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Piranej S, Zhang L, Bazrafshan A, Marin M, Melikyan GB, Salaita K. Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530294. [PMID: 36909543 PMCID: PMC10002644 DOI: 10.1101/2023.02.27.530294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a "mechanical test" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | - Luona Zhang
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
| | | | - Mariana Marin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322 (USA)
- Children’s Healthcare of Atlanta, Atlanta, Georgia 30322 (USA)
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322 (USA)
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322 (USA)
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2
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Fopase R, Panda C, Rajendran AP, Uludag H, Pandey LM. Potential of siRNA in COVID-19 therapy: Emphasis on in silico design and nanoparticles based delivery. Front Bioeng Biotechnol 2023; 11:1112755. [PMID: 36814718 PMCID: PMC9939533 DOI: 10.3389/fbioe.2023.1112755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023] Open
Abstract
Small interfering RNA (siRNA)-mediated mRNA degradation approach have imparted its eminence against several difficult-to-treat genetic disorders and other allied diseases. Viral outbreaks and resulting pandemics have repeatedly threatened public health and questioned human preparedness at the forefront of drug design and biomedical readiness. During the recent pandemic caused by the SARS-CoV-2, mRNA-based vaccination strategies have paved the way for a new era of RNA therapeutics. RNA Interference (RNAi) based approach using small interfering RNA may complement clinical management of the COVID-19. RNA Interference approach will primarily work by restricting the synthesis of the proteins required for viral replication, thereby hampering viral cellular entry and trafficking by targeting host as well as protein factors. Despite promising benefits, the stability of small interfering RNA in the physiological environment is of grave concern as well as site-directed targeted delivery and evasion of the immune system require immediate attention. In this regard, nanotechnology offers viable solutions for these challenges. The review highlights the potential of small interfering RNAs targeted toward specific regions of the viral genome and the features of nanoformulations necessary for the entrapment and delivery of small interfering RNAs. In silico design of small interfering RNA for different variants of SARS-CoV-2 has been discussed. Various nanoparticles as promising carriers of small interfering RNAs along with their salient properties, including surface functionalization, are summarized. This review will help tackle the real-world challenges encountered by the in vivo delivery of small interfering RNAs, ensuring a safe, stable, and readily available drug candidate for efficient management of SARS-CoV-2 in the future.
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Affiliation(s)
- Rushikesh Fopase
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Chinmaya Panda
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - Amarnath P. Rajendran
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada
| | - Hasan Uludag
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB, Canada,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada,Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
| | - Lalit M. Pandey
- Bio-Interface & Environmental Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India,*Correspondence: Lalit M. Pandey, ; Hasan Uludag,
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3
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Li J, Zhang Z, Gu J, Amini R, Mansfield AG, Xia J, White D, Stacey HD, Ang JC, Panesar G, Capretta A, Filipe CDM, Mossman K, Salena BJ, Gubbay JB, Balion C, Soleymani L, Miller MS, Yamamura D, Brennan JD, Li Y. Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer. J Am Chem Soc 2022; 144:23465-23473. [PMID: 36520671 PMCID: PMC9762500 DOI: 10.1021/jacs.2c09870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 12/23/2022]
Abstract
Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 103 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.
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Affiliation(s)
- Jiuxing Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Zijie Zhang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jimmy Gu
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Ryan Amini
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alexandria G. Mansfield
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jianrun Xia
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Dawn White
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Hannah D. Stacey
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jann C. Ang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Gurpreet Panesar
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alfredo Capretta
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Carlos D. M. Filipe
- Department
of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Karen Mossman
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Bruno J. Salena
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | | | - Cynthia Balion
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Leyla Soleymani
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Matthew S. Miller
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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Yang LF, Kacherovsky N, Liang J, Salipante SJ, Pun SH. SCORe: SARS-CoV-2 Omicron Variant RBD-Binding DNA Aptamer for Multiplexed Rapid Detection and Pseudovirus Neutralization. Anal Chem 2022; 94:12683-12690. [PMID: 35972202 PMCID: PMC9397568 DOI: 10.1021/acs.analchem.2c01993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/03/2022] [Indexed: 01/18/2023]
Abstract
During the COVID-19 (coronavirus disease 2019) pandemic, several SARS-CoV-2 variants of concern emerged, including the Omicron variant, which has enhanced infectivity and immune invasion. Many antibodies and aptamers that bind the spike (S) of previous strains of SARS-CoV-2 either do not bind or bind with low affinity to Omicron S. In this study, we report a high-affinity SARS-CoV-2 Omicron RBD-binding aptamer (SCORe) that binds Omicron BA.1 and BA.2 RBD with nanomolar KD1. We employ aptamers SCORe.50 and SNAP4.74 in a multiplexed lateral flow assay (LFA) to distinguish between Omicron and wild-type S at concentrations as low as 100 pM. Finally, we show that SCORe.50 and its dimerized form SCOReD can neutralize Omicron S-pseudotyped virus infection of ACE2-overexpressing cells by >70%. SCORe therefore has potential applications in COVID-19 rapid diagnostics as well as in viral neutralization.
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Affiliation(s)
- Lucy F. Yang
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | - Joey Liang
- Department of Bioengineering, University of Washington, Seattle, WA 98195
| | | | - Suzie H. Pun
- Department of Bioengineering, University of Washington, Seattle, WA 98195
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5
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Silwal AP, Thennakoon SKS, Arya SP, Postema RM, Jahan R, Phuoc CMT, Tan X. DNA aptamers inhibit SARS-CoV-2 spike-protein binding to hACE2 by an RBD- independent or dependent approach. Theranostics 2022; 12:5522-5536. [PMID: 35910791 PMCID: PMC9330529 DOI: 10.7150/thno.74428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022] Open
Abstract
Objective: Nobody knows when the COVID-19 pandemic will end or when and where the next coronavirus will outbreak. Therefore, it is still necessary to develop SARS-CoV-2 inhibitors for different variants or even the new coronavirus. Since SARS-CoV-2 uses its surface spike-protein to recognize hACE2, mediating its entry into cells, ligands that can specifically recognize the spike-protein have the potential to prevent infection. Methods: We have recently discovered DNA aptamers against the S2-domain of the WT spike-protein by exploiting the selection process called SELEX. After optimization, among all candidates, the aptamer S2A2C1 has the shortest sequence and the best binding affinity toward the S2-protein. More importantly, the S2A2C1 aptamer does not bind to the RBD of the spike-protein, but it efficiently blocks the spike-protein/hACE2 interaction, suggesting an RBD-independent inhibition approach. To further improve its performance, we conjugated the S2A2C1 aptamer with a reported anti-RBD aptamer, S1B6C3, using various linkers and constructed hetero-bivalent fusion aptamers. Binding affinities of mono and fusion aptamers against the spike-proteins were measured. The inhibition efficacies of mono and fusion aptamers to prevent the hACE2/spike-protein interaction were determined using ELISA. Results: Anti-spike-protein aptamers, including S2A2C1 and S1B6C3-A5-S2A2C1, maintained high binding affinity toward the WT, Delta, and Omicron spike-proteins and high inhibition efficacies to prevent them from binding to hACE2, rendering them well-suited as diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants. Conclusions: Overall, we discovered the anti-S2 aptamer, S2A2C1, which inhibits the hACE2/spike-protein interaction via an RBD-independent approach. The anti-S2 and anti-RBD aptamers were conjugated to obtain the fusion aptamer, S1B6C3-A5-S2A2C1, which recognizes the spike-protein by an RBD-dependent approach. Our strategies, which discovered aptamer inhibitors targeting the highly conserved S2-protein, as well as the design of fusion aptamers, can be used to target new coronaviruses as they emerge.
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Affiliation(s)
| | | | | | | | | | | | - Xiaohong Tan
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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6
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Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, Li Y. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern. Chemistry 2022; 28:e202200524. [PMID: 35218097 PMCID: PMC9086990 DOI: 10.1002/chem.202200524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Invited for the cover of this issue are John Brennan, Yingfu Li, and co‐workers at McMaster University. The image depicts MSA52 as a universal DNA aptamer that recognizes spike proteins of diverse SARS‐CoV‐2 variants of concern. Read the full text of the article at 10.1002/chem.202200078.
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Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Hannah D Stacey
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Jann C Ang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Dawn White
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Karen Mossman
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Payel Sen
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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