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Jing S, Xue L, Wang H, Peng Z. Global analysis of an age-structured tuberculosis model with an application to Jiangsu, China. J Math Biol 2024; 88:52. [PMID: 38563991 DOI: 10.1007/s00285-024-02066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 08/31/2023] [Accepted: 02/18/2024] [Indexed: 04/04/2024]
Abstract
Diagnostic delay for TB infected individuals and the lack of TB vaccines for adults are the main challenges to achieve the goals of WHO by 2050. In order to evaluate the impacts of diagnostic delay and vaccination for adults on prevalence of TB, we propose an age-structured model with latent age and infection age, and we incorporate Mycobacterium TB in the environment and vaccination into the model. Diagnostic delay is indicated by the age of infection before receiving treatment. The threshold dynamics are established in terms of the basic reproduction number R 0 . WhenR 0 < 1 , the disease-free equilibrium is globally asymptotically stable, which means that TB epidemic will die out; WhenR 0 = 1 , the disease-free equilibrium is globally attractive; there exists a unique endemic equilibrium and the endemic equilibrium is globally attractive whenR 0 > 1 . We estimate that the basic reproduction numberR 0 = 0.5320 (95% CI (0.3060, 0.7556)) in Jiangsu Province, which means that TB epidemic will die out. However, we find that the annual number of new TB cases by 2050 is 1,151 (95%CI: (138, 8,014)), which means that it is challenging to achieve the goal of WHO by 2050. To this end, we evaluate the possibility of achieving the goals of WHO if we start vaccinating adults and reduce diagnostic delay in 2025. Our results demonstrate that when the diagnostic delay is reduced from longer than four months to four months, or 20% adults are vaccinated, the goal of WHO in 2050 can be achieved, and 73,137 (95%CI: (23,906, 234,086)) and 54,828 (95%CI: (15,811, 206,468)) individuals will be prevented from being infected from 2025 to 2050, respectively. The modeling approaches and simulation results used in this work can help policymakers design control measures to reduce the prevalence of TB.
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Affiliation(s)
- Shuanglin Jing
- College of Mathematical Sciences, Harbin Engineering University, Harbin, 150001, Heilongjiang, China
| | - Ling Xue
- College of Mathematical Sciences, Harbin Engineering University, Harbin, 150001, Heilongjiang, China.
| | - Hao Wang
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, T6G 2G1, Canada.
| | - Zhihang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
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Shen M, Xiao Y, Rong L, Zhuang G, Song C, Zhao Q, Huang J, Zhu Q, Liang S, Chen H, Li J, Liao L, Shao Y, Xing H, Ruan Y, Lan G. The impact of attrition on the transmission of HIV and drug resistance. AIDS 2023; 37:1137-1145. [PMID: 36927994 DOI: 10.1097/qad.0000000000003528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BACKGROUND Attrition due to loss to follow-up or termination of antiretroviral therapy (ART) among HIV-infected patients in care may increase the risk of emergence and transmission of drug resistance (TDR), diminish benefit of treatment, and increase morbidity and mortality. Understanding the impact of attrition on the epidemic is essential to provide interventions for improving retention in care. METHODS We developed a comprehensive HIV transmission dynamics model by considering CD4 + cell count dependent diagnosis, treatment, and attrition involving TDR and acquired drug resistance. The model was calibrated by 11 groups HIV/AIDS surveillance data during 2008-2018 from Guangxi, China, and validated by the prevalence of TDR among diagnosed treatment-naive individuals. We aimed to investigate how attrition would affect the transmission of HIV and drug-resistance when expanding ART. RESULTS In the base case with CD4 + cell count dependent per capita attrition rates 0.025∼0.15 and treatment rates 0.23∼0.42, we projected cumulative total new infections, new drug-resistant infections, and HIV-related deaths over 2022-2030 would be 145 391, 7637, and 51 965, respectively. Increasing treatment rates by 0.1∼0.2 can decrease the above total new infections (deaths) by 1.63∼2.93% (3.52∼6.16%). However, even 0.0114∼0.0220 (0.0352∼0.0695) increase in attrition rates would offset this benefit of decreasing infections (deaths). Increasing treatment rates (attrition rates) by 0.05∼0.1 would increase the above drug-resistant infections by 0.16∼0.30% (22.18∼41.15%). CONCLUSION A minor increase in attrition can offset the benefit of treatment expansion and increase the transmission of HIV drug resistance. Reducing attrition rates for patients already in treatment may be as important as expanding treatment for untreated patients.
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Affiliation(s)
- Mingwang Shen
- China-Australia Joint Research Centre for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, Florida, USA
| | - Guihua Zhuang
- China-Australia Joint Research Centre for Infectious Diseases, School of Public Health, Xi'an Jiaotong University Health Science Center
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi
| | - Chang Song
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Quanbi Zhao
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
| | - Jinghua Huang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Qiuying Zhu
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Shujia Liang
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Huanhuan Chen
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Jianjun Li
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Lingjie Liao
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Hui Xing
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Yuhua Ruan
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Guanghua Lan
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
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Larson K, Arampatzis G, Bowman C, Chen Z, Hadjidoukas P, Papadimitriou C, Koumoutsakos P, Matzavinos A. Data-driven prediction and origin identification of epidemics in population networks. ROYAL SOCIETY OPEN SCIENCE 2021; 8:200531. [PMID: 33614060 PMCID: PMC7890494 DOI: 10.1098/rsos.200531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Effective intervention strategies for epidemics rely on the identification of their origin and on the robustness of the predictions made by network disease models. We introduce a Bayesian uncertainty quantification framework to infer model parameters for a disease spreading on a network of communities from limited, noisy observations; the state-of-the-art computational framework compensates for the model complexity by exploiting massively parallel computing architectures. Using noisy, synthetic data, we show the potential of the approach to perform robust model fitting and additionally demonstrate that we can effectively identify the disease origin via Bayesian model selection. As disease-related data are increasingly available, the proposed framework has broad practical relevance for the prediction and management of epidemics.
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Affiliation(s)
- Karen Larson
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Georgios Arampatzis
- Computational Science and Engineering Laboratory, ETH Zürich, CH-8092, Switzerland
- Collegium Helveticum, CH-8092 Zürich, Switzerland
| | - Clark Bowman
- Department of Mathematics and Statistics, Hamilton College, Clinton, NY 13323, USA
| | - Zhizhong Chen
- Department of Physics, Brown University, Providence, RI 02912, USA
| | | | - Costas Papadimitriou
- Department of Mechanical Engineering, University of Thessaly, GR-38334 Volos, Greece
| | - Petros Koumoutsakos
- Computational Science and Engineering Laboratory, ETH Zürich, CH-8092, Switzerland
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Abstract
In recent years, men who have sex with men (MSM) constitute a major group of HIV transmission in China. High primary drug-resistance (PDR) rate in MSM also represents a serious challenge for the Chinese antiretroviral therapy (ART) program. To assess the efficiency of ART in controlling HIV/AIDS infection among MSM, we developed a compartmental model for the annually reported HIV/AIDS MSM from 2007 to 2019 in the Zhejiang Province of China. R0 was 2.3946 (95% CI (2.2961–2.4881)). We predict that 90% of diagnosed HIV/AIDS individuals will have received treatment till 2020, while the proportion of the diagnosed remains as low as 40%. Even when the proportion of the diagnosed reaches 90%, R0 is still larger than the level of AIDS epidemic elimination. ART can effectively control the spread of HIV, even in the presence of drug resistance. The 90-90-90 strategy alone may not eliminate the HIV epidemic in Chinese MSM. Behavioural and biologic interventions are the most effective interventions to control the HIV/AIDS epidemic among MSM.
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Wong RW, Balachandran A, Cheung PK, Cheng R, Pan Q, Stoilov P, Harrigan PR, Blencowe BJ, Branch DR, Cochrane A. An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing. PLoS Pathog 2020; 16:e1008307. [PMID: 32069328 PMCID: PMC7048317 DOI: 10.1371/journal.ppat.1008307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/28/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022] Open
Abstract
The ability of HIV-1 to evolve resistance to combined antiretroviral therapies (cARTs) has stimulated research into alternative means of controlling this infection. We assayed >60 modulators of RNA alternative splicing (AS) to identify new inhibitors of HIV-1 RNA processing-a segment of the viral lifecycle not targeted by current drugs-and discovered compound N-[4-chloro-3-(trifluoromethyl)phenyl]-7-nitro-2,1,3-benzoxadiazol-4-amine (5342191) as a potent inhibitor of both wild-type (Ba-L, NL4-3, LAI, IIIB, and N54) and drug-resistant strains of HIV-1 (IC50: ~700 nM) with no significant effect on cell viability at doses tested. 5342191 blocks expression of four essential HIV-1 structural and regulatory proteins (Gag, Env, Tat, and Rev) without affecting total protein synthesis of the cell. This response is associated with altered unspliced (US) and singly-spliced (SS) HIV-1 RNA accumulation (~60% reduction) and transport to the cytoplasm (loss of Rev) whereas parallel analysis of cellular RNAs revealed less than a 0.7% of host alternative splicing (AS) events (0.25-0.67% by ≥ 10-20%), gene expression (0.01-0.46% by ≥ 2-5 fold), and protein abundance (0.02-0.34% by ≥ 1.5-2 fold) being affected. Decreased expression of Tat, but not Gag/Env, upon 5342191 treatment was reversed by a proteasome inhibitor, suggesting that this compound alters the synthesis/degradation of this key viral factor. Consistent with an affect on HIV-1 RNA processing, 5342191 treatment of cells altered the abundance and phosphorylation of serine/arginine-rich splicing factor (SRSF) 1, 3, and 4. Despite the activation of several intracellular signaling pathways by 5342191 (Ras, MEK1/2-ERK1/2, and JNK1/2/3), inhibition of HIV-1 gene expression by this compound could be reversed by pre-treatment with either a G-protein α-subunit inhibitor or two different MEK1/2 inhibitors. These observations demonstrate enhanced sensitivity of HIV-1 gene expression to small changes in host RNA processing and highlights the potential of modulating host intracellular signaling as an alternative approach for controlling HIV-1 infection.
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Affiliation(s)
- Raymond W. Wong
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Peter K. Cheung
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Qun Pan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Benjamin J. Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Donald R. Branch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Advanced Diagnostics, Infection and Immunity Group, Toronto General Hospital Research Institute, Toronto, Ontario, Canada
- Centre for Innovation, Canadian Blood Services, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
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Shen M, Xiao Y, Rong L, Meyers LA, Bellan SE. The cost-effectiveness of oral HIV pre-exposure prophylaxis and early antiretroviral therapy in the presence of drug resistance among men who have sex with men in San Francisco. BMC Med 2018; 16:58. [PMID: 29688862 PMCID: PMC5914040 DOI: 10.1186/s12916-018-1047-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/28/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Poor adherence to either antiretroviral treatment (ART) or pre-exposure prophylaxis (PrEP) can promote drug resistance, though this risk is thought to be considerably higher for ART. In the population of men who have sex with men (MSM) in San Francisco, PrEP coverage reached 9.6% in 2014 and has continued to rise. Given the risk of drug resistance and high cost of second-line drugs, the costs and benefits of initiating ART earlier while expanding PrEP coverage remain unclear. METHODS We develop an infection-age-structured mathematical model and fit this model to the annual incidence of AIDS cases and deaths directly, and to resistance and demographic data indirectly. We investigate the impact of six various intervention scenarios (low, medium, or high PrEP coverage, with or without earlier ART) over the next 20 years. RESULTS Low (medium, high) PrEP coverage with earlier ART could prevent 22% (42%, 57%) of a projected 44,508 total new infections and 8% (26%, 41%) of a projected 18,426 new drug-resistant infections, and result in a gain of 43,649 (74,048, 103,270) QALYs over 20 years compared to the status quo, at a cost of $4745 ($78,811, $115,320) per QALY gained, respectively. CONCLUSIONS High PrEP coverage with earlier ART is expected to provide the greatest benefit but also entail the highest costs among the strategies considered. This strategy is cost-effective for the San Francisco MSM population, even considering the acquisition and transmission of ART-mediated drug resistance. However, without a substantial increase to San Francisco's annual HIV budget, the most advisable strategy may be initiating ART earlier, while maintaining current strategies of PrEP enrollment.
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Affiliation(s)
- Mingwang Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China.,School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yanni Xiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL, 32611, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.,The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Steven E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, 30602, USA.,Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
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Wong RW, Lingwood CA, Ostrowski MA, Cabral T, Cochrane A. Cardiac glycoside/aglycones inhibit HIV-1 gene expression by a mechanism requiring MEK1/2-ERK1/2 signaling. Sci Rep 2018; 8:850. [PMID: 29339801 PMCID: PMC5770468 DOI: 10.1038/s41598-018-19298-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
The capacity of HIV-1 to develop resistance to current drugs calls for innovative strategies to control this infection. We aimed at developing novel inhibitors of HIV-1 replication by targeting viral RNA processing—a stage dependent on conserved host processes. We previously reported that digoxin is a potent inhibitor of this stage. Herein, we identify 12 other cardiac glycoside/aglycones or cardiotonic steroids (CSs) that impede HIV growth in HIV-infected T cells from clinical patients at IC50s (1.1–1.3 nM) that are 2–26 times below concentrations used in patients with heart conditions. We subsequently demonstrate that CSs inhibit HIV-1 gene expression in part through modulation of MEK1/2-ERK1/2 signaling via interaction with the Na+/K+-ATPase, independent of alterations in intracellular Ca2+. Supporting this hypothesis, depletion of the Na+/K+-ATPase or addition of a MEK1/2-ERK1/2 activator also impairs HIV-1 gene expression. Similar to digoxin, all CSs tested induce oversplicing of HIV-1 RNAs, reducing unspliced (Gag) and singly spliced RNAs (Env/p14-Tat) encoding essential HIV-1 structural/regulatory proteins. Furthermore, all CSs cause nuclear retention of genomic/unspliced RNAs, supporting viral RNA processing as the underlying mechanism for their disruption of HIV-1 replication. These findings call for further in vivo validation and supports the targeting of cellular processes to control HIV-1 infection.
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Affiliation(s)
- Raymond W Wong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Clifford A Lingwood
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S1A8, Canada.,Division of Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, M5G1X8, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S1A8, Canada
| | - Mario A Ostrowski
- Keenan Research Centre for Biomedical Science of St. Michael's Hospital Toronto, Toronto, ON, M5B1W8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, M5S1A8, Canada.,Department of Immunology, University of Toronto, Toronto, ON, M5S1A8, Canada.,Institute of Medical Science, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Tyler Cabral
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Alan Cochrane
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
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