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    A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: case studies

    , Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) Sharifi, F ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
    Sharif University of Technology  2019
    Abstract
    One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II... 

    A perspective to the correlation between brain insulin resistance and alzheimer: medicinal chemistry approach

    , Article Current Diabetes Reviews ; Volume 15, Issue 4 , 2019 , Pages 255-258 ; 15733998 (ISSN) Rabiee, N ; Bagherzadeh, M ; Rabiee, M ; Sharif University of Technology
    Bentham Science Publishers  2019
    Abstract
    Substantial terms have been recognized on the associated risk elements, comorbidities as well as, putative pathophysiological processes of Alzheimer disease and related dementias (ADRDs) as well as, type 2 diabetes mellitus (T2DM), a few from greatest important disease from the moments. Very much is considered regarding the biology and chemistry of each predicament, nevertheless T2DM and ADRDs are an actually similar pattern developing from the similar origins of maturing or synergistic conditions connected by aggressive patho-corporeal terms and continues to be ambiguous. In this depth-critique article, we aimed to investigate all possibilities and represented a novel and applicable... 

    A numerical model for predicting hepatocytes ureagenesis and its related inborn enzyme deficiencies: Case studies

    , Article Scientia Iranica ; Volume 26, Issue 1B , 2019 , Pages 408-420 ; 10263098 (ISSN) Sharifi, F ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
    Sharif University of Technology  2019
    Abstract
    One important functionality of liver cells is ammonia detoxification and urea production. In this study, a numerical model of the urea cycle in hepatocytes was developed. Navier Stokes and convection equations were employed to study the process of ammonia elimination and urea production using a microfluidic channel. The concentration of urea and ammonia throughout the channel was obtained. Furthermore, the urea cycle was modelled with respect to its four main enzymes. This resulted in twelve rate equations that were solved to determine the concentration of each metabolite participating in the urea cycle. Application of results implied common disorders such as hyperammonemia types I and II... 

    A perspective to the correlation between brain insulin resistance and Alzheimer: Medicinal chemistry approach

    , Article Current Diabetes Reviews ; Volume 15, Issue 4 , 2019 , Pages 255-258 ; 15733998 (ISSN) Rabiee, N ; Bagherzadeh, M ; Rabiee, M ; Sharif University of Technology
    Bentham Science Publishers  2019
    Abstract
    Substantial terms have been recognized on the associated risk elements, comorbidities as well as, putative pathophysiological processes of Alzheimer disease and related dementias (ADRDs) as well as, type 2 diabetes mellitus (T2DM), a few from greatest important disease from the moments. Very much is considered regarding the biology and chemistry of each predicament, nevertheless T2DM and ADRDs are an actually similar pattern developing from the similar origins of maturing or synergistic conditions connected by aggressive patho-corporeal terms and continues to be ambiguous. In this depth-critique article, we aimed to investigate all possibilities and represented a novel and applicable... 

    Synthesis and characterization of rGO/Fe2O3 nanocomposite as an efficient supercapacitor electrode material

    , Article Journal of Materials Science: Materials in Electronics ; Volume 31, Issue 17 , 2020 , Pages 14998-15005 Abasali karaj abad, Z ; Nemati, A ; Malek Khachatourian, A ; Golmohammad, M ; Sharif University of Technology
    Springer  2020
    Abstract
    The reduced graphene oxide-Fe2O3 (rGO-Fe2O3) nanocomposites were synthesized by a facile and low-cost hydrothermal method employing rGO and Iron (III) nitrate precursors. The synthesis parameters including the reduction time and presence of reduction aid are studied. The structural and morphological studies of the nanocomposites were investigated by using Raman spectra, Fourier transform infrared spectroscopy, X-ray diffraction, and field emission scanning electron microscopy. The results indicate that Fe2O3 nanoparticles with average particle size of 25 nm are well anchored on graphene sheets and the weight percent of the nanoparticles in the nanocomposites was influenced by the reduction... 

    One-pot microwave synthesis of hierarchical C-doped CuO dandelions/g-C3N4 nanocomposite with enhanced photostability for photoelectrochemical water splitting

    , Article Applied Surface Science ; Volume 530 , 2020 Hosseini Hosseinabad, S. M ; Siavash Moakhar, R ; Soleimani, F ; Sadrnezhaad, S. K ; Masudy Panah, S ; Katal, R ; Seza, A ; Ghane, N ; Ramakrishna, S ; Sharif University of Technology
    Elsevier B.V  2020
    Abstract
    Cupric oxide (CuO) is a semiconductor of choice for photocathode in photoelectrochemical (PEC) applications due to its great sunlight absorption capability. However, photocorrosion is the main drawback of CuO. Herein, CuO/graphitic carbon nitride (g-C3N4) with a unique microstructure, enhanced PEC performance, and considerable photostability is synthesized under microwave irradiation. A facile, one-pot method is utilized to directly deposit the nanocomposite onto fluorine-doped tin oxide from a solution containing copper precursor and urea. Possible mechanism of CuO/g-C3N4 formation through this novel method is investigated. It is elucidated that controlled amounts of urea critically... 

    A hepatocellular carcinoma–bone metastasis-on-a-chip model for studying thymoquinone-loaded anticancer nanoparticles

    , Article Bio-Design and Manufacturing ; Volume 3, Issue 3 , 2020 , Pages 189-202 Sharifi, F ; Yesil Celiktas, O ; Kazan, A ; Maharjan, S ; Saghazadeh, S ; Firoozbakhsh, K ; Firoozabadi, B ; Zhang, Y. S ; Sharif University of Technology
    Springer  2020
    Abstract
    We report the development of a metastasis-on-a-chip platform to model and track hepatocellular carcinoma (HCC)–bone metastasis and to analyze the inhibitory effect of an herb-based compound, thymoquinone (TQ), in hindering the migration of liver cancer cells into the bone compartment. The bioreactor consisted of two chambers, one accommodating encapsulated HepG2 cells and one bone-mimetic niche containing hydroxyapatite (HAp). Above these chambers, a microporous membrane was placed to resemble the vascular barrier, where medium was circulated over the membrane. It was observed that the liver cancer cells proliferated inside the tumor microtissue and disseminated from the HCC chamber to the... 

    Analytical and numerical studies of sequence dependence of passage times for translocation of heterobiopolymers through nanopores

    , Article Journal of Chemical Physics ; Volume 129, Issue 23 , 2008 ; 00219606 (ISSN) Haji Abdolvahab, R ; Roshani, F ; Nourmohammad, A ; Sahimi, M ; Rahimi Tabar, M. R ; Sharif University of Technology
    2008
    Abstract
    We consider chaperone-assisted translocation of biopolymers with two distinct monomers or bases A and B, with the size of the chaperones being λα, where α is a monomer's size. The probability that A and B are neighbors in the biopolymer is PAB. A master equation is used, together with the detailed-balanced condition, in order to derive analytical results for the statistics of the first-passage times of the biopolymer as a function of PAB, λ, and the biopolymer's configuration. Monte Carlo simulations have also been carried out in order to compute the same quantities for biopolymers with 100-900 monomers and several λ. The results indicate nontrivial dependence of the variance of the... 

    Application of support vector machines to 1H NMR data of fish oils: Methodology for the confirmation of wild and farmed salmon and their origins

    , Article Analytical and Bioanalytical Chemistry ; Volume 387, Issue 4 , 2007 , Pages 1499-1510 ; 16182642 (ISSN) Masoum, S ; Malabat, C ; Jalali-Heravi, M ; Guillou, C ; Rezzi, S ; Rutledge, D. N ; Sharif University of Technology
    2007
    Abstract
    Support vector machines (SVMs) were used as a novel learning machine in the authentication of the origin of salmon. SVMs have the advantage of relying on a well-developed theory and have already proved to be successful in a number of practical applications. This paper provides a new and effective method for the discrimination between wild and farm salmon and eliminates the possibility of fraud through misrepresentation of the country of origin of salmon. The method requires a very simple sample preparation of the fish oils extracted from the white muscle of salmon samples. 1H NMR spectroscopic analysis provides data that is very informative for analysing the fatty acid constituents of the... 

    S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Rahnama, S ; Azimzadeh Irani, M ; Amininasab, M ; Ejtehadi, M. R ; Sharif University of Technology
    Nature Research  2021
    Abstract
    SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans... 

    Supported deep eutectic liquid membranes with highly selective interaction sites for efficient CO2 separation

    , Article Journal of Molecular Liquids ; Volume 342 , 2021 ; 01677322 (ISSN) Saeed, U ; Khan, A. L ; Gilani, M. A ; Bilad, M. R ; Khan, A. U ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    This study demonstrates a new strategy in which deep eutectic solvents (DES), a new class of sustainable organic solvents, were impregnated into micro porous polymer support for separation of CO2 from CH4. Three different types of DESs were prepared by mixing and subsequent heating of betaine as hydrogen bond acceptor (HBA) in combination with either glycerol (G), ethylene glycol (EG) or urea (U) as hydrogen bond donors (HBD) in 1:3 stoichiometric mole ratio. The Fourier transform infrared (FTIR) spectroscopy was performed to confirm the formation of DESs. The gas permeation results showed that permeability of CO2 increased from 31.23 to 35.67 Barrer on substitution of HBD from glycerol to... 

    Enzyme-inspired lysine-modified carbon quantum dots performing carbonylation using urea and a cascade reaction for synthesizing 2-benzoxazolinone

    , Article ACS Catalysis ; Volume 11, Issue 17 , 2021 , Pages 10778-10788 ; 21555435 (ISSN) Hasani, M ; Kalhor, H. R ; Sharif University of Technology
    American Chemical Society  2021
    Abstract
    Catalysts as the dynamo of chemical reactions along with solvents play paramount roles in organic transformations in long-lasting modes. Thus, developing effective and biobased catalysts in nontoxic solvents is highly in demand. In this report, carbon quantum dots (CQDs) functionalized with-lysine (Lys-CQDs) were generated from entirely nature-derived materials; they were demonstrated to be a promising catalyst for C-N bond formation in choline chloride urea (ChCl/U), a natural deep eutectic solvent (NADES). Among a number of synthesized CQDs, Lys-CQD turned out to be a powerful catalyst in the model reaction with aniline to afford phenyl urea. This type of transformation is important... 

    Flash photo stimulation of human neural stem cells on graphene/TiO 2 heterojunction for differentiation into neurons

    , Article Nanoscale ; Volume 5, Issue 21 , 2013 , Pages 10316-10326 ; 20403364 (ISSN) Akhavan, O ; Ghaderi, E ; Sharif University of Technology
    2013
    Abstract
    For the application of human neural stem cells (hNSCs) in neural regeneration and brain repair, it is necessary to stimulate hNSC differentiation towards neurons rather than glia. Due to the unique properties of graphene in stem cell differentiation, here we introduce reduced graphene oxide (rGO)/TiO2 heterojunction film as a biocompatible flash photo stimulator for effective differentiation of hNSCs into neurons. Using the stimulation, the number of cell nuclei on rGO/TiO2 increased by a factor of ∼1.5, while on GO/TiO2 and TiO2 it increased only ∼48 and 24%, respectively. Moreover, under optimum conditions of flash photo stimulation (10 mW cm-2 flash intensity and 15.0 mM ascorbic acid in... 

    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) Nassiri, I ; 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... 

    Management of soybean oil refinery wastes through recycling them for producing biosurfactant using Pseudomonas aeruginosa MR01

    , Article World Journal of Microbiology and Biotechnology ; Volume 29, Issue 6 , June , 2013 , Pages 1039-1047 ; 09593993 (ISSN) Partovi, M ; Lotfabad, T. B ; Roostaazad, R ; Bahmaei, M ; Tayyebi, S ; Sharif University of Technology
    2013
    Abstract
    Biosurfactant production through a fermentation process involving the biodegradation of soybean oil refining wastes was studied. Pseudomonas aeruginosa MR01 was able to produce extracellular biosurfactant when it was cultured in three soybean oil refinement wastes; acid oil, deodorizer distillate and soapstock, at different carbon to nitrogen ratios. Subsequent fermentation kinetics in the three types of waste culture were also investigated and compared with kinetic behavior in soybean oil medium. Biodegradation of wastes, biosurfactant production, biomass growth, nitrate consumption and the number of colony forming units were detected in four proposed media, at specified time intervals.... 

    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) Nikkhoo, M ; 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... 

    Nanomechanical properties of lipid bilayer: Asymmetric modulation of lateral pressure and surface tension due to protein insertion in one leaflet of a bilayer

    , Article Journal of Chemical Physics ; Volume 138, Issue 6 , 2013 ; 00219606 (ISSN) Maftouni, N ; Amininasab, M ; Ejtehadi, M. R ; Kowsari, F ; Dastvan, R ; Sharif University of Technology
    2013
    Abstract
    The lipid membranes of living cells form an integral part of biological systems, and the mechanical properties of these membranes play an important role in biophysical investigations. One interesting problem to be evaluated is the effect of protein insertion in one leaflet of a bilayer on the physical properties of lipid membrane. In the present study, an all atom (fine-grained) molecular dynamics simulation is used to investigate the binding of cytotoxin A3 (CTX A3), a cytotoxin from snake venom, to a phosphatidylcholine lipid bilayer. Then, a 5 ms coarse-grained molecular dynamics simulation is carried out to compute the pressure tensor, lateral pressure, surface tension, and first moment... 

    Fabrication of sensitive glutamate biosensor based on vertically aligned CNT nanoelectrode array and investigating the effect of CNTs density on the electrode performance

    , Article Analytical Chemistry ; Volume 84, Issue 14 , June , 2012 , Pages 5932-5938 ; 00032700 (ISSN) Gholizadeh, A ; Shahrokhian, S ; Iraji Zad, A ; Mohajerzadeh, S ; Vosoughi, M ; Darbari, S ; Koohsorkhi, J ; Mehran, M ; Sharif University of Technology
    2012
    Abstract
    In this report, the fabrication of vertically aligned carbon nanotube nanoelectrode array (VACNT-NEA) by photolithography method is presented. Electrochemical impedance spectroscopy as well as cyclic voltammetry was performed to characterize the arrays with respect to different diffusion regimes. The fabricated array illustrated sigmoidal cyclic voltammogram with steady state current dominated by radial diffusion. The fabricated VACNT-NEA and high density VACNTs were employed as electrochemical glutamate biosensors. Glutamate dehydrogenase is covalently attached to the tip of CNTs. The voltammetric biosensor, based on high density VACNTs, exhibits a sensitivity of 0.976 mA mM-1 cm-2 in the... 

    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) Moradi Shoeili, Z ; 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... 

    Protein-nanoparticle interactions: Opportunities and challenges

    , Article Chemical Reviews ; Volume 111, Issue 9 , June , 2011 , Pages 5610-5637 ; 00092665 (ISSN) Mahmoudi, M ; Lynch, I ; Ejtehadi, M. R ; Monopoli, M. P ; Bombelli, F. B ; Laurent, S ; Sharif University of Technology
    2011
    Abstract
    The significant role of protein nanoparticle interactions in nanomedicine and nanotoxicity is emerging recently through the identification of the nanoparticles (NP) protein (biomolecule) corona. The dynamic layer of proteins and/or other biomolecules adsorbed to the nanoparticle surface determines how a NP interacts with living systems and thereby modifies the cellular responses to the NP. Ehrenberg and co-workers used cultured endothelium cells as a model for vascular transport of polystyrene NP with various functional groups, which showed that the capacity of the various NP surfaces to adsorb proteins was indicative of their tendency to associate with cells. The quantification of the...