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    A biomimetic heparinized composite silk-based vascular scaffold with sustained antithrombogenicity

    , Article Scientific Reports ; Volume 7, Issue 1 , 2017 ; 20452322 (ISSN) Zamani, M ; Khafaji, M ; Naji, M ; Vossoughi, M ; Alemzadeh, I ; Haghighipour, N ; Sharif University of Technology
    Autologous grafts, as the gold standard for vascular bypass procedures, associated with several problems that limit their usability, so tissue engineered vessels have been the subject of an increasing number of works. Nevertheless, gathering all of the desired characteristics of vascular scaffolds in the same construct has been a big challenge for scientists. Herein, a composite silk-based vascular scaffold (CSVS) was proposed to consider all the mechanical, structural and biological requirements of a small-diameter vascular scaffold. The scaffold's lumen composed of braided silk fiber-reinforced silk fibroin (SF) sponge covalently heparinized (H-CSVS) using Hydroxy-Iron Complexes (HICs) as... 

    A system-oriented strategy to enhance electron production of Synechocystis sp. PCC6803 in bio-photovoltaic devices: experimental and modeling insights

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Firoozabadi, H ; Mardanpour, M. M ; Motamedian, E ; Sharif University of Technology
    Nature Research  2021
    Bio-photovoltaic devices (BPVs) harness photosynthetic organisms to produce bioelectricity in an eco-friendly way. However, their low energy efficiency is still a challenge. A comprehension of metabolic constraints can result in finding strategies for efficiency enhancement. This study presents a systemic approach based on metabolic modeling to design a regulatory defined medium, reducing the intracellular constraints in bioelectricity generation of Synechocystis sp. PCC6803 through the cellular metabolism alteration. The approach identified key reactions that played a critical role in improving electricity generation in Synechocystis sp. PCC6803 by comparing multiple optimal solutions of... 

    Phenol biodegradation by rotating biological contactor

    , Article Biochemical Engineering Journal ; Volume 11, Issue 1 , 2002 , Pages 19-23 ; 1369703X (ISSN) Alemzadeh, I ; Vossoughi, F ; Houshmandi, M ; Sharif University of Technology
    This study presents the removal performance of phenol in a three-stages cross flow laboratory-scale rotating biological contactor (RBC). The impact of major process and operating variables, such as input hydraulic loading (HL), input COD loading, and temperature of wastewater on the total removal efficiency of the system were examined. It was observed that the phenol removal performance worsened when the HL increased, and optimum total phenol removal efficiency of 99.9% was observed at loading of 4 × 10-3 m-3 m-2 per day and COD concentration of 800 mg dm-3. On the basis of overall treatment of phenol containing wastewater in the RBC, the optimal removal performance was noted at the end of... 

    Controlling the geometry of silver nanostructures for biological applications

    , Article Physics Procedia, Ancona ; Volume 40 , 2013 , Pages 76-83 ; 18753884 (ISSN) Ashkarran, A. A ; Estakhri, S ; Nezhad, M. R. H ; Eshghi, S ; Sharif University of Technology
    Noble metals nanostructures, particularly silver, have attracted much attention in the fields of electronics, chemistry, physics, biology and medicine due to their unique properties which are strongly dependent on the size and shape of metal nanomaterials. This study discusses on silver nanostructures with different geometries including wire, cube, sphere and triangle prepared using solution-phase method and applied for antibacterial activities. X-ray diffraction (XRD), Ultra Violet Visible (UV-Vis) spectroscopy, Dynamic Light Scattering (DLS) and electron microscopy studies of different types of silver nanostructures revealed distinct optical and structural properties of an individual... 

    Personalized disease-specific protein corona influences the therapeutic impact of graphene oxide

    , Article Nanoscale ; Volume 7, Issue 19 , Apr , 2015 , Pages 8978-8994 ; 20403364 (ISSN) Hajipour, M. J ; Raheb, J ; Akhavan, O ; Arjmand, S ; Mashinchian, O ; Rahman, M ; Abdolahad, M ; Serpooshan, V ; Laurent, S ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2015
    The hard corona, the protein shell that is strongly attached to the surface of nano-objects in biological fluids, is recognized as the first layer that interacts with biological objects (e.g., cells and tissues). The decoration of the hard corona (i.e., the type, amount, and conformation of the attached proteins) can define the biological fate of the nanomaterial. Recent developments have revealed that corona decoration strongly depends on the type of disease in human patients from which the plasma is obtained as a protein source for corona formation (referred to as the 'personalized protein corona'). In this study, we demonstrate that graphene oxide (GO) sheets can trigger different... 

    Real time simulation of grasping procedure of large internal organs during laparoscopic surgery

    , Article Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS ; Volume 2012 , 2012 , Pages 924-927 ; 1557170X (ISSN) Dehghani Ashkezari, H ; Mirbagheri, A ; Farahmand, F ; Behzadipour, S ; Firoozbakhsh, K ; Sharif University of Technology
    Surgical simulation systems facilitate safe and efficient training processes of surgical trainees by providing a virtual environment in which the surgical procedure can be repeated unlimitedly in a wide variety of situations. The present study attempted to develop a real time simulation system for the grasping procedure of large internal organs during laparoscopic surgery. A mass-spring-damper model was developed to simulate the nonlinear viscoelastic large deformations of the spleen tissue while interacting with a triple-jaw grasper. A novel collision detection algorithm was designed and implemented to determine the contact points between the tissue and the grasper jaws. Force or... 

    Objective Information in the Empiricist View of von Weizsacker

    , Article Foundations of Science ; Vol. 19, issue. 3 , 2014 , p. 241-255 Khatam, I ; Shafiee, A ; Sharif University of Technology
    We analyze von Weizsacker's view regarding the concept of information in physics. In his view, information arises from the reduction of properties of a physical object to their logical descriptive propositions. The smallest element of a lattice of propositions is an atom of information which is considered as the essence of every physical identity including position space. von Weizsäcker calls this element, "ur". Moreover, Biological evolution is described in terms of enhancement of the variety of forms. Form could be also reduced to descriptive logical propositions, thus to atoms of information. Therefore, information is the fundamental basis in von Weizsäcker's plan for unifying all... 

    Biological removal of phenol from saline wastewater using a moving bed biofilm reactor containing acclimated mixed consortia

    , Article SpringerPlus ; Vol. 3, issue. 1 , 2014 , pp. 1-10 ; ISSN: 21931801 Nakhli, S. A. A ; Ahmadizadeh, K ; Fereshtehnejad, M ; Rostami, M. H ; Safari, M ; Borghei, S. M ; Sharif University of Technology
    In this study, the performance of an aerobic moving bed biofilm reactor (MBBR) was assessed for the removal of phenol as the sole substrate from saline wastewater. The effect of several parameters namely inlet phenol concentration (200-1200 mg/L), hydraulic retention time (8-24 h), inlet salt content (10-70 g/L), phenol shock loading, hydraulic shock loading and salt shock loading on the performance of the 10 L MBBR inoculated with a mixed culture of active biomass gradually acclimated to phenol and salt were evaluated in terms of phenol and chemical oxygen demand (COD) removal efficiencies. The results indicated that phenol and COD removal efficiencies are affected by HRT, phenol and salt... 

    Anaerobic treatment by UASB reactor and aerobic biodegradability test of cutting oil sewage

    , Article Journal of Environmental Studies ; Vol. 40, issue. 1 , 2014 , p. 211-220 Alavi, A. N ; Sajadi, A. A ; Mirzaei, M ; Hoseynian, H ; Sharif University of Technology
    Introduction: Water is consumed in almost all industries. Consequently the used water is turning to a waste that usually should be treated to meet the regulated standard level prior to reuse or discharge into the environment. Cutting oil wastewater is an emulsion normally comprised ofl-10% oil and the remainder water. The main functions of this oil in industry are lubrication, friction reduction, and cooling of instrument s parts. This wastewater is classified as a toxic waste according to the existence of some additive material to prevent corrosion and bacterial growth. Breakage of the emulsion and separation of the water and the oil can alone reduce more than about 90% of the aqueous phase... 

    The propagation of laser light in skin by Monte Carlo-diffusion method: A fast and accurate method to simulate photon migration in biological tissues

    , Article Journal of Lasers in Medical Sciences ; Volume 2, Issue 3 , 2011 , Pages 109-114 ; 20089783 (ISSN) Golshan, M. A ; Tarei, M. G ; Ansari, M. A ; Amjadi, A ; Sharif University of Technology
    Introduction: Due to the importance of laser light penetration and propagation in biological tissues, many researchers have proposed several numerical methods such as Monte Carlo, finite element and green function methods. Among them, the Monte Carlo method is an accurate method which can be applied for different tissues. However, because of its statistical nature, Monte Carlo simulation requires a large number of photon pockets to be traced, so it is computationally expensive and time-consuming. Although other numerical methods based on the diffusion method are fast, they have two important limitations: first, they are not valid near the bounder of sample and source, and second, their... 

    Cell deformation modeling under external force using artificial neural network

    , Article Journal of Solid Mechanics ; Volume 2, Issue 2 , 2010 , Pages 190-198 ; 20083505 (ISSN) Ahmadian, M. T ; Vossoughi, G. R ; Abbasi, A. A ; Raeissi, P ; Sharif University of Technology
    Embryogenesis, regeneration and cell differentiation in microbiological entities are influenced by mechanical forces. Therefore, development of mechanical properties of these materials is important. Neural network technique is a useful method which can be used to obtain cell deformation by the means of force-geometric deformation data or vice versa. Prior to insertion in the needle injection process, deformation and geometry of cell under external point-load is a key element to understand the interaction between cell and needle. In this paper, the goal is the prediction of cell membrane deformation under a certain force and to visually estimate the force of indentation on the membrane from... 

    afpCOOL: a tool for antifreeze protein prediction

    , Article Heliyon ; Volume 4, Issue 7 , 2018 ; 24058440 (ISSN) Eslami, M ; Shirali Hossein Zade, R ; Takalloo, Z ; Mahdevar, G ; Emamjomeh, A ; Sajedi, R. H ; Zahiri, J ; Sharif University of Technology
    Elsevier Ltd  2018
    Various cold-adapted organisms produce antifreeze proteins (AFPs), which prevent the freezing of cell fluids by inhibiting the growth of ice crystals. AFPs are currently being recognized in various organisms, living in extremely low temperatures. AFPs have several important applications in increasing freeze tolerance of plants, maintaining the tissue in frozen conditions and producing cold-hardy plants by applying transgenic technology. Substantial differences in the sequence and structure of the AFPs, pose a challenge for researchers to identify these proteins. In this paper, we proposed a novel method to identify AFPs, using supportive vector machine (SVM) by incorporating 4 types of... 

    FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots

    , Article Bioinformatics ; Volume 36, Issue 12 , 15 June , 2020 , Pages 3662-3668 Etminan, N ; Parvinnia, E ; Sharifi Zarchi, A ; Sharif University of Technology
    Oxford University Press  2020
    Motivation: Multiple sequence alignment (MSA) is important and challenging problem of computational biology. Most of the existing methods can only provide a short length multiple alignments in an acceptable time. Nevertheless, when the researchers confront the genome size in the multiple alignments, the process has required a huge processing space/time. Accordingly, using the method that can align genome size rapidly and precisely has a great effect, especially on the analysis of the very long alignments. Herein, we have proposed an efficient method, called FAME, which vertically divides sequences from the places that they have common areas; then they are arranged in consecutive order. Then... 

    Physico-chemical and biological treatment of olive mill wastewater by rotating biological contactor (RBC) reactors

    , Article Iranian Journal of Chemistry and Chemical Engineering ; Volume 25, Issue 4 , 2006 , Pages 47-53 ; 10219986 (ISSN) Alemzadeh, I ; Nazemi, A ; Sharif University of Technology
    The removal performance of total poly phenols and orthodiphenols (o-diphenols) content in olive mill waste (OMW) was investigated with a three stages cross flow laboratory scale rotating biological contactor (RBC) in the present study. Due to high COD and other pollutant in the original OMW, physico-chemical treatment was effected for COD and other pollutant reduction prior to biological treatment of OMW by the RBC system. Inoculation of RBC was effected by sludge from olive oil factory. In biological treatment, effect of operating parameters such as hydraulic loading (HL) and influent COD were examined. The study of the physicochemical treatment before biological treatment of OMW showed,... 

    Analysis of food resources, host availability and insecticidal impacts on the fecundity, longevity and parasitism efficiency of Diaertiella rapae (M’intosh)

    , Article International Journal of Tropical Insect Science ; Volume 41, Issue 4 , 2021 , Pages 2883-2896 ; 17427584 (ISSN) Nawaz, A ; Ali, H ; Fiaz, S ; Sufyan, M ; Qayyum, M. A ; Azad, R ; Niaz, Y ; Bodlah, M. A ; Khan, K. A ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    The use of pesticides may pose a serious threat to soil and water quality, human health, food safety, aquatic species and beneficial insects. Biological control is an effective component of integrated pest management comprising importation, augmentation and conservation. Conservation of natural enemies could enhance or limit the efficiency of herbivorous insect pests. The present study was designed to evaluate the efficiency of Diaeretiella rapae (McIntosh) and other food resources impacts on parasitoid’s fecundity, survival and efficiency. The effect of different insecticides [Carbosulfan, Imidacloprid, Diafenthiuron and Lufenuron] was also evaluated in a laboratory controlled experiment.... 

    Biological upgrading of heavy oil cuts using native microbial consortia as an environmental-friendly technology in petroleum refineries

    , Article Advances in Environmental Technology ; Volume 8, Issue 3 , 2022 , Pages 215-228 ; 24766674 (ISSN) Ghavipanjeh, F ; Ziaei Rad, Z ; Shayegan, J ; Pazouki, M ; Hossinia, A ; Sharif University of Technology
    Iranian Research Organization for Science and Technology  2022
    Refineries are amongst the most energy-intensive and polluting industries in the world. Biotechnology may serve as an alternative low-cost and environmental-friendly tool to the current costly, toxic and hazardous refining processes. In this study, the compositional redistribution of a heavy hydrocarbon cut is investigated under biological conversion using native microbial consortia. The native consortia were obtained by batch enrichment method applied on oil-polluted soil samples from oil refineries of Iran. The bioconversion experiments were conducted with 20% and 40% (v/v) of the heavy cut as the sole carbon source and 10% (v/v) of the consortia broth in 250 ml flasks containing a mineral... 

    Inferring signaling pathways using interventional data

    , Article Intelligent Data Analysis ; Volume 17, Issue 2 , April , 2013 , Pages 295-308 ; 1088467X (ISSN) Mazloomian, A ; Beigy, H ; Sharif University of Technology
    Studying biological networks helps to gain a better understanding of cellular behaviors. One of the prominent models to study complex interactions in biological networks is the Nested Effects Model (NEM). Based on the Nested Effects Model, we propose two methods for inferring signaling pathways from interventional data. In the first method, we search the space of all feasible solutions with an evolutionary approach to maximize a standard Bayesian score. In the second method, sub-models are constructed with informative features and then combined using an averaging method to make the analysis of larger networks computationally possible. We tested our proposed methods in various noise levels on... 

    Chaos and its degradation-promoting-based control in an antithetic integral feedback circuit

    , Article IEEE Control Systems Letters ; Volume 6 , 2022 , Pages 1622-1627 ; 24751456 (ISSN) Zand, A. M ; Tavazoei, M. S ; Kuznetsov, N. V ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2022
    This letter deals with a novel variant of antithetic integral feedback controller (AIFC) motifs which can feature robust perfect adaptation, a pervasive (desired) ability in natural (synthetic) biomolecular circuits, when coupled with a wide class of process networks to be regulated. Using the separation of time-scales in the proposed kind of AIFC, here we find a reduced-order controller that captures the governing slow part of the original solutions under suitable assumptions. Inspired by Rössler systems, we then make use of such a simpler controller to show that the antithetic circuit can exhibit chaotic behaviors with strange attractors, where the bifurcation from a homeostatic state to... 

    Biological Regeneration of Used Activated Carbon

    , M.Sc. Thesis Sharif University of Technology Noori Ghezeldareh, Maral (Author) ; Borghei, Mehdi (Supervisor)
    Tehran Refinery, as an industrial center that has significant water consumption in Tehran, intends to use the flow of water from the treatment plant south of Tehran after final preparation, with the aim of managing water resources and meeting its needs. And it uses a biological activated carbon (BACF) filter to reduce the DOC concentration. In these filters, the removal of organic matter is performed by the adsorption process as well as the biodegradation process by microorganisms grown on activated carbon. The presence of biofilm leads to continuous bio-regeneration of activated carbon during the water treatment process. Therefore, in this study, by examining the performance of these... 

    Synchronizing hindmarsh-rose neurons over newman-watts networks

    , Article Chaos ; Volume 19, Issue 3 , 2009 ; 10541500 (ISSN) Jalili, M ; Sharif University of Technology
    American Institute of Physics Inc  2009
    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...