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Quantitative Evaluation of Very Low Levels of HIV-1 Reverse Transcriptase by a Novel Highly Sensitive RT-qPCR Assay. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081130. [PMID: 36013309 PMCID: PMC9410348 DOI: 10.3390/life12081130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Based on previous experience in our laboratory, we developed a real-time reverse transcriptase (RT) quantitative PCR (RT-qPCR) assay for the assessment of very low levels of HIV-1 RT activity. The RNA, acting as a template for reverse transcription into cDNA by HIV-1 RT, consisted of a synthetic RNA ad hoc generated by in vitro transcription and included a coding sequence for HSV-1 gD (gD-RNA-synt). Different conditions of variables involved in the RT-qPCR reaction, notably different amounts of gD-RNA-synt, different mixes of the reaction buffer, and different dNTP concentrations, were tested to optimize the assay. The results indicated that the gD-RNA-synt-based RT assay, in its optimized formulation, could detect a specific cDNA reverse transcription even in the presence of 1 × 10-9 U of HIV RT. This achievement greatly improved the sensitivity of the assay over previous versions. In summary, this constructed RT-qPCR assay may be considered a promising tool for providing accurate information on very low HIV-1 RT activity.
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Zhang JY, Zhang Y, Bender AT, Sullivan BP, Olanrewaju AO, Lillis L, Boyle D, Drain PK, Posner JD. HIV pre-exposure prophylaxis adherence test using reverse transcription isothermal amplification inhibition assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1361-1370. [PMID: 35297917 PMCID: PMC8991996 DOI: 10.1039/d2ay00008c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Current HIV antiretroviral therapy (ART) or pre-exposure prophylaxis (PrEP) therapy adherence monitoring relies on either patient self-reported adherence or monitored drug dispensing, which are not reliable. We report a proof-of-concept adherence monitoring assay which directly measures nucleotide reverse transcriptase inhibitor (NRTI) concentration using a reverse transcription isothermal amplification inhibition assay. We measure the concentration of Tenofovir diphosphate (TFV-DP) - an NRTI that functions as a deoxyadenosine triphosphate (dATP) analog and long-term adherence marker for PrEP - by measuring the inhibition of the reverse transcription of an RNA template. The completion or inhibition of reverse transcription is evaluated by recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification assay commonly used for point-of-care diagnostics. We present and validate a model that predicts the amplification probability as a function of dATP and TFV-DP concentrations, nucleotide insertion sites on the RNA template, and RNA template concentration. The model can be used to rationally design and optimize the assay to operate at clinically relevant TFV-DP concentrations. We provide statistical analysis that demonstrates how the assay may be used as a qualitative or semi-quantitative tool for measuring adherence to NRTI drugs and used to support patient compliance. Due to its simple instrumentation and short runtime (<1 hour), this assay has the potential for implementation in low-complexity laboratories or point-of-care settings, which may improve access to ART and PrEP adherence monitoring.
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Affiliation(s)
- Jane Y Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | - Yu Zhang
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
| | | | | | | | - Paul K Drain
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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Mouliou DS, Gourgoulianis KI. False-positive and false-negative COVID-19 cases: respiratory prevention and management strategies, vaccination, and further perspectives. Expert Rev Respir Med 2021; 15:993-1002. [PMID: 33896332 PMCID: PMC8074645 DOI: 10.1080/17476348.2021.1917389] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Introduction: A novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reported via nucleic acid identification in December, 2019. Accuracy of SARS-CoV-2 diagnostic assays has emerged as a major barrier to COVID-19 diagnosis, particularly in cases requiring urgent or emergent treatment. Areas covered: In this review, we explore the major reasons for false-positive and false-negative SARS-CoV-2 test results. How clinical characteristics, specific respiratory comorbidities and SARS-CoV-2 vaccination impact on existing diagnostic assays are highlighted. Different COVID-19 management algorithms based on each test and limitations are thoroughly presented. Expert opinion: The diagnostic accuracy and the capacity of every available assay, which need to be interpreted in the light of the background incidence of SARS-CoV-2 infection in the communities in which they are used, are essential in order to minimize the number of falsely tested cases. Automated testing platforms may enhance diagnostic accuracy by minimizing the potential for human error in assays’ performance. Prior immunization against SARS-CoV-2 impairs the utility of serologic testing of suspected COVID-19 cases. Future avenues of research to evaluate lung tissue innate immune responses hold promise as a target for research to optimize SARS-CoV-2 and future infections’ testing accuracy.
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Affiliation(s)
- Dimitra S Mouliou
- Department of Respiratory Medicine, University of Thessaly, Larissa, Greece
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Sistani P, Dehghan G, Sadeghi L. Structural and kinetic insights into HIV-1 reverse transcriptase inhibition by farnesiferol C. Int J Biol Macromol 2021; 174:309-318. [PMID: 33524481 DOI: 10.1016/j.ijbiomac.2021.01.173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 01/09/2023]
Abstract
Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is the key enzyme for the virus gene replication and the most important target for antiviral therapy. Toxicity, drug resistance and side effects have led to search for new antiviral agents. Farnesiferol C (FC) is a well-known biologically active sesquiterpene coumarin derivative from genus Ferula. The current study was designed to examine the impacts of FC on the structure and function of HIV-1 RT, using some theoretical and experimental methods. FC inhibited HIV-1RT activity via mixed inhibition mechanism (IC50 = 30 μM). Spectroscopic data showed some conformational changes in the secondary as well as tertiary structure of HIV-1RT following the interaction with FC. Results showed that FC could quench the intrinsic fluorescence emission of HIV-1RT through static quenching mechanism. Thermodynamic parameters revealed that hydrogen bondings and van der Waals forces are the major forces in the binding reaction and the low equilibrium constants (KD) value obtained from surface plasmon resonance data, confirmed the high affinity of FC for HIV-1RT. Molecular docking studies indicated that FC interacts with enzyme through hydrophobic pocket. Taken together, the outcomes of this research revealed that, sesquiterpene coumarines can be used to design natural remedies as anti-HIV agents.
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Affiliation(s)
- Parisa Sistani
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Gholamreza Dehghan
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Leila Sadeghi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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Macchi B, Frezza C, Marino-Merlo F, Minutolo A, Stefanizzi V, Balestrieri E, Cerva C, Sarmati L, Andreoni M, Grelli S, Mastino A. Appraisal of a Simple and Effective RT-qPCR Assay for Evaluating the Reverse Transcriptase Activity in Blood Samples from HIV-1 Patients. Pathogens 2020; 9:pathogens9121047. [PMID: 33322208 PMCID: PMC7763350 DOI: 10.3390/pathogens9121047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
Testing HIV-1 RNA in plasma by PCR is universally accepted as the ultimate standard to confirm diagnosis of HIV-1 infection and to monitor viral load in patients under treatment. However, in some cases, this assay could either underestimate or overestimate the replication capacity of a circulating or latent virus. In the present study, we performed the assessment of evaluating the HIV-1 reverse transcriptase (RT) activity by means of a new assay for the functional screening of the status of HIV-1 patients. To this purpose, we utilized, for the first time on blood samples, an adapted version of a real-time RT quantitative PCR assay, utilized to evaluate the HIV-1-RT inhibitory activity of compounds. The study analyzed blood samples from 28 HIV-1-infected patients, exhibiting a wide range of viremia and immunological values. Results demonstrated that plasma HIV-1 RT levels, expressed as cycle threshold values obtained with the assay under appraisal, were inversely and highly significantly correlated with the plasma HIV-1-RNA levels of the patients. Thus, an HIV-1 RT quantitative PCR assay was created which we describe in this study, and it may be considered as a promising basis for an additional tool capable of furnishing information on the functional virological status of HIV-1-infected patients.
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Affiliation(s)
- Beatrice Macchi
- Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Caterina Frezza
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
| | - Francesca Marino-Merlo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy;
| | - Antonella Minutolo
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Valeria Stefanizzi
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
| | - Carlotta Cerva
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Loredana Sarmati
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (C.F.); (C.C.); (L.S.); (M.A.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.M.); (V.S.); (E.B.); (S.G.)
- Tor Vergata University Hospital, 00133 Rome, Italy
| | - Antonio Mastino
- The Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-3388658161
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Olanrewaju AO, Sullivan BP, Zhang JY, Bender AT, Sevenler D, Lo TJ, Fernandez-Suarez M, Drain PK, Posner JD. Enzymatic Assay for Rapid Measurement of Antiretroviral Drug Levels. ACS Sens 2020; 5:952-959. [PMID: 32248685 PMCID: PMC7183420 DOI: 10.1021/acssensors.9b02198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Poor adherence to pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) can lead to human immunodeficiency virus (HIV) acquisition and emergence of drug-resistant infections, respectively. Measurement of antiviral drug levels provides objective adherence information that may help prevent adverse health outcomes. Gold-standard drug-level measurement by liquid chromatography/mass spectrometry is centralized, heavily instrumented, and expensive and is thus unsuitable and unavailable for routine use in clinical settings. We developed the REverSe TRanscrIptase Chain Termination (RESTRICT) assay as a rapid and accessible measurement of drug levels indicative of long-term adherence to PrEP and ART. The assay uses designer single-stranded DNA templates and intercalating fluorescent dyes to measure complementary DNA (cDNA) formation by reverse transcriptase in the presence of nucleotide reverse transcriptase inhibitor drugs. We optimized the RESTRICT assay using aqueous solutions of tenofovir diphosphate (TFV-DP), a metabolite that indicates long-term adherence to ART and PrEP, at concentrations over 2 orders of magnitude above and below the clinically relevant range. We used dilution in water as a simple sample preparation strategy to detect TFV-DP spiked into whole blood and accurately distinguished TFV-DP drug levels corresponding to low and high PrEP adherences. The RESTRICT assay is a fast and accessible test that could be useful for patients and clinicians to measure and improve ART and PrEP adherence.
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Affiliation(s)
| | | | - Jane Y. Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, USA
| | - Andrew T. Bender
- Department of Mechanical Engineering, University of Washington, Seattle, USA
| | - Derin Sevenler
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Tiffany J. Lo
- Department of Materials Science & Engineering, University of Washington, Seattle
| | | | - Paul K. Drain
- Department of Epidemiology, University of Washington, Seattle
- Department of Global Health, University of Washington, Seattle
- Department of Medicine, University of Washington, Seattle
| | - Jonathan D. Posner
- Department of Mechanical Engineering, University of Washington, Seattle, USA
- Department of Chemical Engineering, University of Washington, Seattle
- Department of Family Medicine, University of Washington, Seattle
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Chen J, Zhao Z, Chen Y, Zhang J, Yan L, Zheng X, Liao M, Cao W. Development and application of a SYBR green real-time PCR for detection of the emerging avian leukosis virus subgroup K. Poult Sci 2018; 97:2568-2574. [PMID: 29617900 PMCID: PMC6016701 DOI: 10.3382/ps/pey086] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/19/2018] [Indexed: 12/23/2022] Open
Abstract
Avian leukosis virus subgroup K (ALV-K) is an emerging ALV tumor virus of chickens. We developed a SYBR green-based real-time polymerase chain reaction (PCR) assay for the rapid and economical detection of ALV-K in chicken flocks. The assay was specific for ALV-K and did not cross-react with other ALV subgroup or avian influenza virus, Newcastle disease virus, or Marek's Disease virus. The method was 100 times more sensitive than conventional PCR and 10 times more sensitive than the enzyme-linked immunosorbent assay (ELISA) for the P27 antigen. The assay was also more sensitive than conventional PCR in tests of 86 clinical plasma samples. DF-1 tissue culture cells infected with 1 TCID50 ALV-K particle were identified as negative using ELISA but tested positive with the real-time PCR method. The viral loads in organs and tissues in infected chickens were highest in kidney, lungs, and glandular stomach, and these results matched ELISA findings.
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Affiliation(s)
- Jian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Zijun Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Yangyijun Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Jie Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Lifu Yan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Xiaocui Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China.,Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture.,South China Collaborative Innovation Center for Prevention and Control of Poultry Infectious Diseases and Safety of Poultry Products, Guangzhou, People's Republic of China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, People's Republic of China
| | - Weisheng Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, People's Republic of China.,Key Laboratory of Veterinary Vaccine Innovation of the Ministry of Agriculture.,South China Collaborative Innovation Center for Prevention and Control of Poultry Infectious Diseases and Safety of Poultry Products, Guangzhou, People's Republic of China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, People's Republic of China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, People's Republic of China
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Marino-Merlo F, Macchi B, Armenia D, Bellocchi MC, Ceccherini-Silberstein F, Mastino A, Grelli S. Focus on recently developed assays for detection of resistance/sensitivity to reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2018; 102:9925-9936. [PMID: 30269214 DOI: 10.1007/s00253-018-9390-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022]
Abstract
The biology of HIV is rather complex due to high rate of replication, frequent recombination, and introduction of mutations. This gives rise to a number of distinct variants referred as quasispecies. In addition, the latency within reservoir allows the periodic reactivation of virus replication. The rapid replication of HIV allows immune response escape and establishment of resistance to therapy that can be acquired through drug selection and/or transmitted among individuals. This prompted, over the years, the development of a range of assays aimed to determine drug resistance and sensitivity, to be used both in clinical practice and in antiviral research. Reverse transcriptase (RT) inhibitors have an eminent place among the anti-HIV drugs, being constantly present from the beginning until today in the most commonly used antiviral regimens. This mini-review seeks to provide an up-to-date overview of recent efforts in developing even more reliable and simple methods, of both genotypic and phenotypic types, for specifically detecting drug resistance and sensitivity to RT inhibitors.
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Affiliation(s)
| | - Beatrice Macchi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Antonio Mastino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Via F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,The Institute of Translational Pharmacology, CNR, Rome, Italy.
| | - Sandro Grelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
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DeStefano JJ, Alves Ferreira-Bravo I. A highly sensitive aptamer-based HIV reverse transcriptase detection assay. J Virol Methods 2018; 257:22-28. [PMID: 29630943 DOI: 10.1016/j.jviromet.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
Although many new assays for HIV have been developed, several labs still use simple and reliable radioactivity-based reverse transcriptase (RT) nucleotide incorporation assays for detection and quantification. We describe here a new assay for detection and quantitation of HIV RT activity that is based on a high affinity DNA aptamer to RT. The aptamer is sequestered on 96-well plates where it can bind to RT and other constituents can be removed by extensive washing. Since the aptamer mimics a primer-template, upon radiolabeled nucleotide addition, bound RT molecules can extend the aptamer and the radioactive signal can be detected by standard methods. In addition to being procedurally simple, the assay demonstrated high sensitivity (detection limits for RT and virions were ≤6400 molecules (∼4 × 10-8 units) and ∼100-300 virions, respectively) and was essentially linear over a range of at least 104. Both wild type and drug-resistant forms of HIV-1 RT were detectable as was HIV-2 RT, although there were some modest differences in sensitivity.
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Affiliation(s)
- Jeffrey J DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States; The Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States.
| | - Irani Alves Ferreira-Bravo
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States; The Maryland Pathogen Research Institute, University of Maryland, College Park, MD, United States
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