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biological-model
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The effect of angle and level of exertion on trunk neuromuscular performance during multidirectional isometric activities
, Article Spine ; Volume 34, Issue 5 , 2009 , Pages E170-E177 ; 03622436 (ISSN) ; Olyaei, G. R ; Talebian, S ; Sanjari, M. A ; Parnianpour, M ; Sharif University of Technology
2009
Abstract
STUDY DESIGN.: To quantify trunk muscle capability and controllability in different angles and levels of isometric exertion using a torque tracking system. OBJECTIVE.: To investigate the effect of biaxial isometric exertions on the maximum capability of trunk and to examine the effect of angle and level of isometric exertion on trunk controllability during the tracking task in upright posture. SUMMARY OF BACKGROUND DATA.: Combined motions of trunk at varying exertion levels occur in most daily and occupational activities and are important risk factors of low back pain. Few studies have investigated trunk capability and controllability during multidirectional activities with different...
A quantum mechanical approach towards the calculation of transition probabilities between DNA codons
, Article BioSystems ; Volume 184 , 2019 ; 03032647 (ISSN) ; Shafiee, A ; Sharif University of Technology
Elsevier Ireland Ltd
2019
Abstract
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...
Early cancer detection in blood vessels using mobile nanosensors
, Article IEEE Transactions on Nanobioscience ; Volume 18, Issue 2 , 2019 , Pages 103-116 ; 15361241 (ISSN) ; Ahmadzadeh, A ; Wicke, W ; Jamali, V ; Schober, R ; Nasiri Kenari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2019
Abstract
In this paper, we propose using mobile nanosensors (MNSs) for early stage anomaly detection. For concreteness, we focus on the detection of cancer cells located in a particular region of a blood vessel. These cancer cells produce and emit special molecules, so-called biomarkers, which are symptomatic for the presence of anomaly, into the cardiovascular system. Detection of cancer biomarkers with conventional blood tests is difficult in the early stages of a cancer due to the very low concentration of the biomarkers in the samples taken. However, close to the cancer cells, the concentration of the cancer biomarkers is high. Hence, detection is possible if a sensor with the ability to detect...
Statistical association mapping of population-structured genetic data
, Article IEEE/ACM Transactions on Computational Biology and Bioinformatics ; Volume 16, Issue 2 , 2019 , Pages 636-649 ; 15455963 (ISSN) ; Janghorbani, S ; Motahari, A ; Fatemizadeh, E ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2019
Abstract
Association mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the associated sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease-associated factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability...
Rigid-bar loading on pregnant uterus and development of pregnant abdominal response corridor based on finite element biomechanical model
, Article International Journal for Numerical Methods in Biomedical Engineering ; Volume 36, Issue 1 , January , 2020 ; Ahmadian, M. T ; Mohammadi, H ; Sharif University of Technology
Wiley-Blackwell
2020
Abstract
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...
A multi-scale model for determining the effects of pathophysiology and metabolic disorders on tumor growth
, Article Scientific Reports ; Volume 10, Issue 1 , 20 February , 2020 ; Firoozabadi, B ; Mozafari, A ; Munn, L. L ; Sharif University of Technology
Nature Research
2020
Abstract
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...
Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores
, Article Journal of Chemical Physics ; Volume 129, Issue 23 , 2008 ; 00219606 (ISSN) ; Roshani, F ; Nourmohammad, A ; Sahimi, M ; Rahimi Tabar, M. R ; Sharif University of Technology
2008
Abstract
We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the...
A new approach to C2 continuous piecewise bicubic representation of the articular surfaces of diarthrodial joints
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 220, Issue 4 , 2006 , Pages 553-563 ; 09544119 (ISSN) ; Farahmand, F ; Meghdari, A ; Golestanha, A. S ; Sharif University of Technology
2006
Abstract
Based on the force-deflection equation for a beam subjected to lateral point loads, a C2 continuous piecewise bicubic mathematical representation was proposed to model complicated geometrical surfaces, e.g. the articular surfaces of human joints. The method was then extended so that it could be used for mathematical modelling of incomplete nets of data points, as well as smoothing of noisy and/or filtering of erroneous data points. Mathematical techniques were also developed to calculate the required unknown parameters explicitly, with no need to solve the system of equations simultaneously. The performance of the proposed method was evaluated on a number of surface modelling problems,...
Drug delivery performance of nanocarriers based on adhesion and interaction for abdominal aortic aneurysm treatment
, Article International Journal of Pharmaceutics ; Volume 594 , 2021 ; 03785173 (ISSN) ; Vatani, P ; Amani, A ; Shamloo, A ; Sharif University of Technology
Elsevier B.V
2021
Abstract
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...
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...
Numerical study of the effect of hemodynamic variables on LDL concentration through the single layer of the Left Anterior Descending coronary artery (LAD) under the heart pulse
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 236, Issue 7 , 2022 , Pages 994-1008 ; 09544119 (ISSN) ; Seyedhossein, S. S ; Firoozabadi, B ; MomeniLarimi, M ; Sharif University of Technology
SAGE Publications Ltd
2022
Abstract
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...
Submaximal electromyography-driven musculoskeletal modeling of the human trunk during static tasks: Equilibrium and stability analyses
, Article Journal of Electromyography and Kinesiology ; Volume 65 , 2022 ; 10506411 (ISSN) ; Shirazi Adl, A ; Gagnon, D ; Shahvarpour, A ; Arjmand, N ; Eskandari, A. H ; Larivière, C ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
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 ∼...
Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions
, Article PLoS Computational Biology ; Volume 18, Issue 7 , 2022 ; 1553734X (ISSN) ; Fakharian, M. A ; Ghazizadeh, A ; Sharif University of Technology
Public Library of Science
2022
Abstract
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...
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 ; 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....
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,...
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) ; 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...
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) ; 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...
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) ; 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...
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) ; 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...
Prediction of shape and internal structure of the proximal femur using a modified level set method for structural topology optimisation
, Article Computer Methods in Biomechanics and Biomedical Engineering ; Volume 15, Issue 8 , 2012 , Pages 835-844 ; 10255842 (ISSN) ; Farahmand, F ; Rouhi, G ; Movahhedy, M. R ; Sharif University of Technology
Abstract
A computational framework was developed to simulate the bone remodelling process as a structural topology optimisation problem. The mathematical formulation of the Level Set technique was extended and then implemented into a coronal plane model of the proximal femur to simulate the remodelling of internal structure and external geometry of bone into the optimal state. Results indicated that the proposed approach could reasonably mimic the major geometrical and material features of the natural bone. Simulation of the internal bone remodelling on the typical gross shape of the proximal femur, resulted in a density distribution pattern with good consistency with that of the natural bone. When...