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    A topology-dynamics-based control strategy for multi-dimensional complex networked dynamical systems

    , Article Scientific Reports ; Volume 9, Issue 1 , 2019 ; 20452322 (ISSN) Bahadorian, M ; Alimohammadi, H ; Mozaffari, T ; Rahimi Tabar, M. R ; Peinke, J ; Lehnertz, K ; Sharif University of Technology
    Nature Research  2019
    Abstract
    Complex systems are omnipresent and play a vital role in in our every-day lives. Adverse behavior of such systems has generated considerable interest in being able to control complex systems modeled as networks. Here, we propose a topology-dynamics-based approach for controlling complex systems modeled as networks of coupled multi-dimensional dynamical entities. For given dynamics and topology, we introduce an efficient scheme to identify in polynomial time a finite set of driver nodes, which – when endowed with the control function – steer the network to the desired behavior. We demonstrate the high suitability of our approach by controlling various networked multi-dimensional dynamics,... 

    Alterations of the electroencephalogram sub-bands amplitude during focal seizures in the pilocarpine model of epilepsy

    , Article Physiology and Pharmacology ; Volume 16, Issue 1 , 2012 , Pages 11-20 ; 17350581 (ISSN) Motaghi, S ; Niknazar, M ; Sayyah, M ; babapour, V ; Vahdat, B. V ; Shamsollahi, M. B ; Sharif University of Technology
    2012
    Abstract
    Introduction: Temporal lobe epilepsy (TLE) is the most common and drug resistant epilepsy in adults. Due to behavioral, morphologic and electrographic similarities, pilocarpine model of epilepsy best resembles TLE. This study was aimed at determination of the changes in electroencephalogram (EEG) sub-bands amplitude during focal seizures in the pilocarpine model of epilepsy. Analysis of these changes might help detection of a pre-seizure state before an oncoming seizure. Methods: Rats were treated by scopolamine (1mg/kg, s.c) to prevent cholinergic effects. After 30 min, pilocarpine (380 mg/kg, i.p) was administered to induce status epilepticus (SE) and 2 hours after SE, diazepam (20 mg/kg,... 

    RMet: An automated R based software for analyzing GC-MS and GC×GC-MS untargeted metabolomic data

    , Article Chemometrics and Intelligent Laboratory Systems ; Volume 194 , 2019 ; 01697439 (ISSN) Moayedpour, S ; Parastar, H ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Gas chromatography-mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) are powerful techniques for measurement of all metabolites in complex metabolic samples. However, analyzing GC-MS and especially GC×GC-MS metabolomic data is a major challenge to the researchers in the field of metabolomics mainly due to the complexity and large data size. In this regard, an automated R based software entitled RMet has been developed to overcome the challenges in the metabolomic analysis workflow of GC-MS and GC×GC-MS data sets. Additionally, it is able to facilitate the complex process of extracting reliable and useful biological information from... 

    Optimization of operating parameters and rate of uranium bioleaching from a low-grade ore

    , Article Journal of Radioanalytical and Nuclear Chemistry ; Vol. 301, issue. 2 , 2014 , pp. 341-350 ; ISSN: 02365731 Rashidi, A ; Roosta-Azad, R ; Safdari, S. J ; Sharif University of Technology
    Abstract
    In this study the bioleaching of a low-grade uranium ore containing 480 ppm uranium has been reported. The studies involved extraction of uranium using Acidithiobacillus ferrooxidans derived from the uranium mine samples. The maximum specific growth rate (μ max) and doubling time (t d) were obtained 0.08 h-1 and 8.66 h, respectively. Parameters such as Fe2+ concentration, particle size, temperature and pH were optimized. The effect of pulp density (PD) was also studied. Maximum uranium bio-dissolution of 100 ± 5 % was achieved under the conditions of pH 2.0, 5 % PD and 35 °C in 48 h with the particles of d 80 = 100 μm. The optimum concentration of supplementary Fe2+ was dependent to the PD.... 

    Prevalence of hepatitis e infection in the general population of Iran: a systematic review and meta-analysis

    , Article Future Virology ; Volume 12, Issue 4 , 2017 , Pages 227-236 ; 17460794 (ISSN) Hadifar, S ; Sedighi, M ; Mostafaei, S ; Miri, A ; Amiri, H ; Abiri, R ; Babaei, F ; Kabir, K ; Moghoofei, M ; Sharif University of Technology
    Abstract
    Aim: Hepatitis E is a form of acute viral hepatitis, which is caused by hepatitis E virus (HEV). The study objective was to evaluate the prevalence of HEV to provide an overall relative frequency in Iran. Methods: In this study, databases such as PubMed and Scopus were searched using the following keywords according to MeSH, "Hepatitis E virus", "Epidemiology", "Enzyme-linked immunosorbent assay (ELISA)" and "Iran". Then studies which had reported prevalence of HEV were selected. Results: We selected 36 researches out of 9246 for our study. From all the samples, the pooled estimated prevalence of HEV positive was 9.7%. It should be noted that HEV infection's relative frequency varied from... 

    Quantifying how staining methods bias measurements of neuron morphologies

    , Article Frontiers in Neuroinformatics ; Volume 13 , 2019 ; 16625196 (ISSN) Farhoodi, R ; Lansdell, B. J ; Kording, K. P ; Sharif University of Technology
    Frontiers Media S.A  2019
    Abstract
    The process through which neurons are labeled is a key methodological choice in measuring neuron morphology. However, little is known about how this choice may bias measurements. To quantify this bias we compare the extracted morphology of neurons collected from the same rodent species, experimental condition, gender distribution, age distribution, brain region and putative cell type, but obtained with 19 distinct staining methods. We found strong biases on measured features of morphology. These were largest in features related to the coverage of the dendritic tree (e.g., the total dendritic tree length). Understanding measurement biases is crucial for interpreting morphological data  

    Graphene-based nanoparticles as potential treatment options for parkinson’s disease: A molecular dynamics study

    , Article International Journal of Nanomedicine ; Volume 15 , 2020 , Pages 6887-6903 Alimohammadi, E ; Khedri, M ; Jahromi, A. M ; Maleki, R ; Rezaian, M ; Sharif University of Technology
    Dove Medical Press Ltd  2020
    Abstract
    Introduction: The study of abnormal aggregation of proteins in different tissues of the body has recently earned great attention from researchers in various fields of science. Concerning neurological diseases, for instance, the accumulation of amyloid fibrils can contribute to Parkinson’s disease, a progressively severe neurodegenerative disorder. The most prominent features of this disease are the degeneration of neurons in the substantia nigra and accumulation of α-synuclein aggregates, especially in the brainstem, spinal cord, and cortical areas. Dopamine replacement therapies and other medications have reduced motor impairment and had positive consequences on patients’ quality of life.... 

    Carbosilane dendrimers: Drug and gene delivery applications

    , Article Journal of Drug Delivery Science and Technology ; Volume 59 , 2020 Rabiee, N ; Ahmadvand, S ; Ahmadi, S ; Fatahi, Y ; Dinarvand, R ; Bagherzadeh, M ; Rabiee, M ; Tahriri, M ; Tayebi, L ; Hamblin, M. R ; Sharif University of Technology
    Editions de Sante  2020
    Abstract
    Carbosilane dendrimers are a particular type of dendrimer structure that has been used as delivery vehicles for drugs and nucleic acids. They have a defined structure according to their generation number, and their terminal groups can be rendered cationic or anionic. The cationic charges can address the limitation of electrostatic repulsion between the negatively charged phosphate groups of nucleic acids and negatively charged cell membranes. Specific drugs can be loaded into the central part of the dendrimer or attached at the exterior, and the overall positive charge may improve the efficacy of anti-inflammatory drugs. One promising feature of dendrimers is their non-toxicity both in vitro... 

    Immobilization of Acidithiobacillus ferrooxidans on monolithic packing for biooxidation of ferrous iron

    , Article Iranian Journal of Biotechnology ; Volume 6, Issue 3 , 2008 , Pages 137-143 ; 17283043 (ISSN) Kahrizi, E ; Alemzadeh, I ; Vossoughi, M ; Sharif University of Technology
    2008
    Abstract
    The oxidation of ferrous iron (Fe2+) in solution using Acidithiobacillus ferrooxidans has industrial applications exclusively in the regeneration of ferric iron (Fe3+) as an oxidizing agent for the removal of hydrogen sulfide from waste gases, desulfurization of coal, leaching of non-ferrous metallic sulfides and treatment of acid mine drainage. The aim of this investigation was to increase the bio-oxidation rate of ferrous sulfate by using immobilized cells. Rate of Fe2+ oxidation was determined in a packed-bed bioreactor configuration with monolithic particles being used as support material. Biooxidation of ferrous iron by immobilized cells was investigated in repeated batch culture and... 

    The effect of temperature on eccentric contraction-induced isometric force loss in isolated perfused rat medial gastrocnemius muscle

    , Article Tehran University Medical Journal ; Volume 66, Issue 6 , 2008 , Pages 388-395 ; 16831764 (ISSN) Vasaghi Gharamaleki, B ; Keshavarz, M ; Gharibzadeh, S ; Marvi, H ; Mosayebnejad, J ; Ebrahimi Takamjani, E ; Sharif University of Technology
    Tehran University of Medical Sciences  2008
    Abstract
    Background: The typical features of eccentric exercise-induced muscle damage are delayed-onset muscle soreness (DOMS) and prolonged loss of muscle strength. It has been shown that passive warmth is effective in reducing muscle injury. Due to the interaction of different systems in vivo, we used isolated perfused medial gastrocnemius skeletal muscle to study the direct effect of temperature on the eccentric contraction-induced force loss. Methods: After femoral artery cannulation of a rat, the left medial gastrocnemius muscle was separated and then the entire lower limb was transferred into a prewarmed (35oC) chamber. With the chamber temperature at 31, 35 and 39oC before and during eccentric... 

    Estimation of nitrogen content in cucumber plant (Cucumis sativus L.) leaves using hyperspectral imaging data with neural network and partial least squares regressions

    , Article Chemometrics and Intelligent Laboratory Systems ; Volume 217 , 2021 ; 01697439 (ISSN) Sabzi, S ; Pourdarbani, R ; Rohban, M. H ; García Mateos, G ; Arribas, J. I ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    In recent years, farmers have often mistakenly resorted to overuse of chemical fertilizers to increase crop yield. However, excessive consumption of fertilizers might lead to severe food poisoning. If nutritional deficiencies are detected early, it can help farmers to design better fertigation practices before the problem becomes unsolvable. The aim of this study is to predict the amount of nitrogen (N) content (mg l−1) in cucumber (Cucumis sativus L., var. Super Arshiya-F1) plant leaves using hyperspectral imaging (HSI) techniques and three different regression methods: a hybrid artificial neural networks-particle swarm optimization (ANN-PSO); partial least squares regression (PLSR); and... 

    The olfactory bulb modulates entorhinal cortex oscillations during spatial working memory

    , Article Journal of Physiological Sciences ; Volume 71, Issue 1 , 2021 ; 18806546 (ISSN) Salimi, M ; Tabasi, F ; Nazari, M ; Ghazvineh, S ; Salimi, A ; Jamaati, H ; Raoufy, M. R ; Sharif University of Technology
    BioMed Central Ltd  2021
    Abstract
    Cognitive functions such as working memory require integrated activity among different brain regions. Notably, entorhinal cortex (EC) activity is associated with the successful working memory task. Olfactory bulb (OB) oscillations are known as rhythms that modulate rhythmic activity in widespread brain regions during cognitive tasks. Since the OB is structurally connected to the EC, we hypothesized that OB could modulate EC activity during working memory performance. Herein, we explored OB–EC functional connectivity during spatial working memory performance by simultaneous recording local field potentials when rats performed a Y-maze task. Our results showed that the coherence of delta,... 

    Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

    , Article PLoS ONE ; Volume 16, Issue 1 January 2021 , 2021 ; 19326203 (ISSN) Akbari Rokn Abadi, S ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
    Public Library of Science  2021
    Abstract
    In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

    Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

    , Article PLoS ONE ; Volume 16, Issue 1 , 2021 ; 19326203 (ISSN) Akbari Rokn Abadi, S ; Dijujin, N. H ; Koohi, S ; Sharif University of Technology
    Public Library of Science  2021
    Abstract
    In this study, optical technology is considered as SA issues’ solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome,... 

    WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs

    , Article PLoS ONE ; Volume 17, Issue 4 April , 2022 ; 19326203 (ISSN) Akbari Rokn Abadi, S ; Mohammadi, A ; Koohi, S ; Sharif University of Technology
    Public Library of Science  2022
    Abstract
    The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing customized network structures. However, a few works focus on more effective factors, such as input encoding method or implementation technology, to address accuracy and efficiency issues in this area. Therefore, in this work, we propose an image-based encoding method, called as WalkIm, whose adoption, even in a simple neural network, provides competitive accuracy and superior efficiency, compared to the existing classification methods (e.g. VGDC,... 

    Do the soft tissues located outside tibiofemoral joint have a role in bearing the compressive loads of the joint? An in-vitro study on sheep stifle joints

    , Article Gazzetta Medica Italiana Archivio per le Scienze Mediche ; Volume 172, Issue 7-8 , 2013 , Pages 595-601 ; 03933660 (ISSN) Hakkak, F ; Rostami, M ; Parnianpour, M ; Jabalameli, M ; Sharif University of Technology
    2013
    Abstract
    Aim. The compressive loads on the tibiofemoral joint are normally assumed to be borne solely via contact and pressing of the cartilage surfaces of tibia and femur. However, recent findings suggest that non-contact load-bearing mechanisms are active in the joint as well. In this context, a non-contact load-bearing mechanism involving soft tissue connections outside the tibiofemoral joint has been hypothesized as well. This paper addresses the validity of this hypothesis and the possible involvement of several soft tissue connections outside the joint. Methods. Sheep stifle (knee) joints were studied in vitro. The specimens were loaded in fixed displacement. Various soft tissues outside the... 

    Application of a dissimilarity index of EEG and its sub-bands on prediction of induced epileptic seizures from rat's EEG signals

    , Article IRBM ; Volume 33, Issue 5-6 , December , 2012 , Pages 298-307 ; 19590318 (ISSN) Niknazar, M ; Mousavi, S. R ; Shamsollahi, M. B ; Vosoughi Vahdat, B ; Sayyah, M ; Motaghi, S ; Dehghani, A ; Noorbakhsh, S. M ; Sharif University of Technology
    2012
    Abstract
    Objective: Epileptic seizures are defined as manifest of excessive and hyper-synchronous activity of neurons in the cerebral cortex that cause frequent malfunction of the human central nervous system. Therefore, finding precursors and predictors of epileptic seizure is of utmost clinical relevance to reduce the epileptic seizure induced nervous system malfunction consequences. Researchers for this purpose may even guide us to a deep understanding of the seizure generating mechanisms. The goal of this paper is to predict epileptic seizures in epileptic rats. Methods: Seizures were induced in rats using pentylenetetrazole (PTZ) model. EEG signals in interictal, preictal, ictal and postictal... 

    Effect of mozart music on hippocampal content of BDNF in postnatal rats

    , Article Basic and Clinical Neuroscience ; Volume 2, Issue 3 , 2011 , Pages 21-26 ; 2008126X (ISSN) Marzban, M ; Shahbazi, A ; Tondar, M ; Soleimani, M ; Bakhshayesh, M ; Moshkforoush, A ; Sadati, M ; Zendehrood, S. A ; Joghataei, M. T ; Sharif University of Technology
    2011
    Abstract
    Introduction: It has shown that listening to Mozart music can potentiate spatial tasks in human; and reduce seizure attacks in epileptic patients. A few studies have reported the effects of prenatal plus postpartum exposure of mice to the Mozart music on brain-drived neurotrophic factor (BDNF) in the hippocampus. Here we investigated the effect of postpartum exposure to The Mozart music on BDNF concentration in the hippocampus of rat. Methods: Thirty male one day old newborn Wistar rats divided randomly in two equal experimental and control groups. Experimental group exposed to slow rhythm Mozart music (Mozart Sonata for two pianos KV 448, 6 hour per day; sound pressure levels, between 80... 

    Potential of Calendula alata for phytoremediation of stable cesium and lead from solutions

    , Article Environmental Monitoring and Assessment ; Volume 181, Issue 1-4 , Oct , 2011 , Pages 63-68 ; 01676369 (ISSN) Borghei, M ; Arjmandi, R ; Moogouei, R ; Sharif University of Technology
    2011
    Abstract
    Calendula alata plants were tested for their potential to remove stable cesium and lead from solutions in a 15-day period. The plants were grown hydroponically and placed in solutions containing CsCl and Pb(C 2H 3O 2)2 at different concentrations (0.6, 2 and 5 mg l-1). When plants were incubated in CsCl solutions 46.84 ± 2.12%, 41.35 ± 1.59%, and 52.06 ± 1.02% cesium was found to be remediated after 15 days. Moreover, more than 99% lead was removed from the Pb(C 2H 3O 2)2solution in all three concentrations after 15 days during the same period. When both CsCl and Pb(C 2H 3O 2)2were supplemented together in the solution, 9.92 ± 1.22%, 45.56 ± 3.52%, and 46.16 ± 1.48% cesium and 95.30 ± 0.72%,... 

    Nanomedicine applications in orthopedic medicine: State of the art

    , Article International Journal of Nanomedicine ; Volume 10 , 2015 , Pages 6039-6054 ; 11769114 (ISSN) Mazaheri, M ; Eslahi, N ; Ordikhani, F ; Tamjid, E ; Simchi, A ; Sharif University of Technology
    Dove Medical Press Ltd  2015
    Abstract
    The technological and clinical need for orthopedic replacement materials has led to significant advances in the field of nanomedicine, which embraces the breadth of nanotechnology from pharmacological agents and surface modification through to regulation and toxicology. A variety of nanostructures with unique chemical, physical, and biological properties have been engineered to improve the functionality and reliability of implantable medical devices. However, mimicking living bone tissue is still a challenge. The scope of this review is to highlight the most recent accomplishments and trends in designing nanomaterials and their applications in orthopedics with an outline on future directions...