Aiden Burnett Week 10

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Purpose

To gain a deeper understanding of some prominent databases, as well as how to navigate them in a manner which will be conducive to my future research efforts.

Methods & Results

  1. I performed a search in Google Scholar using the term "Civet ACE2".
    1. Recorded the number of “hits” found: 2,440
    2. Record the top 10 papers, this time using APA format:
      • Li, W., Zhang, C., Sui, J., Kuhn, J. H., Moore, M. J., Luo, S., ... & Murakami, A. (2005). Receptor and viral determinants of SARS‐coronavirus adaptation to human ACE2. The EMBO journal, 24(8), 1634-1643.
      • Li, W., Wong, S. K., Li, F., Kuhn, J. H., Huang, I. C., Choe, H., & Farzan, M. (2006). Animal origins of the severe acute respiratory syndrome coronavirus: insight from ACE2-S-protein interactions. Journal of virology, 80(9), 4211-4219.
      • Ge, X. Y., Li, J. L., Yang, X. L., Chmura, A. A., Zhu, G., Epstein, J. H., ... & Zhang, Y. J. (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature, 503(7477), 535-538.
      • Liu, Z., Xiao, X., Wei, X., Li, J., Yang, J., Tan, H., ... & Liu, L. (2020). Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. Journal of medical virology, 92(6), 595-601.
      • Li, R., Qiao, S., & Zhang, G. (2020). Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV. Journal of Infection, 80(4), 469-496.
      • Li, F. (2008). Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections. Journal of virology, 82(14), 6984-6991.
      • Lopes, L. R., de Mattos Cardillo, G., & Paiva, P. B. (2020). Molecular evolution and phylogenetic analysis of SARS-CoV-2 and hosts ACE2 protein suggest Malayan pangolin as intermediary host. Brazilian Journal of Microbiology, 1-7.
      • Zhai, X., Sun, J., Yan, Z., Zhang, J., Zhao, J., Zhao, Z., ... & Su, S. (2020). Comparison of severe acute respiratory syndrome coronavirus 2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts. Journal of virology, 94(15).
      • Hou, Y., Peng, C., Yu, M., Li, Y., Han, Z., Li, F., ... & Shi, Z. (2010). Angiotensin-converting enzyme 2 (ACE2) proteins of different bat species confer variable susceptibility to SARS-CoV entry. Archives of virology, 155(10), 1563-1569.
      • Li, W., Sui, J., Huang, I. C., Kuhn, J. H., Radoshitzky, S. R., Marasco, W. A., ... & Farzan, M. (2007). The S proteins of human coronavirus NL63 and severe acute respiratory syndrome coronavirus bind overlapping regions of ACE2. Virology, 367(2), 367-374.
  2. Sorted my results by date (instead of relevance), and recorded the top 5 papers, using APA format:
    • Xie, X., Plante, K. S., Weaver, S. C., & Shi, P. Y. Jessica A. Plante1, 2, 3, 12, Yang Liu4, 12, Jianying Liu2, 3, 12, Hongjie Xia4, Bryan A. Johnson2, Kumari G. Lokugamage3, Xianwen Zhang4, Antonio E. Muruato2, 3, Jing Zou4, Camila R. Fontes-Garfias4, Divya Mirchandani1, 2, 3, Dionna Scharton1, 2, 3, John P. Bilello5, Zhiqiang Ku6, Zhiqiang An6, Birte Kalveram7, Alexander N. Freiberg2, 7, 9, 10, Vineet D. Menachery2, 3.
    • Palanivelu, P. (2020). Analyses of the Spike Proteins of Severe Acute Respiratory Syndrome-Related Coronaviruses. Microbiology Research Journal International, 32-50.
    • Pattnaik, B., & Yadav, M. P. (2020). Covid-19 pandemic: History, aetiology, epidemiology, vaccinology and societal impact. Indian Journal of Comparative Microbiology, Immunology and Infectious Diseases, 41(1), 1-18.
    • Öztan, G., & İşsever, H. Yeni Koronavirüsün (Covid-19) Moleküler Yapısı ve Genomik Karakterizasyonu. Sağlık Bilimlerinde İleri Araştırmalar Dergisi, 3(2), 61-71.
    • Bortolini, M. C. Coronavirus Sars-Cov-2 responsible for the COVID-19 pandemic is a specialist in infecting humans.
  3. Filtered my results using “Since 2019”, and recorded the top 5 papers, using APA format:
    • Li, R., Qiao, S., & Zhang, G. (2020). Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV. Journal of Infection, 80(4), 469-496.
    • Liu, Z., Xiao, X., Wei, X., Li, J., Yang, J., Tan, H., ... & Liu, L. (2020). Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. Journal of medical virology, 92(6), 595-601.
    • Lopes, L. R., de Mattos Cardillo, G., & Paiva, P. B. (2020). Molecular evolution and phylogenetic analysis of SARS-CoV-2 and hosts ACE2 protein suggest Malayan pangolin as intermediary host. Brazilian Journal of Microbiology, 1-7.
    • Zhai, X., Sun, J., Yan, Z., Zhang, J., Zhao, J., Zhao, Z., ... & Su, S. (2020). Comparison of severe acute respiratory syndrome coronavirus 2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts. Journal of virology, 94(15).
    • Mou, H., Quinlan, B., Peng, H., Guo, Y., Peng, S., Zhang, L., ... & Alpert, M. (2020). Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2. bioRxiv.
  4. Filtered my results using “Since 2016”, and recorded the top 5 papers, using APA format:
    • Li, R., Qiao, S., & Zhang, G. (2020). Analysis of angiotensin-converting enzyme 2 (ACE2) from different species sheds some light on cross-species receptor usage of a novel coronavirus 2019-nCoV. Journal of Infection, 80(4), 469-496.
    • Liu, Z., Xiao, X., Wei, X., Li, J., Yang, J., Tan, H., ... & Liu, L. (2020). Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2. Journal of medical virology, 92(6), 595-601.
    • Lopes, L. R., de Mattos Cardillo, G., & Paiva, P. B. (2020). Molecular evolution and phylogenetic analysis of SARS-CoV-2 and hosts ACE2 protein suggest Malayan pangolin as intermediary host. Brazilian Journal of Microbiology, 1-7.
    • Zhai, X., Sun, J., Yan, Z., Zhang, J., Zhao, J., Zhao, Z., ... & Su, S. (2020). Comparison of severe acute respiratory syndrome coronavirus 2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts. Journal of virology, 94(15).
    • Mou, H., Quinlan, B., Peng, H., Guo, Y., Peng, S., Zhang, L., ... & Alpert, M. (2020). Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2. bioRxiv.
  5. We then made a list of the search terms that were used by each student in the class. These were recorded below:
    • 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
    • Recorded the search term(s) that have now been assigned specifically to me:
      • 2019-nCoV and immune response
    1. Recorded the number of “hits” found: 2,440
  6. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
    • Recorded the total number of hits on google scholar: "about 25,600"
    • Recorded the total number of hits on pubmed: 1,340
    • Recorded the top 10 papers on PubMed:
      1. Overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses SARS-CoV, MERS-CoV, and 2019-nCo
      2. Immune Response, Inflammation, and the Clinical Spectrum of COVID-19
      3. Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in COVID-19.
      4. COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs.
      5. COVID-19: Unanswered questions on immune response and pathogenesis.
      6. Initial Public Health Response and Interim Clinical Guidance for the 2019 Novel Coronavirus Outbreak - United States, December 31, 2019-February 4, 2020.
      7. Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV.
      8. [Progress and challenge of vaccine development against 2019-novel coronavirus (2019-nCoV)].
      9. COVID-19: Immunology and treatment options.
      10. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic.
  7. Performed a title/abstract search on my assigned keywords.
    • Recorded the total number of hits: 33
    • Record the top 10 papers (you don't need to do APA format for this):
      1. [Progress and challenge of vaccine development against 2019-novel coronavirus (2019-nCoV)].
      2. The pathogenesis and treatment of the `Cytokine Storm' in COVID-19.
      3. The Immune Response and Immunopathology of COVID-19.
      4. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV.
      5. [From SARS to COVID-19: pathogens, receptor, pathogenesis and principles of the treatment].
      6. The Potential Impact of Zinc Supplementation on COVID-19 Pathogenesis.
      7. Assessment of immune response to SARS-CoV-2 with fully automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays.
      8. COVID-19 and what pediatric rheumatologists should know: a review from a highly affected country.
      9. Risk factors associated with disease progression in a cohort of patients infected with the 2019 novel coronavirus.
      10. 2019-nCoV: a worldwide concern and facts.
  8. Add the word “Review” to any articles that are review articles that you listed in question 8.
  9. Picked an author that showed up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and performed an author search on the name Zhonghua Yu
    • Do you find any new articles that you did not find before on PubMed?
      • Zhonghua Yu
    • List up to 5 new articles that were found on the author name search:
      1. High-Risk Factors for Suppurative Mastitis in Lactating Women.
      2. Erastin decreases radioresistance of NSCLC cells partially by inducing GPX4-mediated ferroptosis.
      3. MicroRNA-494-3p Promotes Cell Growth, Migration, and Invasion of Nasopharyngeal Carcinoma by Targeting Sox7.
      4. Enhanced expression of SETDB1 possesses prognostic value and promotes cell proliferation, migration and invasion in nasopharyngeal carcinoma.
      5. Niclosamide sensitizes nasopharyngeal carcinoma to radiation by downregulating Ku70/80 expression.
  10. Now access the Web of Science database. Performed an unrestricted search on my assigned keyword.
    • Recorded the total number of hits: 51
    • Record the top 10 papers (you don't need to use APA format for this):
      1. Harnessing the immune system to overcome cytokine storm and reduce viral load in COVID-19: a review of the phases of illness and therapeutic agents
      2. The CHIR Score for Evaluating the Hyperimmune Response in COVID-19: A Preliminary Concept
      3. Potential Therapeutic Options for COVID-19: Current Status, Challenges, and Future Perspectives
      4. Protection against COVID-19 injury by qingfei paidu decoction via anti-viral, anti-inflammatory activity and metabolic programming
      5. The Immune Response and Immunopathology of COVID-19
      6. Interleukin-6 in Covid-19: A systematic review andmeta-analysis
      7. Overview of the First 6 Months of Clinical Trials for COVID-19 Pharmacotherapy: The Most Studied Drugs
      8. Innate Immune Responses to Highly Pathogenic Coronaviruses and Other Significant Respiratory Viral Infections
      9. The Comparative Immunological Characteristics of SARS-CoV, MERS-CoV, and SARS-CoV-2 Coronavirus Infections
      10. From H1N1 to 2019-nCoV, what do we learn?
  11. We then now created a shared bibliography for the entire class. This can be found at the class shared bibliography page.
    • Put review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, place it in the other articles section.
  12. After we had our shared bibliography, each student was assigned one article. I recorded the citation for my article in APA format:
    • Yuan S, Jiang SC, Li ZL. Analysis of Possible Intermediate Hosts of the New Coronavirus SARS-CoV-2. Front Vet Sci. 2020 Jun 9;7:379. doi: 10.3389/fvets.2020.00379. PMID: 32582786; PMCID: PMC7297130.
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
        • 38
      • How many articles have cited the article you have been assigned?
        • 0
  13. 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: disadvantages
    • PubMed: advantages
    • Pubmed: disadvantages
    • Web of Science: advantages
    • Web of Science: disadvantages
  14. What impact does choice of keywords have on your results?
    • They can exclude or include sources based on which words I use. For example, on PubMed "COVID-19 and immune response" yields 241,000 results while ""SARS-CoV-2 and immune response" yields 48,800. These seemingly similar searches yield drastically different results, illustrating the importance of carefully considering one's keywords.

Scientific Conclusion

Going into this exercise I already had a competent knowledge of how to write search queries. I knew of Google Scholar and PubMed. I did not know about the Wed of Science, which I will make a note about and try to use in future research. Generally my first stop when researching is the William H. Hannon library OneSearch, and then any relevant subject databases that they maintain or link to. Web of Science will be a good option after these. I already knew about the importance of keywords but this exercise has stressed the importance of using "OR" or asterisks to broaden search terms, such as searching "Buddh*" to find sources with Buddhism, Buddha, Buddhist, etc.

Acknowledgments

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Aiden Burnett (talk) 17:07, 11 November 2020 (PST)

References

  1. OpenWetWare. (2020). BIOL368/F20:Week 10. Retrieved 11 November 2020, from https://openwetware.org/wiki/BIOL368/F20:Week_10.
  2. Google Scholar. (2020). Google Scholar. Retrieved 11 November 2020, from https://scholar.google.com/.
  3. PubMed. (2020). Retrieved 11 November 2020, from https://pubmed.ncbi.nlm.nih.gov/?holding=calmulib
  4. Web of Science. (2020). Web of Science. Retrieved 11 November 2020, from http://apps.webofknowledge.com/WOS_GeneralSearch_input.doproduct=WOS&search_mode=GeneralSearch&SID=5B2dLyJmepJiIyQnSaI&preferencesSaved=.

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