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    Seizure Detection in Generalized and Focal Seizure from EEG Signals

    , M.Sc. Thesis Sharif University of Technology Mozafari, Mohsen (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    Epilepsy is one of the diseases that affects the quality of life of epileptic patients. Epileptic patients lose control during epileptic seizures and are more likely to face problems. Designing and creating a seizure detection system can reduce casualties from epileptic attacks. In this study, we present an automatic method that reduces the artifact from the raw signals, and then classifies the seizure and non-seizure epochs. At all stages, it is assumed that no information is available about the patient and this detection is made only based on the information of other patients. The data from this study were recorded in Temple Hospital and the recording conditions were not controlled, so... 

    Emotion Recognition from EEG Signals using Tensor based Algorithms

    , M.Sc. Thesis Sharif University of Technology Einizadeh, Aref (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    The brain electrical signal (EEG) has been widely used in clinical and academic research, due to its ease of recording, non-invasiveness and precision. One of the applications can be emotion recognition from the brain's electrical signal. Generally, two types of parameters (Valence and Arousal) are used to determine the type of emotion, which, in turn, indicate "positive or negative" and "level of extroversion or excitement" for a specific emotion. The significance of emotion is determined by the effects of this phenomenon on daily tasks, especially in cases where the person is confronted with activities that require careful attention and concentration.In the emotion recognition problem,... 

    Evaluation Auditory Attention Using Eeg Signals when Performing Motion and Visual Tasks

    , M.Sc. Thesis Sharif University of Technology Bagheri, Sara (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    Attention is one of the important aspects of brain cognitive activities, which has been widely discussed in psychology and neuroscience and is one of the main fields of research in the education field. The human sense of hearing is very complex, impactful and crucial in many processes such as learning. Human body always does several tasks and uses different senses simultaneously. For example, a student who listens to his/her teacher in the class, at the same time pays attention to the teacher, looks at a text or image, and sometimes writes a note.Using the electroencephalogram (EEG) signal for attention assessment and other cognitive activities is considered because of its facile recording,... 

    Studying Time Perception in Musician and Non-musician Using Auditory Stimuli

    , M.Sc. Thesis Sharif University of Technology Niroomand, Niavash (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    Time perception is a concept that describes how a person interprets the duration of an event. Depending on the circumstances, people may feel that time passes quickly or slowly. So far, the understanding, comparison, and estimation of the time interval have been described using a simple model, a pacemaker accumulator, that is powerful in explaining behavioral and biological data. Also, the role of the frequency band, Contingent Negative Variation (CNV), and Event-Related Potential (ERP) components have been investigated in the passage of time and the perception of time duration. Still, the stimuli used in these studies were not melodic. Predicting is one of the main behaviors of the brain.... 

    Diagnosis of Depressive Disorder using Classification of Graphs Obtained from Electroencephalogram Signals

    , M.Sc. Thesis Sharif University of Technology Moradi, Amir (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    Depression is a type of mental disorder that is characterized by the continuous occurrence of bad moods in the affected person. Studies by the World Health Organization (WHO) show that depression is the second disease that threatens human life, and eight hundred thousand people die due to suicide every year. In order to reduce the damage caused by depression, it is necessary to have an accurate method for diagnosing depression and its rapid treatment, in which electroencephalogram (EEG) signals are considered as one of the best methods for diagnosing depression. Until now, various researches have been conducted to diagnose depression using electroencephalogram signals, most of which were... 

    Design and Implementation of a P300 Speller System by Using Auditory and Visual Paradigm

    , M.Sc. Thesis Sharif University of Technology Jalilpour, Shayan (Author) ; Hajipour Sardouie, Sepideh (Supervisor)
    Abstract
    The use of brain signals in controlling devices and communication with the external environment has been very much considered recently. The Brain-Computer Interface (BCI) systems enable people to easily handle most of their daily physical activity using the brain signal, without any need for movement. One of the most common BCI systems is P300 speller. In this type of BCI systems, the user can spell words without the need for typing with hands. In these systems, the electrical potential of the user's brain signals is distorted by visual, auditory, or tactile stimuli from his/her normal state. An essential principle in these systems is to exploit appropriate feature extraction methods which... 

    An Investigation of Resting-State Eeg Biomarkers Derived from Graph of Brain Connectivity for Diagnosis of Depressive Disorder

    , M.Sc. Thesis Sharif University of Technology Arabpour, Mohammad Reza (Author) ; Hajipour, Sepideh (Supervisor)
    Abstract
    Among the most costly diseases that affect a person's quality of life throughout his or her life, mental disorders (excluding sleep disorders) affect up to 25 percent of people in any community. One of the most common types of these disorders in Iran is depressive disorder, which according to official statistics, 13% of Iranians have some symptoms of it. Until now, the diagnosis of this disease has been traditionally done in clinics with interviews and questionnaires tests based on behavioral psychology and using symptom assessment. Therefore, there is a relatively low accuracy in the treatment process. Nowadays, with the help of functional brain imaging such as electroencephalogram (EEG)... 

    Extraction of Event Related Potentials (ERP) from EEG Signals using Semi-blind Approaches

    , M.Sc. Thesis Sharif University of Technology Jalilpour Monesi, Mohammad (Author) ; Hajipour Sardouie, Sepideh (Supervisor)
    Abstract
    Nowadays, Electroencephalogram (EEG) is the most common method for brain activity measurement. Event Related Potentials (ERP) which are recorded through EEG, have many applications. Detecting ERP signals is an important task since their amplitudes are quite small compared to the background EEG. The usual way to address this problem is to repeat the process of EEG recording several times and use the average signal. Though averaging can be helpful, there is a need for more complicated filtering. Blind source separation methods are frequently used for ERP denoising. These methods don’t use prior information for extracting sources and their use is limited to 2D problems only. To address these... 

    Investigating One-pot Three Component Synthesis of ß-Amino Carbonyl Compounds Exploiting Hydrolases: Protein Splicing Enzyme and N-Acetylmuramide Glycanhydrolase

    , M.Sc. Thesis Sharif University of Technology Fathali, Yasaman (Author) ; Kalhor, Hamidreza (Supervisor)
    Abstract
    The application of biocatalysts in organic reactions refers to the use of enzymes, purified or crude, to increase the reaction rate. The usage of biocatalysts in organic reactions have many advantages, including biocompatibility, ease of separation, high yield, reusability without losing activity, high selectivity, and the use of water as the solvent. Furthermore, the carbon–carbon bond formation is one of the most important reactions in the synthesis of organic compounds, drugs, and biomolecules. Using enzymes in organic reactions can provide insightful information about the enzymes catalytic activities and paves the way for systematic investigation of their mechanisms. The enzymes... 

    DNA Classification Using Optical Processing based on Alignment-free Methods

    , M.Sc. Thesis Sharif University of Technology Kalhor, Reza (Author) ; Koohi, Somayyeh (Supervisor)
    Abstract
    In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually... 

    Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed... 

    Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Nature Research  2022
    Abstract
    DNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of... 

    In silico design of novel anticancer drugs with amino acid and carbohydrate building blocks to inhibit PIM kinases

    , Article Molecular Simulation ; Volume 48, Issue 6 , 2022 , Pages 526-540 ; 08927022 (ISSN) Kalhor, S ; Fattahi, A ; Sharif University of Technology
    Taylor and Francis Ltd  2022
    Abstract
    PIM-1 is a serine-threonine kinase mainly expressed in tissues like the Thymus, spleen, bone marrow, and liver. Overexpression of PIM kinases occurs in various types of human tumours, such as lymphomas, prostate cancer, and oral cancer. As a result, the design of drugs to inhibit PIM-1 in cancerous cells has attracted much attention in recent years. This study aimed to design the alternative inhibitors for PIM-1 kinase, which are based on carbohydrates and amino acids and are expected to be non-toxic with the same chemotherapeutic effects as the traditional known anticancer drugs. The combinatorial use of quantum mechanics (QM) and molecular dynamic simulation (MD) has enabled us to... 

    Design and Implementing an Evaluator Platforn for Cochlear Implent Devices

    , M.Sc. Thesis Sharif University of Technology Asadian, Saeed (Author) ; Hajipour, Sepideh (Supervisor) ; Molaei, Behnam (Co-Supervisor)
    Abstract
    The auditory system with its unique features has been considered by researchers in the past and its various parts from the outside of the body to its internal parts have been studied. The auditory nervous system, as the most important part of the auditory system, is responsible for receiving and processing information from the ear. The auditory system has different anatomical and physiological characteristics. The result of these characteristics is processing power in the field of time and frequency, which has received more attention in this dissertation. This processing power is most evident in the central auditory nervous system. This section includes nerve neurons and synapses from the... 

    Investigating reliable conditions for hewl as an amyloid model in computational studies and drug interactions

    , Article Journal of Chemical Information and Modeling ; Volume 59, Issue 12 , 2019 , Pages 5218-5229 ; 15499596 (ISSN) Kalhor, H. R ; Jabbary, M ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    A number of conformational diseases in humans have been associated with protein/peptide fibrillation known as amyloid. Although extensive studies have been conducted in understanding the molecular basis of amyloid formation, a detailed mechanism is still missing. Experimentally, HEWL (hen egg white lysozyme) has been exploited ubiquitously as a model protein for amyloid fibrillation and drug inhibition. However, computational studies investigating fibril formation of HEWL have been a difficult task to perform mainly due to high stability of lysozymes and the absence of crystal structures of HEWL fibril oligomers. In this study, we have examined various conditions of HEWL amyloid formation... 

    Identification of an aspidospermine derivative from borage extract as an anti-amyloid compound: A possible link between protein aggregation and antimalarial drugs

    , Article Phytochemistry ; Volume 140 , 2017 , Pages 134-140 ; 00319422 (ISSN) Kalhor, H. R ; Ashrafian, H ; Sharif University of Technology
    Elsevier Ltd  2017
    Abstract
    A number of human diseases, including Alzheimer's and Parkinson's have been linked to amyloid formation. To search for an anti-amyloidogenic product, alkaloid enriched extract from borage leaves was examined for anti-amyloidogenic activity using Hen Egg White Lysozyme (HEWL) as a model protein. After isolation of the plant extract using rHPLC, only one fraction indicated a significant bioactivity. TEM analysis confirmed a remarkable reduction of amyloid fibrils in the presence of the bioactive fraction. To identify the effective substance in the fraction, mass spectrometry, FTIR, and NMR were performed. Our analyses determined that the bioactive compound as... 

    Conversion of 3,6-O-dimethylfluorescein to fluorescein-based xanthylium derivative: characterization and covalent attachment to bovine serum albumin

    , Article ChemistrySelect ; Volume 4, Issue 36 , 2019 , Pages 10681-10687 ; 23656549 (ISSN) Kalhor, H. R ; Rezaei, M ; Sharif University of Technology
    Wiley-Blackwell  2019
    Abstract
    Xanthene dyes, such as fluorescein and rhodamine, have played crucial rules in biological sciences especially covalent attachment of these organic compounds to biomolecules. 3-O-methylfluorescein and 3,6-O-dimethylfluorescein were synthesized and purified using a facile procedure. 3,6-O-dimethylfluorescein, which lacks fluorescence, was treated with sodium hydroxide and sulfuric acid solutions, giving rise to yellow and green fluorescent compounds, respectively. In both basic and acidic conditions, donor-acceptor structures were formed. The reaction of 3,6-O-dimethylfluorescein with acids, in a reversible manner, emitted green fluorescence, whereas its reaction with hydroxide ion,... 

    Investigating the effects of amino acid-based surface modification of carbon nanoparticles on the kinetics of insulin amyloid formation

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 176 , 2019 , Pages 471-479 ; 09277765 (ISSN) Kalhor, H. R ; Yahyazadeh, A ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    Surface functionality of nanoparticles has been pivotal in defining interactions of nanoparticles and biomolecules. To explore various functionalities on the surface of nanoparticle through a facile procedure, various carbon-based nanoparticles, modified with a specific natural amino acid, were synthesized; the amino acids were chosen in order that almost all classes of amino acids were included. After characterizations of the nanoparticles using several spectroscopic methods, the effects of surface modification of nanoparticles were examined against amyloid formation, exploiting insulin as a model amyloidogenic polypeptide. Although most amino acids afforded carbon nanoparticles, only... 

    Probe into the molecular mechanism of ibuprofen interaction with warfarin bound to human serum albumin in comparison to ascorbic and salicylic acids: Allosteric inhibition of anticoagulant release

    , Article Journal of Chemical Information and Modeling ; Volume 61, Issue 8 , 2021 , Pages 4045-4057 ; 15499596 (ISSN) Kalhor, H. R ; Taghikhani, E ; Sharif University of Technology
    American Chemical Society  2021
    Abstract
    The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned... 

    Synthesis of Selected Pyridazine-based Organic Compounds and Investigation of Their Inhibitory Effects Against Amyloid Formation

    , M.Sc. Thesis Sharif University of Technology Ghasemi, Elham (Author) ; Kalhor, Hamid Reza (Supervisor)
    Abstract
    At the molecular level, proteins control almost all the biochemical reactions in the cells. In order for proteins to function, they must be able to fold into their unique 3D structure. Deformation of protein structure due to some environmental phenomena such as pH, high temperature, and stress may cause unfolding of proteins and finally result in formation of protein fibrils called "amyloid". Amyloid has been found in a number of human diseases such as Alzheimer, type II diabetes, and Parkinson. Recently pyridazine has been under spotlight due to its unique chemical properties such as high dipole moment and higher solubility in biological solvents. In this study, we aim at using a...