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    The metabolome profiling of obese and non-obese individuals: Metabolically healthy obese and unhealthy non-obese paradox

    , Article Iranian Journal of Basic Medical Sciences ; Volume 23, Issue 2 , 2020 , Pages 186-194 Chashmniam, S ; Madani, N. H ; Ghoochani, B. F. N. M ; Safari Alighiarloo, N ; Khamseh, M. E ; Sharif University of Technology
    Mashhad University of Medical Sciences  2020
    Objective(s): The molecular basis of “metabolically healthy obese” and “metabolically unhealthy non-obese” phenotypes is not fully understood. Our objective was to identify metabolite patterns differing in obese (metabolically healthy vs unhealthy (MHO vs MUHO)) and non-obese (metabolically healthy vs unhealthy (MHNO vs MUHNO)) individuals. Materials and Methods: This case-control study was performed on 86 subjects stratified into four groups using anthropometric and clinical measurements: MHO (21), MUHO (21), MHNO (22), and MUHNO (22). Serum metabolites were profiled using nuclear magnetic resonance (NMR). Multivariate analysis was applied to uncover discriminant metabolites, and enrichment... 

    The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency

    , Article Cell and Bioscience ; Volume 9, Issue 1 , 2019 ; 20453701 (ISSN) Yousefi, M ; Marashi, S. A ; Sharifi Zarchi, A ; Taleahmad, S ; Sharif University of Technology
    BioMed Central Ltd  2019
    Background: Pluripotency is proposed to exist in two different stages: Naive and Primed. Conventional human pluripotent cells are essentially in the primed stage. In recent years, several protocols have claimed to generate naive human embryonic stem cells (hESCs). To the best of our knowledge, none of these protocols is currently recognized as the gold standard method. Furthermore, the consistency of the resulting cells from these diverse protocols at the molecular level is yet to be shown. Additionally, little is known about the principles that govern the metabolic differences between naive and primed pluripotency. In this work, using a computational approach, we tried to shed light on... 

    Context-Specific Reconstruction and Gap-Filling of Metabolic Networks by Sparse Reconciliation of Data Inconsistencies

    , M.Sc. Thesis Sharif University of Technology Fathi, Ali (Author) ; Tefagh, Mojtaba (Supervisor)
    With the increasingly collected biological data, appropriate usage of this data is of great importance for understanding and predicting biological systems and has been the aim of experiments and data collections. A famous category of biological data is known as “omics” which refers to transcriptomics, proteomics, metabolomics, and fluxomics, from different cells or tissues in various media and conditions. This set of data is regularly used for tasks such as studying cells and organisms, understanding cell states, cancer prediction, etc. and is of great importance in Systems Biology.In this thesis, we concentrate on studying cells or organisms using such data, where during that process, we... 

    The Differential Diagnosis of Crohn's Disease and Celiac Disease Using Nuclear Magnetic Resonance Spectroscopy

    , Article Applied Magnetic Resonance ; Volume 45, Issue 5 , May , 2014 , Pages 451-459 Fathi, F ; Kasmaee, L. M ; Sohrabzadeh, K ; Nejad, M. R ; Tafazzoli, M ; Oskouie, A. A ; Sharif University of Technology
    Crohn's disease and celiac disease belong to a group of autoimmune conditions that affect the digestive system, specifically the small intestine. They both attack the digestive tract and share many symptoms. Thus, the discovery of proper methods would be a major step toward differentiating celiac disease from Crohn's disease. The aim of this study was to search for the metabolic biomarkers to differentiate between these two diseases. Proton nuclear magnetic resonance spectroscopy (1H NMR) was employed as the metabolic profiling method to look for serum metabolites that differentiate between celiac disease and Crohn's disease. Classification of celiac disease and Crohn's disease was done... 

    Numerical investigations of hepatic spheroids metabolic reactions in a perfusion bioreactor

    , Article Frontiers in Bioengineering and Biotechnology ; Volume 7 , 2019 ; 22964185 (ISSN) Sharifi, F ; Firoozabadi, B ; Firoozbakhsh, K ; Sharif University of Technology
    Frontiers Media S.A  2019
    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... 

    StrongestPath: a Cytoscape application for protein-protein interaction analysis

    , Article BMC bioinformatics ; Volume 22, Issue 1 , 2021 , Pages 352- ; 14712105 (ISSN) Mousavian, Z ; Khodabandeh, M ; Sharifi Zarchi, A ; Nadafian, A ; Mahmoudi, A ; Sharif University of Technology
    NLM (Medline)  2021
    BACKGROUND: StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can... 

    A mechanobiological mathematical model of liver metabolism

    , Article Biotechnology and Bioengineering ; Volume 117, Issue 9 , 5 June , 2020 , Pages 2861-2874 Nikmaneshi, M. R ; Firoozabadi, B ; Munn, L. L ; Sharif University of Technology
    John Wiley and Sons Inc  2020
    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... 

    Metabolic load comparison between the quarters of a game in elite male basketball players using sport metabolomics

    , Article European Journal of Sport Science ; Volume 21, Issue 7 , 2021 , Pages 1022-1034 ; 17461391 (ISSN) Khoramipour, K ; Gaeini, A. A ; Shirzad, E ; Gilany, K ; Chashniam, S ; Sandbakk, Ø ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Purpose: A basketball match is characterized by intermittent high-intensity activities, thereby relying extensively on both aerobic and anaerobic metabolic pathways. Here, we aimed to compare the metabolic fluctuations between the four 10-min quarters of high-level basketball games using metabolomics analyses. Methods: 70 male basketball players with at least 3 years of experience in the Iran national top-league participated. Before and after each quarter, saliva samples were taken for subsequent untargeted metabolomics analyses, where Principal component analysis (PCA) and Partial least squares-discriminant analysis (PLS-DA) were employed for statistical analysis. Results: Quarters 1 and 3... 

    A novel hybrid systemic modeling into sustainable dynamic urban water metabolism management: Case study

    , Article Sustainable Cities and Society ; Volume 85 , 2022 ; 22106707 (ISSN) Nezami, N ; Zarghami, M ; Tizghadam, M ; Abbasi, M ; Sharif University of Technology
    Elsevier Ltd  2022
    Over the past few years, due to increasing population, limited water resources, and other pressures on the urban water systems (UWS), urban water management has become a major concern for urban policymakers to develop efficient management solutions. In this study, a new hybrid model called sustainable dynamic urban water metabolism management (SDUWMM) is presented, based on urban water metabolism and system dynamics. Isfahan's UWS has been modeled by SDUWMM and its conditions have been simulated until 2041. SDUWMM considers effective internal relationships of the UWS components such as population, climate change, water supply and demand, infrastructures condition, water price, costs and... 

    Numerical Simulation of Glucose Metabolism and Hepatocyte Viability within a Microfluidic

    , M.Sc. Thesis Sharif University of Technology Nejadnasrollah, Farzam (Author) ; Firoozabadi, Bahar (Supervisor)
    The advent of microfluidics as suitable environments for culturing cells is associated with some challenges such as shear stresses applied on the cells. In fact, hepatocytes lose their function as exposed to high shear stresses similar to other cell types. Moreover, among all factors needed for cell viability, feeding hepatocytes with adequate oxygen is of great importance due to their high demand for oxygen compared the other cells. In this thesis, different types of cultures including 2D and 3D has been used in order that shear stresses would be in allowed range and provision of hepatocytes with sufficient oxygen concentrations has been ensured as well. In addition to supplying hepatocytes... 

    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... 

    Metabolomics analysis of the saliva in patients with chronic hepatitis b using nuclear magnetic resonance: A pilot study

    , Article Iranian Journal of Basic Medical Sciences ; Volume 22, Issue 9 , 2019 , Pages 1044-1049 ; 20083866 (ISSN) Gilany, K ; Mohamadkhani, A ; Chashmniam, S ; Shahnazari, P ; Amini, M ; Arjmand, B ; Malekzadeh, R ; Nobakht Motlagh Ghoochani, B. F ; Sharif University of Technology
    Mashhad University of Medical Sciences  2019
    Objective(s): Hepatitis B virus infection causes chronic disease such as cirrhosis and hepatocellular carcinoma. The metabolomics investigations have been demonstrated to be related to pathophysiologic mechanisms in many disorders such as hepatitis B infection. The aim of this study was to investigate the saliva metabolic profile of patients with chronic hepatitis B infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Materials and Methods: Saliva from 16 healthy subjects and 20 patients with chronic hepatitis B virus were analyzed by nuclear magnetic resonance (NMR). Then, multivariate statistical analysis was performed to identify... 

    A facile aerobic copper-catalyzed α-oxygenation of aryl thioacetamides: An efficient access to α-keto aryl thioamides

    , Article Synlett ; Issue 6 , 2008 , Pages 892-896 ; 09365214 (ISSN) Matloubi Moghaddam, F ; Mirjafary, Z ; Saeidian, H ; Jebeli Javan, M ; Sharif University of Technology
    Copper(II) efficiently catalyzes the aerobic oxidation of aryl thioacetamides into the corresponding α-keto aryl thioamides in moderate to high yields in the presence of K2CO3 under O 2 atmosphere. This protocol is simple, clean, and generates water as the only byproduct. A mechanism is proposed for the reaction course. © Georg Thieme Verlag Stuttgart  

    A multi-scale model for determining the effects of pathophysiology and metabolic disorders on tumor growth

    , Article Scientific Reports ; Volume 10, Issue 1 , 20 February , 2020 Nikmaneshi, M. R ; Firoozabadi, B ; Mozafari, A ; Munn, L. L ; Sharif University of Technology
    Nature Research  2020
    The search for efficient chemotherapy drugs and other anti-cancer treatments would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. Because in vivo experimental methods are unable to isolate or control individual factors of the TME and in vitro models often do not include all the contributing factors, some questions are best addressed with systems biology mathematical models. In this work, we present a new fully-coupled, agent-based, multi-scale mathematical model of tumor growth, angiogenesis and metabolism that includes important aspects of the TME spanning subcellular-, cellular- and tissue-level scales. The mathematical model is... 

    The influence of carrier material on the dominance of polyphosphate-accumulating organism metabolism in the biofilm-based biological phosphorus removal process

    , Article Chemical Engineering Journal ; Volume 450 , 2022 ; 13858947 (ISSN) Massoompour, A. R ; Raie, M ; Borghei, S. M ; Appels, L ; Dewil, R ; Sharif University of Technology
    Elsevier B.V  2022
    This study reveals that the type of carrier material affects the stoichiometry of the anaerobic conversion and the metabolism in cultures enriched with polyphosphate-accumulating organisms (PAOs) and helps increase the biological phosphorus removal performance. PAO-enriched biofilms were cultivated in two identical lab-scale sequencing batch reactors containing different carrier types: a typical moving bed bioreactor carrier (MBBR) and a novel carbon-based moving carrier type (CBMC) coated by activated carbon particles. The experiments were conducted at various influent PO43- concentrations (14, 17, 20 mg-PO43--P/L) and two aeration periods (220 and 460 min) under similar operating... 

    A novel metabolic disorder in the degradation pathway of endogenous methanol due to a mutation in the gene of alcohol dehydrogenase

    , Article Clinical Biochemistry ; Volume 90 , 2021 , Pages 66-72 ; 00099120 (ISSN) Razzaghy Azar, M ; Nourbakhsh, M ; Vafadar, M ; Nourbakhsh, M ; Talebi, S ; Sharifi Zarchi, A ; Salehi Siavashani, E ; Garshasbi, M ; Sharif University of Technology
    Elsevier Inc  2021
    Background: A small amount of methanol is produced endogenously in the human body but it is efficiently metabolized by alcohol dehydrogenase (ADH) and other enzymes, and the products eliminated without harm. In this study, we present a new entity of inborn error of methanol metabolism due to a mutation in the ADH1C gene coding for the γ subunit that is part of several ADH isoenzymes. Results: This disorder was discovered in an 11.58-year-old boy. During one 9-month hospital admission, he had periods of 1–4 days during which he was comatose, and between these periods he was sometimes verbose and euphoric, and had ataxia, dysarthria. Following hemodialysis treatments, he became conscious and... 

    Role of carrier characteristics affecting microbial density and population in enhanced nitrogen and phosphorus removal from wastewater

    , Article Journal of Environmental Management ; Volume 302 , 2022 ; 03014797 (ISSN) Massoompour, A.R ; Raie, M ; Borghei, S. M ; Dewil, R ; Appels, L ; Sharif University of Technology
    Academic Press  2022
    This research aims to improve simultaneous nitrification-denitrification and phosphorus removal (SNDPR) using novel carriers and to demonstrate the effect of carrier characteristics on nutrient removal in a biofilm reactor. For this purpose, biofilms enriched with both polyphosphate-accumulating organisms (PAOs) and nitrifiers were cultivated in two parallel sequencing batch reactors containing conventional moving bed bioreactor carriers (MBBR) and a novel type of carriers (carbon-based moving carriers (CBMC)). The new carriers were produced based on recycled waste materials via a chemical-thermal process and their specific surface area were 10.4 times higher than typical MBBR carriers of... 

    Modeling the Endothelial Function in the Brachial Artery Using Photoplethysmography

    , M.Sc. Thesis Sharif University of Technology Mashayekhi, Ghoncheh (Author) ; Zahedi, Edmond (Supervisor) ; Jahed, Mehran (Supervisor)
    Flow Mediated Dilation (FMD) is a non-invasive method for endothelial function assessment providing an index extracted from ultrasonic B-mode images. Although utilized in the research community, the difficulty of its application and high cost of ultrasonic device prevent it from being widely used in clinical settings. In this study we show that substituting the ultrasonic device with more easily handled and low cost photoplethysmography and electrocardiography is possible. We introduce new indices based on the photoplethysmogram (PPG) and electrocardiogram (ECG) and show that they are correlated with the ultrasound-based FMD index. To this end, conventional ultrasound FMD test was carried... 

    Investigation of Anticancer Drug Metabolism in Saccharomyces Cerevisiae as a Drug Resistance Model

    , M.Sc. Thesis Sharif University of Technology Hamed Rahimi, Reza (Author) ; Yaghmaei, Soheila (Supervisor) ; Sardari, Soroush (Supervisor)
    Cancer is a life-threatening group of diseases that arises from the uncontrolled growth and division of cells in the body. Treatment options for cancer include surgery, chemotherapy, radiation therapy, immunotherapy, targeted therapy, and hormone therapy. However, resistance to anticancer drugs can develop through a variety of mechanisms, such as the upregulation of drug efflux pumps and alterations in DNA repair mechanisms. One common mechanism of drug resistance is through changes in metabolism, where cancer cells switch to alternative metabolic pathways to survive and evade the effects of anticancer drugs. The development of new drugs targeting specific molecules and pathways involved in... 

    A Library For Developing Optimization Algorithms In Metabolic Network Analysis

    , M.Sc. Thesis Sharif University of Technology Ghadimi Deylami, Iman (Author) ; Tefagh, Mojtaba (Supervisor)
    In systems biology, one of the most important biological systems that is analyzed and investigated is the metabolic network. A metabolic network is a complete set of metabolic and physical processes that determine the physiological and biochemical characteristics of a cell. These networks encompass metabolic chemical reactions, metabolic pathways, and regulatory interactions that govern these reactions. Therefore, metabolic networks at the genome scale are immensely large, making even efficient algorithms time-consuming for their analysis. To address this issue, reducing metabolic networks is crucial, as it significantly decreases the execution time of algorithms and enhances computational...