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Wielgoss S, Van Dyken JD, Velicer GJ. Mutation Rate and Effective Population Size of the Model Cooperative Bacterium Myxococcus xanthus. Genome Biol Evol 2024; 16:evae066. [PMID: 38526062 PMCID: PMC11069108 DOI: 10.1093/gbe/evae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here, we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation accumulation experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life cycle-such as group-size reduction during fruiting-body development-or its highly structured spatial distribution have significantly influenced how these parameters have evolved.
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Affiliation(s)
- Sébastien Wielgoss
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - James David Van Dyken
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Gregory J Velicer
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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2
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Ouellet V, Erickson A, Wiley K, Morrissey C, Berge V, Moreno CS, Tasken KA, Trudel D, True LD, Lewis MS, Svindland A, Ertunc O, Vidal ID, Osunkoya AO, Jones T, Bova GS, Lamminen T, Achtman AH, Buzza M, Kouspou MM, Bigler SA, Zhou X, Freedland SJ, Mes-Masson AM, Garraway IP, Trock BJ, Taimen P, Saad F, Mirtti T, Knudsen BS, De Marzo AM. The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource. Cancer Epidemiol Biomarkers Prev 2022; 31:715-727. [PMID: 35131885 PMCID: PMC9381093 DOI: 10.1158/1055-9965.epi-21-0600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The need to better understand the molecular underpinnings of the heterogeneous outcomes of patients with prostate cancer is a pressing global problem and a key research priority for Movember. To address this, the Movember Global Action Plan 1 Unique tissue microarray (GAP1-UTMA) project constructed a set of unique and richly annotated tissue microarrays (TMA) from prostate cancer samples obtained from multiple institutions across several global locations. METHODS Three separate TMA sets were built that differ by purpose and disease state. RESULTS The intended use of TMA1 (Primary Matched LN) is to validate biomarkers that help determine which clinically localized prostate cancers with associated lymph node metastasis have a high risk of progression to lethal castration-resistant metastatic disease, and to compare molecular properties of high-risk index lesions within the prostate to regional lymph node metastases resected at the time of prostatectomy. TMA2 (Pre vs. Post ADT) was designed to address questions regarding risk of castration-resistant prostate cancer (CRPC) and response to suppression of the androgen receptor/androgen axis, and characterization of the castration-resistant phenotype. TMA3 (CRPC Met Heterogeneity)'s intended use is to assess the heterogeneity of molecular markers across different anatomic sites in lethal prostate cancer metastases. CONCLUSIONS The GAP1-UTMA project has succeeded in combining a large set of tissue specimens from 501 patients with prostate cancer with rich clinical annotation. IMPACT This resource is now available to the prostate cancer community as a tool for biomarker validation to address important unanswered clinical questions around disease progression and response to treatment.
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Affiliation(s)
- Véronique Ouellet
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
| | - Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Department of Pathology, Helsinki and Uusimaa Hospital District and Medicum, University of Helsinki, Helsinki, Finland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Kathy Wiley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Viktor Berge
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - Carlos S. Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Kristin Austlid Tasken
- Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dominique Trudel
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Pathology and Cellular Biology, Université de Montréal, Montreal, Canada
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Michael S. Lewis
- West Los Angeles Veterans Affairs Medical Center and Departments of Pathology and Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aud Svindland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Onur Ertunc
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Suleyman Demirel University, Department of Pathology, Training and Research Hospital East Campus, Isparta, Turkey
| | - Igor Damasceno Vidal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adeboye O. Osunkoya
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Tracy Jones
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Tarja Lamminen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | | | - Steven A. Bigler
- Department of Pathology, Mississippi Baptist Medical Center, Jackson, Mississippi
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Stephen J. Freedland
- Center for Integrated Research on Cancer and Lifestyle, Cedars-Sinai Medical Center, Los Angeles, California
- Section of Urology, Durham VA Medical Center, Durham, North Carolina
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Medicine, Université de Montréal, Montreal, Canada
| | - Isla P. Garraway
- Department of Urology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California, Los Angeles, California
- Division of Urology, Greater Los Angeles VA Healthcare System, Los Angeles, California
| | - Bruce J. Trock
- Department of Urology and Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pekka Taimen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Fred Saad
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Surgery, Université de Montréal, Montreal, Canada
| | - Tuomas Mirtti
- HUS Diagnostic Center, Department of Pathology, HUS Helsinki University Hospital, Helsinki, Finland
- Medicum and Research Program In Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Beatrice S. Knudsen
- Digital and Computational Pathology, University of Utah, Salt Lake City, Utah
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology and Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
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Simkovich SM, Underhill LJ, Kirby MA, Crocker ME, Goodman D, McCracken JP, Thompson LM, Diaz-Artiga A, Castañaza-Gonzalez A, Garg SS, Balakrishnan K, Thangavel G, Rosa G, Peel JL, Clasen TF, McCollum ED, Checkley W. Resources and Geographic Access to Care for Severe Pediatric Pneumonia in Four Resource-limited Settings. Am J Respir Crit Care Med 2022; 205:183-197. [PMID: 34662531 PMCID: PMC8787246 DOI: 10.1164/rccm.202104-1013oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Rationale: Pneumonia is the leading cause of death in children worldwide. Identifying and appropriately managing severe pneumonia in a timely manner improves outcomes. Little is known about the readiness of healthcare facilities to manage severe pediatric pneumonia in low-resource settings. Objectives: As part of the HAPIN (Household Air Pollution Intervention Network) trial, we sought to identify healthcare facilities that were adequately resourced to manage severe pediatric pneumonia in Jalapa, Guatemala (J-GUA); Puno, Peru (P-PER); Kayonza, Rwanda (K-RWA); and Tamil Nadu, India (T-IND). We conducted a facility-based survey of available infrastructure, staff, equipment, and medical consumables. Facilities were georeferenced, and a road network analysis was performed. Measurements and Main Results: Of the 350 healthcare facilities surveyed, 13% had adequate resources to manage severe pneumonia, 37% had pulse oximeters, and 44% had supplemental oxygen. Mean (±SD) travel time to an adequately resourced facility was 41 ± 19 minutes in J-GUA, 99 ± 64 minutes in P-PER, 40 ± 19 minutes in K-RWA, and 31 ± 19 minutes in T-IND. Expanding pulse oximetry coverage to all facilities reduced travel time by 44% in J-GUA, 29% in P-PER, 29% in K-RWA, and 11% in T-IND (all P < 0.001). Conclusions: Most healthcare facilities in low-resource settings of the HAPIN study area were inadequately resourced to care for severe pediatric pneumonia. Early identification of cases and timely referral is paramount. The provision of pulse oximeters to all health facilities may be an effective approach to identify cases earlier and refer them for care and in a timely manner.
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Affiliation(s)
- Suzanne M. Simkovich
- Division of Pulmonary and Critical Care
- Center for Global Non-Communicable Disease Research and Training, and
- Medstar Health Research Institute, Hyattsville, Maryland
| | - Lindsay J. Underhill
- Division of Pulmonary and Critical Care
- Center for Global Non-Communicable Disease Research and Training, and
| | - Miles A. Kirby
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Mary E. Crocker
- Division of Pulmonary and Sleep Medicine, Seattle Children’s Hospital and School of Medicine, University of Washington, Seattle, Washington
| | - Dina Goodman
- Division of Pulmonary and Critical Care
- Center for Global Non-Communicable Disease Research and Training, and
| | - John P. McCracken
- Global Health Institute, Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia
| | | | - Anaité Diaz-Artiga
- Centro de Estudios de la Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Adly Castañaza-Gonzalez
- Centro de Estudios de la Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Sarada S. Garg
- Department of Environmental Health Engineering, ICMR Center for Advanced Research on Air Quality, Climate and Health, Sri Ramachandra Medical College and Research Institute (Deemed University), Chennai, Tamil Nadu, India
| | - Kalpana Balakrishnan
- Department of Environmental Health Engineering, ICMR Center for Advanced Research on Air Quality, Climate and Health, Sri Ramachandra Medical College and Research Institute (Deemed University), Chennai, Tamil Nadu, India
| | - Gurusamy Thangavel
- Department of Environmental Health Engineering, ICMR Center for Advanced Research on Air Quality, Climate and Health, Sri Ramachandra Medical College and Research Institute (Deemed University), Chennai, Tamil Nadu, India
| | - Ghislaine Rosa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; and
| | - Jennifer L. Peel
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
| | - Thomas F. Clasen
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Eric D. McCollum
- Eudowood Division of Pediatric Respiratory Sciences and
- Global Program for Pediatric Respiratory Sciences, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - William Checkley
- Division of Pulmonary and Critical Care
- Center for Global Non-Communicable Disease Research and Training, and
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Chharia A, Upadhyay R, Kumar V, Cheng C, Zhang J, Wang T, Xu M. Deep-Precognitive Diagnosis: Preventing Future Pandemics by Novel Disease Detection With Biologically-Inspired Conv-Fuzzy Network. IEEE Access 2022; 10:23167-23185. [PMID: 35360503 PMCID: PMC8967064 DOI: 10.1109/access.2022.3153059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Deep learning-based Computer-Aided Diagnosis has gained immense attention in recent years due to its capability to enhance diagnostic performance and elucidate complex clinical tasks. However, conventional supervised deep learning models are incapable of recognizing novel diseases that do not exist in the training dataset. Automated early-stage detection of novel infectious diseases can be vital in controlling their rapid spread. Moreover, the development of a conventional CAD model is only possible after disease outbreaks and datasets become available for training (viz. COVID-19 outbreak). Since novel diseases are unknown and cannot be included in training data, it is challenging to recognize them through existing supervised deep learning models. Even after data becomes available, recognizing new classes with conventional models requires a complete extensive re-training. The present study is the first to report this problem and propose a novel solution to it. In this study, we propose a new class of CAD models, i.e., Deep-Precognitive Diagnosis, wherein artificial agents are enabled to identify unknown diseases that have the potential to cause a pandemic in the future. A de novo biologically-inspired Conv-Fuzzy network is developed. Experimental results show that the model trained to classify Chest X-Ray (CXR) scans into normal and bacterial pneumonia detected a novel disease during testing, unseen by it in the training sample and confirmed to be COVID-19 later. The model is also tested on SARS-CoV-1 and MERS-CoV samples as unseen diseases and achieved state-of-the-art accuracy. The proposed model eliminates the need for model re-training by creating a new class in real-time for the detected novel disease, thus classifying it on all subsequent occurrences. Second, the model addresses the challenge of limited labeled data availability, which renders most supervised learning techniques ineffective and establishes that modified fuzzy classifiers can achieve high accuracy on image classification tasks.
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Affiliation(s)
- Aviral Chharia
- Mechanical Engineering Department, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Rahul Upadhyay
- Electronics and Communication Engineering Department, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Vinay Kumar
- Electronics and Communication Engineering Department, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004, India
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jing Zhang
- Department of Computer Science, University of California at Irvine, Irvine, CA 92697, USA
| | - Tianyang Wang
- Department of Computer Science and Information Technology, Austin Peay State University, Clarksville, TN 37044, USA
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Computer Vision Department, Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates
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Bi W, Xu W, Cheng L, Xue J, Wang Q, Yu F, Xia S, Wang Q, Li G, Qin C, Lu L, Su L, Jiang S. IgG Fc-binding motif-conjugated HIV-1 fusion inhibitor exhibits improved potency and in vivo half-life: Potential application in combination with broad neutralizing antibodies. PLoS Pathog 2019; 15:e1008082. [PMID: 31805154 PMCID: PMC6894747 DOI: 10.1371/journal.ppat.1008082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/16/2019] [Indexed: 12/23/2022] Open
Abstract
The clinical application of conventional peptide drugs, such as the HIV-1 fusion inhibitor enfuvirtide, is limited by their short half-life in vivo. To overcome this limitation, we developed a new strategy to extend the in vivo half-life of a short HIV-1 fusion inhibitory peptide, CP24, by fusing it with the human IgG Fc-binding peptide (IBP). The newly engineered peptide IBP-CP24 exhibited potent and broad anti-HIV-1 activity with IC50 values ranging from 0.2 to 173.7 nM for inhibiting a broad spectrum of HIV-1 strains with different subtypes and tropisms, including those resistant to enfuvirtide. Most importantly, its half-life in the plasma of rhesus monkeys was 46.1 h, about 26- and 14-fold longer than that of CP24 (t1/2 = 1.7 h) and enfuvirtide (t1/2 = 3 h), respectively. IBP-CP24 intravenously administered in rhesus monkeys could not induce significant IBP-CP24-specific antibody response and it showed no obvious in vitro or in vivo toxicity. In the prophylactic study, humanized mice pretreated with IBP-CP24 were protected from HIV-1 infection. As a therapeutic treatment, coadministration of IBP-CP24 and normal human IgG to humanized mice with chronic HIV-1 infection resulted in a significant decrease of plasma viremia. Combining IBP-CP24 with a broad neutralizing antibody (bNAb) targeting CD4-binding site (CD4bs) in gp120 or a membrane proximal external region (MPER) in gp41 exhibited synergistic effect, resulting in significant dose-reduction of the bNAb and IBP-CP24. These results suggest that IBP-CP24 has the potential to be further developed as a new HIV-1 fusion inhibitor-based, long-acting anti-HIV drug that can be used alone or in combination with a bNAb for treatment and prevention of HIV-1 infection.
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Affiliation(s)
- Wenwen Bi
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liang Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jing Xue
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Fei Yu
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qi Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Guangming Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Chuan Qin
- Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Re-emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- * E-mail: (LL); (LS); (SJ)
| | - Lishan Su
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (LL); (LS); (SJ)
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/NHC/CAMS, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York, United States of America
- * E-mail: (LL); (LS); (SJ)
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