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hossein-nazer--tahora
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Link Prediction in Social Networks Using the Diffusion Network Characteristics
, M.Sc. Thesis Sharif University of Technology ; Rabiee, Hamid Reza (Supervisor)
Abstract
Given a snapshot of a network, link preditction methods try to infer future intractions be-tween its nodes. These methods may be used in either analyzing current state of the network or predicting future links of it. Link prediction techniques have many applications among which we can mention recommendation systems. These systems are implemented for com-mercial reasons or preventing user confusion in huge amount of information available.A new perspective toward link prediction is based on supervised random walk. In such methods, a random walker starts from a node in the network and randomly traverses to one of the current node’s neighbours with a probability proportional to the chosen link’s...
Identifying Gene Expression Patterns in Memory T Cell Development
, M.Sc. Thesis Sharif University of Technology ; Mohammadzadeh, Hoda (Supervisor) ; Hossein Khalaj, Babak (Supervisor) ; Basiri, Mohsen (Co-Supervisor)
Abstract
T lymphocytes or T cells are a type of white blood cell that play an important role in the immune system. Memory T cells are a subset of them that are able to reactivate when being re-exposed to the pathogen. Because of the properties of these cells, they are an attractive choice for immunotherapy. Initial memory subgroups were shown to be more persistently effective in immunotherapies. However little is known about development and differentiation of these subgroups. With the discovery of a new subset of T cells, called T memory stem cells (TSCM), They are considered to develop through four stages, naive T cells (TN), T memory stem cells (TSCM), central memory T cells (TCM) and effector...
Investigating the Seismic Behavior of Mid-rise Diagrid Buildings with Irregular Plan
, M.Sc. Thesis Sharif University of Technology ; Rahimzadeh Rofooei, Fayyaz (Supervisor)
Abstract
The utilized structural systems in high-rise buildings are under develop in terms of quantity and quality to increase their resistance under gravity and lateral loads. In addition, widespread researches are conducted to introduce and employ modern structural systems for high-rise buildings to improve there behavior in response to the applied forces, and to reduced the levels of hazards imposed by lateral forces. In this regard in recent years, use of diagrid structural systems has gained most of engineers and architects attention. Architectural limitations and improper site conditions may commonly result in construction of buildings with torsional irregularities. However, presence of...
A comparative overview of epigenomic profiling methods
, Article Frontiers in Cell and Developmental Biology ; Volume 9 , 2021 ; 2296634X (ISSN) ; Sepehri, M. H ; Nazer, N ; Norouzi, M. R ; Sharif University of Technology
Frontiers Media S. A
2021
Abstract
In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments. © Copyright © 2021 Mehrmohamadi, Sepehri, Nazer and Norouzi
Synthesis of Luminescent Carbon Dots for Selectivity Study Towards Metal Ions
, M.Sc. Thesis Sharif University of Technology ; Hormozi-Nezhad, Mohammad Reza (Supervisor)
Abstract
Today, the use of graphene quantum dots has been very much considered due to easy synthesis methods, strong fluorescence emission, and many sources of synthesis. In this study, the effect of changing capping agent of graphene quantum dots toward iron (Ⅲ), copper (Ⅱ) and mercury (Ⅱ) ions was studied. The linear range of response of the graphene quantum dots synthesized with ethylenediamine for mercury (Ⅱ) and iron (Ⅲ) ions was 10-70 µM, and this sensor also responded to Cu (Ⅱ) ions. Urea synthesized graphene quantum dots also responded to all three ions. The linear range of the response for mercury (Ⅱ) , iron (Ⅲ) and copper (Ⅱ) ions was 5-25, 10-70 and 120-120 μM respectively. The linear...
Expression of PIAS genes in migraine patients
, Article Journal of Molecular Neuroscience ; Volume 71, Issue 10 , 2021 , Pages 2053-2059 ; 08958696 (ISSN) ; Hesami, O ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Humana Press Inc
2021
Abstract
Migraine is a complex disabling condition which is associated with dysregulation of several pathways particularly those being associated with immune responses. In order to assess contribution of protein inhibitor of activated STAT (PIAS) in the pathogenesis of migraine, we quantified expression levels of PIAS1–PIAS4 genes in the circulation of patients with migraine compared with controls. Expression of PIAS1 was substantially lower in total migraineurs compared with controls (ratio of mean expressions (RME) = 0.18, SE = 0.29, P value < 0.001) and in both male and female migraineurs compared with sex-matched controls. Expression of PIAS2 was lower in migraineurs without aura compared with...
Expression analysis of BDNF, BACE1 and their antisense transcripts in inflammatory demyelinating polyradiculoneuropathy
, Article Multiple Sclerosis and Related Disorders ; Volume 47 , 2021 ; 22110348 (ISSN) ; Mazdeh, M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Elsevier B.V
2021
Abstract
Acute and chronic inflammatory demyelinating polyradiculoneuropathies (AIDP and CIDP) are two immune-related conditions in the peripheral nervous system. In the current study, we assessed expression levels of Beta-secretase (BACE1), brain-derived neurotrophic factor (BDNF) and their antisense transcripts in the peripheral blood of AIDP and CIDP patients compared with age- and sex-matched controls to assess their potential as biomarkers for these conditions. Expressions of BACE1 and BACE1-AS were down-regulated in CIDP cases compared with controls (Ratios of mean expressions=0.01 and 0.03; P values= 1.07E-08, respectively). On the other hand, expressions of BDNF and BDNF-AS were up-regulated...
Expression analysis of cytokine transcripts in inflammatory demyelinating polyradiculoneuropathy
, Article Metabolic Brain Disease ; Volume 36, Issue 7 , 2021 , Pages 2111-2118 ; 08857490 (ISSN) ; Ghafouri Fard, S ; Omrani, M. D ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Springer
2021
Abstract
Inflammatory demyelinating polyradiculoneuropathies are a group of peripheral nerve system disorders in which immune reactions are dysregulated. Cytokines have noticeable roles in the regulation of these responses. We compared transcript levels of nine cytokine coding genes namely IL-1B, IL-2, IL-4, IL-6, IL-8, IL-17A, IFN-G, TGF-B and TNF-A in the peripheral blood of patients with acute and chronic kinds of this condition (AIDP and CIDP) and healthy persons. Expression of IL-17A was significantly lower in female AIDP cases compared with female controls (Expression Ratio = 0.02, P value = 0.02). Expression of this cytokine was higher in female CIDP cases compared with female AIDP cases...
Expression analysis of protein inhibitor of activated stat in inflammatory demyelinating polyradiculoneuropathy
, Article Frontiers in Immunology ; Volume 12 , 2021 ; 16643224 (ISSN) ; Hussen, B. M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Frontiers Media S.A
2021
Abstract
Protein inhibitors of activated STAT (PIAS) are involved in the regulation of the JAK/STAT signaling pathway and have interactions with NF-κB, p73 and p53. These proteins regulate immune responses; therefore dysregulation in their expression leads to several immune-mediated disorders. In the present study, we examined expression of PIAS1-4 in peripheral blood of patients with acute/chronic inflammatory demyelinating polyradiculoneuropathy (AIDP/CIDP) compared with healthy subjects. We demonstrated down-regulation of all PIAS genes in both AIDP and CIDP cases compared with controls. Similarly, comparisons in gender-based groups revealed down-regulation of these gene0s in patients of each...
Dysregulation of lncRNAs in autoimmune neuropathies
, Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) ; Taheri, M ; Mehvari Habibabadi, J ; Nazer, N ; Sayad, A ; Ghafouri Fard, S ; Sharif University of Technology
Nature Research
2021
Abstract
Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) and Guillain-Barré syndrome (GBS) are inflammatory neuropathies with different clinical courses but similar underlying mechanisms. Long non-coding RNAs (lncRNAs) might affect pathogenesis of these conditions. In the current project, we have selected HULC, PVT1, MEG3, SPRY4-IT1, LINC-ROR and DSCAM-AS1 lncRNAs to appraise their transcript levels in the circulation of CIDP and GBS cases versus controls. Expression of HULC was higher in CIDP patients compared with healthy persons (Ratio of mean expression (RME) = 7.62, SE = 0.72, P < 0.001). While expression of this lncRNA was not different between female CIDP cases and female...
Downregulation of oxytocin-related genes in periodontitis
, Article Frontiers in Molecular Neuroscience ; Volume 15 , 2022 ; 16625099 (ISSN) ; Gholami, L ; Nazer, N ; Hussen, B. M ; Sayad, A ; Hajiesmaeili, M ; Sharif University of Technology
Frontiers Media S.A
2022
Abstract
Periodontitis is a common oral disorder leading to tooth loss in both developed and developing regions of the world. This multifactorial condition is related to the abnormal activity of several molecular pathways, among them are oxytocin-related pathways. In this study, we enrolled 26 patients and 28 controls and assessed the expression of four oxytocin-related genes, namely, FOS, ITPR, RCAN1, and RGS2, in circulation and affected tissues of enrolled individuals using real-time PCR. Expression of FOS was downregulated in total periodontitis tissues compared with total control tissues [ratio of mean expression (RME) = 0.23, P-value = 0.03]. Expression of FOS was also lower in total blood...
Over-Expression of immune-related lncrnas in inflammatory demyelinating polyradiculoneuropathies
, Article Journal of Molecular Neuroscience ; 2020 ; Ghafouri Fard, S ; Mazdeh, M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Humana Press Inc
2020
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles in the pathogenesis of immune-related disorders. However, their role in the pathobiology of inflammatory demyelinating polyradiculoneuropathies remains unclear. In the current study, we measured peripheral expression of four lncRNAs, namely TUG1, FAS-AS1, NEAT1, and GAS5, in patients with acute/chronic inflammatory demyelinating polyradiculoneuropathies (AIDP/CIDP) compared with healthy subjects. Notably, all lncRNAs were over-expressed in patients compared with controls (P < 0.0001 for all lncRNAs). When assessing their expressions in AIDP and CIDP groups separately, TUG1 and NEAT1 were up-regulated in both patient groups compared with...
Abnormal expression of NF-κB-related transcripts in blood of patients with inflammatory peripheral nerve disorders
, Article Metabolic Brain Disease ; Volume 36, Issue 8 , 2021 , Pages 2369-2376 ; 08857490 (ISSN) ; Ghafouri Fard, S ; Badrlou, E ; Omrani, D ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Springer
2021
Abstract
The NF-κB family includes some transcription factors which have important functions in the regulation of immune responses, therefore participating in the pathophysiology of inflammatory conditions such as peripheral neuropathies. We have quantified expression of a number of NF-κB-related transcripts in patients with Guillain-Barré syndrome (GBS) or chronic inflammatory demyelinating polyneuropathy (CIDP) versus healthy subjects. These transcripts have been previously shown to be functionally related with this family of transcription factors. Expressions of ATG5, DICER-AS1, PACER, DILC, NKILA and ADINR have been increased in both CIDP and GBS patients compared with controls. However,...
Over-Expression of immune-related lncrnas in inflammatory demyelinating polyradiculoneuropathies
, Article Journal of Molecular Neuroscience ; Volume 71, Issue 5 , 2021 , Pages 991-998 ; 08958696 (ISSN) ; Ghafouri-Fard, S ; Mazdeh, M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Humana Press Inc
2021
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles in the pathogenesis of immune-related disorders. However, their role in the pathobiology of inflammatory demyelinating polyradiculoneuropathies remains unclear. In the current study, we measured peripheral expression of four lncRNAs, namely TUG1, FAS-AS1, NEAT1, and GAS5, in patients with acute/chronic inflammatory demyelinating polyradiculoneuropathies (AIDP/CIDP) compared with healthy subjects. Notably, all lncRNAs were over-expressed in patients compared with controls (P < 0.0001 for all lncRNAs). When assessing their expressions in AIDP and CIDP groups separately, TUG1 and NEAT1 were up-regulated in both patient groups compared with...
Altered expression of SOCS genes periodontitis
, Article BMC Oral Health ; Volume 22, Issue 1 , 2022 ; 14726831 (ISSN) ; Gholami, L ; Sadeghpour, S ; Nazer, N ; Hussen, B. M ; Sayad, A ; Taheri, M ; Sharif University of Technology
BioMed Central Ltd
2022
Abstract
Suppressor of cytokine signalling (SOCS) family comprises a group of proteins that impede JAK/STAT signalling, thus being involved in the pathogenesis of immune-related conditions. In the present work, we aimed at identification of the role of SOCS genes in the pathogenesis of periodontitis through evaluation of their expression levels both in the circulation and in the affected tissues of patients. Thus, we measured expression levels of SOCS1-3 and SOCS5 transcripts in the blood and gingival samples of patients with periodontitis in comparison with control samples obtained during dental crown lengthening. Expressions of SOCS1, SOCS2, SOCS3 and SOCS5 genes were similar between gingival...
Assessment of expression of NF-κB-related genes in periodontitis
, Article Gene Reports ; Volume 26 , 2022 ; 24520144 (ISSN) ; Gholami, L ; Nazer, N ; Hussen, B. M ; Shadnoush, M ; Sayad, A ; Taheri, M ; Sharif University of Technology
Elsevier Inc
2022
Abstract
Nuclear factor kappa B (NF-κB) is an important regulator of immune responses and is involved in the pathoetiology of periodontitis. We have measured levels of four NF-κB-related genes, namely CEBPA, CEBPA-DT, FBXL19-AS and DILC in blood and tissue samples of patients with chronic periodontitis compared with controls. Expression of CEBPA-DT was significantly lower in blood of patients compared with controls (Ratio of mean expression (RME) = 0.13, P value = 0.01). This pattern was also seen among male subgroups (RME = 0.10, P value = 0.01). FBXL19-AS was down-regulated in venous blood of total patients compared with controls (RME = 0.03, P value < 0.001) and in patients of both sexes compared...
Calculation of the Energy Release Rate of Nano-Cracks in FCC Materials Via the Many Body Atomic Scale FEM
, M.Sc. Thesis Sharif University of Technology ; Mohammadi Shodja, Hossein (Supervisor)
Abstract
Since the classical continuum theory fails to deal with the problems associated with defects, stress concentrators, and relevant deformation phenomena in solids, alternative approaches that can detect the atomistic nature of materials' fracture are required. The deficiency of the capture the size effect which yields delusively high values for some components of the stress field right on the edge of the stress concentrators, and its weakness in describing the complex interaction between small inhomogeneities, cracks and the like when they are only a few nanometers apart, are among some of the disadvantages of the classical approach. In recent years, however, atomistic methods are emerging to...
Dysregulation of lncRNAs in circulation of patients with periodontitis: results of a pilot study
, Article BMC Oral Health ; Volume 21, Issue 1 , 2021 ; 14726831 (ISSN) ; Gholami, L ; Badrlou, E ; Sadeghpour, S ; Nazer, N ; Shadnoush, M ; Sayad, A ; Taheri, M ; Sharif University of Technology
BioMed Central Ltd
2021
Abstract
Background: Periodontitis is a chronic inflammatory disorder with a complex etiology. Long non-coding RNAs (lncRNAs) have been shown to affect pathoetiology of periodontitis. We aimed at identification of expression of five lncRNAs, namely Linc0116, Linc00667, CDK6-AS1, FENDRR and DIRC3 in the circulation and gingival tissues of these patients compared with healthy controls. Methods: In a pilot case–control study, we compared expressions of Linc0116, Linc00667, CDK6-AS1, FENDRR and DIRC3 lncRNAs between blood and tissue samples of patients with periodontitis and healthy controls using real time quantitative PCR technique. The present work was performed on samples got from 26 patients with...
Assessment of expression of a number of immune-related genes in the periodontitis
, Article Ecological Genetics and Genomics ; Volume 22 , 2022 ; 24059854 (ISSN) ; Badrlou, E ; Nazer, N ; Sadeghi, G ; Mehdizadeh, B ; Mirzajani, S ; Sayad, A ; Ghafouri Fard, S ; Sharif University of Technology
Elsevier Inc
2022
Abstract
Immune-related genes have essential roles in the pathobiology of periodontitis. In the current projects, we aimed at appraisal of the expression amounts of three immune-related genes including two mRNA coding genes (NR3C1 and CSTF2) and a long non-coding RNA (CCAT2) in tissue sections and blood of patients with this condition versus healthy controls. Our previous study has shown the susceptibility role of HLA-DRB1*04 allele in development of this disease. So the subjects who were positive for HLA-DRB1*04 allele were excluded. Expression amounts of CCAT2, NR3C1 and CSTF2 genes have been statistically similar between periodontitis patients and controls in both blood samples and tissue samples....
Semisolid Stir Joining of As-Cast Silicon-Aluminum Bronze
, M.Sc. Thesis Sharif University of Technology ; Kokabi, Amir Hossein (Supervisor) ; Ashuri, Hossein (Supervisor)
Abstract
Aluminum Bronzes have many applications in marine environments. These alloys suffer from both hot cracking and cold cracking. In order to overcome the hot cracking and cold cracking, Semisolid Stir Joining method and a proper thermal cycle was used respectively. Effects of temperature, stirring rate, and tool type were investigated in Semisolid Stir joining method. In this method, butt joint design was used in order to place specimens, and the specimens were heated up to specific temperatures (920, 925, 930°C). A stirrer (Cylindrical and Grooved tool) with three rotational speeds (800, 1200, 1600 RPM) was introduced into the stir weld seam. Welded specimens were cooled to the 900°C...