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biological-model
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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...
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....
1H NMR based metabolic profiling in Crohn's disease by random forest methodology
, Article Magnetic Resonance in Chemistry ; Vol. 52, issue. 7 , July , 2014 , p. 370-376 ; Majari-Kasmaee, L ; Mani-Varnosfaderani, A ; Kyani, A ; Rostami-Nejad, M ; Sohrabzadeh, K ; Naderi, N ; Zali, M. R ; Rezaei-Tavirani, M ; Tafazzoli, M ; Arefi-Oskouie, A ; Sharif University of Technology
Abstract
The present study was designed to search for metabolic biomarkers and their correlation with serum zinc in Crohn's disease patients. Crohn's disease (CD) is a form of inflammatory bowel disease that may affect any part of the gastrointestinal tract and can be difficult to diagnose using the clinical tests. Thus, introduction of a novel diagnostic method would be a major step towards CD treatment.Proton nuclear magnetic resonance spectroscopy ( 1H NMR) was employed for metabolic profiling to find out which metabolites in the serum have meaningful significance in the diagnosis of CD. CD and healthy subjects were correctly classified using random forest methodology. The classification model for...
Emergence of molecular chirality due to chiral interactions in a biological environment
, Article Journal of Biological Physics ; Vol. 40, issue. 4 , Jul , 2014 , p. 369-386 ; Ghahramani, F. T ; Shafiee, A ; Sharif University of Technology
Abstract
We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and...
Disc size markedly influences concentration profiles of intravenously administered solutes in the intervertebral disc: A computational study on glucosamine as a model solute
, Article European Spine Journal ; Vol. 23, issue. 4 , April , 2014 , p. 715-723 ; Shirazi-Adl, A ; Parnianpour, M ; Urban, J. P. G ; Sharif University of Technology
Abstract
Purpose: Tests on animals of different species with large differences in intervertebral disc size are commonly used to investigate the therapeutic efficacy of intravenously injected solutes in the disc. We hypothesize that disc size markedly affects outcome. Methods: Here, using a small non-metabolized molecule, glucosamine (GL) as a model solute, we calculate the influence of disc size on transport of GL into rat, rabbit, dog and human discs for 10 h post intravenous-injection. We used transient finite element models and considered an identical GL supply for all animals. Results: Huge effects of disc size on GL concentration profiles were found. Post-injection GL concentration in the rat...
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....
Diagnosis of early Alzheimer's disease based on EEG source localization and a standardized realistic head model
, Article IEEE Journal of Biomedical and Health Informatics ; Volume 17, Issue 6 , 2013 , Pages 1039-1045 ; 21682194 (ISSN) ; Zahedi, E ; Jalili, M ; Keikhosravi, A ; Vahdat, B. V ; Sharif University of Technology
2013
Abstract
In this paper, distributed electroencephalographic (EEG) sources in the brain have been mapped with the objective of early diagnosis of Alzheimer's disease (AD). To this end, records from a montage of a high-density EEG from 17 early AD patients and 17 matched healthy control subjects were considered. Subjects were in eyes-closed, resting-state condition. Cortical EEG sources were modeled by the standardized low-resolution brain electromagnetic tomography (sLORETA) method. Relative logarithmic power spectral density values were obtained in the four conventional frequency bands (alpha, beta, delta, and theta) and 12 cortical regions. Results show that in the left brain hemisphere, the theta...
Protein fibrillation and nanoparticle interactions: Opportunities and challenges
, Article Nanoscale ; Volume 5, Issue 7 , Jan , 2013 , Pages 2570-2588 ; 20403364 (ISSN) ; Kalhor, H. R ; Laurent, S ; Lynch, I ; Sharif University of Technology
2013
Abstract
Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,...
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...
Quantitative determination of optical trapping strength and viscoelastic moduli inside living cells
, Article Physical Biology ; Volume 10, Issue 4 , 2013 ; 14783967 (ISSN) ; Richardson, A. C ; Reihani, S. N. S ; Oddershede, L. B ; Berg Sorensen, K ; Sharif University of Technology
2013
Abstract
With the success of in vitro single-molecule force measurements obtained in recent years, the next step is to perform quantitative force measurements inside a living cell. Optical traps have proven excellent tools for manipulation, also in vivo, where they can be essentially non-invasive under correct wavelength and exposure conditions. It is a pre-requisite for in vivo quantitative force measurements that a precise and reliable force calibration of the tweezers is performed. There are well-established calibration protocols in purely viscous environments; however, as the cellular cytoplasm is viscoelastic, it would be incorrect to use a calibration procedure relying on a viscous environment....
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...
A novel distributed model of the heart under normal and congestive heart failure conditions
, Article Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine ; Volume 227, Issue 4 , 2013 , Pages 362-372 ; 09544119 (ISSN) ; Jahed, M ; Sharif University of Technology
2013
Abstract
Conventional models of cardiovascular system frequently lack required detail and focus primarily on the overall relationship between pressure, flow and volume. This study proposes a localized and regional model of the cardiovascular system. It utilizes noninvasive blood flow and pressure seed data and temporal cardiac muscle regional activity to predict the operation of the heart under normal and congestive heart failure conditions. The analysis considers specific regions of the heart, namely, base, mid and apex of left ventricle. The proposed method of parameter estimation for hydraulic electric analogy model is recursive least squares algorithm. Based on simulation results and comparison...
Spike phase synchronization in delayed-coupled neural networks: Uniform vs. non-uniform transmission delay
, Article Chaos ; Volume 23, Issue 1 , 2013 ; 10541500 (ISSN) ; Sharif University of Technology
2013
Abstract
In this paper, we investigated phase synchronization in delayed dynamical networks. Non-identical spiking Hindmarsh-Rose neurons were considered as individual dynamical systems and coupled through a number of network structures such as scale-free, Erdos-Rényi, and modular. The individual neurons were coupled through excitatory chemical synapses with uniform or distributed time delays. The profile of spike phase synchrony was different when the delay was uniform across the edges as compared to the case when it was distributed, i.e., different delays for the edges. When an identical transmission delay was considered, a quasi-periodic pattern was observed in the spike phase synchrony. There...
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)...
How well do the muscular synergies extracted via non-negative matrix factorisation explain the variation of torque at shoulder joint?
, Article Computer Methods in Biomechanics and Biomedical Engineering ; Volume 16, Issue 3 , 2013 , Pages 291-301 ; 10255842 (ISSN) ; Aminian, K ; Asghari, M ; Parnianpour, M ; Sharif University of Technology
2013
Abstract
The way central nervous system manages the excess degrees of freedom to solve kinetic redundancy of musculoskeletal system remains an open question. In this study, we utilise the concept of synergy formation as a simplifying control strategy to find the muscle recruitment based on summation of identified muscle synergies to balance the biomechanical demands (biaxial external torque) during an isometric shoulder task. A numerical optimisation-based shoulder model was used to obtain muscle activation levels when a biaxial external isometric torque is imposed at the shoulder glenohumeral joint. In the numerical simulations, 12 different shoulder torque vectors in the transverse plane are...
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%
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...
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...