Sharif Digital Repository

Heart attack is one of the most common causes of death in the world. Coronary artery disease is the most recognized cause of heart attack whose onset and progression have been attributed to low-density lipoprotein (LDL) passing through the wall of the artery. In this paper, hemodynamic variables as well as the concentration of LDL through the coronary porous artery at the Left Anterior Descending coronary artery (LAD), and its first diagonal branch (D1) under the heart motion investigated using computational simulation. The geometry that has been studied in this paper is the first bifurcation of Left Anterior Descending (LAD) that has been placed on a perimeter of hypothetical sphere... 

Conventional electromyography-driven (EMG) musculoskeletal models are calibrated during maximum voluntary contraction (MVC) tasks, but individuals with low back pain cannot perform unbiased MVCs. To address this issue, EMG-driven models can be calibrated in submaximal tasks. However, the effects of maximal (when data points include the maximum contraction) and submaximal calibration techniques on model outputs (e.g., muscle forces, spinal loads) remain yet unknown. We calibrated a subject-specific EMG-driven model, using maximal/submaximal isometric contractions, and simulated different independent tasks. Both approaches satisfactorily predicted external moments (Pearson's correlation ∼... 

Passive finite element (FE) models of the spine are commonly used to simulate intact and various pre- and postoperative pathological conditions. Being devoid of muscles, these traditional models are driven by simplistic loading scenarios, e.g., a constant moment and compressive follower load (FL) that do not properly mimic the complex in vivo loading condition under muscle exertions. We aim to develop novel passive FE models that are driven by more realistic yet simple loading scenarios, i.e., in vivo vertebral rotations and pathological-condition dependent FLs (estimated based on detailed musculoskeletal finite element (MS-FE) models). In these novel force–displacement control FE models,... 

Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly... 

Stimulus presentation is believed to quench neural response variability as measured by fano-factor (FF). However, the relative contributions of within-trial spike irregularity and trial-to-trial rate variability to FF fluctuations have remained elusive. Here, we introduce a principled approach for accurate estimation of spiking irregularity and rate variability in time for doubly stochastic point processes. Consistent with previous evidence, analysis showed stimulus-induced reduction in rate variability across multiple cortical and subcortical areas. However, unlike what was previously thought, spiking irregularity, was not constant in time but could be enhanced due to factors such as... 

Atherosclerosis as a common cardiovascular disease is a result of both adverse hemodynamics conditions and monocyte deposition within coronary arteries. It is known that the adhesion of monocytes on the arterial wall and their interaction with the vascular surface are one of the main parameters in the initiation and progression of atherosclerosis. In this work, hemodynamic parameters and monocyte deposition have been investigated in a 3D computational model of the Left Anterior Descending coronary artery (LAD) and its first diagonal branch (D1) under the heart motion. A one-way Lagrangian approach is performed to trace the monocyte particles under different blood flow regimes and heart motion... 

Targeted drug delivery using nanocarriers (NCs) is one of the novel techniques that has recently been used to improve drug delivery to the Abdominal aortic aneurysm (AAA) disease. The purpose of this study is to evaluate the surface density of NCs (SDNC) adhered via ligand-receptor binding to the inner wall of AAA. For this purpose, fluid–structure interaction (FSI) analysis was first performed for the patient-specific and ideal AAA models. Then, by injecting NCs into the aortic artery, the values of SDNC adhered to and interacted with AAA wall were obtained. Two types of NCs, liposomes, and solid particles in four different diameters, were used to investigate the effect of the diameter and... 

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... 

Spine musculoskeletal (MS) models make simplifying assumptions on the intervertebral joint degrees-of-freedom (rotational and/or translational), representation (spherical or beam-like joints), and properties (linear or nonlinear). They also generally neglect the realistic structure of the joints with disc nuclei/annuli, facets, and ligaments. We aim to develop a novel MS model where trunk muscles are incorporated into a detailed finite element (FE) model of the ligamentous T12-S1 spine thus constructing a gold standard coupled MS-FE model. Model predictions are compared under some tasks with those of our earlier spherical joints, beam joints, and hybrid (uncoupled) MS-FE models. The coupled... 

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... 

This paper presents a novel ECG classification algorithm for inclusion as part of real-time cardiac monitoring systems in ultra low-power wearable devices. The proposed solution is based on spiking neural networks which are the third generation of neural networks. In specific, we employ spike-timing dependent plasticity (STDP), and reward-modulated STDP (R-STDP), in which the model weights are trained according to the timings of spike signals, and reward or punishment signals. Experiments show that the proposed solution is suitable for real-time operation, achieves comparable accuracy with respect to previous methods, and more importantly, its energy consumption in real-time classification... 

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... 

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... 

This study presents a novel statistical volume element (SVE) for micromechanical modeling of the white matter structures, with histology-informed randomized distribution of axonal tracts within the extracellular matrix. The model was constructed based on the probability distribution functions obtained from the results of diffusion tensor imaging as well as the histological observations of scanning electron micrograph, at two structures of white matter susceptible to traumatic brain injury, i.e. corpus callosum and corona radiata. A simplistic representative volume element (RVE) with symmetrical arrangement of fully alligned axonal fibers was also created as a reference for comparison. A... 

During pregnancy, traumas can threaten maternal and fetal health. Various trauma effects on a pregnant uterus are little investigated. In the present study, a finite element model of a uterus along with a fetus, placenta, amniotic fluid, and two most effective ligament sets is developed. This model allows numerical evaluation of various loading on a pregnant uterus. The model geometry is developed based on CT-scan data and validated using anthropometric data. Applying Ogden hyper-elastic theory, material properties of uterine wall and placenta are developed. After simulating the “rigid-bar” abdominal loading, the impact force and abdominal penetration are investigated. Findings are compared... 

The search for efficient chemotherapy drugs and other anti-cancer treatments would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. Because in vivo experimental methods are unable to isolate or control individual factors of the TME and in vitro models often do not include all the contributing factors, some questions are best addressed with systems biology mathematical models. In this work, we present a new fully-coupled, agent-based, multi-scale mathematical model of tumor growth, angiogenesis and metabolism that includes important aspects of the TME spanning subcellular-, cellular- and tissue-level scales. The mathematical model is... 

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 role of quantum tunneling in altering the structure of nucleotides to each other and causing a mutational event in DNA has been a topic of debate for years. Here, we introduce a new quantum mechanical approach for analyzing a typical point-mutation in DNA strands. Assuming each codon as a base state, a superposition of codon states could provide a physical description for a set of codons encoding the same amino acid and there are transition amplitudes between them. We choose the amino acids Phe and Ile as our understudy bio-systems which are encoded by two and three codons, respectively. We treat them as large quantum systems and use double- and triple-well potential models to study the... 

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...