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    Urine and serum NMR-based metabolomics in pre-procedural prediction of contrast-induced nephropathy

    , Article Internal and Emergency Medicine ; Volume 15, Issue 1 , 2020 , Pages 95-103 Dalili, N ; Chashmniam, S ; Khoormizi, S. M. H ; Salehi, L ; Jamalian, S. A ; Nafar, M ; Kalantari, S ; Sharif University of Technology
    Springer  2020
    Abstract
    Contrast induced nephropathy (CIN) has been reported to be the third foremost cause of acute renal failure. Metabolomics is a robust technique that has been used to identify potential biomarkers for the prediction of renal damage. We aim to analyze the serum and urine metabolites changes, before and after using contrast for coronary angiography, to determine if metabolomics can predict early development of CIN. 66 patients undergoing elective coronary angiography were eligible for enrollment. Urine and serum samples were collected prior to administration of CM and 72 h post procedure and analyzed by nuclear magnetic resonance. The significant differential metabolites between patients who... 

    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... 

    EEG-based functional networks in schizophrenia

    , Article Computers in Biology and Medicine ; Volume 41, Issue 12 , 2011 , Pages 1178-1186 ; 00104825 (ISSN) Jalili, M ; Knyazeva, M. G ; Sharif University of Technology
    2011
    Abstract
    Schizophrenia is often considered as a dysconnection syndrome in which, abnormal interactions between large-scale functional brain networks result in cognitive and perceptual deficits. In this article we apply the graph theoretic measures to brain functional networks based on the resting EEGs of fourteen schizophrenic patients in comparison with those of fourteen matched control subjects. The networks were extracted from common-average-referenced EEG time-series through partial and unpartial cross-correlation methods. Unpartial correlation detects functional connectivity based on direct and/or indirect links, while partial correlation allows one to ignore indirect links. We quantified the... 

    Nonparametric simulation of signal transduction networks with semi-synchronized update

    , Article PLoS ONE ; Volume 7, Issue 6 , 2012 ; 19326203 (ISSN) Nassiri, I ; Masoudi Nejad, A ; Jalili, M ; Moeini, A ; Sharif University of Technology
    2012
    Abstract
    Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational... 

    A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

    , Article BMC Bioinformatics ; Volume 9 , 2008 ; 14712105 (ISSN) Sheari, A ; Kargar, M ; Katanforoush, A ; Arab, S ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Marashi, S. A ; Sharif University of Technology
    2008
    Abstract
    Background: It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results: In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments?...