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    Whole-genome analysis of de novo somatic point mutations reveals novel mutational biomarkers in pancreatic cancer

    , Article Cancers ; Volume 13, Issue 17 , 2021 ; 20726694 (ISSN) Ghareyazi, A ; Mohseni, A ; Dashti, H ; Beheshti, A ; Dehzangi, A ; Rabiee, H. R ; Alinejad Rokny, H ; Sharif University of Technology
    MDPI  2021
    Abstract
    It is now known that at least 10% of samples with pancreatic cancers (PC) contain a causative mutation in the known susceptibility genes, suggesting the importance of identifying cancer-associated genes that carry the causative mutations in high-risk individuals for early detection of PC. In this study, we develop a statistical pipeline using a new concept, called gene-motif, that utilizes both mutated genes and mutational processes to identify 4211 3-nucleotide PC-associated gene-motifs within 203 significantly mutated genes in PC. Using these gene-motifs as distinguishable features for pancreatic cancer subtyping results in identifying five PC subtypes with distinguishable phenotypes and... 

    Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types

    , Article BMC Bioinformatics ; Volume 23, Issue 1 , 2022 ; 14712105 (ISSN) Ghareyazi, A ; Kazemi, A ; Hamidieh, K ; Dashti, H ; Tahaei, M. S ; Rabiee, H. R ; Alinejad Rokny, H ; Dehzangi, I ; Sharif University of Technology
    BioMed Central Ltd  2022
    Abstract
    Background: The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence, there is no definitive treatment for most cancer types. This reveals the importance of developing new pipelines to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific... 

    CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes

    , Article Scientific Reports ; Volume 10, Issue 1 , 2020 Bayati, M ; Rabiee, H. R ; Mehrbod, M ; Vafaee, F ; Ebrahimi, D ; Forrest, A. R. R ; Alinejad Rokny, H ; Sharif University of Technology
    Nature Research  2020
    Abstract
    Analysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in... 

    MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

    , Article PLoS Computational Biology ; Volume 18, Issue 6 , 2022 ; 1553734X (ISSN) Alinejad Rokny, H ; Modegh, R. G ; Rabiee, H. R ; Sarbandi, E. R ; Rezaie, N ; Tam, K. T ; Forrest, A. R. R ; Sharif University of Technology
    Public Library of Science  2022
    Abstract
    Hi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than transient background and artefactual interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly... 

    Weight Choosability of Graphs

    , M.Sc. Thesis Sharif University of Technology Alinejad, Mohsen (Author) ; Akbari, Saeed (Supervisor)
    Abstract
    Suppose the edges of a graph G are assigned 3-element lists of real weights. Is it possible to choose a weight for each edge from its list so that the sums of weights around adjacent vertices were different?
    A graph G = (V;E) is called (k; k′)-total weight choosable if the following holds: For any total list assignment L which assigns to each vertex x a set L(x) of k real numbers, and assigns to each edge e a set L(e) of k′ real numbers, there is a mapping f : V [ E ! R such that f(y) 2 L(y) for any y 2 V [ E and for any two adjacent vertices x; x′
    Σ e2E(x) f(e) + f(x) ̸=Σ e2E(x′) f(e) + f(x′)
    Is it possible every graph is (2, 2)-total weight choosable and every... 

    Evaluation of Strength Loss due to Diagonal Crack and Parameters Affecting it in Masonry Infill Walls

    , M.Sc. Thesis Sharif University of Technology Alinejad, Nasrollah (Author) ; Moghaddam, Hassan (Supervisor)
    Abstract
    Masonry infills are vastly used as surrounding walls and partitions. Presence of infill in a building causes some change in strength, stiffness, period and generally seismic behavior of the structure.Mainly there are 5 modes of failure including 1- interface cracking 2- sliding along bed joint 3- diagonal cracking 4- corner crushing and 5- ultimate failure. According to these failures, three stages of strength as shear strength, corner strength and ultimate strength can be defined.Diagonal crack can be calculated by slip surface method grown in Sharif university of Technology. Based on this method the strength of infill wall falls down as the cohesive strength of mortar loses and so the slip... 

    Evaluating the Performance of the Concrete Filled Composite Tube Column under Axial Compression Load

    , M.Sc. Thesis Sharif University of Technology Alinejad, Ali (Author) ; Khaloo, Alireza (Supervisor)
    Abstract
    The purpose of this research is evaluating of how the concrete filled composite tube column performs. Nowadays in the construction industry, a new kind of composite column called concrete filled composite tube (CFCT) columns, have become very common. Concrete and composite tubes posses’ complementary performance. Because on one hand, the composite tube makes proper confinement for concrete, on the other hand the concrete prevents internal and local buckling of the composite tube. One of the major advantages of the concrete filled composite tube columns compare to the reinforced concrete column is that there is no further need for reinforcement and molding, which results in swifter... 

    Investigating the behavior of circular concrete filled PVC tube columns under concentric and eccentric load using FEM

    , Article Asian Journal of Civil Engineering ; Volume 22, Issue 4 , 2021 , Pages 589-603 ; 15630854 (ISSN) Alinejad, A ; Khaloo, A ; Hassanpour, S ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    Abstract
    The purpose of this research is to investigate the response of concrete-filled composite tube column under concentric and eccentric loads. To evaluate the influence of PVC pipe on the behavior of concrete-filled composite tubes, concrete-filled PVC pipe (CFPT) were modeled by ABAQUS software. The results demonstrate that the presence of the PVC pipe makes the concrete column more ductile and have a significant effect on the stress–strain curve of the CFPT after the peak strength, in a way that the confinement increased by raising the thickness of PVC pipe, but the confinement effect of the PVC pipe decreased by the increment of the column diameter and compressive strength of the concrete... 

    Investigating the behavior of circular concrete filled PVC tube columns under concentric and eccentric load using FEM

    , Article Asian Journal of Civil Engineering ; Volume 22, Issue 4 , 2021 , Pages 589-603 ; 15630854 (ISSN) Alinejad, A ; Khaloo, A ; Hassanpour, S ; Sharif University of Technology
    Springer Science and Business Media Deutschland GmbH  2021
    Abstract
    The purpose of this research is to investigate the response of concrete-filled composite tube column under concentric and eccentric loads. To evaluate the influence of PVC pipe on the behavior of concrete-filled composite tubes, concrete-filled PVC pipe (CFPT) were modeled by ABAQUS software. The results demonstrate that the presence of the PVC pipe makes the concrete column more ductile and have a significant effect on the stress–strain curve of the CFPT after the peak strength, in a way that the confinement increased by raising the thickness of PVC pipe, but the confinement effect of the PVC pipe decreased by the increment of the column diameter and compressive strength of the concrete... 

    Composite system well-being analysis using sequential Monte Carlo simulation and fuzzy algorithm

    , Article ELECO 2011 - 7th International Conference on Electrical and Electronics Engineering, 1 December 2011 through 4 December 2011, Bursa ; 2011 , Pages I91-I95 ; 9786050102048 (ISBN) Alinejad, B ; Fotuhi-Firuzabad, M ; Parvania, M ; Sharif University of Technology
    2011
    Abstract
    Health, Margin and Risk states which in recent years are known as well-being reliability indices, provide a comprehensive adequacy assessment of bulk power system reliability studies. Conventional reliability information about power system operation only considered health and risk states which were not often adequate criteria both in system planning and utilization. It seems margin state as the intermediate condition between health and risk must be considered. Well-being method which is a approach to power system generation adequacy evaluation incorporates deterministic criteria in a probabilistic framework and provides system operating information in addition to risk assessment and can be... 

    Composite system well-being analysis using sequential Monte Carlo simulation and fuzzy algorithm

    , Article Istanbul University - Journal of Electrical and Electronics Engineering ; Volume 13, Issue 1 , Dec , 2013 , Pages 1575-1580 ; 13030914 (ISSN) Alinejad, B ; Fotuhi Firuzabad, M ; Parvania, M ; Sharif University of Technology
    2013
    Abstract
    Well-Being reliability indices (Health, Margin and Risk), provide a comprehensive measure to assess the adequacy of composite power systems. Conventional reliability information about power system operation only considered health and risk states, which were not often adequate criteria in both power system planning and operation. Well-being approach for power system generation adequacy evaluation incorporates deterministic criteria in a probabilistic framework, and provides system operating information in addition to risk assessment and can be evaluated using analytical techniques. The most important part of this approach is the algorithm for calculating the probability of the states.... 

    Kinetic Analysis of Pyrolysis Modelling of Non-Charring Polymers

    , M.Sc. Thesis Sharif University of Technology Alinejad, Farid (Author) ; Farhanieh, Bijan (Supervisor) ; Afshin, Hossein (Co-Advisor)
    Abstract
    In this research, modelling of pyrolysis in small-scale and a method for calculation of kinetic parameters; activation energy, pre-exponential factor, and model function, have been presented. Calculation of activation energy and frequency factor without any assumption on model function heve been done by presented method. Because, incorrect assumption on model function can be cause to error in estimated values of activation energy and frequency factor.For a bench-scale sample, the heat transfer and mass conservations equations influence the pyrolysis process. In this research for the investigation of kinetic parameter effects, a simple pyrolysis model was presented to predicting the mass flux... 

    Prediction of life-threatening heart arrhythmias using obstructive sleep apnoea characteristics

    , Article 27th Iranian Conference on Electrical Engineering, ICEE 2019, 30 April 2019 through 2 May 2019 ; 2019 , Pages 1761-1764 ; 9781728115085 (ISBN) Mohammad Alinejad, G ; Rasoulinezhad, S ; Shamsollahi, M. B ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2019
    Abstract
    False alarms ratios of up to 86% in Intensive Care Units (ICU) decrease quality of care, impacting both clinical staff and patients through slowing off response time and noise tribulation. We present a novel algorithm to predict heart arrhythmias in ICUs. We focus on five life-threatening arrhythmias: Asystole, Extreme Bradycardia, Extreme Tachycardia, Ventricular Tachycardia, and Ventricular Fibrillation. The algorithm is based on novel features using only 12 seconds of one ECG channel to predict the arrhythmias. Our new feature sets include different SQI and physiological features and the features used in obstructive sleep apnoea detection. We also proposed a new morphological... 

    A charge/discharge plan for electric vehicles in an intelligent parking lot considering destructive random decisions, and V2G and V2V energy transfer modes

    , Article Sustainability (Switzerland) ; Volume 14, Issue 19 , 2022 ; 20711050 (ISSN) Alinejad, M ; Rezaei, O ; Habibifar, R ; Azimian, M ; Sharif University of Technology
    MDPI  2022
    Abstract
    The random decisions of electric vehicle (EV) drivers, together with the vehicle-to-vehicle (V2V) and vehicle-to-grid (V2G) energy transfer modes, make scheduling for an intelligent parking lot (IPL) more complex; thus, they have not been considered simultaneously during IPL planning in other studies. To fill this gap, this paper presents a complete optimal schedule for an IPL in which all the above-mentioned items are considered simultaneously. Additionally, using a complete objective function—including charging/discharging rates and prices, together with penalties, discounts, and reward sets—increases the profits of IPL and EV owners. In addition, during peak times, the demand for energy... 

    Simulation of Phenol Biodegradation by Pseudomonas Putida in a Continuous Stirred Biofilm Reactor

    , M.Sc. Thesis Sharif University of Technology Alinejad, Mahsa (Author) ; Yaghmaei, Soheila (Supervisor) ; Askaripour, Hossein (Supervisor)
    Abstract
    The use of microorganisms to remove or produce a substace is a fundamental part of biotechnology. An example is the bioreactors for phenol removal in wastewater. Biological processes are commonly done in batch reactors in which suspended cells grow in the liquid phase. The batch process needs alternate reactor washes and alternate cell cultivation, which leades to a longer time constant for for each batch. If these reactors operate in continuous conditions, the cells will leave the reactor in liquid flow, and high cell concentrations will be impossible. The biofilm layer makes a batch phase, so the liquid phase flows in and out continuously, but the cells in the biofilm layer stay in the... 

    Using Surface Properties of Immiscible Fluids in Capillary Tubes for Identification and Separation of Cancerous Blood Cells

    , M.Sc. Thesis Sharif University of Technology Alinejad, Amin (Author) ; Ayatollahi, Shahabodin (Supervisor) ; Vossoughi, Manochehr (Supervisor)
    Abstract
    Cancer has been known as one of the main reasons for disease-related deaths in the last decades. Early diagnosis could significantly reduce the level of fatality chances. Among the known cancer types, lung cancer is one of the most malignant ones. The common diagnosticmethods are expensive and using high-technology methods; therefore, the introduction of simple and cheap methods is very urgent to detect it. In this project, surface and interfacial tension measurement of cancerous and normal lung cells have been investigated as an easy detection technique. Among the common measurement methods, Pendant Drop and Capillary height techniques have been utilized in this research work. The obtained... 

    Using genetic alghoritm for distributed generation allocation to reduce losses and improve voltage profile

    , Article 42nd International Universities Power Engineering Conference, UPEC 2007, Brighton, 4 September 2007 through 6 September 2007 ; 2007 , Pages 954-959 ; 1905593368 (ISBN); 9781905593361 (ISBN) Alinejad Beromi, Y ; Sedighizadeh, M ; Bayat, M. R ; Khodayar, M. E ; Sharif University of Technology
    2007
    Abstract
    This paper presents a method for the optimal allocation of Distributed generation in distribution systems. In this paper, our aim would be optimal distributed generation allocation for voltage profile improvement and loss reduction in distribution network. Genetic Algorithm (GA) was used as the solving tool, which referring two determined aim; the problem is defined and objective function is introduced. Considering to fitness values sensitivity in genetic algorithm process, there is needed to apply load flow for decision-making. Load flow algorithm is combined appropriately with GA, till access to acceptable results of this operation. We used MATPOWER package for load flow algorithm and... 

    Nonlinear interstory drift contours for idealized forward directivity pulses using "modified fish-bone" models

    , Article Advances in Structural Engineering ; Volume 18, Issue 5 , May , 2015 , Pages 603-627 ; 13694332 (ISSN) Khalo, A. R ; Khosravi, H ; Jamnani, H. H ; Sharif University of Technology
    Multi-Science Publishing Co. Ltd  2015
    Abstract
    Four 5-, 10-, 20- and 30-story moment frames, representing low-, mid-, and two high-rise structures, were subjected to a great number of idealized directivity pulses. The amplitudes and periods of pulses vary from 0.02 g to 1.0 g and 0.5 to 12 sec, respectively. Over 1400 nonlinear dynamic analyses of low- to high-rise moment frames were performed which were feasible through using modified fish-bone model. The distribution of interstory drift along the height was studied and two applied contours were proposed: (i) the maximum interstory drift contour, and (ii) the critical story contour. These contours were demonstrated versus the ratio of natural period of the structure to the pulse period... 

    Analysis of singularities of a 3DOF parallel manipulator based on a novel geometrical method

    , Article 8th Biennial ASME Conference on Engineering Systems Design and Analysis, ESDA2006, Torino, 4 July 2006 through 7 July 2006 ; Volume 2006 , 2006 ; 0791837793 (ISBN); 9780791837795 (ISBN) Pendar, H ; Sadeghian, H ; Roozbehani, H ; Zohoor, H ; Sharif University of Technology
    2006
    Abstract
    In this article singular points of a parallel manipulator are obtained based on a novel geometrical method. Here we introduce the constrained plain method (CPM) and some of its application in parallel mechanism. Given the definition of constraint plane (CP) and infinite constraint plane (ICP) the dependency conditions of constraints is achieved with the use of a new theorem based on the Ceva geometrical theorem. The direction of angular velocity of a body is achieved by having three ICPs with the use of another theorem. Finally, with the use of the above two novel theorems singularities of the 3UPF_PU mechanism are obtained. It should be emphasized that this method is completely geometrical,... 

    Melting enthalpy and entropy of freestanding metallic nanoparticles based on cohesive energy and average coordination number

    , Article Journal of Physical Chemistry C ; Volume 115, Issue 35 , August , 2011 , Pages 17310-17313 ; 19327447 (ISSN) Omid, H ; Delavari H., H ; Madaah Hosseini, H. R ; Sharif University of Technology
    2011
    Abstract
    An analytical model is proposed to study the effect of particle size on melting enthalpy and entropy of metallic nanoparticles (NPs). The Mott's and Regel's equations for melting entropy in the combination of core average coordination number (CAC) and surface average coordination number (SAC) of freestanding NPs are considered. Clusters of icosahedral (IC), body centered cubic (BCC), and body centered tetragonal (BCT) structure without any vacancies and defects are modeled. Using the variable coordination number made this model to be in good agreement with experimental and molecular dynamic (MD) results of different crystal structures. The model predicts melting entropy and enthalpy of...