Loading...
Search for:
biological-model
0.006 seconds
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...
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...
Subject-specific loads on the lumbar spine in detailed finite element models scaled geometrically and kinematic-driven by radiography images
, Article International Journal for Numerical Methods in Biomedical Engineering ; Volume 35, Issue 4 , 2019 ; 20407939 (ISSN) ; Arjmand, N ; Shirazi Adl, A ; Sharif University of Technology
Wiley-Blackwell
2019
Abstract
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...
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...
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) ; 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...
Evaluation of various energy windows at different radionuclides for scatter and attenuation correction in nuclear medicine
, Article Annals of Nuclear Medicine ; Volume 29, Issue 4 , 2015 , Pages 375-383 ; 09147187 (ISSN) ; Ashoor, M ; Sohrabpour, M ; Shokrani, P ; Rezaei, A ; Sharif University of Technology
Springer-Verlag Tokyo
2015
Abstract
Objective: Improving signal to noise ratio (SNR) and qualified images by the various methods is very important for detecting the abnormalities at the body organs. Scatter and attenuation of photons by the organs lead to errors in radiopharmaceutical estimation as well as degradation of images. The choice of suitable energy window and the radionuclide have a key role in nuclear medicine which appearing the lowest scatter fraction as well as having a nearly constant linear attenuation coefficient as a function of phantom thickness. Methods: The energy windows of symmetrical window (SW), asymmetric window (ASW), high window (WH) and low window (WL) using Tc-99m and Sm-153 radionuclide with...
A study of hyperelastic models for predicting the mechanical behavior of extensor apparatus
, Article Biomechanics and Modeling in Mechanobiology ; Volume 16, Issue 3 , 2017 , Pages 1077-1093 ; 16177959 (ISSN) ; Karimi Taheri, K ; Narooei, K ; Karimi Taheri, A ; Sharif University of Technology
Springer Verlag
2017
Abstract
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...
Margination and adhesion of micro- and nanoparticles in the coronary circulation: A step towards optimised drug carrier design
, Article Biomechanics and Modeling in Mechanobiology ; Volume 17, Issue 1 , 2018 , Pages 205-221 ; 16177959 (ISSN) ; Shamloo, A ; Sharif University of Technology
Springer Verlag
2018
Abstract
Obstruction of left anterior descending artery (LAD) due to the thrombosis or atherosclerotic plaques is the leading cause of death worldwide. Targeted delivery of drugs through micro- and nanoparticles is a very promising approach for developing new strategies in clot-busting or treating restenosis. In this work, we modelled the blood flow characteristics in a patient-specific reconstructed LAD artery by the fluid–solid interaction method and based on physiological boundary conditions. Next, we provided a Lagrangian description of micro- and nanoparticles dynamics in the blood flow considering their Brownian motion and the particle–particle interactions. Our results state that the number of...
Estimation of phase signal change in neuronal current MRI for evoke response of tactile detection with realistic somatosensory laminar network model
, Article Australasian Physical and Engineering Sciences in Medicine ; Volume 39, Issue 3 , 2016 , Pages 717-726 ; 01589938 (ISSN) ; Pouladian, M ; Jameie, S. B ; Abbaspour Tehrani Fard, A ; Sharif University of Technology
Springer Netherlands
2016
Abstract
Magnetic field generated by neuronal activity could alter magnetic resonance imaging (MRI) signals but detection of such signal is under debate. Previous researches proposed that magnitude signal change is below current detectable level, but phase signal change (PSC) may be measurable with current MRI systems. Optimal imaging parameters like echo time, voxel size and external field direction, could increase the probability of detection of this small signal change. We simulate a voxel of cortical column to determine effect of such parameters on PSC signal. We extended a laminar network model for somatosensory cortex to find neuronal current in each segment of pyramidal neurons (PN). 60,000...
A three-dimensional statistical volume element for histology informed micromechanical modeling of brain white matter
, Article Annals of Biomedical Engineering ; Volume 48, Issue 4 , 2020 , Pages 1337-1353 ; Farahmand, F ; Ahmadian, M. T ; Sharif University of Technology
Springer
2020
Abstract
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...
Studying the effect of kinematical pattern on the mechanical performance of paraplegic gait with reciprocating orthosis
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 226, Issue 8 , 2012 , Pages 600-611 ; 09544119 (ISSN) ; Farahmand, F ; Salarieh, H ; Sharif University of Technology
SAGE
2012
Abstract
Paraplegic users of mechanical walking orthoses, e.g. advanced reciprocating gait orthosis (ARGO), often face high energy expenditure and extreme upper body loading during locomotion. We studied the effect of kinematical pattern on the mechanical performance of paraplegic locomotion, in search for an improved gait pattern that leads to lower muscular efforts. A three-dimensional, four segment, six-degrees-of-freedom skeletal model of the advanced reciprocating gait orthosis-assisted paraplegic locomotion was developed based on the data acquired from an experimental study on a single subject. The effect of muscles was represented by ideal joint torque generators. A response surface analysis...
A regenerative approach towards recovering the mechanical properties of degenerated intervertebral discs: Genipin and platelet-rich plasma therapies
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 231, Issue 2 , 2017 , Pages 127-137 ; 09544119 (ISSN) ; Wang, J. L ; Abdollahi, M ; Hsu, Y. C ; Parnianpour, M ; Khalaf, K ; Sharif University of Technology
SAGE Publications Ltd
2017
Abstract
Degenerative disc disease, associated with discrete structural changes in the peripheral annulus and vertebral endplate, is one of the most common pathological triggers of acute and chronic low back pain, significantly depreciating an individual's quality of life and instigating huge socioeconomic costs. Novel emerging therapeutic techniques are hence of great interest to both research and clinical communities alike. Exogenous crosslinking, such as Genipin, and platelet-rich plasma therapies have been recently demonstrated encouraging results for the repair and regeneration of degenerated discs, but there remains a knowledge gap regarding the quantitative degree of effectiveness and...
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...
Healthy and diseasedin vitromodels of vascular systems
, Article Lab on a Chip ; Volume 21, Issue 4 , 2021 , Pages 641-659 ; 14730197 (ISSN) ; Mallone, A ; Nasrollahi, F ; Ostrovidov, S ; Nasiri, R ; Mahmoodi, M ; Haghniaz, R ; Baidya, A ; Salek, M. M ; Darabi, M. A ; Orive, G ; Shamloo, A ; Dokmeci, M. R ; Ahadian, S ; Khademhosseini, A ; Sharif University of Technology
Royal Society of Chemistry
2021
Abstract
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...
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...
MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
, Article PLoS Computational Biology ; Volume 18, Issue 6 , 2022 ; 1553734X (ISSN) ; Modegh, R. G ; Rabiee, H. R ; Sarbandi, E. R ; Rezaie, N ; Tam, K. T ; Forrest, A. R. R ; Sharif University of Technology
Public Library of Science
2022
Abstract
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 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...
EEG-based functional brain networks: does the network size matter?
, Article PloS one ; Volume 7, Issue 4 , 2012 ; 19326203 (ISSN) ; Salehi, N ; Jalili, M ; Knyazeva, M. G ; Sharif University of Technology
PLOS
2012
Abstract
Functional connectivity in human brain can be represented as a network using electroencephalography (EEG) signals. These networks--whose nodes can vary from tens to hundreds--are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which various graph metrics depend upon the network size. To this end, EEGs from 32 normal subjects were recorded and functional networks of three different sizes were extracted. A state-space based method was used to calculate cross-correlation matrices between different brain regions. These correlation matrices were used to construct binary adjacency connectomes, which were assessed with regards to a number of...
Effect of input voltage frequency on the distribution of electrical stresses on the cell surface based on single-cell dielectrophoresis analysis
, Article Scientific Reports ; Volume 10, Issue 1 , 2020 ; Moghimi Zand, M ; Kavand, H ; Javidi, R ; Hadi, A ; Valadkhani, Z ; Renaud, P ; Sharif University of Technology
Nature Research
2020
Abstract
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...