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biological-model
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Total 110 records
Tertiary Treatment of Arak Refinery Dilute Wastewater by Moving Bed Biofilm Reactor (MBBR) Combined with Flocculation and Coagulation Process
, M.Sc. Thesis Sharif University of Technology ;
Abstract
In this research, the capability of an aerobic moving bed biofilm reactor (MBBR) for removal of phenol from Arak refinery dilute wastewater has been investigated. A cubical MBBR with approximate capacity of 10 liters was filled with Kaldnes-K1 biocarriers at filling ratio at 50 percent. Moreover, The MBBR which filled with actual refinery wastewater, combined with Flocculation and Coagulation in order to removing more COD, turbidity and TSS and also reaching to criterion that water can be used by cooling tower. The effects of Phenol concentration (10-100 mgl-1), COD concentration (50-500 mgl-1), Hydraulic Retention Time (HRT) (4-12 h) and Phenol shocks on the performance of MBBR were...
Optimization of Radiotherapy Plan under Uncertainty
, M.Sc. Thesis Sharif University of Technology ; Rafiee, Majid (Supervisor)
Abstract
As a method of cancer treatment or improvement of cancer-related complications, external radiation therapy is prescribed by physicians, in case of detection of a tumor in a region of patient’s body. Over time, various techniques have been developed for external beam radiation therapy. Among which, Intensity Modulated Radiation Therapy (IMRT), due to its ability to adjust the intensity of radiation beams, has a higher capacity to generate appropriate dose distribution based on tumor size and volume and it is one of the most widely used techniques in cancer treatment centers.The core process in treatment planning is using appropriate computer algorithms which results in posing enough damage to...
Hybrid multiscale modeling and prediction of cancer cell behavior
, Article PLoS ONE ; Volume 12, Issue 8 , 2017 ; 19326203 (ISSN) ; Habibi, J ; Sharif University of Technology
Public Library of Science
2017
Abstract
Background: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for...
Experimental feasibility study of estimation of the normalized central blood pressure waveform from radial photoplethysmogram
, Article Journal of Healthcare Engineering ; Volume 6, Issue 1 , 2015 , Pages 121-144 ; 20402295 (ISSN) ; Sohani, V ; Mohd. Ali, M. A ; Chellappan, K ; Beng, G. K ; Sharif University of Technology
Multi-Science Publishing Co. Ltd
2015
Abstract
The feasibility of a novel system to reliably estimate the normalized central blood pressure (CBPN ) from the radial photoplethysmogram (PPG) is investigated. Right-wrist radial blood pressure and left-wrist PPG were simultaneously recorded in five different days. An industry-standard applanation tonometer was employed for recording radial blood pressure. The CBP waveform was amplitude-normalized to determine CBPN . A total of fifteen second-order autoregressive models with exogenous input were investigated using system identification techniques. Among these 15 models, the model producing the lowest coefficient of variation (CV) of the fitness during the five days was...
Search for critical loading condition of the spine-A meta analysis of a nonlinear viscoelastic finite element model
, Article Computer Methods in Biomechanics and Biomedical Engineering ; Volume 8, Issue 5 , 2005 , Pages 323-330 ; 10255842 (ISSN) ; Shirazi Adl, A ; Parnianpour, M ; Sharif University of Technology
2005
Abstract
The relative vulnerability of spinal motion segments to different loading combinations remains unknown. The meta-analysis described here using the results of a validated L2-L3 nonlinear viscoelastic finite element model was designed to investigate the critical loading and its effect on the internal mechanics of the human lumbar spine. A Box-Behnken experimental design was used to design the magnitude of seven independent variables associated with loads, rotations and velocity of motion. Subsequently, an optimization method was used to find the primary and secondary variables that influence spine mechanical output related to facet forces, disc pressure, ligament forces, annulus matrix...
Modeling of interaction between a three-fingered surgical grasper and human spleen
, Article Studies in Health Technology and Informatics, 9 February 2011 through 12 February 2011, Newport Beach, CA ; Volume 163 , 2011 , Pages 663-669 ; 09269630 (ISSN) ; 9781607507055 (ISBN) ; Mirbagheri, A ; Asghari, M ; Farahmand, F ; Sharif University of Technology
2011
Abstract
The aim of this study was to develop a more sophisticated model of the spleen tissue and investigate its interactions with a three-fingered laparoscopic grasper. The spleen tissue, modeled as a hyper viscoelastic material, was subjected to external loadings, imposed by rigid grasping jaws. The tissue deformation as well as the sliding occurrence between tissue and jaws was investigated using nonlinear finite element method. Results indicated that a grasping configuration which aimed a sufficiently large piece of spleen with small radius of curvature was more successful for effective grasping. The trends and magnitudes of the tooltissue interaction forces obtained during effective and...
Emergence of molecular chirality due to chiral interactions in a biological environment
, Article Journal of Biological Physics ; Vol. 40, issue. 4 , Jul , 2014 , p. 369-386 ; Ghahramani, F. T ; Shafiee, A ; Sharif University of Technology
Abstract
We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and...
Self-organization of developing embryo using scale-invariant approach
, Article Theoretical Biology and Medical Modelling ; Volume 8, Issue 1 , 2011 ; 17424682 (ISSN) ; Tiraihi, M ; Tiraihi, T ; Sharif University of Technology
2011
Abstract
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...
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) ; Bavandpour, M ; Ahmadi, A ; Abbott, D ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2014
Abstract
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...
Modeling, simulation, and optimal initiation planning for needle insertion into the liver
, Article Journal of Biomechanical Engineering ; Volume 132, Issue 4 , 2010 ; 01480731 (ISSN) ; Ahmadian, M. T ; Janabi Sharifi, F ; Sharif University of Technology
2010
Abstract
Needle insertion simulation and planning systems (SPSs) will play an important role in diminishing inappropriate insertions into soft tissues and resultant complications. Difficulties in SPS development are due in large part to the computational requirements of the extensive calculations in finite element (FE) models of tissue. For clinical feasibility, the computational speed of SPSs must be improved. At the same time, a realistic model of tissue properties that reflects large and velocity-dependent deformations must be employed. The purpose of this study is to address the aforementioned difficulties by presenting a cost-effective SPS platform for needle insertions into the liver. The study...
A foreign body response-on-a-chip platform
, Article Advanced Healthcare Materials ; Volume 8, Issue 4 , 2019 ; 21922640 (ISSN) ; Htwe, S. S ; Righi, M ; Liu, H ; Pietralunga, A ; Yesil Celiktas, O ; Maharjan, S ; Cha, B. H ; Shin, S. R ; Dokmeci, M. R ; Vrana, N. E ; Ghaemmaghami, A. M ; Khademhosseini, A ; Zhang, Y. S ; Sharif University of Technology
Wiley-VCH Verlag
2019
Abstract
Understanding the foreign body response (FBR) and desiging strategies to modulate such a response represent a grand challenge for implant devices and biomaterials. Here, the development of a microfluidic platform is reported, i.e., the FBR-on-a-chip (FBROC) for modeling the cascade of events during immune cell response to implants. The platform models the native implant microenvironment where the implants are interfaced directly with surrounding tissues, as well as vasculature with circulating immune cells. The study demonstrates that the release of cytokines such as monocyte chemoattractant protein 1 (MCP-1) from the extracellular matrix (ECM)-like hydrogels in the bottom tissue chamber...
Fluid–structure interaction simulation of a cerebral aneurysm: effects of endovascular coiling treatment and aneurysm wall thickening
, Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 74 , 2017 , Pages 72-83 ; 17516161 (ISSN) ; Nejad, M. A ; Saeedi, M ; Sharif University of Technology
Abstract
In the present study, we investigate the effect of the hemodynamic factors of the blood flow on the cerebral aneurysms. To this end, a hypothetical geometry of the aneurysm in the circle of Willis, located in the bifurcation point of the anterior cerebral artery (ACA) and anterior communicating artery (ACoA) is modeled in a three-dimensional manner. Three cases are chosen in the current study: an untreated thin wall (first case), untreated thick wall (second case), and a treated aneurysm (third case). The effect of increasing the aneurysm wall thickness on the deformation and stress distribution of the walls are studied. The obtained results showed that in the second case, a reduction in the...
Using distance on the Riemannian manifold to compare representations in brain and in models
, Article NeuroImage ; Volume 239 , 2021 ; 10538119 (ISSN) ; Shirali, A ; Aghajan, H ; Nili, H ; Sharif University of Technology
Academic Press Inc
2021
Abstract
Representational similarity analysis (RSA) summarizes activity patterns for a set of experimental conditions into a matrix composed of pairwise comparisons between activity patterns. Two examples of such matrices are the condition-by-condition inner product and correlation matrix. These representational matrices reside on the manifold of positive semidefinite matrices, called the Riemannian manifold. We hypothesize that representational similarities would be more accurately quantified by considering the underlying manifold of the representational matrices. Thus, we introduce the distance on the Riemannian manifold as a metric for comparing representations. Analyzing simulated and real fMRI...
Feedback control of the neuromusculoskeletal system in a forward dynamics simulation of stair locomotion
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 223, Issue 6 , 2009 , Pages 663-675 ; 09544119 (ISSN) ; Meghdari, A ; Vossoughi, G ; Sharif University of Technology
2009
Abstract
The aim of this study is to employ feedback control loops to provide a stable forward dynamics simulation of human movement under repeated position constraint conditions in the environment, particularly during stair climbing. A ten-degrees-of-freedom skeletal model containing 18 Hill-type musculotendon actuators per leg was employed to simulate the model in the sagittal plane. The postural tracking and obstacle avoidance were provided by the proportional-integral-derivative controller according to the modulation of the time rate change of the joint kinematics. The stability of the model was maintained by controlling the velocity of the body's centre of mass according to the desired centre of...
Utility of a nonlinear joint dynamical framework to model a pair of coupled cardiovascular signals
, Article IEEE Journal of Biomedical and Health Informatics ; Volume 17, Issue 4 , 2013 , Pages 881-890 ; 21682194 (ISSN) ; Shamsollahi, M. B ; Sharif University of Technology
2013
Abstract
We have recently proposed a correlated model to provide a Gaussian mixture representation of the cardiovascular signals, with promising results in identifying rhythm disturbances. The approach provides a transformation of the data into a set of integrable Gaussians distributed over time. Looking into the model from a new joint modeling perspective, it is capable of assembling a filtered estimation, and can be used to derive temporal information of the waveforms. In this paper, we present a step-by-step derivation of the joint model putting correlation assumptions together to conclude a minimal joint description for a pair of ECG-ABP signals. We then probe novel applications of this model,...
Synthetic ECG generation and bayesian filtering using a Gaussian wave-based dynamical model
, Article Physiological Measurement ; Volume 31, Issue 10 , 2010 , Pages 1309-1329 ; 09673334 (ISSN) ; Shamsollahi, M. B ; Clifford, G. D ; Sharif University of Technology
2010
Abstract
In this paper, we describe a Gaussian wave-based state space to model the temporal dynamics of electrocardiogram (ECG) signals. It is shown that this model may be effectively used for generating synthetic ECGs as well as separate characteristic waves (CWs) such as the atrial and ventricular complexes. The model uses separate state variables for each CW, i.e. P, QRS and T, and hence is capable of generating individual synthetic CWs as well as realistic ECG signals. The model is therefore useful for generating arrhythmias. Simulations of sinus bradycardia, sinus tachycardia, ventricular flutter, atrial fibrillation and ventricular tachycardia are presented. In addition, discrete versions of...
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) ; Sameni, R ; Shamsollahi, M. B ; Sharif University of Technology
2007
Abstract
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
Validation of the revised stressful life event questionnaire using a hybrid model of genetic algorithm and artificial neural networks
, Article Computational and Mathematical Methods in Medicine ; Volume 2013 , 2013 ; 1748670X (ISSN) ; Roohafza, H ; Sadeghi, M ; Andalib, E ; Shavandi, H ; Sarrafzadegan, N ; Sharif University of Technology
2013
Abstract
Objectives. Stressors have a serious role in precipitating mental and somatic disorders and are an interesting subject for many clinical and community-based studies. Hence, the proper and accurate measurement of them is very important. We revised the stressful life event (SLE) questionnaire by adding weights to the events in order to measure and determine a cut point. Methods. A total of 4569 adults aged between 18 and 85 years completed the SLE questionnaire and the general health questionnaire-12 (GHQ-12). A hybrid model of genetic algorithm (GA) and artificial neural networks (ANNs) was applied to extract the relation between the stressful life events (evaluated by a 6-point Likert scale)...
Extreme bendability of DNA double helix due to bending asymmetry
, Article Journal of Chemical Physics ; Volume 143, Issue 10 , 2015 ; 00219606 (ISSN) ; Eslami Mossallam, B ; Naderi, S ; Ejtehadi, M. R ; Sharif University of Technology
American Institute of Physics Inc
2015
Abstract
Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule...
Phenomenological tissue fracture modeling for an Endoscopic Sinus and Skull Base Surgery training system based on experimental data
, Article Medical Engineering and Physics ; Volume 68 , 2019 , Pages 85-93 ; 13504533 (ISSN) ; Farahmand, F ; Vossoughi, G ; Moradi, H ; Mousa Sadr Hosseini, S ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
The ideal simulator for Endoscopic Sinus and Skull Base Surgery (ESSS)training must be supported by a physical model and provide repetitive behavior in a controlled environment. Development of realistic tissue models is a key part of ESSS virtual reality (VR)-based surgical simulation. Considerable research has been conducted to address haptic or force feedback and propose a phenomenological tissue fracture model for sino-nasal tissue during surgical tool indentation. Mechanical properties of specific sino-nasal regions of the sheep head have been studied in various indentation and relaxation experiments. Tool insertion at different indentation rates into coronal orbital floor (COF)tissue is...