Macie Duran Week 10

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Macie M. Duran

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Purpose

The purpose of this exercise was to use several different databases to find scholarly and relevant information. Using different search keywords, databases, and filters all play a role in the results that a search yields. Understanding how to sort through articles to find relevant and accurate sources is an important skill to have when conducting research.

Methods & Results

  1. I completed the warm-up exercise using Google Scholar. I searched SARS-CoV-2 ACE2 therapeutics.
    1. The search yielded about 12,000 results in 0.13 seconds.
    2. I recorded the top 10 papers using APA format:
      • Paper 1: Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive care medicine, 46(4), 586-590.
      • Paper 2: Gurwitz, D. (2020). Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics. Drug development research.
      • Paper 3: Kalra, R. S., Tomar, D., Meena, A. S., & Kandimalla, R. (2020). SARS-CoV-2, ACE2, and hydroxychloroquine: cardiovascular complications, therapeutics, and clinical readouts in the current settings. Pathogens, 9(7), 546.
      • Paper 4: Albini, A., Noonan, D. M., Pelosi, G., Di Guardo, G., & Lombardo, M. (2020). The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based antihypertensive therapies—reply. Internal and emergency medicine, 1-2.
      • Paper 5: Pang, X., Cui, Y., & Zhu, Y. (2020). Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication. Acta Pharmacologica Sinica, 41(9), 1255-1257.
      • Paper 6: Fu, Y., Cheng, Y., & Wu, Y. (2020). Understanding SARS-CoV-2-mediated inflammatory responses: from mechanisms to potential therapeutic tools. Virologica Sinica, 1-6.
      • Paper 7: Zhao, Y., Zhao, Z., Wang, Y., Zhou, Y., Ma, Y., & Zuo, W. (2020). Single-cell RNA expression profiling of ACE2, thereceptor of SARS-CoV-2. Biorxiv.
      • Paper 8: Davidson, A. M., Wysocki, J., & Batlle, D. (2020). Interaction of SARS-CoV-2 and Other Coronavirus With ACE (Angiotensin-Converting Enzyme)-2 as Their Main Receptor: Therapeutic Implications. Hypertension, 76(5), 1339-1349.
      • Paper 9: Smith, M., & Smith, J. C. (2020). Repurposing therapeutics for COVID-19: supercomputer-based docking to the SARS-CoV-2 viral spike protein and viral spike protein-human ACE2 interface.
      • Paper 10: He, Y., Wang, J., Li, F., & Shi, Y. (2020). Main clinical features of COVID-19 and potential prognostic and therapeutic value of the microbiota in SARS-CoV-2 infections. Frontiers in Microbiology, 11, 1302.
    3. I sorted my results by date (instead of relevance), and recorded the top 5 papers, using APA format:
      • Paper 1: Chowdhury, T., Baindara, P., & Mandal, S. M. (2020). LPD-12, a Promising Lipopeptide to Control COVID-19. International Journal of Antimicrobial Agents, 106218.
      • Paper 2: Jena, S., Munusami, P., Balamurali, M. M., & Chanda, K. (2020). Computationally approached inhibition potential of Tinospora Cordifolia towards COVID-19 targets.
      • Paper 3: Liu, L., Shan, H., Lei, C., Hui, D. S. C., Du, B., Li, L., ... & Wang, T. (2020). Angiotensin Converting Enzyme 2 May Mediate Disease Severity In COVID-19 Identification of vulnerability to. Circ Res, 126, 1671-1681.
      • Paper 4: Thakur, S. S. (2020). Proteomics and Its Application in Pandemic Diseases.
      • Paper 5: Toor, H. G., Banerjee, D. I., Rath, S. L., & Darji, S. A. (2020). Computational drug re-purposing targeting the spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19. European Journal of Pharmacology, 173720.
    4. I filtered my results using “Since 2019”, and recorded the top 5 papers, using APA format:
      • Paper 1: Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive care medicine, 46(4), 586-590.
      • Paper 2: Gurwitz, D. (2020). Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics. Drug development research.
      • Paper 3: Kalra, R. S., Tomar, D., Meena, A. S., & Kandimalla, R. (2020). SARS-CoV-2, ACE2, and hydroxychloroquine: cardiovascular complications, therapeutics, and clinical readouts in the current settings. Pathogens, 9(7), 546.
      • Paper 4: Albini, A., Noonan, D. M., Pelosi, G., Di Guardo, G., & Lombardo, M. (2020). The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based antihypertensive therapies—reply. Internal and emergency medicine, 1-2.
      • Paper 5: Fu, Y., Cheng, Y., & Wu, Y. (2020). Understanding SARS-CoV-2-mediated inflammatory responses: from mechanisms to potential therapeutic tools. Virologica Sinica, 1-6.
    5. I then filtered my results using “Since 2016”, and recorded the top 5 papers, using APA format:
      • Paper 1: Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target. Intensive care medicine, 46(4), 586-590.
      • Paper 2: Gurwitz, D. (2020). Angiotensin receptor blockers as tentative SARS‐CoV‐2 therapeutics. Drug development research.
      • Paper 3: Albini, A., Noonan, D. M., Pelosi, G., Di Guardo, G., & Lombardo, M. (2020). The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor-and angiotensin II receptor blocker-based antihypertensive therapies—reply. Internal and emergency medicine, 1-2.
      • Paper 4: Kalra, R. S., Tomar, D., Meena, A. S., & Kandimalla, R. (2020). SARS-CoV-2, ACE2, and hydroxychloroquine: cardiovascular complications, therapeutics, and clinical readouts in the current settings. Pathogens, 9(7), 546.
      • Paper 5: Pang, X., Cui, Y., & Zhu, Y. (2020). Recombinant human ACE2: potential therapeutics of SARS-CoV-2 infection and its complication. Acta Pharmacologica Sinica, 41(9), 1255-1257.
  2. Below is a list of the search terms that were used by each student in the class:
    • Warm-up exercise keywords
      • COVID-19 deaths
      • COVID-19 transmission
      • SARS-CoV-2 dying, getting better/worse
      • COVID-19 transmission
      • D614G
      • civet
      • long-term respiratory effects of COVID
      • SARS-CoV-2 antibodies
      • D614G mutation
      • SARS-CoV-2 immune response
      • 2019-nCoV transmission
      • SARS-CoV-2 antibodies
    • Assigned keywords
      • Nathan: COVID-19 and immune response (241,000)
      • Yaniv: COVID-19 and antibodies (62,900)
      • Ian: COVID-19 and immunity (77,500)
      • JT: COVID-19 and immune reaction (104,000)
      • Taylor: SARS-CoV-2 and immune response (48,800)
      • Nida: SARS-CoV-2 and antibodies (48,200)
      • Owen: SARS-CoV-2 and immunity (57,000)
      • Anna: SARS-CoV-2 and immune reaction (97,700)
      • Aiden: 2019-nCoV and immune response (25,600)
      • Fatimah: 2019-nCoV and antibodies (17,400)
      • Kam: 2019-nCoV and immunity (24,500)
      • Macie: 2019-nCoV and immune reaction (20,800)
  3. I used the LMU-specific link to access PubMed. I performed an unrestricted search on my assigned keywords (2019-nCoV and immune reaction).
    1. My search yielded 294 results.
    2. I recorded the top 10 papers below:
      • Paper 1: Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC. Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. JAMA. 2020 Aug 25;324(8):782-793. doi: 10.1001/jama.2020.12839. PMID: 32648899.
      • Paper 2: Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, Guo L, Guo R, Chen T, Hu J, Xiang Z, Mu Z, Chen X, Chen J, Hu K, Jin Q, Wang J, Qian Z. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun. 2020 Mar 27;11(1):1620. doi: 10.1038/s41467-020-15562-9. PMID: 32221306; PMCID: PMC7100515.
      • Paper 3: Folegatti PM, Ewer KJ, Aley PK, Angus B, Becker S, Belij-Rammerstorfer S, Bellamy D, Bibi S, Bittaye M, Clutterbuck EA, Dold C, Faust SN, Finn A, Flaxman AL, Hallis B, Heath P, Jenkin D, Lazarus R, Makinson R, Minassian AM, Pollock KM, Ramasamy M, Robinson H, Snape M, Tarrant R, Voysey M, Green C, Douglas AD, Hill AVS, Lambe T, Gilbert SC, Pollard AJ; Oxford COVID Vaccine Trial Group. Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet. 2020 Aug 15;396(10249):467-478. doi: 10.1016/S0140-6736(20)31604-4. Epub 2020 Jul 20. Erratum in: Lancet. 2020 Aug 15;396(10249):466. PMID: 32702298; PMCID: PMC7445431.
      • Paper 4: Yao XH, Li TY, He ZC, Ping YF, Liu HW, Yu SC, Mou HM, Wang LH, Zhang HR, Fu WJ, Luo T, Liu F, Guo QN, Chen C, Xiao HL, Guo HT, Lin S, Xiang DF, Shi Y, Pan GQ, Li QR, Huang X, Cui Y, Liu XZ, Tang W, Pan PF, Huang XQ, Ding YQ, Bian XW. [A pathological report of three COVID-19 cases by minimal invasive autopsies]. Zhonghua Bing Li Xue Za Zhi. 2020 May 8;49(5):411-417. Chinese. doi: 10.3760/cma.j.cn112151-20200312-00193. PMID: 32172546.
      • Paper 5: Korakas E, Ikonomidis I, Kousathana F, Balampanis K, Kountouri A, Raptis A, Palaiodimou L, Kokkinos A, Lambadiari V. Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes. Am J Physiol Endocrinol Metab. 2020 Jul 1;319(1):E105-E109. doi: 10.1152/ajpendo.00198.2020. Epub 2020 May 27. PMID: 32459524; PMCID: PMC7322508.
      • Paper 6: Wang H, Li X, Li T, Zhang S, Wang L, Wu X, Liu J. The genetic sequence, origin, and diagnosis of SARS-CoV-2. Eur J Clin Microbiol Infect Dis. 2020 Sep;39(9):1629-1635. doi: 10.1007/s10096-020-03899-4. Epub 2020 Apr 24. PMID: 32333222; PMCID: PMC7180649.
      • Paper 7: Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, Marrama D, de Silva AM, Frazier A, Carlin AF, Greenbaum JA, Peters B, Krammer F, Smith DM, Crotty S, Sette A. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell. 2020 Jun 25;181(7):1489-1501.e15. doi: 10.1016/j.cell.2020.05.015. Epub 2020 May 20. PMID: 32473127; PMCID: PMC7237901.
      • Paper 8: Xu X, Han M, Li T, Sun W, Wang D, Fu B, Zhou Y, Zheng X, Yang Y, Li X, Zhang X, Pan A, Wei H. Effective treatment of severe COVID-19 patients with tocilizumab. Proc Natl Acad Sci U S A. 2020 May 19;117(20):10970-10975. doi: 10.1073/pnas.2005615117. Epub 2020 Apr 29. PMID: 32350134; PMCID: PMC7245089.
      • Paper 9: Li L, Zhang W, Hu Y, Tong X, Zheng S, Yang J, Kong Y, Ren L, Wei Q, Mei H, Hu C, Tao C, Yang R, Wang J, Yu Y, Guo Y, Wu X, Xu Z, Zeng L, Xiong N, Chen L, Wang J, Man N, Liu Y, Xu H, Deng E, Zhang X, Li C, Wang C, Su S, Zhang L, Wang J, Wu Y, Liu Z. Effect of Convalescent Plasma Therapy on Time to Clinical Improvement in Patients With Severe and Life-threatening COVID-19: A Randomized Clinical Trial. JAMA. 2020 Aug 4;324(5):460-470. doi: 10.1001/jama.2020.10044. Erratum in: JAMA. 2020 Aug 4;324(5):519. PMID: 32492084; PMCID: PMC7270883.
      • Paper 10: Le Bert N, Tan AT, Kunasegaran K, Tham CYL, Hafezi M, Chia A, Chng MHY, Lin M, Tan N, Linster M, Chia WN, Chen MI, Wang LF, Ooi EE, Kalimuddin S, Tambyah PA, Low JG, Tan YJ, Bertoletti A. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020 Aug;584(7821):457-462. doi: 10.1038/s41586-020-2550-z. Epub 2020 Jul 15. PMID: 32668444.
  4. Next, I performed a title/abstract search on my assigned keywords.
    1. My search yielded 12 results.
    2. I recorded the top 10 papers below:
      • Paper 1: Iyer M, Jayaramayya K, Subramaniam MD, Lee SB, Dayem AA, Cho SG, Vellingiri B. COVID-19: an update on diagnostic and therapeutic approaches. BMB Rep. 2020 Apr;53(4):191-205. doi: 10.5483/BMBRep.2020.53.4.080. PMID: 32336317; PMCID: PMC7196187.
      • Paper 2: Jothimani D, Venugopal R, Abedin MF, Kaliamoorthy I, Rela M. COVID-19 and the liver. J Hepatol. 2020 Nov;73(5):1231-1240. doi: 10.1016/j.jhep.2020.06.006. Epub 2020 Jun 15. PMID: 32553666; PMCID: PMC7295524.
        • Review
      • Paper 3: Heneka MT, Golenbock D, Latz E, Morgan D, Brown R. Immediate and long-term consequences of COVID-19 infections for the development of neurological disease. Alzheimers Res Ther. 2020 Jun 4;12(1):69. doi: 10.1186/s13195-020-00640-3. PMID: 32498691; PMCID: PMC7271826.
        • Review
      • Paper 4: Allegra A, Di Gioacchino M, Tonacci A, Musolino C, Gangemi S. Immunopathology of SARS-CoV-2 Infection: Immune Cells and Mediators, Prognostic Factors, and Immune-Therapeutic Implications. Int J Mol Sci. 2020 Jul 6;21(13):4782. doi: 10.3390/ijms21134782. PMID: 32640747; PMCID: PMC7370171.
        • Review
      • Paper 5: Li K, Hao Z, Zhao X, Du J, Zhou Y. SARS-CoV-2 infection-induced immune responses: Friends or foes? Scand J Immunol. 2020 Aug;92(2):e12895. doi: 10.1111/sji.12895. Epub 2020 Jun 17. PMID: 32445403; PMCID: PMC7267129.
        • Review
      • Paper 6: Tilocca B, Soggiu A, Musella V, Britti D, Sanguinetti M, Urbani A, Roncada P. Molecular basis of COVID-19 relationships in different species: a one health perspective. Microbes Infect. 2020 May-Jun;22(4-5):218-220. doi: 10.1016/j.micinf.2020.03.002. Epub 2020 Mar 17. PMID: 32194253; PMCID: PMC7102648.
      • Paper 7: Amiral J, Vissac AM, Seghatchian J. Covid-19, induced activation of hemostasis, and immune reactions: Can an auto-immune reaction contribute to the delayed severe complications observed in some patients? Transfus Apher Sci. 2020 Jun;59(3):102804. doi: 10.1016/j.transci.2020.102804. Epub 2020 May 3. PMID: 32387238; PMCID: PMC7252011.
      • Paper 8: Sanchez-Gonzalez MA, Moskowitz D, Issuree PD, Yatzkan G, Rizvi SAA, Day K. A Pathophysiological Perspective on COVID-19's Lethal Complication: From Viremia to Hypersensitivity Pneumonitis-like Immune Dysregulation. Infect Chemother. 2020 Sep;52(3):335-344. doi: 10.3947/ic.2020.52.3.335. Epub 2020 Jul 15. PMID: 32537960; PMCID: PMC7533209.
        • Review
      • Paper 9: Elkind MSV, Boehme AK, Smith CJ, Meisel A, Buckwalter MS. Infection as a Stroke Risk Factor and Determinant of Outcome After Stroke. Stroke. 2020 Oct;51(10):3156-3168. doi: 10.1161/STROKEAHA.120.030429. Epub 2020 Sep 8. PMID: 32897811; PMCID: PMC7530056.
        • Review
      • Paper 10: Burtscher J, Cappellano G, Omori A, Koshiba T, Millet GP. Mitochondria: In the Cross Fire of SARS-CoV-2 and Immunity. iScience. 2020 Oct 23;23(10):101631. doi: 10.1016/j.isci.2020.101631. Epub 2020 Sep 29. PMID: 33015593; PMCID: PMC7524535.
        • Review
  5. I then added the word Review to any review articles I listed in the previous step.
  6. I picked an author that showed up in multiple citations and performed an author search on the name.
    1. I searched the author Sebastiano Gangemi.
    2. My search yielded 194 results.
    3. I recorded the top 5 articles below:
      • Paper 1: Minciullo PL, Catalano A, Mandraffino G, Casciaro M, Crucitti A, Maltese G, Morabito N, Lasco A, Gangemi S, Basile G. Inflammaging and Anti-Inflammaging: The Role of Cytokines in Extreme Longevity. Arch Immunol Ther Exp (Warsz). 2016 Apr;64(2):111-26. doi: 10.1007/s00005-015-0377-3. Epub 2015 Dec 12. PMID: 26658771.
      • Paper 2: Ventura MT, Casciaro M, Gangemi S, Buquicchio R. Immunosenescence in aging: between immune cells depletion and cytokines up-regulation. Clin Mol Allergy. 2017 Dec 14;15:21. doi: 10.1186/s12948-017-0077-0. PMID: 29259496; PMCID: PMC5731094.
      • Paper 3: Imbalzano E, Casciaro M, Quartuccio S, Minciullo PL, Cascio A, Calapai G, Gangemi S. Association between urticaria and virus infections: A systematic review. Allergy Asthma Proc. 2016 Jan-Feb;37(1):18-22. doi: 10.2500/aap.2016.37.3915. Epub 2015 Dec 3. PMID: 26637522.
      • Paper 4: Pennisi P, Tonacci A, Tartarisco G, Billeci L, Ruta L, Gangemi S, Pioggia G. Autism and social robotics: A systematic review. Autism Res. 2016 Feb;9(2):165-83. doi: 10.1002/aur.1527. Epub 2015 Oct 20. PMID: 26483270.
      • Paper 5: Allegra A, Spatari G, Mattioli S, Curti S, Innao V, Ettari R, Allegra AG, Giorgianni C, Gangemi S, Musolino C. Formaldehyde Exposure and Acute Myeloid Leukemia: A Review of the Literature. Medicina (Kaunas). 2019 Sep 25;55(10):638. doi: 10.3390/medicina55100638. PMID: 31557975; PMCID: PMC6843642.
  7. I used the Web of Science database to perform an unrestricted search on my assigned keywords (2019-nCoV and immune reaction).
    1. My search yielded 4 results.
    2. I recorded the 4 papers below:
      • Paper 1: Goli, M. (2020). Review of novel human β‐coronavirus (2019‐nCoV or SARS‐CoV‐2) from the food industry perspective—Appropriate approaches to food production technology. Food Science & Nutrition, 8(10), 5228-5237. doi:10.1002/fsn3.1892
      • Paper 2: Singh, S. P., Pritam, M., Pandey, B., & Yadav, T. P. (2020). Microstructure, pathophysiology, and potential therapeutics of COVID‐19: A comprehensive review. Journal of Medical Virology. doi:10.1002/jmv.26254
      • Paper 3: Mungroo, M. R., Khan, N. A., & Siddiqui, R. (2020). Novel Coronavirus: Current Understanding of Clinical Features, Diagnosis, Pathogenesis, and Treatment Options. Pathogens, 9(4), 297. doi:10.3390/pathogens9040297
      • Paper 4: Zhang, D., Wu, K., Zhang, X., Deng, S., & Peng, B. (2020). In silico screening of Chinese herbal medicines with the potential to directly inhibit 2019 novel coronavirus. Journal of Integrative Medicine, 18(2), 152-158. doi:10.1016/j.joim.2020.02.005
  8. The class created a shared bibliography. I went through the search results that I have found and added articles to the shared bibliography page.
  9. After creating the shared bibliography, each student chose one article. I have recorded the APA citation for my article below:
    • Xu, X., Han, M., Li, T., Sun, W., Wang, D., Fu, B., ... & Zhang, X. (2020). Effective treatment of severe COVID-19 patients with tocilizumab. Proceedings of the National Academy of Sciences, 117(20), 10970-10975.
  10. I used Web of Science to search for the article I chose.
    • The article has 22 cited references.
    • The article has been cited in other articles 391 times.
  11. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
    • Google Scholar: advantages
      • Google Scholar provides more search results, as it is able to search through many databases at once. It is also very easy to get citations in MLA, APA, Chicago, etc.
    • Google Scholar: disadvantages
      • The results vary in their quality and reliability. Articles need to be more closely analyzed to ensure they are peer-reviewed and accurate.
    • PubMed: advantages
      • PubMed has many advanced search options, allowing you to get more relevant results. PubMed is very useful when researching topics related to health and medicine.
    • Pubmed: disadvantages
      • Citing articles from PubMed is not as simple as it is on Google Scholar, and the results are not always the full text version. PubMed is also has more limited results, as its search is not as broad as Google Scholar's.
    • Web of Science: advantages
      • Web of Science allows you to save articles and searches, making it easy to search through any articles without having to open all of them. There are also more advanced search options, making it possible to find more relevant results. Lastly, you can search through articles that have not yet been published.
    • Web of Science: disadvantages
      • Web of Science is not a free database, so it isn't as accessible as Google Scholar or PubMed. It also requires that you do manual citations of the articles, as there is no cite option on the site.
  12. What impact does choice of keywords have on your results?
    • Slight changes in keywords can have pretty dramatic effects on the results you receive. This exercise how important it is to take your time when conducting research and complete multiple searches on a variety of databases. This provides a more diverse array of articles.

Scientific Conclusion

This exercise demonstrated how results differ greatly based on different databases, search keywords, and search filters that are used. I was already very familiar with Google Scholar and fairly familiar with PubMed, but I had never used Web of Science. I will definitely be using it in the future, as it is an extremely useful source for conducting research. By using a variety of search engines and filters, I was able to find many interesting and useful articles, despite only searching one specific phrase, "2019-nCoV and immune reaction."

Acknowledgments

  1. I worked with my homework partner Fatimah Alghanem to complete this week's assignment.
  2. I copied and modified procedures from the Week 10 assignment page.
  3. Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

(Macie Duran (talk) 20:42, 11 November 2020 (PST))

References