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metabolism
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A mechanobiological mathematical model of liver metabolism
, Article Biotechnology and Bioengineering ; Volume 117, Issue 9 , 5 June , 2020 , Pages 2861-2874 ; Firoozabadi, B ; Munn, L. L ; Sharif University of Technology
John Wiley and Sons Inc
2020
Abstract
The liver plays a complex role in metabolism and detoxification, and better tools are needed to understand its function and to develop liver-targeted therapies. In this study, we establish a mechanobiological model of liver transport and hepatocyte biology to elucidate the metabolism of urea and albumin, the production/detoxification of ammonia, and consumption of oxygen and nutrients. Since hepatocellular shear stress (SS) can influence the enzymatic activities of liver, the effect of SS on the urea and albumin synthesis are empirically modeled through the mechanotransduction mechanisms. The results demonstrate that the rheology and dynamics of the sinusoid flow can significantly affect...
Preparation of Ag-Al₂O₃ nano structures by combustion method and investigation of photocatalytic activity
, Article International Journal of Applied Ceramic Technology ; Volume 18, Issue 6 , 2021 , Pages 2064-2074 ; 1546542X (ISSN) ; Khodadadipoor, Z ; Fazli, M ; Einafshar, N ; Mohebbi Zinab, J ; Asaei, S ; Sharif University of Technology
John Wiley and Sons Inc
2021
Abstract
In this research, Ag-Al2O3 nanostructures have been prepared via combustion synthesis and ammonium acetate and urea have been applied as fuels. The prepared Ag-Al2O3 nanostructures were characterized by DTA, XRD, SEM, TEM, and BET spectroscopy. The effect of different ratios of silver to alumina and fuel percentage on morphology and particle size of prepared products were investigated. The results showed that using ammonium acetate fuel led to the production of Ag-γ-Al2O3 nanocompounds, while using urea produced Ag-α-Al2O3. Also, the photocatalytic activity of Ag-Al2O3 nanostructures for Congo red degradation was evaluated by UV-Vis diffuse reflectance spectroscopy. The photocatalytic...
Comparison of engineered cartilage based on BMSCs and chondrocytes seeded on PVA-PPU scaffold in a sheep model
, Article Journal of Biomedical Materials Research - Part B Applied Biomaterials ; Volume 110, Issue 11 , 2022 , Pages 2411-2421 ; 15524973 (ISSN) ; Sepahdar, A ; Rabiee, N ; Nazbar, A ; Farzad Mohajeri, S ; Dehghan, M. M ; Shokrgozar, M. A ; Majidi, M ; Mardjanmehr, S. H ; Aminianfar, H ; Akbari Javar, H ; Bonakdar, S ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
In this study, polyvinyl alcohol hydrogel chains were crosslinked by polyurethane in order to synthesize a suitable substrate for cartilage lesions. The substrate was fully characterized, and in vitro and in vivo investigations were conducted based on a sheep model. In vitro tests were performed based on the chondrocyte cells with the Alcian Blue and safranin O staining in order to prove the presence of proteoglycan on the surface of the synthesized substrate, which has been secreted by cultures of chondrocytes. Furthermore, the expression of collagen type I, collagen type II, aggrecan, and Sox9 was presented in the chondrocyte cultures on the synthesized substrate through RT-PCR. In...
The highest inhibition coefficient of phenol biodegradation using an acclimated mixed culture
, Article Water Science and Technology ; Volume 73, Issue 5 , 2016 , Pages 1033-1040 ; 02731223 (ISSN) ; Sharifi Abdar, P. S ; Borghei, S. M ; Sharif University of Technology
IWA Publishing
2016
Abstract
In this study a membrane biological reactor (MBR) was operated at 25±1 °C and pH = 7.5±0.5 to treat synthetic wastewater containing high phenol concentrations. Removal efficiencies of phenol and chemical oxygen demand (COD)were evaluated at four various hydraulic retention times (HRTs) of 24, 12, 8, and 4 hours. The removal rate of phenol (5.51 kg-Phenol kg-VSS-1 d-1), observed at HRT of 4 h,was the highest phenol degradation rate in the literature.According toCODtests, therewere no significant organic matter in the effluent, and phenol was degraded completely by mixed culture. Substrate inhibition was calculated from experimental growth parameters using the Haldane, Yano, and Edward...
Efficient biodegradation of naphthalene by a newly characterized indigenous achromobacter sp. FBHYA2 isolated from Tehran oil refinery complex
, Article Water Science and Technology ; Volume 66, Issue 3 , March , 2012 , Pages 594-602 ; 02731223 (ISSN) ; Borghei, S. M ; Hassani, A. H ; Yakhchali, B ; Ardjmand, M ; Zeinali, M ; Sharif University of Technology
IWA Pub
2012
Abstract
A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30°C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals...
The metabolomics signature associated with responsiveness to steroid therapy in focal segmental glomerulosclerosis: A pilot study
, Article Revista de Investigacion Clinica ; Volume 71, Issue 2 , 2019 , Pages 106-115 ; 00348376 (ISSN) ; Kalantari, S ; Nafar, M ; Boroumandnia, N ; Sharif University of Technology
Instituto Nacional de la Nutricion Salvador Zubiran
2019
Abstract
Background: Focal segmental glomerulosclerosis (FSGS) is considered one of the most severe glomerular diseases and around 80% of cases are resistant to steroid treatment. Since a large proportion of steroid-resistant (SR) FSGS patients progress to end-stage renal disease, other therapeutic strategies may benefit this population. However, identification of non-invasive biomarkers to predict this high-risk population is needed. Objective: We aimed to identify the biomarker candidates to distinguish SR from steroid-sensitive (SS) patients using metabolomics approach and to identify the possible molecular mechanism of resistance. Methods: Urine was collected from biopsy-proven FSGS patients...
Numerical modeling of ureagenesis in a microfluidic channel mimicking a liver lobule
, Article 2015 22nd Iranian Conference on Biomedical Engineering, ICBME 2015, 25 November 2015 through 28 November 2015 ; 2015 , Pages 54-59 ; 9781467393515 (ISBN) ; Firoozabadi, B ; Saidi, M. S ; Firoozbakhsh, K ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
Ammonia detoxification is one of the main functions of the liver results in production of urea. In this study ammonia elimination and urea production was simulated in a microchannel mimicking the hepatic porto central axis. Navier- Stockes equations along with convection equations were solved for the related species in the entire domain. Since the Reynolds number was small (~1) the fluid flow regime was laminar. Urea cycle was modeled regarding its four main enzymes. Twelve rate equations were also solved in order to obtain the concentration of each metabolites participating in urea cycle. Concentration of the urea reached its maximum ca. 1.2e-5 M at the end of the channel which is in good...
Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein
, Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
Hindawi Limited
2021
Abstract
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for...
Numerical investigations of hepatic spheroids metabolic reactions in a perfusion bioreactor
, Article Frontiers in Bioengineering and Biotechnology ; Volume 7 , 2019 ; 22964185 (ISSN) ; Firoozabadi, B ; Firoozbakhsh, K ; Sharif University of Technology
Frontiers Media S.A
2019
Abstract
Miniaturized culture systems of hepatic cells are emerging as a strong tool facilitating studies related to liver diseases and drug discovery. However, the experimental optimization of various parameters involved in the operation of these systems is time-consuming and expensive. Hence, developing numerical tools predicting the function of such systems can significantly reduce the associated cost. In this paper, a perfusion-based three dimensional (3D) bioreactor comprising encapsulated human liver hepatocellular carcinoma (HepG2) spheroids are analyzed. The flow and mass transfer equations for oxygen as well as different metabolites such as albumin, glucose, glutamine, ammonia, and urea were...
Expression analysis of protein inhibitor of activated stat in inflammatory demyelinating polyradiculoneuropathy
, Article Frontiers in Immunology ; Volume 12 , 2021 ; 16643224 (ISSN) ; Hussen, B. M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Frontiers Media S.A
2021
Abstract
Protein inhibitors of activated STAT (PIAS) are involved in the regulation of the JAK/STAT signaling pathway and have interactions with NF-κB, p73 and p53. These proteins regulate immune responses; therefore dysregulation in their expression leads to several immune-mediated disorders. In the present study, we examined expression of PIAS1-4 in peripheral blood of patients with acute/chronic inflammatory demyelinating polyradiculoneuropathy (AIDP/CIDP) compared with healthy subjects. We demonstrated down-regulation of all PIAS genes in both AIDP and CIDP cases compared with controls. Similarly, comparisons in gender-based groups revealed down-regulation of these gene0s in patients of each...
Synthesis, crystal structure and catalytic activity of a novel Mo(VI)-oxazoline complex in highly efficient oxidation of sulfides to sulfoxides by urea hydrogen peroxide
, Article Inorganica Chimica Acta ; Volume 361, Issue 7 , 2008 , Pages 2019-2024 ; 00201693 (ISSN) ; Tahsini, L ; Latifi, R ; Ellern, A ; Woo, L. K ; Sharif University of Technology
Elsevier S.A
2008
Abstract
Novel molybdenum complex, cis-[MoO2(phox)2] has been synthesized and characterized by IR, 1H NMR, elemental analyses (CHN), and X-ray molecular structure determination methods. This complex was found to be an efficient, selective catalyst for the oxidation of various sulfides to sulfoxides with urea hydrogen peroxide (UHP) in excellent yields (100% for diallylsulfide) and short reaction times (20 min) at room temperature. The catalytic system oxidizes diallylsulfide chemoselectively to its corresponding sulfoxide without any over oxidation in double bond. © 2007 Elsevier B.V. All rights reserved
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) ; 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...
A viscoelastic model for axonal microtubule rupture
, Article Journal of Biomechanics ; Volume 48, Issue 7 , 2015 , Pages 1241-1247 ; 00219290 (ISSN) ; Manuchehrfar, F ; Rafii Tabar, H ; Sharif University of Technology
Elsevier Ltd
2015
Abstract
Axon is an important part of the neuronal cells and axonal microtubules are bundles in axons. In axons, microtubules are coated with microtubule-associated protein tau, a natively unfolded filamentous protein in the central nervous system. These proteins are responsible for cross-linking axonal microtubule bundles. Through complimentary dimerization with other tau proteins, bridges are formed between nearby microtubules creating bundles. Formation of bundles of microtubules causes their transverse reinforcement and has been shown to enhance their ability to bear compressive loads. Though microtubules are conventionally regarded as bearing compressive loads, in certain circumstances during...
Characterization of a microfluidic microbial fuel cell as a power generator based on a nickel electrode
, Article Biosensors and Bioelectronics ; Volume 79 , 2016 , Pages 327-333 ; 09565663 (ISSN) ; Yaghmaei, S ; Sharif University of Technology
Elsevier Ltd
2016
Abstract
This study reports the fabrication of a microfluidic microbial fuel cell (MFC) using nickel as a novel alternative for conventional electrodes and a non-phatogenic strain of Escherichia coli as the biocatalyst. The feasibility of a microfluidic MFC as an efficient power generator for production of bioelectricity from glucose and urea as organic substrates in human blood and urine for implantable medical devices (IMDs) was investigated. A maximum open circuit potential of 459mV was achieved for the batch-fed microfluidic MFC. During continuous mode operation, a maximum power density of 104Wm-3 was obtained with nutrient broth. For the glucose-fed microfluidic MFC, the maximum power density of...
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) ; 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...
Fabrication of hierarchically porous silk fibroin-bioactive glass composite scaffold via indirect 3D printing: Effect of particle size on physico-mechanical properties and in vitro cellular behavior
, Article Materials Science and Engineering C ; Volume 103 , 2019 ; 09284931 (ISSN) ; Alemzadeh, I ; Tamjid, E ; Khafaji, M ; Vossoughi, M ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
In order to regenerate bone defects, bioactive hierarchically scaffolds play a key role due to their multilevel porous structure, high surface area, enhanced nutrient transport and diffusion. In this study, novel hierarchically porous silk fibroin (SF) and silk fibroin-bioactive glass (SF-BG) composite were fabricated with controlled architecture and interconnected structure, by combining indirect three-dimensional (3D) inkjet printing and freeze-drying methods. Further, the effect of 45S5 Bioactive glass particles of different sizes (<100 nm and 6 μm) on mechanical strength and cell behavior was investigated. The results demonstrated that the hierarchical structure in this scaffold was...
A novel niosome formulation for encapsulation of anthocyanins and modelling intestinal transport
, Article Food Chemistry ; Volume 293 , 2019 , Pages 57-65 ; 03088146 (ISSN) ; Akay, S ; Sharifi, F ; Sevimli Gur, C ; Ongen, G ; Yesil Celiktas, O ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
The bioavailability of drugs can be improved by regulating the structural properties, particularly lipoid systems, such as niosomes, can increase cellular uptake. Herein, we optimized double emulsion and niosomal formulations for encapsulating anthocyanin-rich black carrot extract. Nanoparticles obtained by selected formulation were characterized in terms of morphology, particle size, drug encapsulation efficiency, in vitro release and cytotoxicity. The optimum conditions for niosomal formulation were elicited as 30 mg of cholesterol, 150 mg of Tween 20 and feeding time of 1 min at a stirring rate of 900 rpm yielding the lowest average particle size of 130 nm. In vitro release data showed...
You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome
, Article Computers in Biology and Medicine ; Volume 106 , 2019 , Pages 106-113 ; 00104825 (ISSN) ; Hasani Bidgoli, M ; Motahari, S. A ; Sedaghat, N ; Modarressi, M. H ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
Background: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. Methods: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally...
Dynamics of a magnetically rotated micro swimmer inspired by paramecium metachronal wave
, Article Progress in Biophysics and Molecular Biology ; Volume 142 , 2019 , Pages 32-42 ; 00796107 (ISSN) ; Shamloo, A ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple...
Porous shape memory dental implant by reactive sintering of TiH2–Ni-Urea mixture
, Article Materials Science and Engineering C ; Volume 107 , 2020 ; Sadrnezhaad, S .K ; Hosseini, S. A ; Sharif University of Technology
Elsevier Ltd
2020
Abstract
We produced bifurcated bone-like shape memory implant (BL-SMI) with desirable tooth-root fixation capability by compact-sintering of TiH2–Ni-urea mixture. The primary constituents of the porous product were Ni and Ti. We could adjust the pores' shape, size, and interconnectivity for favorite bone ingrowth by using urea as a space holder. Without urea, we obtained an average porosity of 0.30, and a mean void size of 100 μm. With 70 vol % urea, we got 62% interconnected pores of 400 μm average size. Aging allowed us to tune the austenite-martensite transformation temperatures towards the needed body tissue arouse. Differential scanning calorimetry measured the transformation temperatures....