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Prajapati S, Ngono AE, Cauley MM, Timis J, Shrestha S, Bastola A, Mandal SK, Yadav SR, Napit R, Moi ML, Yamabhai M, Sessions OM, Shresta S, Manandhar KD. Genomic sequencing and neutralizing serological profiles during acute dengue infection: A 2017 cohort study in Nepal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597174. [PMID: 38895290 PMCID: PMC11185687 DOI: 10.1101/2024.06.03.597174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus that poses a threat to nearly 50% of the global population. DENV has been endemic in Nepal since 2006; however, little is known about how DENV is evolving or the prevalence of anti-DENV immunity within the Nepalese population. To begin to address these gaps, we performed a serologic and genetic study of 49 patients from across Nepal who presented at central hospitals during the 2017 dengue season with suspected DENV infection. Of the 49 subjects assessed, 21 (43%) were positive for DENV NS1 antigen; of these; 5 were also anti-DENV IgM + IgG + ; 7 were DENV IgM + IgG - , 2 were IgM - IgG + , and 7 were IgM - IgG - by specific ELISAs. Seven of the 21 NS1+ sera were RNA+ by RT-PCR (six DENV2, one DENV3), suggesting that DENV2 was the dominant serotype in our cohort. Whole-genome sequencing of two DENV2 isolates showed similarity with strains circulating in Singapore in 2016, and the envelope genes were also similar to strains circulating in India in 2017. DENV-neutralizing antibodies (nAbs) were present in 31 of 47 sera tested (66%); among these, 20, 24, 26, and 12 sera contained nAbs against DENV1, 2, 3, and 4 serotypes, respectively. Serology analysis suggested that 12 (26%) and 19 (40%) of the 49 subjects were experiencing primary and secondary DENV infections, respectively. Collectively, our results provide evidence for current and/or past exposure to multiple DENV serotypes in our cohort, and the RNA analyses further indicate that DENV2 was the likely dominant serotype circulating in Nepal in 2017. These data suggest that expanded local surveillance of circulating DENV genotypes and population immunity will be important to effectively manage and mitigate future dengue outbreaks in Nepal.
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Anam V, Guerrero BV, Srivastav AK, Stollenwerk N, Aguiar M. Within-host models unravelling the dynamics of dengue reinfections. Infect Dis Model 2024; 9:458-473. [PMID: 38385021 PMCID: PMC10879676 DOI: 10.1016/j.idm.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/23/2024] Open
Abstract
Caused by four serotypes, dengue fever is a major public health concern worldwide. Current modeling efforts have mostly focused on primary and heterologous secondary infections, assuming that lifelong immunity prevents reinfections by the same serotype. However, recent findings challenge this assumption, prompting a reevaluation of dengue immunity dynamics. In this study, we develop a within-host modeling framework to explore different scenarios of dengue infections. Unlike previous studies, we go beyond a deterministic framework, considering individual immunological variability. Both deterministic and stochastic models are calibrated using empirical data on viral load and antibody (IgM and IgG) concentrations for all dengue serotypes, incorporating confidence intervals derived from stochastic realizations. With good agreement between the mean of the stochastic realizations and the mean field solution for each model, our approach not only successfully captures primary and heterologous secondary infection dynamics facilitated by antibody-dependent enhancement (ADE) but also provides, for the first time, insights into homotypic reinfection dynamics. Our study discusses the relevance of homotypic reinfections in dengue transmission at the population level, highlighting potential implications for disease prevention and control strategies.
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Affiliation(s)
- Vizda Anam
- Basque Center for Applied Mathematics, Basque Country, Spain
- Department of Mathematics and Statistics, University of Basque Country, Basque Country, Spain
| | | | | | | | - Maíra Aguiar
- Basque Center for Applied Mathematics, Basque Country, Spain
- Ikerbasque, Basque Foundation for Science, Basque Country, Spain
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Stollenwerk N, Estadilla CDS, Mar J, Bidaurrazaga Van-Dierdonck J, Ibarrondo O, Blasco-Aguado R, Aguiar M. The effect of mixed vaccination rollout strategy: A modelling study. Infect Dis Model 2023; 8:318-340. [PMID: 36945695 PMCID: PMC9998287 DOI: 10.1016/j.idm.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/11/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Vaccines have measurable efficacy obtained first from vaccine trials. However, vaccine efficacy (VE) is not a static measure and long-term population studies are needed to evaluate its performance and impact. COVID-19 vaccines have been developed in record time and the currently licensed vaccines are extremely effective against severe disease with higher VE after the full immunization schedule. To assess the impact of the initial phase of the COVID-19 vaccination rollout programmes, we used an extended Susceptible - Hospitalized - Asymptomatic/mild - Recovered (SHAR) model. Vaccination models were proposed to evaluate different vaccine types: vaccine type 1 which protects against severe disease only but fails to block disease transmission, and vaccine type 2 which protects against both severe disease and infection. VE was assumed as reported by the vaccine trials incorporating the difference in efficacy between one and two doses of vaccine administration. We described the performance of the vaccine in reducing hospitalizations during a momentary scenario in the Basque Country, Spain. With a population in a mixed vaccination setting, our results have shown that reductions in hospitalized COVID-19 cases were observed five months after the vaccination rollout started, from May to June 2021. Specifically in June, a good agreement between modelling simulation and empirical data was well pronounced.
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Affiliation(s)
- Nico Stollenwerk
- BCAM-Basque Center for Applied Mathematics, Bilbao, Basque Country, Spain
- Dipartimento di Matematica, Universitá degli Studi di Trento, Povo, Trento, Italy
| | - Carlo Delfin S Estadilla
- BCAM-Basque Center for Applied Mathematics, Bilbao, Basque Country, Spain
- Preventive Medicine and Public Health Department, University of the Basque Country, Leioa, Basque Country, Spain
| | - Javier Mar
- Osakidetza Basque Health Service, Guipúzcoa, Basque Country, Spain
- Biodonostia Health Research Institute, Guipúzcoa, Basque Country, Spain
| | | | - Oliver Ibarrondo
- Osakidetza Basque Health Service, Guipúzcoa, Basque Country, Spain
| | | | - Maíra Aguiar
- BCAM-Basque Center for Applied Mathematics, Bilbao, Basque Country, Spain
- Dipartimento di Matematica, Universitá degli Studi di Trento, Povo, Trento, Italy
- Ikerbasque, Basque Foundation for Science, Bilbao, Basque Country, Spain
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Modeling the initial phase of COVID-19 epidemic: The role of age and disease severity in the Basque Country, Spain. PLoS One 2022; 17:e0267772. [PMID: 35830439 PMCID: PMC9278753 DOI: 10.1371/journal.pone.0267772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022] Open
Abstract
Declared a pandemic by the World Health Organization (WHO), COVID-19 has spread rapidly around the globe. With eventually substantial global underestimation of infection, by the end of March 2022, more than 470 million cases were confirmed, counting more than 6.1 million deaths worldwide. COVID-19 symptoms range from mild (or no) symptoms to severe illness, with disease severity and death occurring according to a hierarchy of risks, with age and pre-existing health conditions enhancing risks of disease severity. In order to understand the dynamics of disease severity during the initial phase of the pandemic, we propose a modeling framework stratifying the studied population into two groups, older and younger, assuming different risks for severe disease manifestation. The deterministic and the stochastic models are parametrized using epidemiological data for the Basque Country population referring to confirmed cases, hospitalizations and deaths, from February to the end of March 2020. Using similar parameter values, both models were able to describe well the existing data. A detailed sensitivity analysis was performed to identify the key parameters influencing the transmission dynamics of COVID-19 in the population. We observed that the population younger than 60 years old of age would contribute more to the overall force of infection than the older population, as opposed to the already existing age-structured models, opening new ways to understand the effect of population age on disease severity during the COVID-19 pandemic. With mild/asymptomatic cases significantly influencing the disease spreading and control, our findings support the vaccination strategy prioritising the most vulnerable individuals to reduce hospitalization and deaths, as well as the non-pharmaceutical intervention measures to reduce disease transmission.
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Aguiar M, Anam V, Blyuss KB, Estadilla CDS, Guerrero BV, Knopoff D, Kooi BW, Srivastav AK, Steindorf V, Stollenwerk N. Mathematical models for dengue fever epidemiology: A 10-year systematic review. Phys Life Rev 2022; 40:65-92. [PMID: 35219611 PMCID: PMC8845267 DOI: 10.1016/j.plrev.2022.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/11/2023]
Abstract
Mathematical models have a long history in epidemiological research, and as the COVID-19 pandemic progressed, research on mathematical modeling became imperative and very influential to understand the epidemiological dynamics of disease spreading. Mathematical models describing dengue fever epidemiological dynamics are found back from 1970. Dengue fever is a viral mosquito-borne infection caused by four antigenically related but distinct serotypes (DENV-1 to DENV-4). With 2.5 billion people at risk of acquiring the infection, it is a major international public health concern. Although most of the cases are asymptomatic or mild, the disease immunological response is complex, with severe disease linked to the antibody-dependent enhancement (ADE) - a disease augmentation phenomenon where pre-existing antibodies to previous dengue infection do not neutralize but rather enhance the new infection. Here, we present a 10-year systematic review on mathematical models for dengue fever epidemiology. Specifically, we review multi-strain frameworks describing host-to-host and vector-host transmission models and within-host models describing viral replication and the respective immune response. Following a detailed literature search in standard scientific databases, different mathematical models in terms of their scope, analytical approach and structural form, including model validation and parameter estimation using empirical data, are described and analyzed. Aiming to identify a consensus on infectious diseases modeling aspects that can contribute to public health authorities for disease control, we revise the current understanding of epidemiological and immunological factors influencing the transmission dynamics of dengue. This review provide insights on general features to be considered to model aspects of real-world public health problems, such as the current epidemiological scenario we are living in.
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Affiliation(s)
- Maíra Aguiar
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Vizda Anam
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Konstantin B Blyuss
- VU University, Faculty of Science, De Boelelaan 1085, NL 1081, HV Amsterdam, the Netherlands
| | - Carlo Delfin S Estadilla
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Bruno V Guerrero
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Damián Knopoff
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Centro de Investigaciones y Estudios de Matemática CIEM, CONICET, Medina Allende s/n, Córdoba, 5000, Argentina
| | - Bob W Kooi
- University of Sussex, Department of Mathematics, Falmer, Brighton, UK
| | - Akhil Kumar Srivastav
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Vanessa Steindorf
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain
| | - Nico Stollenwerk
- Basque Center for Applied Mathematics, Alameda de Mazarredo 14, Bilbao, E-48009, Basque Country, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Via Sommarive 14, Povo, Trento, 38123, Italy
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Aguiar M, Van-Dierdonck JB, Mar J, Stollenwerk N. The role of mild and asymptomatic infections on COVID-19 vaccines performance: A modeling study. J Adv Res 2021; 39:157-166. [PMID: 35777906 PMCID: PMC8592646 DOI: 10.1016/j.jare.2021.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Maíra Aguiar
- Basque Center for Applied Mathematics (BCAM), Bilbao, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Italy; Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | | | - Javier Mar
- Osakidetza Basque Health Service, Debagoiena Integrated Healthcare Organisation, Research Unit, Arrasate-Mondragón, Guipúzcoa, Spain; Biodonostia Health Research Institute, Donostia-San Sebastián, Guipúzcoa, Spain; Kronikgune Institute for Health Services Research, Economic Evaluation Unit, Barakaldo, Spain
| | - Nico Stollenwerk
- Basque Center for Applied Mathematics (BCAM), Bilbao, Spain; Dipartimento di Matematica, Università degli Studi di Trento, Italy
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Sebayang AA, Fahlena H, Anam V, Knopoff D, Stollenwerk N, Aguiar M, Soewono E. Modeling Dengue Immune Responses Mediated by Antibodies: A Qualitative Study. BIOLOGY 2021; 10:biology10090941. [PMID: 34571818 PMCID: PMC8464952 DOI: 10.3390/biology10090941] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary With more than one-third of the world population at risk of acquiring the disease, dengue fever is a major public health problem. Caused by four antigenically distinct but related serotypes, disease severity is associated with the immunological status of the individual, seronegative or seropositive, prior to a natural dengue infection. While a primary natural dengue infection is often asymptomatic or mild, individuals experiencing a secondary dengue infection with a heterologous serotype have higher risk of developing the severe form of the disease, linked to the antibody-dependent enhancement (ADE) process. We develop a modeling framework to describe the dengue immune responses mediated by antibodies. Our model framework can describe qualitatively the dynamic of the viral load and antibodies production for scenarios of primary and secondary infections, as found in the empirical immunology literature. Studies such as the one described here serve as a baseline to further model extensions. Future refinements of our framework will be of use to evaluate the impact of imperfect dengue vaccines. Abstract Dengue fever is a viral mosquito-borne infection and a major international public health concern. With 2.5 billion people at risk of acquiring the infection around the world, disease severity is influenced by the immunological status of the individual, seronegative or seropositive, prior to natural infection. Caused by four antigenically related but distinct serotypes, DENV-1 to DENV-4, infection by one serotype confers life-long immunity to that serotype and a period of temporary cross-immunity (TCI) to other serotypes. The clinical response on exposure to a second serotype is complex with the so-called antibody-dependent enhancement (ADE) process, a disease augmentation phenomenon when pre-existing antibodies to previous dengue infection do not neutralize but rather enhance the new infection, used to explain the etiology of severe disease. In this paper, we present a minimalistic mathematical model framework developed to describe qualitatively the dengue immunological response mediated by antibodies. Three models are analyzed and compared: (i) primary dengue infection, (ii) secondary dengue infection with the same (homologous) dengue virus and (iii) secondary dengue infection with a different (heterologous) dengue virus. We explore the features of viral replication, antibody production and infection clearance over time. The model is developed based on body cells and free virus interactions resulting in infected cells activating antibody production. Our mathematical results are qualitatively similar to the ones described in the empiric immunology literature, providing insights into the immunopathogenesis of severe disease. Results presented here are of use for future research directions to evaluate the impact of dengue vaccines.
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Affiliation(s)
- Afrina Andriani Sebayang
- Department of Mathematics, Institut Teknologi Bandung, Bandung 40132, Indonesia; (A.A.S.); (H.F.)
| | - Hilda Fahlena
- Department of Mathematics, Institut Teknologi Bandung, Bandung 40132, Indonesia; (A.A.S.); (H.F.)
| | - Vizda Anam
- Basque Centre for Applied Mathematics (BCAM), Alameda Mazarredo, 14, 48009 Bilbao, Spain; (V.A.); (D.K.); (N.S.)
| | - Damián Knopoff
- Basque Centre for Applied Mathematics (BCAM), Alameda Mazarredo, 14, 48009 Bilbao, Spain; (V.A.); (D.K.); (N.S.)
| | - Nico Stollenwerk
- Basque Centre for Applied Mathematics (BCAM), Alameda Mazarredo, 14, 48009 Bilbao, Spain; (V.A.); (D.K.); (N.S.)
- Dipartimento di Matematica, Universita degli Studi di Trento, Via Sommarive 14, 38123 Trento, Italy
| | - Maíra Aguiar
- Basque Centre for Applied Mathematics (BCAM), Alameda Mazarredo, 14, 48009 Bilbao, Spain; (V.A.); (D.K.); (N.S.)
- Dipartimento di Matematica, Universita degli Studi di Trento, Via Sommarive 14, 38123 Trento, Italy
- Ikerbasque, Basque Foundation for Science, Euskadi Plaza, 5, 48009 Bilbo, Spain
- Correspondence: (M.A.); (E.S.)
| | - Edy Soewono
- Department of Mathematics, Institut Teknologi Bandung, Bandung 40132, Indonesia; (A.A.S.); (H.F.)
- Center for Mathematical Modeling and Simulation, Institut Teknologi Bandung, Bandung 40132, Indonesia
- Correspondence: (M.A.); (E.S.)
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Critical fluctuations in epidemic models explain COVID-19 post-lockdown dynamics. Sci Rep 2021; 11:13839. [PMID: 34226646 PMCID: PMC8257671 DOI: 10.1038/s41598-021-93366-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
As the COVID-19 pandemic progressed, research on mathematical modeling became imperative and very influential to understand the epidemiological dynamics of disease spreading. The momentary reproduction ratio r(t) of an epidemic is used as a public health guiding tool to evaluate the course of the epidemic, with the evolution of r(t) being the reasoning behind tightening and relaxing control measures over time. Here we investigate critical fluctuations around the epidemiological threshold, resembling new waves,
even when the community disease transmission rate \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β is not significantly changing. Without loss of generality, we use simple models that can be treated analytically and results are applied to more complex models describing COVID-19 epidemics. Our analysis shows that, rather than the supercritical regime (infectivity larger than a critical value, \documentclass[12pt]{minimal}
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\begin{document}$$\beta > \beta _c$$\end{document}β>βc) leading to new exponential growth of infection, the subcritical regime (infectivity smaller than a critical value, \documentclass[12pt]{minimal}
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\begin{document}$$\beta < \beta _c$$\end{document}β<βc) with small import is able to explain the dynamic behaviour of COVID-19 spreading after a lockdown lifting, with \documentclass[12pt]{minimal}
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\begin{document}$$r(t) \approx 1$$\end{document}r(t)≈1 hovering around its threshold value.
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Zhao R, Wang M, Cao J, Shen J, Zhou X, Wang D, Cao J. Flavivirus: From Structure to Therapeutics Development. Life (Basel) 2021; 11:life11070615. [PMID: 34202239 PMCID: PMC8303334 DOI: 10.3390/life11070615] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/25/2022] Open
Abstract
Flaviviruses are still a hidden threat to global human safety, as we are reminded by recent reports of dengue virus infections in Singapore and African-lineage-like Zika virus infections in Brazil. Therapeutic drugs or vaccines for flavivirus infections are in urgent need but are not well developed. The Flaviviridae family comprises a large group of enveloped viruses with a single-strand RNA genome of positive polarity. The genome of flavivirus encodes ten proteins, and each of them plays a different and important role in viral infection. In this review, we briefly summarized the major information of flavivirus and further introduced some strategies for the design and development of vaccines and anti-flavivirus compound drugs based on the structure of the viral proteins. There is no doubt that in the past few years, studies of antiviral drugs have achieved solid progress based on better understanding of the flavivirus biology. However, currently, there are no fully effective antiviral drugs or vaccines for most flaviviruses. We hope that this review may provide useful information for future development of anti-flavivirus drugs and vaccines.
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Affiliation(s)
- Rong Zhao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Meiyue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Shen
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Xin Zhou
- Department of Medical Imaging, Shanxi Medical University, Taiyuan 030001, China;
| | - Deping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
| | - Jimin Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
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