abstract
    In percutaneous applications, needle insertion into soft tissue is considered as a challenging procedure, and hence, it has been the subject of many recent studies. This study considers a model-based dynamics equation to evaluate the needle movement through prostate soft tissue. The proposed model estimates the applied force to the needle using the tissue deformation data and finite element model of the tissue. To address the role of mechanical properties of the soft tissue, an inverse dynamics control method based on sliding mode approach is used to demonstrate system performance in the presence of uncertainties. Furthermore, to deal with inaccurate estimation of mechanical parameters of... 

    Effect of microthread design of dental implants on stress and strain patterns: A three-dimensional finite element analysis

    , Article Biomedizinische Technik ; Volume 58, Issue 5 , September , 2013 , Pages 457-467 ; 00135585 (ISSN) Amid, R ; Raoofi, S ; Kadkhodazadeh, M ; Movahhedi, M. R ; Khademi, M ; Sharif University of Technology
    Walter de Gruyter and Co  2013
    Abstract
    The aim of this study was to use finite element analysis (FEA) to assess the influence of microthread design at the implant neck on stress distribution in the surrounding bone. A commercially available implant with 3.5 mm diameter and 10.5 mm length was selected and used as a model. For the purpose of designing the microthread implant model, microthreads were added to the implant neck in a computerized model. A force measuring 100 N was then applied to the entire surface of the abutment in the vertical direction. The results showed that in both models, stress was mainly concentrated at the cortical bone adjacent to the neck of the implant. Maximum stress values in the cortical bone... 

    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
    2013
    Abstract
    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 ×... 

    Prediction of particle deposition in the respiratory track using 3D-1D modeling

    , Article Scientia Iranica ; Volume 19, Issue 6 , December , 2012 , Pages 1479-1486 ; 10263098 (ISSN) Monjezi, M ; Dastanpour, R ; Saidi, M. S ; Pishevar, A. R ; Sharif University of Technology
    2012
    Abstract
    Airflow simulation of the whole respiratory system is still unfeasible due to the geometrical complexity of the lung airways and the diversity of the length scales involved in the problem. Even the new CT imaging system is not capable of providing accurate 3D geometries for smaller tubes, and a complete 3D simulation is impeded by the limited computational resources available. The aim of this study is to develop a fully coupled 3D-1D model to make accurate prediction of airflow and particle deposition in the whole respiratory track, with reasonable computational cost and efficiency. In the new proposed method, the respiratory tree is divided into three parts to be dealt with using different... 

    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
    2012
    Abstract
    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  

    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
    2012
    Abstract
    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 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
    2012
    Abstract
    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... 

    Computational pharmacokinetics of solute penetration into human intervertebral discs-Effects of endplate permeability, solute molecular weight and disc size

    , Article Journal of Biomechanics ; Volume 45, Issue 13 , 2012 , Pages 2195-2202 ; 00219290 (ISSN) Motaghinasab, S ; Shirazi Adl, A ; Urban, J. P. G ; Parnianpour, M ; Sharif University of Technology
    Abstract
    A finite element model is developed to predict the penetration time-history of three different solutes into the human lumbar disc following intravenous injection. Antibiotics are routinely administered intravenously in spinal surgery to prevent disc infection. Successful prophylaxis requires antibiotics to reach adequate inhibitory levels. Here, the transient diffusion of cephazolin is investigated over 10. h post-injection in a human disc model subject to reported concentrations in the blood stream as the prescribed boundary sources. Post-injection variation of cephazolin concentrations in the disc adjacent to supply sources closely followed the decay curve in the blood stream and fell...