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    Development of simple and efficient Lab-on-a-Disc platforms for automated chemical cell lysis

    , Article Scientific Reports ; Volume 10, Issue 1 , 6 July , 2020 Khorrami Jahromi, A ; Saadatmand, M ; Eghbal, M ; Parsa Yeganeh, L ; Sharif University of Technology
    Nature Research  2020
    Abstract
    Cell lysis is the most important first step for molecular biology and diagnostic testing. Recently, microfluidic systems have attracted considerable attention due to advantages associated with automation, integration and miniaturization, especially in resource-limited settings. In this work, novel centrifugal microfluidic platforms with new configurations for chemical cell lysis are presented. The developed systems employ passive form of pneumatic and inertial forces for effective mixing of lysis reagents and cell samples as well as precise fluidic control. Characterizations of the developed Lab-on-a-Discs (LoaDs) have been conducted with dyed deionized (DI) waters and white blood cells... 

    A large dataset of white blood cells containing cell locations and types, along with segmented nuclei and cytoplasm

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Kouzehkanan, Z. M ; Saghari, S ; Tavakoli, S ; Rostami, P ; Abaszadeh, M ; Mirzadeh, F ; Satlsar, E. S ; Gheidishahran, M ; Gorgi, F ; Mohammadi, S ; Hosseini, R ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Accurate and early detection of anomalies in peripheral white blood cells plays a crucial role in the evaluation of well-being in individuals and the diagnosis and prognosis of hematologic diseases. For example, some blood disorders and immune system-related diseases are diagnosed by the differential count of white blood cells, which is one of the common laboratory tests. Data is one of the most important ingredients in the development and testing of many commercial and successful automatic or semi-automatic systems. To this end, this study introduces a free access dataset of normal peripheral white blood cells called Raabin-WBC containing about 40,000 images of white blood cells and color... 

    High-throughput, label-free isolation of white blood cells from whole blood using parallel spiral microchannels with u-shaped cross-section

    , Article Biosensors ; Volume 11, Issue 11 , 2021 ; 20796374 (ISSN) Mehran, A ; Rostami, P ; Saidi, M. S ; Firoozabadi, B ; Kashaninejad, N ; Sharif University of Technology
    MDPI  2021
    Abstract
    Rapid isolation of white blood cells (WBCs) from whole blood is an essential part of any WBC examination platform. However, most conventional cell separation techniques are labor-intensive and low throughput, require large volumes of samples, need extensive cell manipulation, and have low purity. To address these challenges, we report the design and fabrication of a passive, label-free microfluidic device with a unique U-shaped cross-section to separate WBCs from whole blood using hydrodynamic forces that exist in a microchannel with curvilinear geometry. It is shown that the spiral microchannel with a U-shaped cross-section concentrates larger blood cells (e.g., WBCs) in the inner... 

    Prediction of HLA-Peptide Binding using 3D Structural Features

    , M.Sc. Thesis Sharif University of Technology Bagh Golshani, Marjan (Author) ; Sharifi Zarchi, Ali (Supervisor)
    Abstract
    The human leukocyte antigen protein, commonly known as HLA, has the ability to present small protein fragments called peptides on the surface of cells, whether they originate from within the cell or externally. The binding of these peptides to HLA receptors is a crucial step that triggers an immune response. By estimating the affinity between peptides and HLA class I, we can identify novel antigens that have the potential to be targeted by cancer therapeutic vaccines. Computational methods that predict the binding affinity between peptides and HLA receptors have the potential to expedite the design process of cancer vaccines. Currently, most computational methods exclusively rely on... 

    A Data-Driven Optimization Methodology to Improve Unmatched Pairs Assignment in Kidney Exchange Problem

    , M.Sc. Thesis Sharif University of Technology Dadashi, Hossein (Author) ; Najafi, Mahdi (Supervisor) ; Rafiee, Majid (Supervisor)
    Abstract
    One of the most common and effective ways to treat end-stage renal disease is the use of kidney exchange techniques. However, the main problem with this treatment is the presence of many barriers to allocating kidney pairs to each other, which reduces the success of kidney transplants. Among different types of kidney transplantation methods, the present study utilizes kidney transplantation cycles to develop the allocation of unmatched pairs in kidney transplantation using a data-driven optimization technique. In this study, HLA patients were considered as simulated and also a two-objective model in the kidney exchange network was designed to maximize the probability of kidney... 

    Distinct dynamics of migratory response to pd-1 and ctla-4 blockade reveals new mechanistic insights for potential t-cell reinvigoration following immune checkpoint blockade

    , Article Cells ; Volume 11, Issue 22 , 2022 ; 20734409 (ISSN) Safaeifard, F ; Goliaei, B ; Aref, A. R ; Foroughmand-Araabi, M. H ; Goliaei, S ; Lorch, J ; Jenkins, R. W ; Barbie, D. A ; Shariatpanahi, S. P ; Rüegg, C ; Sharif University of Technology
    MDPI  2022
    Abstract
    Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1), two clinically relevant targets for the immunotherapy of cancer, are negative regulators of T-cell activation and migration. Optimizing the therapeutic response to CTLA-4 and PD-1 blockade calls for a more comprehensive insight into the coordinated function of these immune regulators. Mathematical modeling can be used to elucidate nonlinear tumor–immune interactions and highlight the underlying mechanisms to tackle the problem. Here, we investigated and statistically characterized the dynamics of T-cell migration as a measure of the functional response to these pathways. We used a previously... 

    Investigation of a two-step device implementing magnetophoresis and dielectrophoresis for separation of circulating tumor cells from blood cells

    , Article Engineering in Life Sciences ; Volume 20, Issue 7 , 2020 , Pages 296-304 Shamloo, A ; Yazdani, A ; Saghafifar, F ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Identifying tumor cells from a pool of other cells has always been an appealing topic for different purposes. The objective of this study is to discriminate circulating tumor cells (CTCs) from blood cells for diagnostic purposes in a novel microfluidic device using two active methods: magnetophoresis and dielectrophoresis. The most specific feature of this device is the differentiation of CTCs without labeling them in order to achieve a more reliable and less complicated method. This device was analyzed and evaluated using finite element method. Four cell lines are separated in this device containing red blood cells, platelets, white blood cells, and CTCs. Primarily, red blood cells and... 

    Association between human leukocyte antigens and cutaneous adverse drug reactions to antiepileptics and antibiotics in the Iranian population

    , Article Dermatologic Therapy ; Volume 35, Issue 5 , 2022 ; 13960296 (ISSN) Mortazavi, H ; Rostami, A ; Firooz, A ; Esmaili, N ; Ghiasi, M ; Lajevardi, V ; Amirzargar, A. A ; Sheykhi, I ; Khamesipour, A ; Akhdar, M ; Sharif University of Technology
    John Wiley and Sons Inc  2022
    Abstract
    In this case–control study, class І and ІІ human leukocyte antigen (HLA) alleles in Iranian patients with benign and severe cutaneous adverse drug reactions (CADRs) due to aromatic anticonvulsants and antibiotics were evaluated. Patients diagnosed with CADRs (based on clinical and laboratory findings) with a Naranjo score of ≥ 4 underwent blood sampling and HLA-DNA typing. The control group comprised 90 healthy Iranian adults. Alleles with a frequency of more than two were reported. Deviations from Hardy–Weinberg equilibrium were not observed. Eighty patients with CADRs including 54 females and 26 males with a mean age of 41.49 ± 16.08 years were enrolled in this study. The culprit drugs... 

    Numerical analysis of a dielectrophoresis field-flow fractionation device for the separation of multiple cell types

    , Article Journal of Separation Science ; Volume 40, Issue 20 , 2017 , Pages 4067-4075 ; 16159306 (ISSN) Shamloo, A ; Kamali, A ; Sharif University of Technology
    Abstract
    In this study, a dielectrophoresis field-flow fractionation device was analyzed using a numerical simulation method and the behaviors of a set of different cells were investigated. By reducing the alternating current frequency of the electrodes from the value used in the original setup configuration and increasing the number of exit channels, total discrimination in cell trajectories and subsequent separation of four cell types were achieved. Cells were differentiated based on their size and dielectric response that are represented in their real part of Clausius–Mossotti factor at different frequencies. A number of novel designs were also proposed based on the original setup configuration.... 

    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... 

    Personalised deposition maps for micro- and nanoparticles targeting an atherosclerotic plaque: attributions to the receptor-mediated adsorption on the inflamed endothelial cells

    , Article Biomechanics and Modeling in Mechanobiology ; Volume 18, Issue 3 , 2019 , Pages 813-828 ; 16177959 (ISSN) Shamloo, A ; Forouzandehmehr, M ; Sharif University of Technology
    Springer Verlag  2019
    Abstract
    Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer...