BIOL368/S19 Week 10

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BIOL368/F20 BIOL368/F20:People

Purpose

The purpose of this lab is that we learn the different results that different scientific search engines give. Also how results from our search are affected by keywords used and specifications of date, and other factors like author name. In this lab, we learn how to navigate through the different search engines like Pubmed and Google Scholar and be able to determine the one that would provide the most suitable results for our research.

Answers

  1. Warm up exercise (announced in class)
  2. Perform a search in Google Scholar.
    • Record the number of “hits” you found:
      • 180,000
    • Record the top 10 papers, this time using APA format:
    1. Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature medicine, 26(4), 450-452.
    2. Lu, X., Zhang, L., Du, H., Zhang, J., Li, Y. Y., Qu, J., ... & Wu, C. (2020). SARS-CoV-2 infection in children. New England Journal of Medicine, 382(17), 1663-1665.
    3. Van Doremalen, N., Bushmaker, T., Morris, D. H., Holbrook, M. G., Gamble, A., Williamson, B. N., ... & Lloyd-Smith, J. O. (2020). Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. New England Journal of Medicine, 382(16), 1564-1567.
    4. Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell.
    5. Wang, W., Xu, Y., Gao, R., Lu, R., Han, K., Wu, G., & Tan, W. (2020). Detection of SARS-CoV-2 in different types of clinical specimens. Jama, 323(18), 1843-1844.
    6. Gudbjartsson, D. F., Norddahl, G. L., Melsted, P., Gunnarsdottir, K., Holm, H., Eythorsson, E., ... & Thorsteinsdottir, B. (2020). Humoral immune response to SARS-CoV-2 in Iceland. New England Journal of Medicine, 383(18), 1724-1734.
    7. Liu, Y., Ning, Z., Chen, Y., Guo, M., Liu, Y., Gali, N. K., ... & Liu, X. (2020). Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Nature, 582(7813), 557-560.
    8. Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221-224.
    9. Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., ... & Xiang, Z. (2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature communications, 11(1), 1-12.
    10. Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., ... & Peter, A. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 1-6.
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    1. Paramasivam, A. (2020). RNA 2′-O-methylation modification and its implication in COVID-19 immunity. Cell Death Discovery, 6(1), 1-3.
    2. Burić, N., & Stojanović, S. (2020). Occupational hazard for Dental staff exposed to the SARS-CoV-2 virus during Dental procedures. Acta stomatologica Naissi, 36(81), 1995-2006.
    3. Sahu, K. K., & Cerny, J. (2020). A review on how to do hematology consults during COVID-19 pandemic. Blood Reviews, 100777.
    4. Sofi, M. S., Hamid, A., & Bhat, S. U. (2020). Coronavirus COVID-19: A critical review of its history, pathogenesis, transmission, diagnosis and treatment. Biosafety and Health.
    5. Aralova, N. I. (2020). Integrated Mathematical Model of Self-Organization of Functional Systems of Organism for Simulation of Viral Diseases. Journal of Automation and Information Sciences, 52(7).
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    1. Lu, X., Zhang, L., Du, H., Zhang, J., Li, Y. Y., Qu, J., ... & Wu, C. (2020). SARS-CoV-2 infection in children. New England Journal of Medicine, 382(17), 1663-1665.
    2. Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221-224.
    3. Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., ... & Peter, A. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 1-6.
    4. Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., ... & Xiang, Z. (2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature communications, 11(1), 1-12.
    5. Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020). Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences, 117(21), 11727-11734.
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    1. Lu, X., Zhang, L., Du, H., Zhang, J., Li, Y. Y., Qu, J., ... & Wu, C. (2020). SARS-CoV-2 infection in children. New England Journal of Medicine, 382(17), 1663-1665.
    2. Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221-224.
    3. Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F. (2020). The proximal origin of SARS-CoV-2. Nature medicine, 26(4), 450-452.
    4. Petersen, E., Koopmans, M., Go, U., Hamer, D. H., Petrosillo, N., Castelli, F., ... & Simonsen, L. (2020). Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics. The Lancet infectious diseases.
    5. Pinto, D., Park, Y. J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., ... & Peter, A. (2020). Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature, 1-6.
  6. We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
    • 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
    • Record the search terms that have now been assigned specifically to yo
      • 2019-nCoV and antibodies
  7. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits
      • 2,098
    • Record the top 10 papers (you don't need to do APA format for this):
    1. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260-1263. doi: 10.1126/science.abb2507. Epub 2020 Feb 19. PMID: 32075877; PMCID: PMC7164637.
    2. Jiang S, Hillyer C, Du L. Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses. Trends Immunol. 2020 May;41(5):355-359. doi: 10.1016/j.it.2020.03.007. Epub 2020 Apr 2. Erratum in: Trends Immunol. 2020 Apr 24;: PMID: 32249063; PMCID: PMC7129017.
    3. AminJafari A, Ghasemi S. The possible of immunotherapy for COVID-19: A systematic review. Int Immunopharmacol. 2020 Jun;83:106455. doi: 10.1016/j.intimp.2020.106455. Epub 2020 Apr 2. PMID: 32272396; PMCID: PMC7128194.
    4. Jin Y, Wang M, Zuo Z, Fan C, Ye F, Cai Z, Wang Y, Cui H, Pan K, Xu A. Diagnostic value and dynamic variance of serum antibody in coronavirus disease 2019. Int J Infect Dis. 2020 May;94:49-52. doi: 10.1016/j.ijid.2020.03.065. Epub 2020 Apr 3. PMID: 32251798; PMCID: PMC7194885.
    5. Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, Lu L, Jiang S, Yang Z, Wu Y, Ying T. Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerg Microbes Infect. 2020 Feb 17;9(1):382-385. doi: 10.1080/22221751.2020.1729069. PMID: 32065055; PMCID: PMC7048180.
    6. Klasse PJ, Moore JP. Antibodies to SARS-CoV-2 and their potential for therapeutic passive immunization. Elife. 2020 Jun 23;9:e57877. doi: 10.7554/eLife.57877. PMID: 32573433; PMCID: PMC7311167.
    7. Kruse RL. Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China. F1000Res. 2020 Jan 31;9:72. doi: 10.12688/f1000research.22211.2. PMID: 32117569; PMCID: PMC7029759.
    8. Saghazadeh A, Rezaei N. Towards treatment planning of COVID-19: Rationale and hypothesis for the use of multiple immunosuppressive agents: Anti-antibodies, immunoglobulins, and corticosteroids. Int Immunopharmacol. 2020 Jul;84:106560. doi: 10.1016/j.intimp.2020.106560. Epub 2020 May 8. PMID: 32413736; PMCID: PMC7205724.
    9. Liu W, Liu L, Kou G, Zheng Y, Ding Y, Ni W, Wang Q, Tan L, Wu W, Tang S, Xiong Z, Zheng S. Evaluation of Nucleocapsid and Spike Protein-Based Enzyme-Linked Immunosorbent Assays for Detecting Antibodies against SARS-CoV-2. J Clin Microbiol. 2020 May 26;58(6):e00461-20. doi: 10.1128/JCM.00461-20. PMID: 32229605; PMCID: PMC7269413.
    10. Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C, Song G, Woehl J, Yang L, Abbott RK, Callaghan S, Garcia E, Hurtado J, Parren M, Peng L, Ramirez S, Ricketts J, Ricciardi MJ, Rawlings SA, Wu NC, Yuan M, Smith DM, Nemazee D, Teijaro JR, Voss JE, Wilson IA, Andrabi R, Briney B, Landais E, Sok D, Jardine JG, Burton DR. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science. 2020 Aug 21;369(6506):956-963. doi: 10.1126/science.abc7520. Epub 2020 Jun 15. PMID: 32540903; PMCID: PMC7299280.
  8. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits
      • 48
    • Record the top 10 papers (you don't need to do APA format for this):
    1. Wrapp D, Wang N, Corbett KS, Goldsmith JA, Hsieh CL, Abiona O, Graham BS, McLellan JS. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020 Mar 13;367(6483):1260-1263. doi: 10.1126/science.abb2507. Epub 2020 Feb 19. PMID: 32075877; PMCID: PMC7164637.
    2. Tu YF, Chien CS, Yarmishyn AA, Lin YY, Luo YH, Lin YT, Lai WY, Yang DM, Chou SJ, Yang YP, Wang ML, Chiou SH. A Review of SARS-CoV-2 and the Ongoing Clinical Trials. Int J Mol Sci. 2020 Apr 10;21(7):2657. doi: 10.3390/ijms21072657. PMID: 32290293; PMCID: PMC7177898. (review)
    3. Jiang S, Hillyer C, Du L. Neutralizing Antibodies against SARS-CoV-2 and Other Human Coronaviruses. Trends Immunol. 2020 May;41(5):355-359. doi: 10.1016/j.it.2020.03.007. Epub 2020 Apr 2. Erratum in: Trends Immunol. 2020 Apr 24;: PMID: 32249063; PMCID: PMC7129017.
    4. Tian X, Li C, Huang A, Xia S, Lu S, Shi Z, Lu L, Jiang S, Yang Z, Wu Y, Ying T. Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody. Emerg Microbes Infect. 2020 Feb 17;9(1):382-385. doi: 10.1080/22221751.2020.1729069. PMID: 32065055; PMCID: PMC7048180.
    5. Chen Y, Guo Y, Pan Y, Zhao ZJ. Structure analysis of the receptor binding of 2019-nCoV. Biochem Biophys Res Commun. 2020 Feb 17;525(1):135–40. doi: 10.1016/j.bbrc.2020.02.071. Epub ahead of print. PMID: 32081428; PMCID: PMC7092824.
    6. Li H, Wang YM, Xu JY, Cao B. [Potential antiviral therapeutics for 2019 Novel Coronavirus]. Zhonghua Jie He He Hu Xi Za Zhi. 2020 Feb 5;43(0):E002. Chinese. doi: 10.3760/cma.j.issn.1001-0939.2020.0002. Epub ahead of print. PMID: 32023685.
    7. Li H, Wang YM, Xu JY, Cao B. [Potential antiviral therapeutics for 2019 Novel Coronavirus]. Zhonghua Jie He He Hu Xi Za Zhi. 2020 Mar 12;43(3):170-172. Chinese. doi: 10.3760/cma.j.issn.1001-0939.2020.03.004. PMID: 32164080.
    8. Tai W, He L, Zhang X, Pu J, Voronin D, Jiang S, Zhou Y, Du L. Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Cell Mol Immunol. 2020 Jun;17(6):613-620. doi: 10.1038/s41423-020-0400-4. Epub 2020 Mar 19. PMID: 32203189; PMCID: PMC7091888.
    9. Pillay TS. Gene of the month: the 2019-nCoV/SARS-CoV-2 novel coronavirus spike protein. J Clin Pathol. 2020 Jul;73(7):366-369. doi: 10.1136/jclinpath-2020-206658. Epub 2020 May 6. PMID: 32376714. (review)
    10. Shanmugaraj B, Siriwattananon K, Wangkanont K, Phoolcharoen W. Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19). Asian Pac J Allergy Immunol. 2020 Mar;38(1):10-18. doi: 10.12932/AP-200220-0773. PMID: 32134278. (review)
  9. Add the word “Review” to any articles that are review articles that you listed in question 8.
  10. Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
    • Do you find any new articles that you did not find before on PubMed?
      • Yes I found new articles that I did not find before.
    • Record the top 10 papers (you don't need to use APA format for this):
    1. Xu JY, Zhang C, Wang X, Zhai L, Ma Y, Mao Y, Qian K, Sun C, Liu Z, Jiang S, Wang M, Feng L, Zhao L, Liu P, Wang B, Zhao X, Xie H, Yang X, Zhao L, Chang Y, Jia J, Wang X, Zhang Y, Wang Y, Yang Y, Wu Z, Yang L, Liu B, Zhao T, Ren S, Sun A, Zhao Y, Ying W, Wang F, Wang G, Zhang Y, Cheng S, Qin J, Qian X, Wang Y, Li J, He F, Xiao T, Tan M. Integrative Proteomic Characterization of Human Lung Adenocarcinoma. Cell. 2020 Jul 9;182(1):245-261.e17. doi: 10.1016/j.cell.2020.05.043. PMID: 32649877.
    2. Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell. 2020 Jul 23;182(2):497-514.e22. doi: 10.1016/j.cell.2020.05.039. Epub 2020 Jun 23. Erratum in: Cell. 2020 Sep 17;182(6):1661-1662. PMID: 32579974; PMCID: PMC7391009.
    3. Li L, Li X, Xia Y, Chu Y, Zhong H, Li J, Liang P, Bu Y, Zhao R, Liao Y, Yang P, Lu X, Jiang S. Recommendation of Antimicrobial Dosing Optimization During Continuous Renal Replacement Therapy. Front Pharmacol. 2020 May 29;11:786. doi: 10.3389/fphar.2020.00786. PMID: 32547394; PMCID: PMC7273837.
    4. Su S, Du L, Jiang S. Learning from the past: development of safe and effective COVID-19 vaccines. Nat Rev Microbiol. 2020 Oct 16:1–9. doi: 10.1038/s41579-020-00462-y. Epub ahead of print. PMID: 33067570; PMCID: PMC7566580.
    5. Wang X, Xu W, Hu G, Xia S, Sun Z, Liu Z, Xie Y, Zhang R, Jiang S, Lu L. Retraction Note to: SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion. Cell Mol Immunol. 2020 Aug;17(8):894. doi: 10.1038/s41423-020-0498-4. PMID: 32651469; PMCID: PMC7348563.
    6. Guo L, Zhao S, Li W, Wang Y, Li L, Jiang S, Ren W, Yuan Q, Zhang F, Kong F, Lei J, Yuan M. Absence of SARS-CoV-2 in semen of a COVID-19 patient cohort. Andrology. 2020 Jun 29:10.1111/andr.12848. doi: 10.1111/andr.12848. Epub ahead of print. PMID: 32598557; PMCID: PMC7362062.
    7. Gu H, Chen Q, Yang G, He L, Fan H, Deng YQ, Wang Y, Teng Y, Zhao Z, Cui Y, Li Y, Li XF, Li J, Zhang NN, Yang X, Chen S, Guo Y, Zhao G, Wang X, Luo DY, Wang H, Yang X, Li Y, Han G, He Y, Zhou X, Geng S, Sheng X, Jiang S, Sun S, Qin CF, Zhou Y. Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Science. 2020 Sep 25;369(6511):1603-1607. doi: 10.1126/science.abc4730. Epub 2020 Jul 30. PMID: 32732280; PMCID: PMC7574913.
    8. Fan L, Jiang S, Yang X, Wang Z, Yang C. COVID-19 Drug Treatment in China. Curr Pharmacol Rep. 2020 Jun 19:1-9. doi: 10.1007/s40495-020-00218-5. Epub ahead of print. PMID: 32837851; PMCID: PMC7302922.
    9. Jiang Y, Chen D, Cai D, Yi Y, Jiang S. Effectiveness of remdesivir for the treatment of hospitalized COVID-19 persons: A network meta-analysis. J Med Virol. 2020 Aug 19:10.1002/jmv.26443. doi: 10.1002/jmv.26443. Epub ahead of print. PMID: 32813283; PMCID: PMC7461548.
    10. Zhang H, Liu M, Zhang H, Cao S, Li Y, Jiang S, Song Y, Liu S. Detection of p53 mutation and serum monitoring alert caused by Marek's disease virus in poultry. BMC Vet Res. 2020 Aug 24;16(1):303. doi: 10.1186/s12917-020-02520-2. PMID: 32831091; PMCID: PMC7444044.
  11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:
      • 67
    • Record the top 10 papers (you don't need to use APA format for this):
    1. Interpretive discrepancies caused by target values inter-batch variations in chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG by MAGLUMI
    2. Structures of theSARS-CoV-2 nucleocapsid and their perspectives for drug design
    3. 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
    4. Stroke and Novel Coronavirus Infection in Humans: A Systematic Review and Meta-Analysis
    5. Addition of Tocilizumab to the Standard of Care Reduces Mortality in Severe COVID-19: A Systematic Review and Meta-Analysis
    6. Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscape
    7. SARS-CoV-2 pathophysiology and assessment of coronaviruses in CNS diseases with a focus on therapeutic targets
    8. COVID-19: benefits and risks of passive immunotherapeutics
    9. Structures of theSARS-CoV-2 nucleocapsid and their perspectives for drug design
    10. Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19: An evidence-based clinical practice guideline (updated version)
  12. We will now create a shared bibliography for the entire class. Go through the search results that you have found and add articles to the class shared bibliography page.
    • Only add articles that are unique (everyone will be adding to the page and we do not want redundant articles)
    • 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.
    • Add the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Add your wiki signature to the end of the citation.
    • Ideally, each student will contribute 2-3 unique articles that would be worthy of a journal club. Add articles that are related to what you are interested in investigating for the second research project.
  13. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
    • Wu, J. L., Tseng, W. P., Lin, C. H., Lee, T. F., Chung, M. Y., Huang, C. H., ... & Chen, S. C. (2020). Four point-of-care lateral flow immunoassays for diagnosis of COVID-19 and for assessing dynamics of antibody responses to SARS-CoV-2. Journal of Infection, 81(3), 435-442.
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have? 22 cited references
      • How many articles have cited the article you have been assigned? One article has cited the article that I chose.
  14. 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 gives a large number of papers as it gives a wide amount of results, also it gives citations in APA, MLA, Chicago, etc.. for each article.
    • Google Scholar: disadvantages
      • One disadvantage of google scholar is that it doesn't provide advanced search options. Another disadvantage is that the results are not as specific to the topic searched.
    • PubMed: advantages
      • One advantage of Pubmed is that it provides an advanced search option. Another advantage is that it's easy to cite a paper from it.
    • PubMed: disadvantages
      • PubMed gives a low number of results, there are not many options when compared to other search engines. Also navigating could be a little confusing.
    • Web of Science: advantages
      • Web of science gives the abstract of a paper without having to open it which is helpful. Also, it provides science categories that help in specifying the type of paper one is looking for.
    • Web of Science: disadvantages
      • It's not easy to cite a paper from Web of Science, one has to do manual citation. Additionally, it provides a low number of results when compared to other search engines like google scholar
  15. What impact does the choice of keywords have on your results?
    • choice of keywords could impact the number of results that you get. Also how recent the papers are depending on how often the keyword searched is used recently in the field.

Scientific Conclusion

This exercise helped me learn about scientific databases that I did not know about before. prior to this exercise, I learned about how searching for the same thing using different words could result in having significantly different results which is something that I should pay attention to more in my future researches.

Acknowledgments

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Falghane (talk) 04:23, 12 November 2020 (PST)

References

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