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    Evolution of costly signaling and partial cooperation

    , Article Scientific Reports ; Volume 9, Issue 1 , 2019 ; 20452322 (ISSN) Salahshour, M ; Sharif University of Technology
    Nature Publishing Group  2019
    Abstract
    Two seemingly unrelated, but fundamental challenges in evolutionary theory, are the evolution of costly signals and costly cooperative traits, both expected to reduce an individual’s fitness and diminish by natural selection. Here, by considering a well mixed population of individuals who produce signals and decide on their strategies in a game they play, based on the signals, we show that costly signals and costly cooperative strategies can co-evolve as a result of internal dynamics of the system. Costly signals evolve, despite their apparent cost, due to a favorable cooperative response they elicit. This favorable strategic response can be quantified in a fitness term which governs the... 

    Altered expression of SOCS genes periodontitis

    , Article BMC Oral Health ; Volume 22, Issue 1 , 2022 ; 14726831 (ISSN) Ghafouri Fard, S ; Gholami, L ; Sadeghpour, S ; Nazer, N ; Hussen, B. M ; Sayad, A ; Taheri, M ; Sharif University of Technology
    BioMed Central Ltd  2022
    Abstract
    Suppressor of cytokine signalling (SOCS) family comprises a group of proteins that impede JAK/STAT signalling, thus being involved in the pathogenesis of immune-related conditions. In the present work, we aimed at identification of the role of SOCS genes in the pathogenesis of periodontitis through evaluation of their expression levels both in the circulation and in the affected tissues of patients. Thus, we measured expression levels of SOCS1-3 and SOCS5 transcripts in the blood and gingival samples of patients with periodontitis in comparison with control samples obtained during dental crown lengthening. Expressions of SOCS1, SOCS2, SOCS3 and SOCS5 genes were similar between gingival... 

    Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data

    , Article PloS one ; Volume 12, Issue 2 , 2017 , Pages e0171240- ; 19326203 (ISSN) Narimani, Z ; Beigy, H ; Ahmad, A ; Masoudi Nejad, A ; Fröhlich, H ; Sharif University of Technology
    2017
    Abstract
    Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model. We devise a novel Bayesian network reverse engineering approach using ordinary... 

    Plant hormones as signals in arbuscular mycorrhizal symbiosis

    , Article Critical Reviews in Biotechnology ; Vol. 34, issue. 2 , 2014 , p. 123-133 Miransari, M ; Abrishamchi, A ; Khoshbakht, K ; Niknam, V ; Sharif University of Technology
    Abstract
    Arbuscular mycorrhizal (AM) fungi are non-specific symbionts developing mutual and beneficial symbiosis with most terrestrial plants. Because of the obligatory nature of the symbiosis, the presence of the host plant during the onset and proceeding of symbiosis is necessary. However, AM fungal spores are able to germinate in the absence of the host plant. The fungi detect the presence of the host plant through some signal communications. Among the signal molecules, which can affect mycorrhizal symbiosis are plant hormones, which may positively or adversely affect the symbiosis. In this review article, some of the most recent findings regarding the signaling effects of plant hormones, on... 

    Carbon nanotubes in microfluidic lab-on-a-chip technology: current trends and future perspectives

    , Article Microfluidics and Nanofluidics ; Volume 21, Issue 9 , 2017 ; 16134982 (ISSN) Ghasemi, A ; Amiri, H ; Zare, H ; Masroor, M ; Hasanzadeh, A ; Beyzavi, A ; Aref, A. R ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Abstract
    Advanced nanomaterials such as carbon nanotubes (CNTs) display unprecedented properties such as strength, electrical conductance, thermal stability, and intriguing optical properties. These properties of CNT allow construction of small microfluidic devices leading to miniaturization of analyses previously conducted on a laboratory bench. With dimensions of only millimeters to a few square centimeters, these devices are called lab-on-a-chip (LOC). A LOC device requires a multidisciplinary contribution from different fields and offers automation, portability, and high-throughput screening along with a significant reduction in reagent consumption. Today, CNT can play a vital role in many parts... 

    Recent clinical findings on the role of kinase inhibitors in COVID-19 management

    , Article Life Sciences ; Volume 306 , 2022 ; 00243205 (ISSN) Malekinejad, Z ; Baghbanzadeh, A ; Nakhlband, A ; Baradaran, B ; Jafari, S ; Bagheri, Y ; Raei, F ; Montazersaheb, S ; Farahzadi, R ; Sharif University of Technology
    Elsevier Inc  2022
    Abstract
    The highly pathogenic, novel coronavirus disease (COVID-19) outbreak has emerged as a once-in-a-century pandemic with poor consequences, urgently calling for new therapeutics, cures, and supportive interventions. It has already affected over 250 million people worldwide; thereby, there is a need for novel therapies to alleviate the related complications. There is a paradigm shift in developing drugs and clinical practices to combat COVID-19. Several clinical trials have been performed or are testing diverse pharmacological interventions to alleviate viral load and complications such as cytokine release storm (CRS). Kinase-inhibitors have appeared as potential antiviral agents for COVID-19... 

    Effects of short term and long term Extremely Low Frequency Magnetic Field on depressive disorder in mice: Involvement of nitric oxide pathway

    , Article Life Sciences ; Volume 146 , 2016 , Pages 52-57 ; 00243205 (ISSN) Madjid Ansari, A ; Farzam Pour, S ; Sadr, A ; Shekarchi, B ; Majid Zadeh, A. K ; Sharif University of Technology
    Elsevier Inc 
    Abstract
    Aims Previous reports on the possible effects of Extremely Low Frequency Magnetic Fields (ELF MF) on mood have been paradoxical in different settings while no study has yet been conducted on animal behavior. In addition, it was shown that ELF MF exposure makes an increase in brain nitric oxide level. Therefore, in the current study, we aimed to assess the possible effect(s) of ELF MF exposure on mice Forced Swimming Test (FST) and evaluate the probable role of the increased level of nitric oxide in the observed behavior. Main methods Male adult mice NMRI were recruited to investigate the short term and long term ELF MF exposure (0.5 mT and 50 Hz, single 2 h and 2 weeks 2 h a day). Locomotor... 

    Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis

    , Article BMC Medical Genomics ; Volume 12, Issue 1 , 2019 ; 17558794 (ISSN) Karimizadeh, E ; Sharifi Zarchi, A ; Nikaein, H ; Salehi, S ; Salamatian, B ; Elmi, N ; Gharibdoost, F ; Mahmoudi, M ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Background: Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been entirely understood. This study intended to investigate the common and tissue-specific pathways involved in different tissues of SSc patients. Methods: An integrative gene expression analysis of ten independent microarray datasets of three tissues was conducted to identify differentially expressed genes (DEGs). DEGs were mapped to the search tool for retrieval of interacting genes (STRING) to acquire protein-protein interaction (PPI) networks. Then, functional clusters in PPI... 

    Comparing the effects of endurance and resistance trainings on gene expression involved in protein synthesis and degradation signaling pathways of Wistar rat soleus muscle

    , Article Tehran University Medical Journal ; Volume 77, Issue 11 , 2020 , Pages 668-677 Gholipour, M ; Seifabad, M ; Asad, M. R ; Sharif University of Technology
    Tehran University of Medical Sciences  2020
    Abstract
    Background: Skeletal muscle mass, which is regulated by a balance between muscle protein synthesis and degradation, is an important factor for movement to meet everyday needs, especially in pathological conditions and aging. The purpose of the present investigation was to compare the alterations of the gene expression involved in muscle protein synthesis and degradation signaling pathways induced by two exercise training protocols. Methods: Eight weeks old Wistar rats have been assigned to the present experimental study, which was conducted from August 2018 to October 2018 at the animal laboratory of Tehran University. They were randomly divided into two resistance and endurance training... 

    The performances of the chi-square test and complexity measures for signal recognition in biological sequences

    , Article Journal of Theoretical Biology ; Volume 251, Issue 2 , 2008 , Pages 380-387 ; 00225193 (ISSN) Pirhaji, L ; Kargar, M ; Sheari, A ; Poormohammadi, H ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Sharif University of Technology
    2008
    Abstract
    With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the... 

    Model-based fiducial points extraction for baseline wandered electrocardiograms

    , Article IEEE Transactions on Biomedical Engineering ; Volume 55, Issue 1 , 2008 , Pages 347-351 ; 00189294 (ISSN) Sayadi, O ; Shamsollahi, M. B ; Sharif University of Technology
    2008
    Abstract
    A fast algorithm based on the nonlinear dynamical model for the electrocardiogram (ECG) is presented for the precise extraction of the characteristic points of these signals with baseline drift. Using the adaptive bionic wavelet transform, the baseline wander is removed efficiently. In fact by the means of the bionic wavelet transform, the resolution in the time-frequency domain can be adaptively adjusted not only by the signal frequency but also by the signal instantaneous amplitude and its first-order differential, which results in a better baseline wander cancellation. At the next step the parameters of the model are chosen to have the least square error with the original ECG. Determining... 

    Altered expression of STAT genes in periodontitis

    , Article Human Antibodies ; Volume 29, Issue 3 , 2021 , Pages 209-216 ; 10932607 (ISSN) Gholami, L ; Movafagh, A ; Badrlou, E ; Nazer, N ; Yari, M ; Sadeghi, G ; Mirzajani, S ; Shadnoush, M ; Sayad, A ; Ghafouri Fard, S ; Sharif University of Technology
    IOS Press BV  2021
    Abstract
    Signal Transducer and Activator of Transcription (STAT) pathway is functionally located downstream of Janus kinases proteins and can integrate signals from diverse pathways, thus regulating several aspects of immune responses. Although contribution of STAT proteins in the pathogenesis of several inflammatory conditions has been confirmed, their role in the development of periodontitis has been less appraised. Thus, we assessed levels of STAT transcripts in the periodontal tissues and circulation of affected individuals compared with the corresponding controls. Expression of STAT1 was remarkably lower in tissues samples of patients compared with control tissues (Ratio of mean expression (RME)... 

    Overexpression of protein kinase Mζ in the hippocampus mitigates alzheimer's disease-related cognitive deficit in rats

    , Article Brain Research Bulletin ; Volume 166 , 2021 , Pages 64-72 ; 03619230 (ISSN) Amini, N ; Roosta Azad, R ; Motamedi, F ; Mirzapour Delavar, H ; Ghasemi, S ; Aliakbari, S ; Pourbadie, H. G ; Sharif University of Technology
    Elsevier Inc  2021
    Abstract
    Accumulation of amyloid beta (Aβ) soluble forms in the cerebral parenchyma is the mainstream concept underlying memory deficit in the early phase of Alzheimer's disease (AD). PKMζ plays a critical role in the maintenance of long-term memory. Yet, the role of this brain-specific enzyme has not been addressed in AD. We examined the impact of hippocampal PKMζ overexpression on AD-related memory impairment in rats. Oligomeric form of Aβ (oAβ) or vehicle was bilaterally microinjected into the dorsal hippocampus of male Wistar rats under stereotaxic surgery. One week later, 2 μl of lentiviral vector (108 T.U. / ml.) encoding PKMζ genome was microinjected into the dorsal hippocampus. Seven days... 

    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... 

    Inferring causal molecular networks: Empirical assessment through a community-based effort

    , Article Nature Methods ; Volume 13, Issue 4 , 2016 , Pages 310-322 ; 15487091 (ISSN) Hill, S. M ; Heiser, L.M ; Cokelaer, T ; Linger, M ; Nesser, N. K ; Carlin, D. E ; Zhang, Y ; Sokolov, A ; Paull, E. O ; Wong, C. K ; Graim, K ; Bivol, A ; Wang, H ; Zhu, F ; Afsari, B ; Danilova, L. V ; Favorov, A. V ; Lee, W. S ; Taylor, D ; Hu, C. W ; Long, B. L ; Noren, D. P ; Bisberg, A. J ; Mills, G. B ; Gray, J. W ; Kellen, M ; Norman, T ; Friend, S ; Qutub, A. A ; Fertig, E. J ; Guan, Y ; Song, M ; Stuart, J. M ; Spellman, P. T ; Koeppl, H ; Stolovitzky, G ; Saez Rodriguez, J ; Mukherjee, S ; Afsari, B ; Al-Ouran, R ; Anton, B ; Arodz, T ; Askari Sichani, O ; Bagheri, N ; Berlow, N ; Bisberg, A. J ; Bivol, A ; Bohler, A ; Bonet, J ; Bonneau, R ; Budak, G ; Bunescu, R ; Caglar, M ; Cai, B ; Cai, C ; Carlin, D. E ; Carlon, A ; Chen, L ; Ciaccio, M. F ; Cokelaer, T ; Cooper, G ; Coort, S ; Creighton, C. J ; Daneshmand, S. M. H ; De La Fuente, A ; Di Camillo, B ; Danilova, L. V ; Dutta-Moscato, J ; Emmett, K ; Evelo, C ; Fassia, M. K. H ; Favorov, A. V ; Fertig, E. J ; Finkle, J. D ; Finotello, F ; Friend, S ; Gao, X ; Gao, J ; Garcia Garcia, J ; Ghosh, S ; Giaretta, A ; Graim, K ; Gray, J. W ; Großeholz, R ; Guan, Y ; Guinney, J ; Hafemeister, C ; Hahn, O ; Haider, S ; Hase, T ; Heiser, L. M ; Hill, S. M ; Hodgson, J ; Hoff, B ; Hsu, C. H ; Hu, C. W ; Hu, Y ; Huang, X ; Jalili, M ; Jiang, X ; Kacprowski, T ; Kaderali, L ; Kang, M ; Kannan, V ; Kellen, M ; Kikuchi, K ; Kim, D. C ; Kitano, H ; Knapp, B ; Komatsoulis, G ; Koeppl, H ; Krämer, A ; Kursa, M. B ; Kutmon, M ; Lee, W. S ; Li, Y ; Liang, X ; Liu, Z ; Liu, Y ; Long, B. L ; Lu, S ; Lu, X ; Manfrini, M ; Matos, M. R. A ; Meerzaman, D ; Mills, G. B ; Min, W ; Mukherjee, S ; Müller, C. L ; Neapolitan, R. E ; Nesser, N. K ; Noren, D. P ; Norman, T ; Oliva, B ; Opiyo, S. O ; Pal, R ; Palinkas, A ; Paull, E. O ; Planas Iglesias, J ; Poglayen, D ; Qutub, A. A ; Saez Rodriguez, J ; Sambo, F ; Sanavia, T ; Sharifi-Zarchi, A ; Slawek, J ; Sokolov, A ; Song, M ; Spellman, P. T ; Streck, A ; Stolovitzky, G ; Strunz, S ; Stuart, J. M ; Taylor, D ; Tegnér, J ; Thobe, K ; Toffolo, G. M ; Trifoglio, E ; Unger, M ; Wan, Q ; Wang, H ; Welch, L ; Wong, C. K ; Wu, J. J ; Xue, A. Y ; Yamanaka, R ; Yan, C ; Zairis, S ; Zengerling, M ; Zenil, H ; Zhang, S ; Zhang, Y ; Zhu, F ; Zi, Z ; Sharif University of Technology
    Nature Publishing Group  2016
    Abstract
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was... 

    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
    Abstract
    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... 

    Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues

    , Article Journal of Assisted Reproduction and Genetics ; Volume 36, Issue 8 , 2019 , Pages 1743-1752 ; 10580468 (ISSN) Barjaste, N ; Shahhoseini, M ; Afsharian, P ; Sharifi Zarchi, A ; Masoudi Nejad, A ; Sharif University of Technology
    Springer New York LLC  2019
    Abstract
    Purpose: Endometriosis is a gynecological disease that causes the uterine lining to appear in other organs outside the uterus. As DNA methylation has an important role in this disorder, its profiling can reveal new information to improve the diagnosis and treatment of endometriosis patients. Methods: We conducted a genome-wide methylation profiling of ectopic and eutopic endometrial tissues from women with and without endometriosis using Infinium Human Methylation 450K BeadChip arrays. DNA methylation samples were collected from nine ectopic and nine eutopic endometrial tissues of endometriosis and six endometrial tissues of healthy controls. Results: Correlation heatmaps and the principal... 

    An integrative Bayesian network approach to highlight key drivers in systemic lupus erythematosus

    , Article Arthritis Research and Therapy ; Volume 22, Issue 1 , June , 2020 Maleknia, S ; Salehi, Z ; Rezaei Tabar, V ; Sharifi Zarchi, A ; Kavousi, K ; Sharif University of Technology
    BioMed Central  2020
    Abstract
    Background: A comprehensive intuition of the systemic lupus erythematosus (SLE), as a complex and multifactorial disease, is a biological challenge. Dealing with this challenge needs employing sophisticated bioinformatics algorithms to discover the unknown aspects. This study aimed to underscore key molecular characteristics of SLE pathogenesis, which may serve as effective targets for therapeutic intervention. Methods: In the present study, the human peripheral blood mononuclear cell (PBMC) microarray datasets (n = 6), generated by three platforms, which included SLE patients (n = 220) and healthy control samples (n = 135) were collected. Across each platform, we integrated the datasets by... 

    Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response

    , Article Journal of Biomolecular Structure and Dynamics ; Volume 40, Issue 6 , 2022 , Pages 2575-2585 ; 07391102 (ISSN) Azimzadeh Irani, M ; Ejtehadi, M. R ; Sharif University of Technology
    Taylor and Francis Ltd  2022
    Abstract
    Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of ‘compact’ and ‘extended’ conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic... 

    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...