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    Design and Construction of Novel Intein Mediated Biosensor in Order to Detect Amyloid Fibrils

    , M.Sc. Thesis Sharif University of Technology Miri, Mohammad (Author) ; Kalhor, Hamid Reza (Supervisor)
    The most important factor in protein's function and its 3D structure is folding. Misfolding or native folding perturbation in some peptides and proteins force them get into amyloid fibril aggregation. It has been observed that these aggregations are the cause of some debilitative diseases especially ones that are related to aging like Alzheimer disease, Hantington's disease, typeII diabets etc. Recently it has been shown that specific regions in human catalase protein interact with some amyloid fibrils, such as Aß, IAPP, PrP etc. Inteins are self-splicing protein enzymes, which excise themselves from the mature protein and join the two flanking adjacent sequences by a new peptide bond in a... 

    Paroxysmal atrial fibrillation prediction using Kalman filter

    , Article ACM International Conference Proceeding Series, 26 October 2011 through 29 October 2011, Barcelona ; 2011 ; 9781450309134 (ISBN) Montazeri, N ; Shamsollahi, M. B ; Carrault, G ; Hernández, A. I ; Sharif University of Technology
    In this paper, we proposed a method based on Kalman Filter for predicting the onset of paroxysmal atrial fibrillation (PAF) from the electrocardiogram (ECG) using clinical data available from the Computers in Cardiology (CinC) Challenge 2001. To predict PAF, we developed an algorithm based upon the number of atrial premature complexes (APCs) in the ECG. The algorithm detects classical isolated APCs by monitoring fidelity signals, which is defined here as a function of the innovation signal of Kalman filter, in vicinity of premature heartbeats and decides whether one beat is APC or not then predicts PAF, based on the number of APC. The challenge database consists of 56 pairs of 30-minute ECG... 

    Predicting atrial fibrillation termination using ECG features, a comparison

    , Article 2008 1st International Symposium on Applied Sciences in Biomedical and Communication Technologies, ISABEL 2008, Aalborg, 25 October 2008 through 28 October 2008 ; 2008 ; 9781424426478 (ISBN) Saberi, S ; Esmaeili, V ; Towhidkhah, F ; Moradi, M. H ; Sharif University of Technology
    In this study, surface ECG recordings have been used to accomplish a non-invasive method which can predict spontaneous termination of Atrial Fibrillation (AF) and discriminate terminating (T) and non-terminating (N) AF episodes. The data set was provided by Physionet including holter recordings of 50 patients (20 training and 30 test sets). Concerning that most relevant information about the AF exists in the atrial fibrillatory wave, Several spectral and time-frequency parameters were extracted from the ECG signal after canceling the QRST complex. Also a temporal feature, RR interval variation, representing the ventricular activity was calculated. These parameters were evaluated using a... 

    Fabrication and Characterization of a Drug Release System Based on Mesoporous Silica Nanoparticles for Hydrophobic Drugs

    , M.Sc. Thesis Sharif University of Technology Taebnia, Nayyera (Author) ; Yaghmaei, Soheila (Supervisor) ; Arpanaei, Ayyoob (Supervisor) ; Morshedi, Dina (Co-Advisor)
    This research aims to develop a drug delivery system based on mesoporous silica nanoparticles (MSNPs) for hydrophobic drugs and evaluating their cytotoxicity. The internal environment of the body is aqueous, while most of effective drugs display poor aqueous solubility, resulting in insufficient bioavailability. Due to their several unique properties, such as a large surface area, tunable pore size, facile surface multi functionalization and excellent biocompatibility, MSNPs are recognized as promising and powerful tools to overcome this hurdle. In the present study, MSNPs were synthesized using template removing method and then were functionalized through grafting procedure. They were... 

    Design and Fabrication of Drug-loaded Nanoparticles to Prevent Fibrillation of Alpha-synuclein in Parkinson

    , M.Sc. Thesis Sharif University of Technology Nayebzadeh, Ramin (Author) ; Mashayekhan, Shohreh (Supervisor) ; Morshedi, Dina (Supervisor)
    The purpose of this study is to assess the inhibitory effects of an appropriate nanoparticles loaded with gallic acid on the fibrillation of alpha-synuclein. Alpha-synuclein is a major component of protein plaques in synucleinopathies, particularly Parkinson’s disease. Gallic acid (GA, 3,4,5-trihydroxy benzoic acid) is a well–known small molecule which can inhibit the formation of α-synuclein fibrils. For the process of fibrillation, purified protein was incubated at 37◦C and pH 7.2. Fibrillation was analyzed by the standard fibril methods.after that investigated fabricating of gallic acid trapped in the chitosan nanoparticles and gallic acid loaded in chitosan –coated mesoporous silica... 

    Controlling Atrial fibrillation using Cohen's model

    , Article 2011 18th Iranian Conference of Biomedical Engineering, ICBME 2011, 14 December 2011 through 16 December 2011 ; December , 2011 , Pages 60-63 ; 9781467310055 (ISBN) Aghajari, S ; Bahrami, F ; Sharif University of Technology
    Drug administration using infusion pumps can find application in treating patients with arrhythmias. These pumps can obviate the need to use drugs several times a day and automatically adapt the dosage to patient situation. Considering the importance of administration of right dosage, a perfect-controlled pump is needed to approach this goal. This paper focuses on controlling Atrial fibrillation (AF) arrhythmia. The abnormal heart rhythm that affects RR interval sequence and there have been some attempts to model these effects. One of these models is proposed by Cohen and colleges. Searching through the variables of this model, selecting the potential control variable (the one that its... 

    The hot sites of α-synuclein in amyloid fibril formation

    , Article Scientific Reports ; Volume 10, Issue 1 , 22 July , 2020 Khammari, A ; Arab, S. S ; Ejtehadi, M. R ; Sharif University of Technology
    Nature Research  2020
    The role of alpha-synuclein (αS) amyloid fibrillation has been recognized in various neurological diseases including Parkinson’s Disease (PD). In early stages, fibrillation occurs by the structural transition from helix to extended states in monomeric αS followed by the formation of beta-sheets. This alpha-helix to beta-sheet transition (αβT) speeds up the formation of amyloid fibrils through the formation of unstable and temporary configurations of the αS. In this study, the most important regions that act as initiating nuclei and make unstable the initial configuration were identified based on sequence and structural information. In this regard, a Targeted Molecular Dynamics (TMD)... 

    Prediction of Heart Arrhythmias Related to Pramature Beats

    , M.Sc. Thesis Sharif University of Technology Sabeti, Elyas (Author) ; Shamsollahi, Mohammad Bagher (Supervisor)
    About 42 percent of annual mortality in all around the world is originated from cardiovascular arrhythmias and diseases. One of these arrhythmias is atrial fibrillation whose onset and persistence can produce clot and consequently cause stroke. The basis of our research are upon this idea that dangerous heart arrhythmias do not happen abruptly and there always are some background signs before occurrence of them. In our approach to predict the onset of atrial fibrillation, by analyzing ECG signal in order to extract distinguishing features, we want to classify signals which will terminate Paroxysmal Atrial Fibrillation (PAF) from signals which won’t end with PAF. In this thesis, we propose... 

    Physiological temperature has a crucial role in amyloid beta in the absence and presence of hydrophobic and hydrophilic nanoparticles

    , Article ACS Chemical Neuroscience ; Volume 4, Issue 3 , December , 2013 , Pages 375-378 ; 19487193 (ISSN) Ghavami, M ; Rezaei, M ; Ejtehadi, R ; Lotfi, M ; Shokrgozar, M. A ; Abd Emamy, B ; Raush, J ; Mahmoudi, M ; Sharif University of Technology
    Amyloid beta fibrillation can lead to major disorder of neurons processes and is associated with several neuronal diseases (e.g., Alzheimer's disease). We report here an importance of slight temperature changes, in the physiological range (35-42 °C), on the amyloid fibrillation process in the presence and absence of hydrophilic (silica) and hydrophobic (polystyrene) nanoparticles (NPs). The results highlight the fact that slight increases in temperature can induce inhibitory and acceleratory effects of hydrophobic and hydrophilic NPs on the fibrillation process, respectively. Using further in vivo considerations, the outcomes of this study can be used for considerable modifications on the... 

    Prediction of Paroxysmal Atrial Fibrillation using Empirical Mode Decomposition and RR intervals

    , Article 2012 IEEE-EMBS Conference on Biomedical Engineering and Sciences, IECBES 2012, 17 December 2012 through 19 December 2012 ; December , 2012 , Pages 750-754 ; 9781467316668 (ISBN) Sabeti, E ; Shamsollahi, M. B ; Afdideh, F ; Sharif University of Technology
    In this paper, we proposed a method based on time-frequency dependent features extracted from Intrinsic Mode Functions (IMFs) and physiological feature such as the number of premature beats (PBs) to predict the onset of Paroxysmal Atrial Fibrillation (PAF) by using electrocardiogram (ECG) signal. To extract IMFs, we used Empirical Mode Decomposition (EMD). In order to predict PAF, we used variance of IMFs of signals, the area under the absolute of IMF curves and the number of PBs, since increasing of all of these parameters are a clear sign of PAF occurrence. We used clinical database which was provided for the 2001 Computer in Cardiology Challenge (CinC). The test set of this database... 

    Characteristics of early repolarization pattern in the Iranian population

    , Article Iranian Red Crescent Medical Journal ; Volume 19, Issue 3 , 2017 ; 20741804 (ISSN) Mollazadeh, R ; Sehhati, F ; Eslami, M ; Nemati, F ; Monfarednasab, M ; Sefidbakht, S ; Sharif University of Technology
    Kowsar Medical Publishing Company  2017
    Background: The early repolarization pattern (ERP) has been considered a normal variant in electrocardiography (ECG) for a long time. Nevertheless, increasing evidence has demonstrated its association with adverse outcomes. Objectives: The present study aimed to evaluate the prevalence of ERP in the Iranian general population and demonstrate its clinical and ECG correlates. Methods: A cross sectional study, comprising 1424 consecutive healthy adult individuals, was conducted at two university based hospitals in Tehran, Iran in 2012-2013. The ERP prevalence, clinical characteristics and ECG morphology were investigated in volunteers. Results: ERP was present in 136 out of 1,424 people (9.6%).... 

    Prediction of life-threatening heart arrhythmias using obstructive sleep apnoea characteristics

    , Article 27th Iranian Conference on Electrical Engineering, ICEE 2019, 30 April 2019 through 2 May 2019 ; 2019 , Pages 1761-1764 ; 9781728115085 (ISBN) Mohammad Alinejad, G ; Rasoulinezhad, S ; Shamsollahi, M. B ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    False alarms ratios of up to 86% in Intensive Care Units (ICU) decrease quality of care, impacting both clinical staff and patients through slowing off response time and noise tribulation. We present a novel algorithm to predict heart arrhythmias in ICUs. We focus on five life-threatening arrhythmias: Asystole, Extreme Bradycardia, Extreme Tachycardia, Ventricular Tachycardia, and Ventricular Fibrillation. The algorithm is based on novel features using only 12 seconds of one ECG channel to predict the arrhythmias. Our new feature sets include different SQI and physiological features and the features used in obstructive sleep apnoea detection. We also proposed a new morphological... 

    Protein corona composition of gold nanoparticles/nanorods affects amyloid beta fibrillation process

    , Article Nanoscale ; Volume 7, Issue 11 , Feb , 2015 , Pages 5004-5013 ; 20403364 (ISSN) Mirsadeghi, S ; Dinarvand, R ; Ghahremani, M. H ; Hormozi-Nezhad, M. R ; Mahmoudi, Z ; Hajipour, M. J ; Atyabi, F ; Ghavami, M ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2015
    Protein fibrillation process (e.g., from amyloid beta (Aβ) and α-synuclein) is the main cause of several catastrophic neurodegenerative diseases such as Alzheimer's and Parkinson diseases. During the past few decades, nanoparticles (NPs) were recognized as one of the most promising tools for inhibiting the progress of the disease by controlling the fibrillation kinetic process; for instance, gold NPs have a strong capability to inhibit Aβ fibrillations. It is now well understood that a layer of biomolecules would cover the surface of NPs (so called "protein corona") upon the interaction of NPs with protein sources. Due to the fact that the biological species (e.g., cells and amyloidal... 

    Mechanistic understanding of the interactions between nano-objects with different surface properties and α-synuclein

    , Article ACS Nano ; Volume 13, Issue 3 , 2019 , Pages 3243-3256 ; 19360851 (ISSN) Mohammad Beigi, H ; Hosseini, A ; Adeli, M ; Ejtehadi, M. R ; Christiansen, G ; Sahin, C ; Tu, Z ; Tavakol, M ; Dilmaghani Marand, A ; Nabipour, I ; Farzadfar, F ; Otzen, D. E ; Mahmoudi, M ; Hajipour, M. J ; Sharif University of Technology
    American Chemical Society  2019
    Aggregation of the natively unfolded protein α-synuclein (α-syn) is key to the development of Parkinson's disease (PD). Some nanoparticles (NPs) can inhibit this process and in turn be used for treatment of PD. Using simulation strategies, we show here that α-syn self-assembly is electrostatically driven. Dimerization by head-to-head monomer contact is triggered by dipole-dipole interactions and subsequently stabilized by van der Waals interactions and hydrogen bonds. Therefore, we hypothesized that charged nano-objects could interfere with this process and thus prevent α-syn fibrillation. In our simulations, positively and negatively charged graphene sheets or superparamagnetic iron oxide... 

    Discovery of a tetracyclic indole alkaloid that postpones fibrillation of hen egg white lysozyme protein

    , Article International Journal of Biological Macromolecules ; Volume 183 , 2021 , Pages 1939-1947 ; 01418130 (ISSN) Ashrafian, H ; Zadeh, E.H ; Tajbakhsh, M ; Majid, N ; Srivastava, G.N ; Khan, R.H ; Sharif University of Technology
    Elsevier B.V  2021
    Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril... 

    Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer’s disease therapy

    , Article Biophysical Reviews ; Volume 11, Issue 6 , 2019 , Pages 901-925 ; 18672450 (ISSN) Jokar, S ; Khazaei, S ; Behnammanesh, H ; Shamloo, A ; Erfani, M ; Beiki, D ; Bavi, O ; Sharif University of Technology
    Springer  2019
    Alzheimer’s disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported...