Sharif Digital Repository

Instrumental responses are hypothesized to be of two kinds: habitual and goal-directed, mediated by the sensorimotor and the associative cortico-basal ganglia circuits, respectively. The existence of the two heterogeneous associative learning mechanisms can be hypothesized to arise from the comparative advantages that they have at different stages of learning. In this paper, we assume that the goal-directed system is behaviourally flexible, but slow in choice selection. The habitual system, in contrast, is fast in responding, but inflexible in adapting its behavioural strategy to new conditions. Based on these assumptions and using the computational theory of reinforcement learning, we... 

This study investigates the effect of body acceleration on human cardiac function. Finite element analysis is conducted to simulate geometrical and mechanical properties of human heart. Heart geometrical modeling in three-dimension is performed by segmentation of cardiac MRI images. The nonlinear mechanical behavior of myocardium is modeled by Mooney-Rivlin, Polynomial, Ogden and Yeoh hyperelastic material models. Stress-strain curves of myocardial tissue are obtained from experimental compression tests on bovine heart samples. The experimental results are employed for the evaluation of material coefficients by the nonlinear least squares method. Among hyperelastic models, the Yeoh model... 

A hallmark of more advanced models is their higher details of trunk muscles represented by a larger number of muscles. The question is if in reality we control these muscles individually as independent agents or we control groups of them called "synergy". To address this, we employed a 3-D biomechanical model of the spine with 18 trunk muscles that satisfied equilibrium conditions at L4/5, with different cost functions. The solutions of several 2-D and 3-D tasks were arranged in a data matrix and the synergies were computed by using non-negative matrix factorization (NMF) algorithms. Variance accounted for (VAF) was used to evaluate the number of synergies that emerged by the analysis, which... 

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... 

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... 

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... 

An essential input to the musculoskeletal (MS) trunk models that estimate muscle and spine forces is kinematics of the thorax, pelvis, and lumbar vertebrae. While thorax and pelvis kinematics are usually measured via skin motion capture devices (with inherent errors on the proper identification of the underlying bony landmarks and the relative skin-sensor-bone movements), those of the intervening lumbar vertebrae are commonly approximated at fixed proportions based on the thorax-pelvis kinematics. This study proposes an image-based kinematics measurement approach to drive subject-specific (musculature, geometry, mass, and center of masses) MS models. Kinematics of the thorax, pelvis, and... 

In this paper, a constitutive and micromechanical model for prediction of rate-dependent behavior of connective tissues (CTs) is presented. Connective tissues are considered as nonlinear viscoelastic material. The rate-dependent behavior of CTs is incorporated into model using the well-known quasi-linear viscoelasticity (QLV) theory. A planar wavy representative volume element (RVE) is considered based on the tissue microstructure histological evidences. The presented model parameters are identified based on the available experiments in the literature. The presented constitutive model introduced to ABAQUS by means of UMAT subroutine. Results show that, monotonic uniaxial test predictions of... 

Background: Sudden trunk perturbations occur in various occupational and sport activities. Despite numerous measurement studies, no comprehensive modeling simulations have yet been attempted to investigate trunk biodynamics under sudden loading/unloading. Methods: Dynamic kinematics-driven approach was used to evaluate the temporal variation of trunk muscle forces, internal loads and stability before and after a sudden release of a posterior horizontal load. Measured post-disturbance trunk kinematics, as input, and muscle electromyography (EMG) activities, for qualitative validation, were considered. Findings: Computed agonist and antagonist muscle forces before and after release agreed well... 

In this study, the influence of vascular bed comprising terminal arterial branches on heat transfer in a liver tumor exposed to high intensity focused ultrasound (HIFU) is studied numerically. Also, the effect of vascular density on temperature distribution is investigated. A coupled set of acoustics, thermal, and fluid models is used to calculate the temperature distribution in the liver. The numerical model is established based on the Westervelt and bioheat equations along with the Navier-Stokes equations. Moreover, the acoustic streaming effect is included with Newtonian and non-Newtonian flow assumptions. It is found that in a vascular bed comprising terminal arterial branches, the... 

Background: The purpose of this study was to propose a methodology for mechanical characterization of the ligaments in subject-specific models of the patellofemoral joint (PFJ) of living individuals. Method: PFJ laxity tests were performed on a healthy volunteer using a specially designed loading apparatus under biplane fluoroscopy. A three-dimensional (3D) parametric model of the PFJ was developed in the framework of the rigid body spring model using the geometrical data acquired from the subject's computed tomography and magnetic resonance images. The stiffness and pre-strains of the medial and lateral PFJ ligaments were characterized using a two-step optimization procedure which minimized... 

The present study investigates the diversification and dynamic behavior of a multi-population microfluidic microbial fuel cell (MFC) as a biosensor. The cost effective microfluidic MFC coupled to a comprehensive model, presents a novel platform for monitoring chemical and biological phenomena. The importance of competition among different microbial groups, hierarchical biochemical processes, bacterial chemotaxis and different mechanisms of electron transfer were significant considerations in the present model. The validation of the model using experimental data from a microfluidic MFC shows an appropriate match with the hierarchal biodegradation processes of a complex substrate as well as... 

Traditional load-control musculoskeletal and finite element (FE) models of the spine fail to accurately predict in vivo intervertebral joint loads due mainly to the simplifications and assumptions when estimating redundant trunk muscle forces. An alternative powerful protocol that bypasses the calculation of muscle forces is to drive the detailed FE models by image-based in vivo displacements. Development of subject-specific models, however, both involves the risk of extensive radiation exposures while imaging in supine and upright postures and is time consuming in terms of the reconstruction of the vertebrae, discs, ligaments, and facets geometries. This study therefore aimed to introduce a... 

Laccase production by indigenous fungus, Phanerochaete chrysosporium, requires solving optimal problems to determine the maximum production of the enzyme within a definite time period and conditions specified in the solid-state fermentation process. For this purpose, parallel to response surface methodology, an analytical approach has been proposed based on the advanced concepts of Poisson geometry and Lie groups, which lead to a system of the Hamiltonian equations. Despite the dating of the Hamiltonian approach to solving biological problems, the novelty of this paper is based on the expression of a Hamiltonian system in notions of Poisson geometry, Lie algebras and symmetry groups and... 

In this work, a mathematical model was developed to simulate the urinary concentration mechanism. A 3-D geometry was derived based on the detail physiological pictures of rat kidney. The approximate region of each tubule was obtained from the volume distribution of structures based on Walter Pfaller's monograph and Layton's region-based model. Mass and momentum balances were applied to solve for the change in solutes concentration and osmolality. The osmolality of short and long descending nephrons at the end of the outer medulla was obtained to be 530 mOsmol/kgH2O and 802 mOsmol/kgH2O, respectively, which were in acceptable agreement with experimental data. The fluid osmolality of the short... 

The Calcium ion Ca2+ plays a critical role as an initiator and preserving agent of the cross-bridge cycle in the force generation of skeletal muscle. A new multi-scale chemo-mechanical model is presented in order to analyze the role of Ca2+ in muscle fatigue and to predict fatigue behavior. To this end, a cross-bridge kinematic model was incorporated in a continuum based mechanical model, considering a thermodynamic compatible framework. The contractile velocity and the generated active force were directly related to the force-bearing states that were considered for the cross-bridge cycle. In order to determine the values of the model parameters, the output results of an isometric simulation... 

Biomechanical modeling approaches require body posture to evaluate the risk of spine injury during manual material handling. The procedure to measure body posture via motion-analysis techniques as well as the subsequent calculations of lumbosacral moments and spine loads by, respectively, inverse-dynamic and musculoskeletal models are complex and time-consuming. We aim to develop easy-to-use yet accurate artificial neural networks (ANNs) that predict 3D whole-body posture (ANNposture), segmental orientations (ANNangle), and lumbosacral moments (ANNmoment) based on our measurements during load-handling activities. Fifteen individuals each performed 135 load-handling activities by reaching (0... 

The effect of the variation in the femoral groove geometry on patellofemoral joint stability was studied using a two dimensional transverse plane model with deformable articular surfaces. The femoral and patellar bony structures were modelled as rigid bodies with their profiles expressed by splines. The articular cartilage was discretized into compression springs, distributed along the femoral and patellar profiles, based on the rigid-body spring model. The medial and lateral retinacula were modelled as linear tensile springs, and the quadriceps muscles and patellar tendon as strings with known tension. The anatomical data were obtained from the transverse plane magnetic resonance images of... 

In this paper, a heuristic method for determining the optimal number of clusters is proposed. Four clustering algorithms, namely K-means, Growing Neural Gas, Simulated Annealing based technique, and Fuzzy C-means in conjunction with three well known cluster validity indices, namely Davies-Bouldin index, Calinski-Harabasz index, Maulik-Bandyopadhyay index, in addition to the proposed index are used. Our simulations evaluate capability of mentioned indices in some artificial and medical datasets. © 2008 IEEE  

Irregular hemodynamics affects the progression of various vascular diseases, such atherosclerosis or aneurysms. Despite the extensive hemodynamics studies on animal models, the inter-species differences between humans and animals hamper the translation of such findings. Recent advances in vascular tissue engineering and the suitability ofin vitromodels for interim analysis have increased the use ofin vitrohuman vascular tissue models. Although the effect of flow on endothelial cell (EC) pathophysiology and EC-flow interactions have been vastly studied in two-dimensional systems, they cannot be used to understand the effect of other micro- and macro-environmental parameters associated with...