Sharif Digital Repository

BACKGROUND: StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can... 

Background: Self-organization is a fundamental feature of living organisms at all hierarchical levels from molecule to organ. It has also been documented in developing embryos. Methods. In this study, a scale-invariant power law (SIPL) method has been used to study self-organization in developing embryos. The SIPL coefficient was calculated using a centro-axial skew symmetrical matrix (CSSM) generated by entering the components of the Cartesian coordinates; for each component, one CSSM was generated. A basic square matrix (BSM) was constructed and the determinant was calculated in order to estimate the SIPL coefficient. This was applied to developing C. elegans during early stages of... 

Purpose: Presence of photon attenuation severely challenges quantitative accuracy in single-photon emission computed tomography (SPECT) imaging. Subsequently, various attenuation correction methods have been developed to compensate for this degradation. The present study aims to implement an attenuation correction method and then to evaluate quantification accuracy of attenuation correction in small-animal SPECT imaging. Methods: Images were reconstructed using an iterative reconstruction method based on the maximum-likelihood expectation maximization (MLEM) algorithm including resolution recovery. This was implemented in our designed dedicated small-animal SPECT (HiReSPECT) system. For... 

OBJECTIVES: Recent advances in the field of acoustics and piezoelectric and ultrasound transducers have led to new approaches to the diagnosis and treatment of certain diseases. One method of treatment with ultrasonic waves is high-intensity focused ultrasound (HIFU) treatment, which is a thermal therapeutic method used to treat malignant tumors. Although a variety of treatment-planning strategies using ultrasonic waves have been investigated, little clinical success has been achieved. Computational modeling is a powerful tool for predicting device performance. METHODS: The heating induced by a concave transducer with operating powers of 85 and 135 W was studied, and the experimental results... 

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,... 

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... 

Support vector machines (SVMs) were used as a novel learning machine in the authentication of the origin of salmon. SVMs have the advantage of relying on a well-developed theory and have already proved to be successful in a number of practical applications. This paper provides a new and effective method for the discrimination between wild and farm salmon and eliminates the possibility of fraud through misrepresentation of the country of origin of salmon. The method requires a very simple sample preparation of the fish oils extracted from the white muscle of salmon samples. 1H NMR spectroscopic analysis provides data that is very informative for analysing the fatty acid constituents of the... 

In this study, physically cross-linked hydrogels were developed by freezing-thawing method while different concentrations of honey were included into the hydrogels for accelerated wound healing. The hydrogel was composed of chitosan, polyvinyl alcohol (PVA), and gelatin with the ratio of 2:1:1 (v/v), respectively. Further, the effect of honey concentrations on antibacterial properties, and cell behavior was investigated. In vivo studies, including wound healing mechanism using rat model and histological analysis of section tissue samples were performed. The results illustrated that the incorporation of honey in hydrogels increased the ultimate strain of hydrogels approximately two times,... 

Background & Objective: The potent antioxidant property of fullerene C60 nanoparticles and their derivatives has been demonstrated in a wide range of in vitro and in vivo studies. Hence, we examined the effects of fullerene C60 on the oxidative stress parameters in brain and liver of the rats in normal situation. Materials & Methods: The study was performed in two groups of Wistar rats (each group, n = 6); normal and fullerene-treated normal animals. Treated rats received fullerene via oral gavage at dose of 1 mg/kg/day for 60 days. At termination of the study, the oxidative stress parameters were determined in brain and liver tissues, including the contents of glutathione (GSH) and... 

With increasing use of computers in everyday life, improved communication between machines and human is needed. To make a right communication and understand a humankind face which is made in a graphical environment, implementing the audio and visual projects like lip reading, audio and visual speech recognition and lip making are needed. Lack of a complete audio and visual database for this application in Farsi language made us provide a new complete Farsi database for this project that is called SFAVD. It is a unique audio and visual database which in addition to considering Farsi conceptual and speech structure, it considers influence of speech on lip changes. This database is created for... 

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... 

In this paper, we describe the design, development and preliminary evaluation of a novel animation tool for smartphones and tablets, with the goal of improving creativity and problem-solving ability among novice users, mainly young children. The user first draws the objects with markers and crayons on paper and takes a photo with their mobile or tablet to import their drawings into the app as game sprites. They then design their animation scene and point to a part of the character and selecting its animation type from existing buttons. Hence the selected part is animated in a vertex shader while ensuring a smooth transition with the non-pointed part. The results of a preliminary evaluation... 

In the present study, a detailed biocompatibility testing of a novel class of hybrid nanostructure based on hyperbranched polyglycerol and β-cyclodextrin is conducted. This highly water soluble nanostructure with size of less than 10 nm, polydispersity of less than 1.3, chemical tenability and highly branched architecture with the control over branching structure could be potentially used as a carrier in drug delivery systems. To this end, extensive studies in vitro and in vivo conditions have to be demonstrated. The in vitro studies include in vitro cytotoxicity tests; MTT and Neutral Red assay as an indicator of mitochondrial and lysosomal function, and blood biocompatibility tests such as... 

Purpose: Tests on animals of different species with large differences in intervertebral disc size are commonly used to investigate the therapeutic efficacy of intravenously injected solutes in the disc. We hypothesize that disc size markedly affects outcome. Methods: Here, using a small non-metabolized molecule, glucosamine (GL) as a model solute, we calculate the influence of disc size on transport of GL into rat, rabbit, dog and human discs for 10 h post intravenous-injection. We used transient finite element models and considered an identical GL supply for all animals. Results: Huge effects of disc size on GL concentration profiles were found. Post-injection GL concentration in the rat... 

Objective: Epileptic seizure detection is a key step for epilepsy assessment. In this work, using the pentylenetetrazole (PTZ) model, seizures were induced in rats, and ECoG signals in interictal, preictal, ictal, and postictal periods were recorded. The recorded ECoG signals were then analyzed to detect epileptic seizures in the epileptic rats. Methods: Two different approaches were considered in this work: thresholding and classification. In the thresholding approach, a feature is calculated in consecutive windows, and the resulted index is tracked over time and compared with a threshold. The moment the index crosses the threshold is considered as the moment of seizure onset. In the... 

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... 

Background: An essential requirement for performing robotic-assisted surgery on a freely beating heart is a prediction algorithm that can estimate the future heart trajectory. Method: Heart motion, respiratory volume (RV) and electrocardiogram (ECG) signal were measured from two dogs during thoracotomy surgery. A comprehensive multimodality prediction algorithm was developed based on the multivariate autoregressive model to incorporate the heart trajectory and cardiorespiratory data with multiple inherent measurement rates explicitly. Results: Experimental results indicated strong relationships between the dominant frequencies of heart motion with RV and ECG. The prediction algorithm... 

This article presents the result of an analysis to determine the distance that the fuselage of a Flapping Flyer moves up and down when the wing flap and comparison it with experiments that was done on fuselage phenomena during flight of an ornithopters and Winged animals in Wind tunnel. It is suggested that this motion may reduce the efficiency of design, whereas the tendency for fuselage motion may be largely cancelled in the bi plane configuration. The article also answers a question that has puzzled for scientist. Why bodies of winged animals don't move up and down noticeably when they flaps their wing during flight? Finally we offer one solution for reduce this unwanted motion near 50 %... 

Mechanical ventilation (MV) can result in long-term brain impairments that are resistant to treatment. The mechanisms underlying MV-induced brain function impairment remain unclear. Since nasal airflow modulates brain activity, here we evaluated whether reinstating airflow during MV could influence the memory performance of rats after recovery. Rats were allocated into two study groups: one group received rhythmic air-puff into the nasal cavity during MV and a control group that underwent ventilation without air-puff. During MV, air-puffs induced time-locked event potentials in OB, mPFC and vHPC and significantly increased the oscillatory activity at the air-puff frequency. Furthermore, in...