Sharif Digital Repository

Techniques available in graph theory can be applied to signals recorded from human brain. In network analysis of EEG signals, the individual nodes are EEG sensor locations and the edges correspond to functional relations between them that are extracted from EEG time series. In this paper, we study EEG-based directed functional networks in Alzheimer's disease (AD). To this end, directed connectivity matrices of 25 AD patients and 26 healthy subjects are processed and a number of meaningful graph theory metrics are studied. Our data show that functional networks of AD brains have significantly reduced global connectivity in alpha and beta bands (P < 0.05). The AD brains have significantly... 

We have investigated hydrogen sensing properties of electrodeposited Pd clusters on macroporous silicon substrates. Porous layer was prepared by electrochemical etching of p-type silicon (100) wafer in organic electrolyte DMF (dimethylformamide) diluted by HF (%95 Vol. %). The deposition of Pd was carried out by linear voltammetry (LV) technique. This technique was taken for reduction of palladium ions in the potential range from 0.4 V to -1 V vs. SCE, at the scan rate of 20 mV s-1. Some samples were annealed at 300°C for an hour in air to study the effect of heat treatment on their gas sensitivity. Surface structural and chemical properties of the samples were characterised using Scanning... 

This study presents a novel statistical volume element (SVE) for micromechanical modeling of the white matter structures, with histology-informed randomized distribution of axonal tracts within the extracellular matrix. The model was constructed based on the probability distribution functions obtained from the results of diffusion tensor imaging as well as the histological observations of scanning electron micrograph, at two structures of white matter susceptible to traumatic brain injury, i.e. corpus callosum and corona radiata. A simplistic representative volume element (RVE) with symmetrical arrangement of fully alligned axonal fibers was also created as a reference for comparison. A... 

Gas chromatography-mass spectrometry (GC-MS) combined with Chemometric resolution techniques were proposed as a method for the analysis of volatile components of Iranian damask rose oil. The essential oil of damask rose was extracted using hydrodistillation method and analyzed with GC-MS in optimized conditions. A total of 70 components were identified using similarity searches between mass spectra and MS database. This number was extended to 95 components with concentrations higher than 0.01% accounting for 94.75% of the total relative content using Chemometric techniques. For the first time in this work, an approach based upon subspace comparison is used for determination of the chemical... 

Background: Electromyography (EMG) is the study of muscle function through the inquiry of electrical signals that the muscles emanate. EMG signals collected from the surface of the skin (Surface Electromyogram: sEMG) can be used in different applications such as recognizing musculoskeletal neural based patterns intercepted for hand prosthesis movements. Current systems designed for controlling the prosthetic hands either have limited functions or can only be used to perform simple movements or use excessive amount of electrodes in order to achieve acceptable results. In an attempt to overcome these problems we have proposed an intelligent system to recognize hand movements and have provided... 

Superparamagnetic iron oxide nanoparticles (SPION) with narrow size distribution and stabilized by polyvinyl alcohol (PVA) were synthesized. The particles were prepared by a coprecipitation technique using ferric and ferrous salts with a molar Fe3+/Fe2+ ratio of 2. Using a design of experiments (DOE) approach, the effect of different synthesis parameters (stirring rate and base molarity) on the structure, morphology, saturation magnetization, purity, size, and size distribution of the synthesized magnetite nanoparticles was studied by various analysis techniques including X-ray powder diffraction (XRD), thermogravimetric analysis (TGA) with differential scanning calorimetry (DSC)... 

The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be... 

The novel coronavirus pandemic has rapidly spread around the world since December 2019. Various techniques have been applied in identification of SARS-CoV-2 or COVID-19 infection including computed tomography imaging, whole genome sequencing, and molecular methods such as reverse transcription polymerase chain reaction (RT-PCR). This review article discusses the diagnostic methods currently being deployed for the SARS-CoV-2 identification including optical biosensors and point-of-care diagnostics that are on the horizon. These innovative technologies may provide a more accurate, sensitive and rapid diagnosis of SARS-CoV-2 to manage the present novel coronavirus outbreak, and could be... 

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... 

Mean field independent component analysis (MF-ICA) along with other chemometric techniques was proposed for obtaining more information from multi-component gas chromatographic-mass spectrometric (GC-MS) signals of essential oils (mandarin and lemon as examples). Using these techniques, some fundamental problems during the GC-MS analysis of essential oils such as varying baseline, presence of different types of noise and co-elution have been solved. The parameters affecting MF-ICA algorithm were screened using a 25 factorial design. The optimum conditions for MF-ICA algorithm were followed by deconvolution of complex GC-MS peak clusters. The number of independent components (ICs) (chemical... 

The spatiotemporal variability of ambient volatile organic compounds (VOCs) in Tehran, Iran, is not well understood. Here we present the design, methods, and results of the Tehran Study of Exposure Prediction for Environmental Health Research (Tehran SEPEHR) on ambient concentrations of benzene, toluene, ethylbenzene, p-xylene, m-xylene, o-xylene (BTEX), and total BTEX. To date, this is the largest study of its kind in a low- and middle-income country and one of the largest globally. We measured BTEX concentrations at five reference sites and 174 distributed sites identified by a cluster analytic method. Samples were taken over 25 consecutive 2-weeks at five reference sites (to be used for... 

The current study was designed to assess the association between temporal variations in urban PM2.5 chemical composition, sources, and the oxidative stress and inflammatory response in an alveolar macrophage (AM) model. A year-long sampling campaign collected PM2.5 samples at the Sharif University in Tehran, Iran. PM-induced reactive oxygen species (ROS) production was measured both with an acellular dithiothreitol consumption assay (DTT-ROS; ranged from 2.1 to 9.3 nmoles min−1 m−3) and an in vitro macrophage-mediated ROS production assay (AM-ROS; ranged from 125 to 1213 μg Zymosan equivalents m−3). The production of tumor necrosis factor alpha (TNF-α; ranged from ~60 to 518 pg TNF-α m−3)... 

A Zn-Rich (GaN)1−x(ZnO)xnanostructure was synthesized with the assistance of a high-gravity technique in order to reduce the reaction time and temperature. The synthesized inorganic nanomaterial has been applied in both drug and gene delivery systems, and as the first fully inorganic nanomaterial, it was investigated in a comprehensive cellular investigation as well. In order to increase the potential bioavailability, as well as the interactions with the pCRISPR, the nanomaterial was enriched with additional Zn ions. The nanomaterial and the final nanocarrier were characterized at each step before and after any biological analysisviaFESEM, AFM, TEM, FTIR and XRD. The polymer coated... 

Overexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression of ssDNA and the related antigens in the population and brisk activity in gene-editing technologies in the treatment/detection may lead to the presence of pCRISPR in the blood. Therefore, the detection and evaluation of their trace concentrations are of... 

Introduction: B lymphocyte-induced maturation protein 1 (BLIMP1) encoded by the positive regulatory domain 1 gene (PRDM1), is a key regulator in T cell differentiation in mouse models. BLIMP1-deficiency results in a lower effector phenotype and a higher memory phenotype. Methods: In this study, we aimed to determine the role of transcription factor BLIMP1 in human T cell differentiation. Specifically, we investigated the role of BLIMP1 in memory differentiation and exhaustion of human T cells. We used CRISPR interference (CRISPRi) to knock-down BLIMP1 and investigated the differential expressions of T cell memory and exhaustion markers in BLIMP1-deficient T cells in comparison with...