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    Magnetic resonance imaging tracking of stem cells in vivo using iron oxide nanoparticles as a tool for the advancement of clinical regenerative medicine

    , Article Chemical Reviews ; Volume 111, Issue 2 , November , 2011 , Pages 253-280 ; 00092665 (ISSN) Mahmoudi, M ; Hosseinkhani, H ; Hosseinkhani, M ; Boutry, S ; Simchi, A ; Shane Journeay, W ; Subramani, K ; Laurent, S ; Sharif University of Technology
    2011
    Abstract
    Fetal stem cells, which can be isolated from the organs of fetuses, differentiate along multiple lineages. Their advantages over their adult counterparts include better intrinsic homing and engraftment and lower immunogenicity, and they are less ethically contentious. It is noteworthy that Mesenchymal Stem Cells (MSC) can be activated and mobilized at the site of damaged tissue. Since vascular delivery suffers from a pulmonary first pass effect, direct or systemic injection of MSCs into the damaged tissue is preferred, particularly in the case of versatile tissue ischemia. Ultrasound applies acoustic energy with a frequency above human hearing (20 kHz). Ultrasound imaging or sonography... 

    Controlled release of doxorubicin from electrospun PEO/chitosan/graphene oxide nanocomposite nanofibrous scaffolds

    , Article Materials Science and Engineering C ; Volume 48 , March , 2015 , Pages 384-390 ; 09284931 (ISSN) Ardeshirzadeh, B ; Aboutalebi Anaraki, N ; Irani, M ; Roshanfekr Rad, L ; Shamshiri, S ; Sharif University of Technology
    Elsevier Ltd  2015
    Abstract
    Polyethylene oxide (PEO)/chitosan (CS)/graphene oxide (GO) electrospun nanofibrous scaffolds were successfully developed via electrospinning process for controlled release of doxorubicin (DOX). The SEM analysis of nanofibrous scaffolds with different contents of GO (0.1, 0.2, 0.5 and 0.7 wt.%) indicated that the minimum diameter of nanofibers was found to be 85 nm for PEO/CS/GO 0.5% nanofibers. The π-π stacking interaction between DOX and GO with fine pores of nanofibrous scaffolds exhibited higher drug loading (98%) and controlled release of the DOX loaded PEO/CS/GO nanofibers. The results of DOX release from nanofibrous scaffolds at pH 5.3 and 7.4 indicated strong pH dependence. The... 

    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
    Abstract
    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... 

    Optimizing fuzzy logic controller for diabetes type I by genetic algorithm

    , Article 2010 The 2nd International Conference on Computer and Automation Engineering, ICCAE 2010, 26 February 2010 through 28 February 2010, Singapore ; Volume 2 , 2010 , Pages 4-8 ; 9781424455850 (ISBN) Ghaemi Osgouie, K ; Azizi, A ; Sharif University of Technology
    2010
    Abstract
    Biological systems are highly nonlinear, and there is a significant amount of variability from one patient to another. A controller for drug infusion has to be able to achieve good performance for most of the potential patient population. These controllers are designed for the general population, as no knowledge is available before hand for each particular patient. This necessitates perforce an algorithm that will be able to compensate for the differences between individuals and external factors. Of the possibilities, fuzzy logic direct model reference adaptive control (DMRAC) is the choice for Insulin infusion control for diabetes type I as results presented herein. Safety and robustness... 

    Use of the freely-swimming, Serratia marcescens bacteria to enhance mixing in microfluidic systems

    , Article ASME 2009 International Mechanical Engineering Congress and Exposition, 13 November 2009 through 19 November 2009 ; Volume 12, Issue PART A , 2010 , Pages 463-467 ; 9780791843857 (ISBN) Peysepar, M ; Shafii, M. B ; Rasoulian, R ; Jamalifar, H ; Fazeli, M. R ; Sharif University of Technology
    American Society of Mechanical Engineers (ASME) 
    Abstract
    Mixing has become a challenge in micro-fluidic systems because of the low Reynolds number in micro-channels. The method which is implemented in this paper is to use freely-swimming bacteria to enhance the mixing process. Accordingly, the Serratia marcescens bacteria were used for this matter. The mixing performance of the system is quantified by measuring the diffusion rate of Rhodamine B in a particular section of a channel connected to a chamber with varying Rhodamine B concentration. The concentration of Rhodamine B was measured using the Laser Induced Fluorescence (LIF) technique. The channel is in the form of a pipe and is closed on the extending side. In this paper, it is demonstrated... 

    Specific targeting delivery to MUC1 overexpressing tumors by albumin-chitosan nanoparticles conjugated to DNA aptamer

    , Article International Journal of Pharmaceutics ; Volume 515, Issue 1-2 , 2016 , Pages 607-615 ; 03785173 (ISSN) Esfandyari Manesh, M ; Mohammadi, A ; Atyabi, F ; Nabavi, S. M ; Ebrahimi, S. M ; Shahmoradi, E ; Shiri Varnamkhasti, B ; Ghahremani, M. H ; Dinarvand, R ; Sharif University of Technology
    Elsevier B.V  2016
    Abstract
    Chitosan-coated human serum albumin nanoparticles were functionalized by MUC1 aptamer to obtain a selective drug carrier toward cancers overexpressing MUC1. The negative charges of albumin nanoparticles were shifted to positive charges by surface modification with chitosan, and MUC1 was conjugated through an acrylate spacer. The cytotoxicity of targeted nanoparticles was significantly more than non-aptamer nanoparticles, and also the chitosan-coated nanoparticles had more cytotoxic effects than the negatively charged albumin nanoparticles. The IC50 of targeted nanoparticles was 28 and 26% of free paclitaxel in MCF7 and T47D cells at 48 h, respectively. Confocal laser scanning electron... 

    Effects of short term and long term Extremely Low Frequency Magnetic Field on depressive disorder in mice: Involvement of nitric oxide pathway

    , Article Life Sciences ; Volume 146 , 2016 , Pages 52-57 ; 00243205 (ISSN) Madjid Ansari, A ; Farzam Pour, S ; Sadr, A ; Shekarchi, B ; Majid Zadeh, A. K ; Sharif University of Technology
    Elsevier Inc 
    Abstract
    Aims Previous reports on the possible effects of Extremely Low Frequency Magnetic Fields (ELF MF) on mood have been paradoxical in different settings while no study has yet been conducted on animal behavior. In addition, it was shown that ELF MF exposure makes an increase in brain nitric oxide level. Therefore, in the current study, we aimed to assess the possible effect(s) of ELF MF exposure on mice Forced Swimming Test (FST) and evaluate the probable role of the increased level of nitric oxide in the observed behavior. Main methods Male adult mice NMRI were recruited to investigate the short term and long term ELF MF exposure (0.5 mT and 50 Hz, single 2 h and 2 weeks 2 h a day). Locomotor... 

    Inhibitory activity on type 2 diabetes and hypertension key-enzymes, and antioxidant capacity of veronica persica phenolic-rich extracts

    , Article Cellular and Molecular Biology ; Volume 62, Issue 6 , 2016 , Pages 80-85 ; 01455680 (ISSN) Sharifi Rad, M ; Tayeboon, G. S ; Sharifi Rad, J ; Iriti, M ; Varoni, E. M ; Razazi, S ; Sharif University of Technology
    Cellular and Molecular Biology Association  2016
    Abstract
    Veronica genus (Plantaginaceae) is broadly distributed in different habitats. In this study, the inhibitory activity of free soluble and conjugated phenolic extracts of Veronica persica on key enzymes associated to type 2 diabetes (α-glucosidase and α-amylase) and hypertension (angiotensin I converting enzyme, ACE) was assessed, as well as their antioxidant power. Our results showed that both the extracts inhibited α-amylase, α-glucosidase and ACE in a dose-dependent manner. In particular, free phenolic extract significantly (P < 0.05) inhibited α-glucosidase (IC50 532.97 μg/mL), whereas conjugated phenolic extract significantly (P < 0.05) inhibited a-amylase (IC50 489.73 μg/mL) and ACE... 

    Urine concentrating mechanism modelling in rat kidney inner medulla

    , Article 2016 23rd Iranian Conference on Biomedical Engineering and 2016 1st International Iranian Conference on Biomedical Engineering, ICBME 2016, 23 November 2016 through 25 November 2016 ; 2017 , Pages 111-116 ; 9781509034529 (ISBN) Sanatkhani, S ; Saidi, M. S ; Banazadeh, M. H ; Sharif University of Technology
    Abstract
    Physicians use charts that are prepared by experiments on animals or humans to prescribe drug dosage for patients. This method requires some precious amount of time by the Ministry of Health to approve new drugs to be used in healthcare centers. Three-dimensional modeling of the inner medulla by considering the known physiological features help us to predict the distribution of a drug or any minerals in the kidney. In this study we present modeling of the important species distribution including Na+ and urea in the rat inner medulla that influence the urine concentrating mechanism. We use a C++ code to develop the inner medulla geometry based on physiological data to better capture the... 

    Meta-aligner: long-read alignment based on genome statistics

    , Article BMC Bioinformatics ; Volume 18, Issue 1 , 2017 ; 14712105 (ISSN) Nashta Ali, D ; Aliyari, A ; Ahmadian Moghadam, A ; Edrisi, M. A ; Motahari, S. A ; Khalaj, B. H ; Sharif University of Technology
    Abstract
    Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

    Apoptotic and anti-apoptotic genes transcripts patterns of graphene in mice

    , Article Materials Science and Engineering C ; Volume 71 , 2017 , Pages 460-464 ; 09284931 (ISSN) Ahmadian, H ; Hashemi, E ; Akhavan, O ; Shamsara, M ; Hashemi, M ; Farmany, A ; Daliri Joupari, M ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    Recent studies showed that a large amount of graphene oxide accumulated in kidney and liver when it injected intravenously. Evaluation of lethal and apoptosis gene expression in these tissues, which are under stress is very important. In this paper the in vivo dose-dependent effects of graphene oxide and reduced graphene oxide nanoplatelets on kidney and liver of mice were studied. Balb/C mice were treated by 20 mg/kg body weight of nanoplatelets. Molecular biology analysis showed that graphene nanoplatelets injected intravenously lead to overexpression of BAX gene in both kidney and liver tissues (P ≥ 0.01). In addition these nanoparticles significantly increase BCL2 gene expression in both... 

    Novel microwave-assisted synthesis of porous g-C3N4/SnO2 nanocomposite for solar water-splitting

    , Article Applied Surface Science ; Volume 440 , 15 May , 2018 , Pages 153-161 ; 01694332 (ISSN) Seza, A ; Soleimani, F ; Naseri, N ; Soltaninejad, M ; Montazeri, S.M ; Sadrnezhaad, S.K ; Mohammadi, M.R ; Moghadam, H.A ; Forouzandeh, M ; Amin, M.H ; Sharif University of Technology
    Elsevier B.V  2018
    Abstract
    Highly porous nanocomposites of graphitic-carbon nitride and tin oxide (g-C3N4/SnO2) were prepared through simple pyrolysis of urea molecules under microwave irradiation. The initial amount of tin was varied in order to investigate the effect of SnO2 content on preparation and properties of the composites. The synthesized nanocomposites were well-characterized by XRD, FE-SEM, HR-TEM, BET, FTIR, XPS, DRS, and PL. A homogeneous distribution of SnO2 nanoparticles with the size of less than 10 nm on the porous C3N4 sheets could be obtained, suggesting that in-situ synthesis of SnO2 nanoparticles was responsible for the formation of g-C3N4. The process likely occurred by the aid of the large... 

    Construction of scaffolds composed of acellular cardiac extracellular matrix for myocardial tissue engineering

    , Article Biologicals ; Volume 53 , 2018 , Pages 10-18 ; 10451056 (ISSN) Esmaeili Pourfarhangi, K ; Mashayekhan, S ; Ghanbari Asl, S ; Hajebrahimi, Z ; Sharif University of Technology
    Academic Press  2018
    Abstract
    High rates of mortality and morbidity stemming from cardiovascular diseases unveil extreme limitations in current therapies despite enormous advances in medical and pharmaceutical sciences. Following myocardial infarction (MI), parts of myocardium undergo irreversible remodeling and is substituted by a scar tissue which eventually leads to heart failure (HF). To address this issue, cardiac patches have been utilized to initiate myocardial regeneration. In this study, a porous cardiac patch is fabricated using a mixture of decellularized myocardium extracellular matrix (ECM) and chitosan (CS). Results of rheological measurements, SEM, biodegradation test, and MTT assay showed that the... 

    Molecular dynamics simulations of orai reveal how the third transmembrane segment contributes to hydration and ca2+ selectivity in calcium release-activated calcium channels

    , Article Journal of Physical Chemistry B ; Volume 122, Issue 16 , 2018 , Pages 4407-4417 ; 15206106 (ISSN) Alavizargar, A ; Berti, C ; Ejtehadi, M. R ; Furini, S ; Sharif University of Technology
    American Chemical Society  2018
    Abstract
    Calcium release-activated calcium (CRAC) channels open upon depletion of Ca2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison... 

    Covalent immobilization of cellulase using magnetic poly(ionic liquid) support: improvement of the enzyme activity and stability

    , Article Journal of Agricultural and Food Chemistry ; Volume 66, Issue 4 , 2018 , Pages 789-798 ; 00218561 (ISSN) Hosseini, H ; Hosseini, A ; Zohreh, N ; Yaghoubi, M ; Pourjavadi, A ; Sharif University of Technology
    American Chemical Society  2018
    Abstract
    A magnetic nanocomposite was prepared by entrapment of Fe3O4 nanoparticles into the cross-linked ionic liquid/epoxy type polymer. The resulting support was used for covalent immobilization of cellulase through the reaction with epoxy groups. The ionic surface of the support improved the adsorption of enzyme, and a large amount of enzyme (106.1 mg/g) was loaded onto the support surface. The effect of the presence of ionic monomer and covalent binding of enzyme was also investigated. The structure of support was characterized by various instruments such as FT-IR, TGA, VSM, XRD, TEM, SEM, and DLS. The activity and stability of immobilized cellulase were investigated in the prepared support. The... 

    Molecular simulation of protein dynamics in nanopores. II. Diffusion

    , Article Journal of Chemical Physics ; Volume 130, Issue 8 , 2009 ; 00219606 (ISSN) Javidpour, L ; Tabar, M.R.R ; Sahimi, M ; Sharif University of Technology
    2009
    Abstract
    A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the α-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the... 

    Self-supported nanoporous Zn–Ni–Co/Cu selenides microball arrays for hybrid energy storage and electrocatalytic water/urea splitting

    , Article Chemical Engineering Journal ; Volume 375 , 2019 ; 13858947 (ISSN) Hosseini, H ; Shahrokhian, S ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    The phase-pure multiple ternary or quaternary metal selenides in energy boosting, have not been reported yet. Here, self-supported porous crystalline Zn–Ni–Co/Cu selenides microballs arrays were constructed by selenation of the designed tubular Cu(OH)2 arrays decorated with ultrathin Zn–Co–Ni tri-metallic hydroxide on carbon cloth substrate. For this rational engineering, a novel precursor sample was firstly prepared by conversion of deposited Cu layer to hollow tubular Cu(OH)2 arrays on carbon cloth, then, Zn-Co–Ni layered ternary hydroxides with a thin layer structure was deposited around this tubular arrays. The selenation with an exciting morphology change from amorphous tube to highly... 

    GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation

    , Article Glycobiology ; Volume 29, Issue 11 , 2019 , Pages 803-812 ; 14602423 (ISSN) Azimzadeh Irani, M ; Ejtehadi, M. R ; Sharif University of Technology
    NLM (Medline)  2019
    Abstract
    IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring... 

    A Boolean network control algorithm guided by forward dynamic programming

    , Article PLoS ONE ; Volume 14, Issue 5 , 2019 ; 19326203 (ISSN) Moradi, M ; Goliaei, S ; Foroughmand Araabi, M. H ; Sharif University of Technology
    Public Library of Science  2019
    Abstract
    Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source... 

    Cis-trans proline isomers in the catalytic domain of calcineurin

    , Article FEBS Journal ; Volume 286, Issue 6 , 2019 , Pages 1230-1239 ; 1742464X (ISSN) Teixeira, J. M. C ; Guasch, A ; Biçer, A ; Aranguren Ibáñez, Á ; Chashmniam, S ; Paniagua, J. C ; Pérez Riba, M ; Fita, I ; Pons, M ; Sharif University of Technology
    Blackwell Publishing Ltd  2019
    Abstract
    Calcineurin is an essential calcium-activated serine/threonine phosphatase. The six NMR-observable methionine methyl groups in the catalytic domain of human calcineurin Aα (CNA) were assigned and used as reporters of the presence of potential cis-trans isomers in solution. Proline 84 is found in the cis conformation in most calcineurin X-ray structures, and proline 309, which is part of a highly conserved motif in phosphoprotein phosphatases, was modeled with a cis peptide bond in one of the two molecules present in the asymmetric unit of CNA. We mutated each of the two prolines to alanine to force the trans conformation. Solution NMR shows that the P84A CNA mutant exists in two forms,...