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    Effect of Cu2+ ion on biological performance of nanostructured uorapatite doped with copper

    , Article Scientia Iranica ; Volume 24, Issue 6 , 2017 , Pages 2845-2855 ; 10263098 (ISSN) Nikonam Mofrad, R ; Sadrnezhaad, S. K ; Vahdati Khaki, J ; Sharif University of Technology
    Nanostructured copper-doped uorapatite (Cux.Ca(10X).(PO4)6.F2) having crystallite sizes of 19, 29, and 34 nm at x = 0:9, 0.4, and 0.0, respectively, was synthesized by planetary ball milling of CaO, P2O5, CaF2, and CuO powders. Specifications of the products were determined by Fourier-transform infrared spectroscopy, eld emission scanning electron microscopy, transmission electron microscopy, and X-ray di raction analyses. In-vitro studies and Mossman's Tetrazole Test (MTT) assays were also conducted by incubating Cux.Ca(10X).(PO6).F2 powder into Kokubo's Simulated Body Fluid (SBF) and against BT-20 cell, respectively, to determine bioactivity and biocompatibility of the materials.... 

    Hybrid multiscale modeling and prediction of cancer cell behavior

    , Article PLoS ONE ; Volume 12, Issue 8 , 2017 ; 19326203 (ISSN) Zangooei, M. H ; Habibi, J ; Sharif University of Technology
    Public Library of Science  2017
    Background: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for... 

    NMR spectroscopy-based metabolomic study of serum in sulfur mustard exposed patients with lung disease

    , Article Biomarkers ; Volume 22, Issue 5 , 2017 , Pages 413-419 ; 1354750X (ISSN) Nobakht, B.F., M. Gh ; Arefi Oskouie, A ; Rezaei Tavirani, M ; Aliannejad, R ; Taheri, S ; Fathi, F ; Naseri, M. T ; Sharif University of Technology
    Taylor and Francis Ltd  2017
    Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the... 

    Modeling and optimization of gelatin-chitosan micro-carriers preparation for soft tissue engineering: using response surface methodology

    , Article Materials Science and Engineering C ; Volume 75 , 2017 , Pages 545-553 ; 09284931 (ISSN) Radaei, P ; Mashayekhan, S ; Vakilian, S ; Sharif University of Technology
    Electrospray ionization is a wide spread technique for producing polymeric microcarriers (MCs) by applying electrostatic force and ionic cross-linker, simultaneously. In this study, fabrication process of gelatin-chitosan MCs and its optimization using the Response Surface Methodology (RSM) is reported. Gelatin/chitosan (G/C) blend ratio, applied voltage and feeding flow rate, their individual and interaction effects on the diameter and mechanical strength of the MCs were investigated. The obtained models for diameter and mechanical strength of MCs have a quadratic relationship with G/C blend ratio, applied voltage and feeding flow rate. Using the desirability curve, optimized G/C blend... 

    Fabrication of new magnetite-graphene nanocomposite and comparison of its laser-hyperthermia properties with conventionally prepared magnetite-graphene hybrid

    , Article Materials Science and Engineering C ; Volume 75 , 2017 , Pages 572-581 ; 09284931 (ISSN) Tayyebi, A ; Moradi, S ; Azizi, F ; Outokesh, M ; Shadanfar, K ; Mousavi, S. S ; Sharif University of Technology
    A single step supercritical method was introduced for synthesis of “magnetite - reduced graphene oxide (M-rGO)” composite in supercritical methanol. Modified surface, smaller size, lesser cytotoxicity, and homogenous dispersion of Fe3O4 nanoparticles on the graphene surface were advantages of this new M-rGO composite in comparison to the materials synthesized by conventional wet chemical method (M-GO). Nanocomposites were injected in tissue equivalent phantoms of agarose gel in 10 mg/g dosage, and were irradiated by a 1600 mW laser beam at wavelength of 800–810 nm. The M-rGO and M-GO were found to be the most and the least efficient samples for increasing the temperature of the phantom. As... 

    Study of epithelial differentiation and protein expression of keratinocyte-mesenchyme stem cell co-cultivation on electrospun nylon/B. vulgaris extract composite scaffold

    , Article Materials Science and Engineering C ; Volume 75 , 2017 , Pages 653-662 ; 09284931 (ISSN) Hosseinzadeh, S ; Soleimani, M ; Vossoughi, M ; Ranjbarvan, P ; Hamedi, S ; Zamanlui, S ; Mahmoudifard, M ; Sharif University of Technology
    Employing of the composite electrospun scaffold containing herbal extract in conjugation with co-culturing of cells can open up new window to the design of efficient biomaterials for skin tissue regeneration. Here, we introduce the synergistic effect of composite electrospun nanofibrous scaffold of nylon66 loaded with Beta vulgaris (B. vulgaris) (extract of beet roots, a plants whose widely used in Iranian folk medicine as wound healing medicine) and co-culture of mesenchymal stem-cells (MSCs)-human keratinocyte (H-keratino) differentiation towards epithelial lineage. In vitro biocompatibility was examined through MTT assay and epithelial differentiation checked by real-time PCR and... 

    Nanomechanical properties of MscL α helices: A steered molecular dynamics study

    , Article Channels ; Volume 11, Issue 3 , 2017 , Pages 209-223 ; 19336950 (ISSN) Bavi, N ; Bavi, O ; Vossoughi, M ; Naghdabadi, R ; Hill, A. P ; Martinac, B ; Jamali, Y ; Sharif University of Technology
    Taylor and Francis Inc  2017
    Gating of mechanosensitive (MS) channels is driven by a hierarchical cascade of movements and deformations of transmembrane helices in response to bilayer tension. Determining the intrinsic mechanical properties of the individual transmembrane helices is therefore central to understanding the intricacies of the gating mechanism of MS channels. We used a constant-force steered molecular dynamics (SMD) approach to perform unidirectional pulling tests on all the helices of MscL in M. tuberculosis and E. coli homologs. Using this method, we could overcome the issues encountered with the commonly used constant-velocity SMD simulations, such as low mechanical stability of the helix during... 

    Challenges and future prospects for the delivery of biologics: oral mucosal, pulmonary, and transdermal routes

    , Article AAPS Journal ; Volume 19, Issue 3 , 2017 , Pages 652-668 ; 15507416 (ISSN) Morales, J. O ; Fathe, K. R ; Brunaugh, A ; Ferrati, S ; Li, S ; Montenegro Nicolini, M ; Mousavikhamene, Z ; McConville, J. T ; Prausnitz, M. R ; Smyth, H. D. C ; Sharif University of Technology
    Springer New York LLC  2017
    Biologic products are large molecules such as proteins, peptides, nucleic acids, etc., which have already produced many new drugs for clinical use in the last decades. Due to the inherent challenges faced by biologics after oral administration (e.g., acidic stomach pH, digestive enzymes, and limited permeation through the gastrointestinal tract), several alternative routes of administration have been investigated to enable sufficient drug absorption into systemic circulation. This review describes the buccal, sublingual, pulmonary, and transdermal routes of administration for biologics with relevant details of the respective barriers. While all these routes avoid transit through the... 

    Two schemes for production of biosurfactant from Pseudomonas aeruginosa MR01: Applying residues from soybean oil industry and silica sol–gel immobilized cells

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 152 , 2017 , Pages 159-168 ; 09277765 (ISSN) Bagheri Lotfabad, T ; Ebadipour, N ; Roostaazad, R ; Partovi, M ; Bahmaei, M ; Sharif University of Technology
    Elsevier B.V  2017
    Rhamnolipids are the most common biosurfactants and P. aeruginosa strains are the most frequently studied microorganisms for the production of rhamnolipids. Eco-friendly advantages and promising applications of rhamnolipids in various industries are the major reasons for pursuing the economic production of these biosurfactants. This study shows that cultivation of P. aeruginosa MR01 in medium contained inexpensive soybean oil refinery wastes which exhibited similar levels and homologues of rhamnolipids. Mass spectrometry indicated that the Rha-C10-C10 and Rha-Rha-C10-C10 constitute the main rhamnolipids in different cultures of MR01 including one of oil carbon source analogues. Moreover,... 

    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
    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
    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
    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... 

    Theoretical modeling of actin-retrograde-flow passing clusters of confined T cell receptors

    , Article Mathematical Biosciences ; Volume 283 , 2017 , Pages 1-6 ; 00255564 (ISSN) Ghasemi V., A ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Elsevier Inc  2017
    Through the activation process of T cells, actin filaments move from the cell periphery toward the cell center. The moving filaments engage with T cell receptors and thus contribute to transportation of the signaling molecules. To study the connection between the moving actin filaments and T cell receptors, an experiment available in the literature has measured filaments flow velocity passing over a region of confined clusters of receptors. It shows that flow velocity decreases in the proximity of the receptors, and then regains its normal value after traversing the region, suggesting a dissipative friction-like connection. In this work, we develop a minimal theoretical model to re-examine... 

    Short-term effects of particle size fractions on circulating biomarkers of inflammation in a panel of elderly subjects and healthy young adults

    , Article Environmental Pollution ; Volume 223 , 2017 , Pages 695-704 ; 02697491 (ISSN) Hassanvand, M. S ; Naddafi, K ; Kashani, H ; Faridi, S ; Kunzli, N ; Nabizadeh, R ; Momeniha, F ; Gholampour, A ; Arhami, M ; Zare, A ; Pourpak, Z ; Hoseini, M ; Yunesian, M ; Sharif University of Technology
    Systemic inflammation biomarkers have been associated with risk of cardiovascular morbidity and mortality. We aimed to clarify associations of acute exposure to particulate matter (PM10(PM < 10 μm), PM2.5-10(PM 2.5–10 μm), PM2.5(PM < 2.5 μm), PM1-2.5(PM 1–2.5 μm), and PM1 (PM < 1 μm)) with systemic inflammation using panels of elderly subjects and healthy young adults. We followed a panel of 44 nonsmoking elderly subjects living in a retirement home and a panel of 40 healthy young adults living in a school dormitory in Tehran city, Iran from May 2012 to May 2013. Blood biomarkers were measured one every 7–8 weeks and included white blood cells (WBC), high sensitive C-reactive protein... 

    Cell shape affects nanoparticle uptake and toxicity: An overlooked factor at the nanobio interfaces

    , Article Journal of Colloid and Interface Science ; Volume 531 , 2018 , Pages 245-252 ; 00219797 (ISSN) Farvadi, F ; Ghahremani, M. H ; Hashemi, F ; Hormozi Nezhad, M. R ; Raoufi, M ; Zanganeh, S ; Atyabi, F ; Dinarvand, R ; Mahmoudi, M ; Sharif University of Technology
    Academic Press Inc  2018
    Hypothesis: It is now being increasingly accepted that cells in their native tissue show different morphologies than those grown on a culture plate. Culturing cells on the conventional two-dimensional (2D) culture plates does not closely resemble the in vivo three-dimensional (3D) structure of cells which in turn seems to affect cellular function. This is one of the reasons, among many others, that nanoparticles uptake and toxicology data from 2D culture plates and in vivo environments are not correlated with one another. In this study, we offer a novel platform technology for producing more in vivo-like models of in vitro cell culture. Experiments: The normal fibroblast cells (HU02) were... 

    Magnetic carbon nanotubes: preparation, physical properties, and applications in biomedicine

    , Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 46, Issue 7 , 2018 , Pages 1314-1330 ; 21691401 (ISSN) Samadishadlou, M ; Farshbaf, M ; Annabi, N ; Kavetskyy, T ; Khalilov, R ; Saghfi, S ; Akbarzadeh, A ; Mousavi, S ; Sharif University of Technology
    Magnetic carbon nanotubes (MCNTs) have been widely studied for their potential applications in medicine, diagnosis, cell biology, analytical chemistry, and environmental technology. Introduction of MCNTs paved the way for the emergence of new approaches in nanobiotechnology and biomedicine as a result of their multifarious properties embedded within either the carbon nanotubes (CNTs) or magnetic parts. Numerous preparation techniques exists for functionalizing CNTs with magnetic nanoparticles, and these versatile strategies lay the ground for the generation of novel and versatile systems which are applicable to many industries and biological areas. Here, we review and discuss the recent... 

    Development of a novel nano-sized anti-VEGFA nanobody with enhanced physicochemical and pharmacokinetic properties

    , Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 46, Issue 7 , 2018 , Pages 1402-1414 ; 21691401 (ISSN) Khodabakhsh, F ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
    Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD... 

    Smart liposomal drug delivery for treatment of oxidative stress model in human embryonic stem cell-derived retinal pigment epithelial cells

    , Article International Journal of Pharmaceutics ; Volume 548, Issue 1 , 2018 , Pages 62-72 ; 03785173 (ISSN) Behroozi, F ; Abdkhodaie, M. J ; Sadeghi Abandansari, H ; Satarian, L ; Kazemi Ashtiani, M ; Jaafari, M. R ; Baharvand, H ; Sharif University of Technology
    Oxidative stress has been implicated in the progression of age-related macular degeneration (AMD). Treatment with antioxidants seems to delay progression of AMD. In this study, we suggested an antioxidant delivery system based on redox-sensitive liposome composed of phospholipids and a diselenide centered alkyl chain. Dynamic light scattering assessment indicated that the liposomes had an average size of 140 nm with a polydispersity index below 0.2. The percentage of encapsulation efficiency of the liposomes was calculated by high-performance liquid chromatography. The carriers were loaded with N-acetyl cysteine as a model antioxidant drug. We demonstrated responsiveness of the nanocarrier... 

    Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

    , Article Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN) Rahimi, T ; Niazi, A ; Deihimi, T ; Taghavi, S. M ; Ayatollahi, S ; Ebrahimie, E ; Sharif University of Technology
    Springer Verlag  2018
    One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison... 

    Design and parameter study of integrated microfluidic platform for CTC isolation and enquiry; a numerical approach

    , Article Biosensors ; Volume 8, Issue 2 , 18 June , 2018 ; 20796374 (ISSN) Shamloo, A ; Ahmad, S ; Momeni, M ; Sharif University of Technology
    Being the second cause of mortality across the globe, there is now a persistent effort to establish new cancer medication and therapies. Any accomplishment in treating cancers entails the existence of accurate identification systems empowering the early diagnosis. Recent studies indicate CTCs’ potential in cancer prognosis as well as therapy monitoring. The chief shortcoming with CTCs is that they are exceedingly rare cells in their clinically relevant concentration. Here, we simulated a microfluidic construct devised for immunomagnetic separation of the particles of interest from the background cells. This separation unit is integrated with a mixer subunit. The mixer is envisioned for...