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Polyhedral Oligomeric Silsesquioxanes based Materials as Sorbent and Sensor
, Ph.D. Dissertation Sharif University of Technology ; Bagheri, Habib (Supervisor) ; Jamali, Sirous (Supervisor)
Abstract
The main approach in this thesis is the synthesis and identification of polyhedral oligomeric silsesquisans (POSS) and their modification with suitable functional groups to induce desired properties and use them as adsorbents or sensor. In the first work, POSSs were used as three-dimensional porous compounds with special properties as extractant phase in solid phase croextraction. Selective extraction of polar and non-polar molecules to particle size and functional groups on POSS. In this research, a threedimensional network of POSS including naphthalene diimide (POSS-NDI) and perylene diimide (POSS-PDI) as an extractant phase capable of absorbing volatile organic compounds was used to...
Exploring Pivot Genes and Clinical Prognosis Using Combined Bioinformatics Approaches in the Colon Cancer
,
M.Sc. Thesis
Sharif University of Technology
;
Foroughmand Araabi, Mohammad Hadi
(Supervisor)
Abstract
Colorectal cancer (CRC) is one of the most common cause of cancer death worldwide. Identification of pivot genes in colorectal cancer can play an important role as biomarkers in predicting and early diagnosis and reducing the number of deaths caused by this disease. In this study, the aim of which is to discover pivot genes in colorectal cancer, six microarray datasets selected from the GEO database including 277 tumor tissue samples and 325 normal colon tissue samples. After data processing, differentially expressed genes and CRC-related genes were screened and 285 shared genes between them were identified for subsequent analysis. Based on 285 shared genes, the protein-protein interaction...
Cell Sepration of Cancer Cells by Using Electrical Field
, M.Sc. Thesis Sharif University of Technology ; Asempour, Ahmad (Supervisor) ; Ahmadian, Mohamadtaghi (Supervisor)
Abstract
Cancer is the second leading cause of death in the world, with a high annual cost of treatment. As the cancer progresses, the cancer cells in the bloodstream metastasize to other parts of the body, causing the disease to spread throughout the patient's body and disrupt organ functions. sepration of cancer cells in the bloodstream inhibits the growth of cancer. Cancer cells differ from healthy cells in some features, such as size, electrical charge and polarization. These features can be used to seprate cancer cells from healthy cells.In this study, cell surface electrical charge was used as a biomarker to seprate cancer cells. By passing blood flow through a chanal and applying an electrical...
Evaluation of the Possibility of Diagnosing Female Gynecologic Cancer using X-Ray Fluorescence (XRF)Spectroscopy of Hair and Nail
, M.Sc. Thesis Sharif University of Technology ; Hosseini, Abulfazl (Supervisor) ; Salimi, Ehsan (Supervisor)
Abstract
In recent years, indirect methods of cancer detection that utilize changes in trace element levels in various parts of the body, such as hair and nails, have garnered significant attention from researchers.The primary objective of these methods is to identify alterations in trace element levels that serve as biological markers in the presence of disease. While direct examination of affected organs remains the gold standard for cancer diagnosis, it is often expensive, time-consuming, inconvenient, and associated with potential side effects. Therefore, if the effectiveness of this approach is validated, it could serve as a cost-effective, non-invasive, safe, and early diagnostic method in...
Cancer Prediction Using cfDNA Methylation Patterns With Deep Learning Approach
, M.Sc. Thesis Sharif University of Technology ; Soleymani Baghshah, Mahdieh (Supervisor)
Abstract
Liquid biopsy includes information about the progress of the tumor, the effectiveness of the treatment and the possibility of tumor metastasis. This type of biopsy obtains this information by doing diagnosis and enumerating genetic variations in cells and cell-free DNA (cfDNA). Only a small fraction of cfDNA which might be free circulation tumor DNA (ctDNA) fragments, has mutations and is usually identified by epigenetic variations. On the other hand, the use of liquid biopsy has decreased, and tumors in the final stages are often untreatable due to the low accuracy in prediction of cancer. In this research, the aim is to predict cancer using cfDNA methylation patterns. We obtain these...
Metabolic profiling of seminal plasma from teratozoospermia patients
, Article Journal of Pharmaceutical and Biomedical Analysis ; Volume 178 , January , 2020 ; Chashmniam, S ; Nobakht, F ; Amini, M ; Javidi, A ; Minai Tehrani, A ; Arjmand, B ; Gilany, K ; Sharif University of Technology
Elsevier B. V
2020
Abstract
Teratozoospermia is one of conditions that can cause male infertility. The mechanism of teratozoospermia remains unclear. The knowledge of the metabolites in human seminal plasma (HSP) is meaningful for the pathological study of teratozoospermia. Analysis of changed metabolites in HSP can help understand the cellular mechanism, find the novel biomarkers and subsequently design a diagnosis test. In this study, the analysis of samples performed by proton nuclear magnetic resonance spectroscopy (1H NMR spectroscopy) to identify the various metabolites, with the aim of finding metabolic profiles and biomarkers related to male infertility. Eighteen de-regulated metabolites were identified in...
Untargeted metabolomics based on nuclear magnetic resonance spectroscopy and multivariate classification techniques for identifying metabolites associated with breast cancer patients
, Article Chemometrics and Intelligent Laboratory Systems ; Volume 223 , 2022 ; 01697439 (ISSN) ; Khalilvand, M ; Tavakolizadeh, H ; Parastar, H ; Sharif University of Technology
Elsevier B.V
2022
Abstract
In this study, multivariate classification techniques combined with proton nuclear magnetic resonance (1HNMR) spectroscopy is proposed to identify breast cancer biomarkers that can precisely distinguish between healthy control and breast cancer (BC) patients. In this regard, first optimizing the metabolite extraction procedure was performed using Box-Behnken design (BBD). Then, data-driven soft independent modeling of class analogy (DD-SIMCA) model and partial least squares-discriminant analysis (PLS-DA) were successfully utilized for separating healthy from BC patient's classes. On this matter, both DD-SIMCA and PLS-DA models could successfully distinguish the healthy class from the BC...
The metabolomics signature associated with responsiveness to steroid therapy in focal segmental glomerulosclerosis: A pilot study
, Article Revista de Investigacion Clinica ; Volume 71, Issue 2 , 2019 , Pages 106-115 ; 00348376 (ISSN) ; Kalantari, S ; Nafar, M ; Boroumandnia, N ; Sharif University of Technology
Instituto Nacional de la Nutricion Salvador Zubiran
2019
Abstract
Background: Focal segmental glomerulosclerosis (FSGS) is considered one of the most severe glomerular diseases and around 80% of cases are resistant to steroid treatment. Since a large proportion of steroid-resistant (SR) FSGS patients progress to end-stage renal disease, other therapeutic strategies may benefit this population. However, identification of non-invasive biomarkers to predict this high-risk population is needed. Objective: We aimed to identify the biomarker candidates to distinguish SR from steroid-sensitive (SS) patients using metabolomics approach and to identify the possible molecular mechanism of resistance. Methods: Urine was collected from biopsy-proven FSGS patients...
Perylene diimide-POSS network for semi selective solid-phase microextraction of lung cancer biomarkers in exhaled breath
, Article Analytica Chimica Acta ; Volume 1198 , 2022 ; 00032670 (ISSN) ; Bagheri, H ; Yeganeh Rad, L ; Minaeian, S ; Sharif University of Technology
Elsevier B.V
2022
Abstract
Lung cancer (LC) is the leading cause of cancer mortality so, the analysis of exhaled human breath has great significance for early non-invasive diagnosis. Poor selectivity and strong humidity are two bottlenecks for the application of gas sensors to exhaled breath analysis. The development of novel extractive phases for the analysis of exhaled breath by chromatography is therefore a lucrative object. Polyhedral oligomeric silsesquioxanes (POSS) are among the 3D porous materials whose unique properties make them promising coatings for solid-phase microextraction (SPME). Selective enrichment of polar or nonpolar targets depends on the pore size and functional groups on the POSSs. Herein, we...
Prognostic Biomarker Selection for Breast Cancer using Bioinformatics and Deep Learning
, M.Sc. Thesis Sharif University of Technology ; Sharifi Zarchi, Ali (Supervisor)
Abstract
Triple Negative Breast Cancer (TNBC) is an invasive subtype of breast cancer. Finding prognostic biomarkers is helpful in choosing the appropriate treatment procedure for patients of this cancer. In recent years, the role of microRNAs in various biological processes, including cancer, has been identified, and their accessibility and stability have made these types of molecules an ideal biomarker. In the first phase of this study, with the aim of overcoming the limitations of previous studies, a new bioinformatics protocol has been proposed to investigate the prognostic miRNAs of triple negative breast cancer. First, using survival analysis, 56 prognostic miRNAs which had a significant...
NMR- and GC/MS-based metabolomics of sulfur mustard exposed individuals: a pilot study
, Article Biomarkers ; Volume 21, Issue 6 , 2016 , Pages 479-489 ; 1354750X (ISSN) ; Aliannejad, R ; Rezaei Tavirani, M ; Arefi Oskouie, A ; Naseri, M. T ; Parastar, H ; Aliakbarzadeh, G ; Fathi, F ; Taheri, S ; Sharif University of Technology
Taylor and Francis Ltd
Abstract
Sulfur Mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and...
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types
, Article BMC Bioinformatics ; Volume 23, Issue 1 , 2022 ; 14712105 (ISSN) ; Kazemi, A ; Hamidieh, K ; Dashti, H ; Tahaei, M. S ; Rabiee, H. R ; Alinejad Rokny, H ; Dehzangi, I ; Sharif University of Technology
BioMed Central Ltd
2022
Abstract
Background: The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence, there is no definitive treatment for most cancer types. This reveals the importance of developing new pipelines to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific...
Pattern recognition analysis of chromatographic fingerprints of Crocus sativus L. secondary metabolites towards source identification and quality control
, Article Analytical and Bioanalytical Chemistry ; Volume 408, Issue 12 , 2016 , Pages 3295-3307 ; 16182642 (ISSN) ; Sereshti, H ; Parastar, H ; Sharif University of Technology
Springer Verlag
2016
Abstract
Chromatographic fingerprinting is an effective methodology for authentication and quality control of herbal products. In the presented study, a chemometric strategy based on multivariate curve resolution-alternating least squares (MCR-ALS) and multivariate pattern recognition methods was used to establish a gas chromatography-mass spectrometry (GC-MS) fingerprint of saffron. For this purpose, the volatile metabolites of 17 Iranian saffron samples, collected from different geographical regions, were determined using the combined method of ultrasound-assisted solvent extraction (UASE) and dispersive liquid-liquid microextraction (DLLME), coupled with GC-MS. The resolved elution profiles and...
Metabolomics analysis of the saliva in patients with chronic hepatitis b using nuclear magnetic resonance: A pilot study
, Article Iranian Journal of Basic Medical Sciences ; Volume 22, Issue 9 , 2019 , Pages 1044-1049 ; 20083866 (ISSN) ; Mohamadkhani, A ; Chashmniam, S ; Shahnazari, P ; Amini, M ; Arjmand, B ; Malekzadeh, R ; Nobakht Motlagh Ghoochani, B. F ; Sharif University of Technology
Mashhad University of Medical Sciences
2019
Abstract
Objective(s): Hepatitis B virus infection causes chronic disease such as cirrhosis and hepatocellular carcinoma. The metabolomics investigations have been demonstrated to be related to pathophysiologic mechanisms in many disorders such as hepatitis B infection. The aim of this study was to investigate the saliva metabolic profile of patients with chronic hepatitis B infection and to identify underlying mechanisms as well as potential biomarkers associated with the disease. Materials and Methods: Saliva from 16 healthy subjects and 20 patients with chronic hepatitis B virus were analyzed by nuclear magnetic resonance (NMR). Then, multivariate statistical analysis was performed to identify...
A selective chemiresistive sensor for the cancer-related volatile organic compound hexanal by using molecularly imprinted polymers and multiwalled carbon nanotubes
, Article Microchimica Acta ; Volume 186, Issue 3 , 2019 ; 00263672 (ISSN) ; Banan Nojavani, M ; Nikkhah, M ; Alizadeh, T ; Esfandiar, A ; Ganjali, M. R ; Sharif University of Technology
Springer-Verlag Wien
2019
Abstract
A chemiresistive sensor is described for the lung cancer biomarker hexanal. A composite consisting of molecularly imprinted polymer nanoparticles and multiwalled carbon nanotubes was used in the sensor that is typically operated at a voltage of 4 V and is capable of selectively sensing gaseous hexanal at room temperature. It works in the 10 to 200 ppm concentration range and has a 10 ppm detection limit (at S/N = 3). The sensor signal recovers to a value close to its starting value without the need for heating even after exposure to relatively high levels of hexanal
Association of biomarkers of systemic inflammation with organic components and source tracers in quasi-ultrafine particles
, Article Environmental Health Perspectives ; Volume 118, Issue 6 , 2010 , Pages 756-762 ; 00916765 (ISSN) ; Staimer, N ; Tjoa, T ; Arhami, M ; Polidori, A ; Gillen, D. L ; Kleinman, M. T ; Schauer, J. J ; Sioutas, C ; Sharif University of Technology
2010
Abstract
Background: Evidence is needed regarding the air pollutant components and their sources responsible for associations between particle mass concentrations and human cardiovascular outcomes. We previously found associations between circulating biomarkers of inflammation and mass concentrations of quasi-ultrafine particles ≤ 0.25 μm in aerodynamic diameter (PM0.25) in a panel cohort study of 60 elderly subjects with coronary artery disease living in the Los Angeles Basin.Objectives: We reassessed biomarker associations with PM0.25 using new particle composition data.Methods: Weekly biomarkers of inflammation were plasma interleukin-6 (IL-6) and soluble tumor necrosis factor-α receptor II...
Fabrication, modeling and optimization of lyophilized advanced platelet rich fibrin in combination with collagen-chitosan as a guided bone regeneration membrane
, Article International Journal of Biological Macromolecules ; Volume 125 , 2019 , Pages 383-391 ; 01418130 (ISSN) ; Mashayekhan, S ; Saadatmand, M ; Sharif University of Technology
Elsevier B.V
2019
Abstract
In this study, lyophilized advanced platelet rich fibrin (A-PRF) was used in combination with collagen-chitosan membrane for the first time to combine advantages of both collagen and A-PRF membranes. Response surface methodology (RSM) was used to design the experimental condition and to correlate the effects of parameters, including chitosan/collagen (chit/col) weight ratio and A-PRF concentration on Young's modulus, mesenchymal stem cell (MSCs) viability and degradation rate of the membranes. Results showed that Young's modulus of the membranes was intensified by increasing chit/col weight ratio and decreasing A-PRF concentration from 3 to 8 MPa. Cell viability of MSCs was improved by both...
A noninvasive urine metabolome panel as potential biomarkers for diagnosis of t cell-mediated renal transplant rejection
, Article OMICS A Journal of Integrative Biology ; Volume 24, Issue 3 , March , 2020 , Pages 140-147 ; Chashmniam, S ; Nafar, M ; Samavat, S ; Rezaie, D ; Dalili, N ; Sharif University of Technology
Mary Ann Liebert Inc
2020
Abstract
Acute T cell-mediated rejection (TCMR)is a major complication after renal transplantation. TCMR diagnosis is very challenging and currently depends on invasive renal biopsy and nonspecific markers such as serum creatinine. A noninvasive metabolomics panel could allow early diagnosis and improved accuracy and specificity. We report, in this study, on urine metabolome changes in renal transplant recipients diagnosed with TCMR, with a view to future metabolomics-based diagnostics in transplant medicine. We performed urine metabolomic analyses in three study groups: (1) 7 kidney transplant recipients with acute TCMR, (2) 15 kidney transplant recipients without rejection but with impaired kidney...
ZnO nanoparticle/nanorod-based label-free electrochemical immunoassay for rapid detection of MMP-9 biomarker
, Article Biochemical Engineering Journal ; Volume 164 , 2020 ; Abdekhodaie, M. J ; Mousavi, S. A ; Taghipour, F ; Sharif University of Technology
Elsevier B.V
2020
Abstract
A label-free electrochemical biosensor was developed for the rapid detection of the matrix metalloproteinase 9 (MMP-9) biomarker on the basis of antibody immobilizing on the zinc oxide (ZnO) nanoparticle and ZnO nanorod electrodes. The charge transfer resistance (Rct) of the electrodes was used as the indicator for MMP-9 concentration, which was obtained through cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The ZnO nanorod-based biosensor exhibited linear behavior in the MMP-9 concentration range of 1–1000 ng/ml, which is a wider range than the available concentration ranges for most of the conventional methods. The biosensor sensitivity was 32.5 μA/(decade × cm2)...
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...