Sharif Digital Repository

Ankylosing spondylitis (AS) is a systemic inflammatory disorder of joints and entheses. Recent studies have reported an increased prevalence of dementia in AS patients. However, data for exploring the association between dementia and AS remain uncertain. In this study, enriched pathways and differentially expressed genes (DEGs) were identified in whole blood transcription data of AS patients obtained from the gene expression omnibus (GEO) database; using gene set enrichment analysis (GSEA) and differential expression analysis. Four pathways, including oxidative phosphorylation, Alzheimer's, Parkinson's, and Huntington's diseases were significantly enriched in AS patients compared to the... 

In recent years, analyzing genome-wide expression profiles to find genetic markers has received much attention as a challenging field of research aiming at unveiling biological mechanisms behind complex disorders. The identification of reliable and reproducible markers has lately been achieved by integrating genome-scale functional relationships and transcriptome datasets, and a number of algorithms have been developed to support this strategy. In this paper, we present a promising and easily applicable tool to accomplish this goal, namely CytoGTA, which is a Cytoscape plug-in that relies on an optimistic game theoretic approach (GTA) for identifying subnetwork markers. Given transcriptomic... 

In this paper, the Extended Kalman filtering (EKF) approach has been used to infer gene regulatory networks using time-series gene expression data. Gene expression values are considered stochastic processes and the gene regulatory network, a dynamical nonlinear stochastic model. Using these values and a modified Kalman filtering approach, the model's parameters and consequently the interactions amongst genes are predicted. In this paper, each gene-gene interaction is modeled using a linear term, a nonlinear one, and a constant term. The linear and nonlinear term coefficients are included in the state vector together with the gene expressions' true values. Through the extended Kalman... 

Gelatin methacrylate (GelMA) was proved to be a promising bioink for corneal stromal cell delivery. However, GelMA has low mechanical properties which makes it difficult to be suturable and handled for clinical applicattion. In this study, three different ratios of 12.5 % GelMA and 10 % PEGDA were investigated for corneal stromal cells delivery. The mixture containing 75 % GelMA and 25 % PEGDA (75G25P) was found to have reasonable cell viability and suturing strength. Moreover, collagen nanofibers were incorporated into 75G25P hydrogel to improve the mechanical and biomimetic properties of the construct (75G25P-E). A hybrid structure was obtained by injecting the optimized bioink on the... 

Titanium carbonated hydroxyapatite (Ti/CHA) nanobiocomposites have extensive biological applications due to the excellent biocompatibility and similar characteristics to the human bone. Ti/CHA nanobiocomposite has good biological properties but it suffer from diverse characteristics especially in hardness, Young's modulus, apparent porosity and relative density. This investigation is an attempt to propose the predictive models using gene expression programming (GEP) to estimate these characteristics. In this regards, GEP is used to model and compare the effect of practical variables including pressure, Ti/CHA contents and sintering temperature on their monitored properties. To achieve this... 

Background: The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. However, these algorithms often produce classifiers with weaknesses in terms of accuracy, robustness, and interpretability. This paper introduces fuzzy support vector machine which is a learning algorithm based on combination of fuzzy classifiers and kernel machines for microarray classification.Results: Experimental results on public leukemia, prostate, and colon cancer datasets show that fuzzy support vector machine applied in combination with filter or wrapper feature selection... 

Motivation: Single-cell RNA-sequencing (scRNA-seq) offers the opportunity to dissect heterogeneous cellular compositions and interrogate the cell-type-specific gene expression patterns across diverse conditions. However, batch effects such as laboratory conditions and individual-variability hinder their usage in cross-condition designs. Results: Here, we present a single-cell Generative Adversarial Network (scGAN) to simultaneously acquire patterns from raw data while minimizing the confounding effect driven by technical artifacts or other factors inherent to the data. Specifically, scGAN models the data likelihood of the raw scRNA-seq counts by projecting each cell onto a latent embedding.... 

3D hydrogel environment with both unique properties of nanofibrous structure and electrical character can provide a promising scaffold for skeletal muscle tissue engineering approaches. Herein, the poly acrylic acid (PAA)-based hydrogel was engineered to conductive one by aniline polymerization in the form of nanofibers. The poly aniline (PANi) nanofibers were made by the optimized chemical reactions between the surface carboxylate groups of based hydrogel and protonated aniline monomers. We found that the strong bonding which was created between PANi and camphor sulphonic acid (CSA) as a doping agent supporting the stable electrical property of composite hydrogel after incubation in cell... 

Recent studies showed that a large amount of graphene oxide accumulated in kidney and liver when it injected intravenously. Evaluation of lethal and apoptosis gene expression in these tissues, which are under stress is very important. In this paper the in vivo dose-dependent effects of graphene oxide and reduced graphene oxide nanoplatelets on kidney and liver of mice were studied. Balb/C mice were treated by 20 mg/kg body weight of nanoplatelets. Molecular biology analysis showed that graphene nanoplatelets injected intravenously lead to overexpression of BAX gene in both kidney and liver tissues (P ≥ 0.01). In addition these nanoparticles significantly increase BCL2 gene expression in both... 

Background: Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been entirely understood. This study intended to investigate the common and tissue-specific pathways involved in different tissues of SSc patients. Methods: An integrative gene expression analysis of ten independent microarray datasets of three tissues was conducted to identify differentially expressed genes (DEGs). DEGs were mapped to the search tool for retrieval of interacting genes (STRING) to acquire protein-protein interaction (PPI) networks. Then, functional clusters in PPI... 

One of the main issues of wastewater treatment is the silica deposition in steam turbines. Evaporation of silica with the steam in adequate concentration is one of the main sources of scale formation in steam turbines. In this study, the authors introduce the utilization of a genetic-based approach—gene expression programming (GEP)—for solubility prognostication of the silica in superheated steam of boilers with respect to water silica content and pressure. The result of GEP mathematical approach is a new algebraic formula to achieve our goals. Developed model predicts the silica solubility in the range of 0.8–22.1 MPa and 1–500 mg/kg for pressure and boiler water silica content,...