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biological-model
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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...
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)...
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,...
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...
Transient analysis of trunk response in sudden release loading using kinematics-driven finite element model
, Article Clinical Biomechanics ; Volume 24, Issue 4 , 2009 , Pages 341-347 ; 02680033 (ISSN) ; Shirazi Adl, A ; Parnianpour, M ; Sharif University of Technology
2009
Abstract
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...
Tool-tissue force estimation in laparoscopic surgery using geometric features
, Article Studies in Health Technology and Informatics ; Volume 184 , 2013 , Pages 225-229 ; 09269630 (ISSN) ; Behzadipour, S ; Farahmand, F ; Sharif University of Technology
IOS Press
2013
Abstract
This paper introduces three geometric features, from deformed shape of a soft tissue, which demonstrate good correlation with probing force and maximum local stress. Using FEM simulation, 2D and 3D model of an in vivo porcine liver was built for different probing tasks. Maximum deformation angle, maximum deformation depth and width of displacement constraint of the reconstructed shape of the deformed body were calculated. Two neural networks were trained from these features and the calculated interaction forces. The features are shown to have high potential to provide force estimation either for haptic devices or to assess the damage to the tissue in large deformations of up to 40%
The use of a cis-dioxomolybdenum(VI) dinuclear complex with quadradentate 1,4-benzenediylbis(benzyldithiocarbamate)(2-) as model compound for the active site of oxo transfer molybdoenzymes: Reactivity, kinetics, and catalysis
, Article Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy ; Volume 88 , 2012 , Pages 210-215 ; 13861425 (ISSN) ; Boghaei, D. M ; Sharif University of Technology
2012
Abstract
Dinuclear cis-dioxomolybdenum(VI) complex [{MoO 2(Bz 2Benzenediyldtc)} 2] coordinated by a quadradentate dithiocarbamate (Bz 2Benzenediyldtc 2- = 1,4-benzenediylbis(benzyldithiocarbamate)(2-)) has been prepared and characterized by elemental analysis, 13C NMR, IR and UV-vis spectroscopy. The kinetics of the oxygen atom transfer between [{MoO 2(Bz 2Benzenediyldtc)} 2] and PPh 3 was studied spectrophotometrically in CH 2Cl 2 medium at 520 nm and four different temperatures, 288, 293, 298 and 303 K, respectively. The reaction follows second order kinetics with the rate constant k = 0.163(2) M -1 S -1 and its increasingly strong absorption at 520 nm clearly indicate the formation of a μ-oxo...
The impact of including tRNA content on the optimality of the genetic code
, Article Bulletin of Mathematical Biology ; Volume 67, Issue 6 , 2005 , Pages 1355-1368 ; 00928240 (ISSN) ; Shateri Najafabadi, H ; Ahmadi Nejad, H ; Torabi, N ; Sharif University of Technology
2005
Abstract
Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, since it is known that, when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The...
The effects of trochlear groove geometry on patellofemoral joint stability - A computer model study
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 222, Issue 1 , 2008 , Pages 75-88 ; 09544119 (ISSN) ; Farahmand, F ; Meghdari, A ; Sharif University of Technology
2008
Abstract
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...
The effect of parameters of equilibrium-based 3-D biomechanical models on extracted muscle synergies during isometric lumbar exertion
, Article Journal of Biomechanics ; Volume 49, Issue 6 , 2016 , Pages 967-973 ; 00219290 (ISSN) ; Sedaghat Nejad, E ; Rashedi, E ; Sedighi, A ; Arjmand, N ; Parnianpour, M ; Sharif University of Technology
Elsevier Ltd
Abstract
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...
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...
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...
Synchronizing hindmarsh-rose neurons over newman-watts networks
, Article Chaos ; Volume 19, Issue 3 , 2009 ; 10541500 (ISSN) ; Sharif University of Technology
American Institute of Physics Inc
2009
Abstract
In this paper, the synchronization behavior of the Hindmarsh-Rose neuron model over Newman-Watts networks is investigated. The uniform synchronizing coupling strength is determined through both numerically solving the network's differential equations and the master-stability-function method. As the average degree is increased, the gap between the global synchronizing coupling strength, i.e., the one obtained through the numerical analysis, and the strength necessary for the local stability of the synchronization manifold, i.e., the one obtained through the master-stability-function approach, increases. We also find that this gap is independent of network size, at least in a class of networks...
Switching kalman filter based methods for apnea bradycardia detection from ECG signals
, Article Physiological Measurement ; Volume 36, Issue 9 , 2015 , Pages 1763-1783 ; 09673334 (ISSN) ; Shamsollahi, M. B ; Ge, D ; Hernandez, A. I ; Sharif University of Technology
Abstract
Apnea bradycardia (AB) is an outcome of apnea occurrence in preterm infants and is an observable phenomenon in cardiovascular signals. Early detection of apnea in infants under monitoring is a critical challenge for the early intervention of nurses. In this paper, we introduce two switching Kalman filter (SKF) based methods for AB detection using electrocardiogram (ECG) signal. The first SKF model uses McSharry's ECG dynamical model integrated in two Kalman filter (KF) models trained for normal and AB intervals. Whereas the second SKF model is established by using only the RR sequence extracted from ECG and two AR models to be fitted in normal and AB intervals. In both SKF approaches, a...
Substrate oscillations boost recombinant protein release from Escherichia coli
, Article Bioprocess and Biosystems Engineering ; Volume 37, Issue 5 , May , 2014 , Pages 881-890 ; ISSN: 16157591 ; Herwig, C ; Sharif University of Technology
Abstract
Intracellular production of recombinant proteins in prokaryotes necessitates subsequent disruption of cells for protein recovery. Since the cell disruption and subsequent purification steps largely contribute to the total production cost, scalable tools for protein release into the extracellular space is of utmost importance. Although there are several ways for enhancing protein release, changing culture conditions is rather a simple and scalable approach compared to, for example, molecular cell design. This contribution aimed at quantitatively studying process technological means to boost protein release of a periplasmatic recombinant protein (alkaline phosphatase) from E. coli....
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 ∼...
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...
Subject-specific 2D/3D image registration and kinematics-driven musculoskeletal model of the spine
, Article Journal of Biomechanics ; Volume 57 , 2017 , Pages 18-26 ; 00219290 (ISSN) ; Arjmand, N ; Shirazi Adl, A ; Farahmand, F ; Sharif University of Technology
Abstract
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...
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...