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van der Kuyl AC. Contemporary Distribution, Estimated Age, and Prehistoric Migrations of Old World Monkey Retroviruses. EPIDEMIOLGIA (BASEL, SWITZERLAND) 2021; 2:46-67. [PMID: 36417189 PMCID: PMC9620922 DOI: 10.3390/epidemiologia2010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022]
Abstract
Old World monkeys (OWM), simians inhabiting Africa and Asia, are currently affected by at least four infectious retroviruses, namely, simian foamy virus (SFV), simian immunodeficiency virus (SIV), simian T-lymphotropic virus (STLV), and simian type D retrovirus (SRV). OWM also show chromosomal evidence of having been infected in the past with four more retroviral species, baboon endogenous virus (BaEV), Papio cynocephalus endogenous virus (PcEV), simian endogenous retrovirus (SERV), and Rhesus endogenous retrovirus-K (RhERV-K/SERV-K1). For some of the viruses, transmission to other primates still occurs, resulting, for instance, in the HIV pandemic. Retroviruses are intimately connected with their host as they are normally spread by close contact. In this review, an attempt to reconstruct the distribution and history of OWM retroviruses will be made. A literature overview of the species infected by any of the eight retroviruses as well as an age estimation of the pathogens will be given. In addition, primate genomes from databases have been re-analyzed for the presence of endogenous retrovirus integrations. Results suggest that some of the oldest retroviruses, SERV and PcEV, have travelled with their hosts to Asia during the Miocene, when a higher global temperature allowed simian expansions. In contrast, younger viruses, such as SIV and SRV, probably due to the lack of a primate continuum between the continents in later times, have been restricted to Africa and Asia, respectively.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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2
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Natoli M, Gallon J, Lu H, Amgheib A, Pinato DJ, Mauri FA, Marafioti T, Akarca AU, Ullmo I, Ip J, Aboagye EO, Brown R, Karadimitris A, Ghaem-Maghami S. Transcriptional analysis of multiple ovarian cancer cohorts reveals prognostic and immunomodulatory consequences of ERV expression. J Immunother Cancer 2021; 9:jitc-2020-001519. [PMID: 33436485 PMCID: PMC7805370 DOI: 10.1136/jitc-2020-001519] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Endogenous retroviruses (ERVs) play a role in a variety of biological processes, including embryogenesis and cancer. DNA methyltransferase inhibitors (DNMTi)-induced ERV expression triggers interferon responses in ovarian cancer cells via the viral sensing machinery. Baseline expression of ERVs also occurs in cancer cells, though this process is poorly understood and previously unexplored in epithelial ovarian cancer (EOC). Here, the prognostic and immunomodulatory consequences of baseline ERV expression was assessed in EOC. METHODS ERV expression was assessed using EOC transcriptional data from The Cancer Genome Atlas (TCGA) and from an independent cohort (Hammersmith Hospital, HH), as well as from untreated or DNMTi-treated EOC cell lines. Least absolute shrinkage and selection operator (LASSO) logistic regression defined an ERV expression score to predict patient prognosis. Immunohistochemistry (IHC) was conducted on the HH cohort. Combination of DNMTi treatment with γδ T cells was tested in vitro, using EOC cell lines and patient-derived tumor cells. RESULTS ERV expression was found to define clinically relevant subsets of EOC patients. An ERV prognostic score was successfully generated in TCGA and validated in the independent cohort. In EOC patients from this cohort, a high ERV score was associated with better survival (log-rank p=0.0009) and correlated with infiltration of CD8+PD1+T cells (r=0.46, p=0.0001). In the TCGA dataset, a higher ERV score was found in BRCA1/2 mutant tumors, compared to wild type (p=0.015), while a lower ERV score was found in CCNE1 amplified tumors, compared to wild type (p=0.019). In vitro, baseline ERV expression dictates the level of ERV induction in response to DNMTi. Manipulation of an ERV expression threshold by DNMTi resulted in improved EOC cell killing by cytotoxic immune cells. CONCLUSIONS These findings uncover the potential for baseline ERV expression to robustly inform EOC patient prognosis, influence tumor immune infiltration and affect antitumor immunity.
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Affiliation(s)
- Marina Natoli
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - John Gallon
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Haonan Lu
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ala Amgheib
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Francesco A Mauri
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Teresa Marafioti
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Ayse U Akarca
- Department of Pathology, University College London Cancer Institute, London, UK
| | - Ines Ullmo
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jacey Ip
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Eric O Aboagye
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Robert Brown
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Pathology, Institute of Cancer Research, London, UK
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Yee JL, Grant RF, Van Rompay KKA, Roberts JA, Kuller L, Cunningham JL, Simmons JH, Papin JF. In vitro and In vivo Susceptibility of Baboons ( Papio sp.) to Infection with and Apparent Antibody Reactivity to Simian Betaretrovirus (SRV). Comp Med 2020; 70:75-82. [PMID: 31747991 PMCID: PMC7024778 DOI: 10.30802/aalas-cm-19-000014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/04/2019] [Accepted: 04/19/2019] [Indexed: 11/05/2022]
Abstract
Despite the lack of confirmed reports of an exogenous Simian betaretrovirus (SRV) isolated from baboons (Papio sp.), reports of simian endogenous gammaretrovirus (SERV) in baboons with complete genomes suggest that such viruses may be potentially infectious. In addition, serologic tests have repeatedly demonstrated antibody reactivity to SRV in baboons from multiple colonies. These findings complicate the management and use of such animals for research. To provide further insight into this situation, we performed in vitro and in vivo studies to determine if baboons are or can be infected with SRV. In our initial experiment, we were not able to isolate SRV from 6 seropositive or sero-indeterminate baboons by coculturing their peripheral blood mononuclear cells (PBMC) with macaque PBMC or permissive cell lines. In a subsequent experiment, we found that baboon PBMC infected in vitro with high dose SRV were permissive to virus replication. To test in vivo infectibil- ity, groups of naive baboons were infused intravenously with either (i) the same SRV tissue culture virus stocks used for the in vitro studies, (ii) SRV antibody positive and PCR positive macaque blood, (iii) SRV antibody positive or indeterminate, but PCR negative baboon blood, or (iv) SRV antibody and PCR negative baboon blood. Sustained SRV infection, as defined by reproducible PCR detection and/or antibody seroconversion, was confirmed in 2 of 3 baboons receiving tissue culture virus but not in any recipients of transfused blood from seropositive macaques or baboons. In conclusion, the data indicate that even though baboon cells can be infected experimentally with high doses of tissue culture grown SRV, baboons that are repeatedly SRV antibody positive and PCR negative are unlikely to be infected with exogenous SRV and thus are unlikely to transmit a virus that would threaten the SPF status of captive baboon colonies.
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Affiliation(s)
- JoAnn L Yee
- California National Primate Research Center, University of California, Davis, California
| | - Richard F Grant
- Washington National Primate Research Center, University of Washington, Seattle, Washington
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, California
| | - Jeffrey A Roberts
- California National Primate Research Center, University of California, Davis, California
| | - LaRene Kuller
- Washington National Primate Research Center, University of Washington, Seattle, Washington
| | - Jesse L Cunningham
- California National Primate Research Center, University of California, Davis, California
| | - Joe H Simmons
- Michale E. Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas; and
| | - James F Papin
- Department of Pathology, Division of Comparative Medicine, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma
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Wang X, Wang B, Liu Z, Garber PA, Pan H. Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys. PeerJ 2019; 7:e6602. [PMID: 30918756 PMCID: PMC6428148 DOI: 10.7717/peerj.6602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely distributed in snub-nosed monkeys, and their phylogenetic history can mirror that of their hosts over long evolutionary time scales. In addition, ERV sequences appear to have an important influence on the evolution of host pathology.
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Affiliation(s)
- Xiao Wang
- Beijing Forestry University, School of Nature Conservation, Beijing, China
| | - Boshi Wang
- Chinese Academy of Sciences, Institute of Zoology, CAS Key laboratory of Animal Ecology and Conservation Biology, Beijing, China
| | - Zhijin Liu
- Chinese Academy of Sciences, Institute of Zoology, CAS Key laboratory of Animal Ecology and Conservation Biology, Beijing, China
| | - Paul A Garber
- University of Illinois, Department of Anthropology and Program in Ecology and Evolutionary Biology, Urbana, IL, America
| | - Huijuan Pan
- Beijing Forestry University, School of Nature Conservation, Beijing, China
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5
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Panda A, de Cubas AA, Stein M, Riedlinger G, Kra J, Mayer T, Smith CC, Vincent BG, Serody JS, Beckermann KE, Ganesan S, Bhanot G, Rathmell WK. Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma. JCI Insight 2018; 3:121522. [PMID: 30135306 PMCID: PMC6141170 DOI: 10.1172/jci.insight.121522] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/05/2018] [Indexed: 12/16/2022] Open
Abstract
Although a subset of clear cell renal cell carcinoma (ccRCC) patients respond to immune checkpoint blockade (ICB), predictors of response remain uncertain. We investigated whether abnormal expression of endogenous retroviruses (ERVs) in tumors is associated with local immune checkpoint activation (ICA) and response to ICB. Twenty potentially immunogenic ERVs (πERVs) were identified in ccRCC in The Cancer Genome Atlas data set, and tumors were stratified into 3 groups based on their expression levels. πERV-high ccRCC tumors showed increased immune infiltration, checkpoint pathway upregulation, and higher CD8+ T cell fraction in infiltrating leukocytes compared with πERV-low ccRCC tumors. Similar results were observed in ER+/HER2- breast, colon, and head and neck squamous cell cancers. ERV expression correlated with expression of genes associated with histone methylation and chromatin regulation, and πERV-high ccRCC was enriched in BAP1 mutant tumors. ERV3-2 expression correlated with ICA in 11 solid cancers, including the 4 named above. In a small retrospective cohort of 24 metastatic ccRCC patients treated with single-agent PD-1/PD-L1 blockade, ERV3-2 expression in tumors was significantly higher in responders compared with nonresponders. Thus, abnormal expression of πERVs is associated with ICA in several solid cancers, including ccRCC, and ERV3-2 expression is associated with response to ICB in ccRCC.
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Affiliation(s)
- Anshuman Panda
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.,Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, USA
| | | | - Mark Stein
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.,Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | | | - Joshua Kra
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Tina Mayer
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Christof C. Smith
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Benjamin G. Vincent
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jonathan S. Serody
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kathryn E. Beckermann
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA.,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.,Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.,Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey, USA.,Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA
| | - W. Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA.,Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Yee JL, Grant R, Van Rompay KK, Kuller L, Carpenter A, Watanabe R, Huebner R, Agricola B, Smedley J, Roberts JA. Emerging diagnostic challenges and characteristics of simian betaretrovirus infections in captive macaque colonies. J Med Primatol 2018; 46:149-153. [PMID: 28748661 DOI: 10.1111/jmp.12295] [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] [Accepted: 06/26/2017] [Indexed: 11/27/2022]
Abstract
To better understand Simian betaretrovirus (SRV) seropositivity in virus-negative macaques, we transfused blood from SRV-infected or suspect donors into immunosuppressed naive recipients. Our results do not support typical SRV1-5 infection as the cause, but provide evidence for several possibilities including serological artifact, new/different SRV, or an endogenous virus.
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Affiliation(s)
- JoAnn L Yee
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Richard Grant
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Koen K Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - LaRene Kuller
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Amanda Carpenter
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Robin Watanabe
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Rebeca Huebner
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Brian Agricola
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jeremy Smedley
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jeffrey A Roberts
- California National Primate Research Center, University of California, Davis, CA, USA
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Grant R, Keele B, Kuller L, Watanabe R, Perret A, Smedley J. Identification of novel simian endogenous retroviruses that are indistinguishable from simian retrovirus (SRV) on current SRV diagnostic assays. J Med Primatol 2018; 46:158-161. [PMID: 28748668 DOI: 10.1111/jmp.12297] [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] [Accepted: 06/26/2017] [Indexed: 01/05/2023]
Abstract
Simian betaretroviruses include the well-known exogenous simian retroviruses (SRV-1 through SRV-8), and some closely related simian endogenous retroviruses (SERV). Here, we characterized two new viral genomes, which appear to represent novel SERVs but have characteristics of both SRV and SERV highlighting the need to develop new assays providing molecular and serologic differentiation of SERV and SRV to avoid false positives.
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Affiliation(s)
- Richard Grant
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Brandon Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - LaRene Kuller
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Robin Watanabe
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Alex Perret
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jeremy Smedley
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
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Ma Y, Liu R, Lv H, Han J, Zhong D, Zhang X. A computational method for prediction of matrix proteins in endogenous retroviruses. PLoS One 2017; 12:e0176909. [PMID: 28472185 PMCID: PMC5417524 DOI: 10.1371/journal.pone.0176909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 04/19/2017] [Indexed: 11/18/2022] Open
Abstract
Human endogenous retroviruses (HERVs) encode active retroviral proteins, which may be involved in the progression of cancer and other diseases. Matrix protein (MA), in group-specific antigen genes (gag) of retroviruses, is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. However, the amount of annotated MAs in ERVs is still at a low level so far. No computational method to predict the exact start and end coordinates of MAs in gags has been proposed yet. In this paper, a computational method to identify MAs in ERVs is proposed. A divide and conquer technique was designed and applied to the conventional prediction model to acquire better results when dealing with gene sequences with various lengths. Initiation sites and termination sites were predicted separately and then combined according to their intervals. Three different algorithms were applied and compared: weighted support vector machine (WSVM), weighted extreme learning machine (WELM) and random forest (RF). G − mean (geometric mean of sensitivity and specificity) values of initiation sites and termination sites under 5-fold cross validation generated by random forest models are 0.9869 and 0.9755 respectively, highest among the algorithms applied. Our prediction models combine RF & WSVM algorithms to achieve the best prediction results. 98.4% of all the collected ERV sequences with complete MAs (125 in total) could be predicted exactly correct by the models. 94,671 HERV sequences from 118 families were scanned by the model, 104 new putative MAs were predicted in human chromosomes. Distributions of the putative MAs and optimizations of model parameters were also analyzed. The usage of our predicting method was also expanded to other retroviruses and satisfying results were acquired.
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Affiliation(s)
- Yucheng Ma
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Ruiling Liu
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (RLL); (HQL)
| | - Hongqiang Lv
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
- * E-mail: (RLL); (HQL)
| | - Jiuqiang Han
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Dexing Zhong
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Xinman Zhang
- School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
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