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    Hybrid multiscale modeling and prediction of cancer cell behavior

    , Article PLoS ONE ; Volume 12, Issue 8 , 2017 ; 19326203 (ISSN) Zangooei, M. H ; Habibi, J ; Sharif University of Technology
    Public Library of Science  2017
    Abstract
    Background: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for... 

    Atomic scale interactions between RNA and DNA aptamers with the TNF- α protein

    , Article BioMed Research International ; Volume 2021 , 2021 ; 23146133 (ISSN) Asadzadeh, H ; Moosavi, A ; Alexandrakis, G ; Mofrad, M. R. K ; Sharif University of Technology
    Hindawi Limited  2021
    Abstract
    Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

    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) Delfino, R. J ; 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... 

    Detection and a possible link between parvovirus B19 and thyroid cancer

    , Article Tumor Biology ; Volume 39, Issue 6 , 2017 ; 10104283 (ISSN) Etemadi, A ; Mostafaei, S ; Yari, K ; Ghasemi, A ; Chenar, H. M ; Moghoofei, M ; Sharif University of Technology
    Abstract
    Human parvovirus B19 (B19) is a small, non-enveloped virus and belongs to Parvoviridae family. B19 persists in many tissues such as thyroid tissue and even thyroid cancer. The main aim of this study was to determine the presence of B19, its association with increased inflammation in thyroid tissue, and thus its possible role in thyroid cancer progression. Studies have shown that virus replication in non-permissive tissue leads to overexpression of non-structural protein and results in upregulation of proinflammatory cytokines such as interleukin 6 and tumor necrosis factor alpha. A total of 36 paraffin-embedded thyroid specimens and serum were collected from patients and 12 samples were used... 

    Seasonal variations in the oxidative stress and inflammatory potential of PM2.5 in Tehran using an alveolar macrophage model; The role of chemical composition and sources

    , Article Environment International ; Volume 123 , 2019 , Pages 417-427 ; 01604120 (ISSN) Al Hanai, A. H ; Antkiewicz, D. S ; Hemming, J. D. C ; Shafer, M. M ; Lai, A. M ; Arhami, M ; Hosseini, V ; Schauer, J. J ; Sharif University of Technology
    Elsevier Ltd  2019
    Abstract
    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)... 

    Short-term effects of particle size fractions on circulating biomarkers of inflammation in a panel of elderly subjects and healthy young adults

    , Article Environmental Pollution ; Volume 223 , 2017 , Pages 695-704 ; 02697491 (ISSN) Hassanvand, M. S ; Naddafi, K ; Kashani, H ; Faridi, S ; Kunzli, N ; Nabizadeh, R ; Momeniha, F ; Gholampour, A ; Arhami, M ; Zare, A ; Pourpak, Z ; Hoseini, M ; Yunesian, M ; Sharif University of Technology
    Abstract
    Systemic inflammation biomarkers have been associated with risk of cardiovascular morbidity and mortality. We aimed to clarify associations of acute exposure to particulate matter (PM10(PM < 10 μm), PM2.5-10(PM 2.5–10 μm), PM2.5(PM < 2.5 μm), PM1-2.5(PM 1–2.5 μm), and PM1 (PM < 1 μm)) with systemic inflammation using panels of elderly subjects and healthy young adults. We followed a panel of 44 nonsmoking elderly subjects living in a retirement home and a panel of 40 healthy young adults living in a school dormitory in Tehran city, Iran from May 2012 to May 2013. Blood biomarkers were measured one every 7–8 weeks and included white blood cells (WBC), high sensitive C-reactive protein... 

    Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis

    , Article BMC Medical Genomics ; Volume 12, Issue 1 , 2019 ; 17558794 (ISSN) Karimizadeh, E ; Sharifi Zarchi, A ; Nikaein, H ; Salehi, S ; Salamatian, B ; Elmi, N ; Gharibdoost, F ; Mahmoudi, M ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    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... 

    Effect of synthesis temperature of magnetic–fluorescent nanoparticles on properties and cellular imaging

    , Article Journal of Inorganic and Organometallic Polymers and Materials ; Volume 30, Issue 11 , 2020 , Pages 4597-4605 Sahebalzamani, H ; Mehrani, K ; Madaah Hosseini, H. R ; Zare, K ; Sharif University of Technology
    Springer  2020
    Abstract
    The excellent photoluminescent properties of Fe3O4-graphene quantum dots (Fe3O4/GQD) nanoparticles prepared at 30 and 90 °C have made them as promising optical probes for imaging. Herein, the cytotoxicity of GQD and Fe3O4/GQD nanoparticles in L929 cells was investigated using MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromide] assay. The cellular apoptosis or necrosis was then evaluated by flow cytometry analysis. The Fe3O4/GQD nanoparticles were characterized by transmission electron microscopy (TEM), Raman spectroscopy (Raman), Fourier-transform infrared spectroscopy (FT-IR), photoluminescence (PL). Characterization results obtained, clearly show that Fe3O4/GQD nanoparticles... 

    Expression analysis of cytokine transcripts in inflammatory demyelinating polyradiculoneuropathy

    , Article Metabolic Brain Disease ; Volume 36, Issue 7 , 2021 , Pages 2111-2118 ; 08857490 (ISSN) Nicknafs, F ; 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... 

    Fullerene C60 nanoparticle attenuates pain and tumor necrosis factor-α protein expression in the hippocampus following diabetic neuropathy in rats

    , Article Physiology and Pharmacology (Iran) ; Volume 26, Issue 4 , 2022 , Pages 451-458 ; 24765236 (ISSN) Namdar, F ; Bahrami, F ; Bahari, Z ; Ghanbari, B ; Shahyad, S ; Mohammadi, M. T ; Sharif University of Technology
    Iranian Society of Physiology and Pharmacology  2022
    Abstract
    Introduction: Diabetic neuropathy is a common complication of diabetes mellitus. It is associated with nerve damage due to oxidative stress and high levels of pro-inflammatory mediators. In the present study, we examined the anti-nociceptive effects of Fullerene nanoparticle, as a potent anti-oxidant, during diabetic neuropathy. Methods: Diabetes mellitus induced through injection of streptozotocin (STZ) (40 mg/kg). Four groups were used in the study as follows: the control, control+fullerene, diabetes, and diabetes +fullerene groups. All four groups received sesame oil. Treatment rats received fullerene C60 (1mg/kg/day) for 9 weeks by intra-gastric gavage. Then, cold allodynia, histology,... 

    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) Chashmniam, S ; 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... 

    Human papilloma virus and breast cancer: The role of inflammation and viral expressed proteins

    , Article BMC Cancer ; Volume 19, Issue 1 , 2019 ; 14712407 (ISSN) Khodabandehlou, N ; Mostafaei, S ; Etemadi, A ; Ghasemi, A ; Payandeh, M ; Hadifar, S ; Norooznezhad, A. H ; Kazemnejad, A ; Moghoofei, M ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Background: Breast cancer is currently the most common neoplasm diagnosed in women globally. There is a growing body of evidence to suggest that human papillomavirus (HPV) infection may play a key role in invasiveness of breast cancer. The aim of this study was to determine the presence of HPV in patients with breast cancer and its possible association with cancer progression. Methods: Breast specimens were collected from 72 patients with breast cancer and 31 healthy controls. The presence of HPV was investigated by polymerase chain reaction (PCR) and genotyping was performed for positive cases. We also evaluated the viral factors such as E6, E2, and E7 in HPV positive cases. Enzyme-linked...