Nathan R Beshai Week 10

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Nathan R. Beshai

Course assignments

  1. Week 1
  2. Week 2
  3. Week 3
  4. Week 4
  5. Week 5
  6. Week 6
  7. Week 7
  8. Week 8
  9. Week 9
  10. Week 10
  11. Week 11
  12. Week 12
  13. Week 14

Individual journal assignments

  1. Nathan R Beshai Week 2
  2. Nathan R Beshai Week 3
  3. Nathan R Beshai Week 4
  4. Nathan R Beshai Week 5
  5. Nathan R Beshai Week 6
  6. Nathan R Beshai Week 7
  7. Nathan R Beshai Week 8
  8. Nathan R Beshai Week 9
  9. Nathan R Beshai Week 10
  10. Nathan R Beshai Week 11
  11. The D614G Research Group Week 12
  12. The D614G Research Group Week 14

Class Journals

  1. Class Journal 1
  2. Class Journal 2
  3. Class Journal 3
  4. Class Journal 4
  5. Class Journal 5
  6. Class Journal 6
  7. Class Journal 7
  8. Class Journal 8
  9. Class Journal 9
  10. Class Journal 10
  11. Class Journal 11
  12. Class Journal 12
  13. Class Journal 14

Link to Brightspace and LMU's Homepage

  1. Link to Brightspace
  2. Link to LMU's Homepage

Purpose

  • Learning how to choose a more efficient database and being able to navigate through databases. This will help filter out articles that are not needed and produce the most relevant articles.

Methods and Results

  1. Performed a search in Google Scholar.
    • Covid-19 transmission
    1. Recorded the number of “hits” I found:
      • 495,000 results
    2. Recorded the top 10 papers, this time using APA format:
      • Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K. A., ... & Sim, E. M. (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature medicine, 26(9), 1398-1404.
      • Badr, H. S., Du, H., Marshall, M., Dong, E., Squire, M. M., & Gardner, L. M. (2020). Association between mobility patterns and COVID-19 transmission in the USA: a mathematical modeling study. The Lancet Infectious Diseases.
      • Qian, G., Yang, N., Ma, A. H. Y., Wang, L., Li, G., Chen, X., & Chen, X. (2020). COVID-19 transmission within a family cluster by presymptomatic carriers in China. Clinical Infectious Diseases.
      • Mitjà, O., & Clotet, B. (2020). Use of antiviral drugs to reduce COVID-19 transmission. The Lancet Global Health, 8(5), e639-e640.
      • Nishiura, H., Oshitani, H., Kobayashi, T., Saito, T., Sunagawa, T., Matsui, T., ... & Suzuki, M. (2020). Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19). MedRxiv.
      • Izzetti, R., Nisi, M., Gabriele, M., & Graziani, F. (2020). COVID-19 transmission in dental practice: brief review of preventive measures in Italy. Journal of Dental Research, 0022034520920580.
      • Yu, X., & Yang, R. (2020). COVID‐19 transmission through asymptomatic carriers is a challenge to containment. Influenza and Other Respiratory Viruses.
      • Lee, B., & Raszka, W. V. (2020). COVID-19 transmission and children: the child is not to blame. Pediatrics, 146(2).
      • Liu, J., Zhou, J., Yao, J., Zhang, X., Li, L., Xu, X., ... & Yan, J. (2020). Impact of meteorological factors on the COVID-19 transmission: A multi-city study in China. Science of the Total Environment, 138513.
      • Tuite, A. R., Fisman, D. N., & Greer, A. L. (2020). Mathematical modelling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada. CMAJ, 192(19), E497-E505.
  2. Sorted my results by date (instead of relevance), and recorded the top 5 papers, using APA format:
    • Liu, N., Chen, Z., & Bao, G. (2020). Role of Media Coverage in Mitigating COVID-19 Transmission: Evidence from China. Technological Forecasting and Social Change, 120435.
    • Chisale, M. R., Ramazanu, S., Wu, J. T. S., Sinyiza, F. W., Bvumbwe, T., Nyambalo, B., & Mbakaya, B. C. (2020). Community-based interventions for preventing COVID-19 transmission in low-and middle-income countries: A systematic review.
    • Hassard, F., Lundy, L., Singer, A. C., Grimsley, J., & Di Cesare, M. (2020). Innovation in wastewater near-source tracking for rapid identification of COVID-19 in schools. The Lancet Microbe.
    1. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Arif, M., & Sengupta, S. (2020). Nexus between population density and novel coronavirus (COVID-19) pandemic in the south Indian states: A geo-statistical approach. Environment, Development and Sustainability, 1-29.
    • Palialol, B., Pereda, P., & Azzoni, C. Does weather influence COVID‐19 transmission?. Regional Science Policy & Practice.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Mitjà, O., & Clotet, B. (2020). Use of antiviral drugs to reduce COVID-19 transmission. The Lancet Global Health, 8(5), e639-e640.
    • Yu, X., & Yang, R. (2020). COVID‐19 transmission through asymptomatic carriers is a challenge to containment. Influenza and Other Respiratory Viruses.
    • Baker, M. G., Wilson, N., & Anglemyer, A. (2020). Successful elimination of Covid-19 transmission in New Zealand. New England Journal of Medicine, 383(8), e56.
    • Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K. A., ... & Sim, E. M. (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature medicine, 26(9), 1398-1404.
    • Badr, H. S., Du, H., Marshall, M., Dong, E., Squire, M. M., & Gardner, L. M. (2020). Association between mobility patterns and COVID-19 transmission in the USA: a mathematical modeling study. The Lancet Infectious Diseases.
  4. Filtered my results using “Since 2016”, and recorded the top 5 papers, using APA format:
    • Baker, M. G., Wilson, N., & Anglemyer, A. (2020). Successful elimination of Covid-19 transmission in New Zealand. New England Journal of Medicine, 383(8), e56.
    • Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K. A., ... & Sim, E. M. (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nature medicine, 26(9), 1398-1404.
    • Mitjà, O., & Clotet, B. (2020). Use of antiviral drugs to reduce COVID-19 transmission. The Lancet Global Health, 8(5), e639-e640.
    • Yu, X., & Yang, R. (2020). COVID‐19 transmission through asymptomatic carriers is a challenge to containment. Influenza and Other Respiratory Viruses.
    • Badr, H. S., Du, H., Marshall, M., Dong, E., Squire, M. M., & Gardner, L. M. (2020). Association between mobility patterns and COVID-19 transmission in the USA: a mathematical modelling study. The Lancet Infectious Diseases.
  5. Made a list of the searched terms that were used by each student in the class. Recorded the list written on the board here:
  • 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: 15,500
    • Recorded the searched terms that have now been assigned specifically to me:
      • Covid-19 and immune response: 241,000 results
  2. Now accessed the PubMed database by using the LMU-specific link. Performed an unrestricted search on my assigned keywords.
    • Recorded the total number of hits:
      • 2,506
    • Recorded the top 10 papers:
      1. García L. F. (2020). Immune Response, Inflammation, and the Clinical Spectrum of COVID-19. Frontiers in immunology, 11, 1441. https://doi.org/10.3389/fimmu.2020.01441
      2. Tufan, A., Avanoğlu Güler, A., & Matucci-Cerinic, M. (2020). COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs. Turkish journal of medical sciences, 50(SI-1), 620–632. https://doi.org/10.3906/sag-2004-168
      3. Maggi, E., Canonica, G. W., & Moretta, L. (2020). COVID-19: Unanswered questions on immune response and pathogenesis. The Journal of allergy and clinical immunology, 146(1), 18–22.
      4. Paces, J., Strizova, Z., Smrz, D., & Cerny, J. (2020). COVID-19 and the immune system. Physiological research, 69(3), 379–388. https://doi.org/10.33549/physiolres.934492
      5. Tay, M. Z., Poh, C. M., Rénia, L., MacAry, P. A., & Ng, L. (2020). The trinity of COVID-19: immunity, inflammation and intervention. Nature reviews. Immunology, 20(6), 363–374. https://doi.org/10.1038/s41577-020-0311-8
      6. Vardhana SA, Wolchok JD. The many faces of the anti-COVID immune response. J Exp Med. 2020 Jun 1;217(6):e20200678. doi: 10.1084/jem.20200678. PMID: 32353870; PMCID: PMC7191310.
      7. Prompetchara, E., Ketloy, C., & Palaga, T. (2020). Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pacific journal of allergy and immunology, 38(1), 1–9. https://doi.org/10.12932/AP-200220-0772
      8. Muniyappa, R., & Gubbi, S. (2020). COVID-19 pandemic, coronaviruses, and diabetes mellitus. American journal of physiology. Endocrinology and metabolism, 318(5), E736–E741. https://doi.org/10.1152/ajpendo.00124.2020
      9. Gosain, R., Abdou, Y., Singh, A., Rana, N., Puzanov, I., & Ernstoff, M. S. (2020). COVID-19 and Cancer: a Comprehensive Review. Current oncology reports, 22(5), 53. https://doi.org/10.1007/s11912-020-00934-7
      10. Blanco-Melo, D., Nilsson-Payant, B. E., Liu, W. C., Uhl, S., Hoagland, D., Møller, R., Jordan, T. X., Oishi, K., Panis, M., Sachs, D., Wang, T. T., Schwartz, R. E., Lim, J. K., Albrecht, R. A., & tenOever, B. R. (2020). Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell, 181(5), 1036–1045.e9. https://doi.org/10.1016/j.cell.2020.04.026
  3. Performed a title/abstract search on my assigned keywords.
    • Record the total number of hits:
      • 1,007
    • Recorded the top 10 papers:
      1. García LF. Immune Response, Inflammation, and the Clinical Spectrum of COVID-19. Front Immunol. 2020 Jun 16;11:1441. doi: 10.3389/fimmu.2020.01441. PMID: 32612615; PMCID: PMC7308593. Review
      2. Azkur AK, Akdis M, Azkur D, Sokolowska M, van de Veen W, Brüggen MC, O'Mahony L, Gao Y, Nadeau K, Akdis CA. Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in C Review OVID-19. Allergy. 2020 Jul;75(7):1564-1581. doi: 10.1111/all.14364. PMID: 32396996; PMCID: PMC7272948.
      3. Prompetchara E, Ketloy C, Palaga T. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol. 2020 Mar;38(1):1-9. doi: 10.12932/AP-200220-0772. PMID: 32105090.
      4. Tufan A, Avanoğlu Güler A, Matucci-Cerinic M. COVID-19, immune system response, hyperinflammation and repurposing antirheumatic drugs. Turk J Med Sci. 2020 Apr 21;50(SI-1):620-632. doi: 10.3906/sag-2004-168. PMID: 32299202; PMCID: PMC7195984. Review
      5. Hussain A, Bhowmik B, do Vale Moreira NC. COVID-19 and diabetes: Knowledge in progress. Diabetes Res Clin Pract. 2020 Apr;162:108142. doi: 10.1016/j.diabres.2020.108142. Epub 2020 Apr 9. PMID: 32278764; PMCID: PMC7144611.
      6. Maggi E, Canonica GW, Moretta L. COVID-19: Unanswered questions on immune response and pathogenesis. J Allergy Clin Immunol. 2020 Jul;146(1):18-22. doi: 10.1016/j.jaci.2020.05.001. Epub 2020 May 8. PMID: 32389590; PMCID: PMC7205667.
      7. Vardhana SA, Wolchok JD. The many faces of the anti-COVID immune response. J Exp Med. 2020 Jun 1;217(6):e20200678. doi: 10.1084/jem.20200678. PMID: 32353870; PMCID: PMC7191310. Review
      8. Qin C, Zhou L, Hu Z, Zhang S, Yang S, Tao Y, Xie C, Ma K, Shang K, Wang W, Tian DS. Dysregulation of Immune Response in Patients With Coronavirus 2019 (COVID-19) in Wuhan, China. Clin Infect Dis. 2020 Jul 28;71(15):762-768. doi: 10.1093/cid/ciaa248. PMID: 32161940; PMCID: PMC7108125.
      9. Wilk AJ, Rustagi A, Zhao NQ, Roque J, Martínez-Colón GJ, McKechnie JL, Ivison GT, Ranganath T, Vergara R, Hollis T, Simpson LJ, Grant P, Subramanian A, Rogers AJ, Blish CA. A single-cell atlas of the peripheral immune response in patients with severe COVID-19. Nat Med. 2020 Jul;26(7):1070-1076. doi: 10.1038/s41591-020-0944-y. Epub 2020 Jun 8. PMID: 32514174; PMCID: PMC7382903.
      10. Gosain R, Abdou Y, Singh A, Rana N, Puzanov I, Ernstoff MS. COVID-19 and Cancer: a Comprehensive Review. Curr Oncol Rep. 2020 May 8;22(5):53. doi: 10.1007/s11912-020-00934-7. PMID: 32385672; PMCID: PMC7206576. Review
  4. Added the word “Review” to any articles that are review articles that I listed in question 8.
  5. Picked an author that shows up in multiple citations (if there isn’t one, just picked the last author from one of the papers) and performed an author search on the name.
    • Listed number of any new articles that you did not find before on PubMed?
      • Yes, 5
    • Listed up to 5 new articles that were found on the author name search:
      1. do Vale Moreira NC, Hussain A, Bhowmik B, Mdala I, Siddiquee T, Fernandes VO, Montenegro Júnior RM, Meyer HE. Prevalence of Metabolic Syndrome by different definitions, and its association with type 2 diabetes, pre-diabetes, and cardiovascular disease risk in Brazil. Diabetes Metab Syndr. 2020 Sep-Oct;14(5):1217-1224. doi: 10.1016/j.dsx.2020.05.043. Epub 2020 Jul 12. PMID: 32682310.
      2. Riaz M, Shaikh F, Fawwad A, Hakeem R, Shera AS, Hitman GA, Bhowmik B, do Vale Moreira NC, Basit A, Hussain A. Maternal Nutrition during Early Pregnancy and Cardiometabolic Status of Neonates at Birth. J Diabetes Res. 2018 Apr 24;2018:7382946. doi: 10.1155/2018/7382946. PMID: 29850608; PMCID: PMC5941780.
      3. Guo L, Shi Z, Zhang Y, Wang C, Do Vale Moreira NC, Zuo H, Hussain A. Comorbid diabetes and the risk of disease severity or death among 8807 COVID-19 patients in China: A meta-analysis. Diabetes Res Clin Pract. 2020 Aug;166:108346. doi: 10.1016/j.diabres.2020.108346. Epub 2020 Jul 22. PMID: 32710998; PMCID: PMC7375287.
      4. do Vale Moreira NC, Montenegro RM Jr, Meyer HE, Bhowmik B, Mdala I, Siddiquee T, Oliveira Fernandes V, Hussain A. Glycated Hemoglobin in the Diagnosis of Diabetes Mellitus in a Semi-Urban Brazilian Population. Int J Environ Res Public Health. 2019 Sep 26;16(19):3598. doi: 10.3390/ijerph16193598. PMID: 31561434; PMCID: PMC6801550.
      5. Hussain A, Bhowmik B, do Vale Moreira NC. COVID-19 and diabetes: Knowledge in progress. Diabetes Res Clin Pract. 2020 Apr;162:108142. doi: 10.1016/j.diabres.2020.108142. Epub 2020 Apr 9. PMID: 32278764; PMCID: PMC7144611.
  6. Now accessed the Web of Science database. Performed an unrestricted search on my assigned keywords.
    • Recorded the total number of hits:
      1. There are 1,243 results for Covid-19 and immune response
    • Recorded the top 10 papers:
      1. Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19) By: Arora, Shweta; Singh, Prithvi; Dohare, Ravins; et al.
      2. BCG is a Good Immunotherapeutic Agent for Viral and Autoimmune Diseases: Is it a New Weapon against Coronavirus (COVID-19)? By: Sharquie, Inas K.
      3. Behavioral immune system linked to responses to the threat of COVID-19 By: Makhanova, Anastasia; Shepherd, Melissa A.
      4. The role of host genetics in susceptibility to severe viral infections in humans and insights into host genetics of severe COVID-19: A systematic review By: Elhabyan, Abdelazeem; Elyaacoub, Saja; Sanad, Ehab; et al
      5. IFN-gamma is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection By: Gadotti, Ana Carolina; Deus, Marina de Castro; Telles, Joao Paulo; et al.
      6. SARS-CoV-2 IgG antibody responses in New York City By: Reifer, Josh; Hayum, Nosson; Heszkel, Benzion; et al.
      7. Immunological features of coronavirus disease 2019 in patients with cancer By: Thibaudin, Marion; Fumet, Jean-David; Bon, Marjorie; et al.
      8. Safety assessment of drug combinations used in COVID-19 treatment: in silico toxicogenomic data-mining approach By: Baralic, Katarina; Jorgovanovic, Dragica; Zivancevic, Katarina; et al.
      9. Histopathologic and Autopsy Findings in Patients Diagnosed With Coronavirus Disease 2019 (COVID-19): What We Know So Far Based on Correlation With Clinical, Morphologic and Pathobiological Aspects By: Al Nemer, Areej
      10. Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach By: Ahammad, Ishtiaque; Lira, Samia Sultana
  7. We will now create a shared bibliography for the entire class. Went through the search results that I have found and added articles to the class shared bibliography page.
    • Only added articles that are unique (everyone will be adding to the page and we do not want redundant articles)
    • Put reviewed articles and primary research articles in their respective sections. If the article did not fit either of those two categories, placed it in the other articles section.
    • Added the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Added my wiki signature to the end of the citation.
    • Ideally, each student will contribute 2-3 unique articles.
  8. Now that we have our shared bibliography, each student will be assigned one article. Recorded the citation for your article in APA format: Maggi, E., Canonica, G. W., & Moretta, L. (2020). COVID-19: Unanswered questions on immune response and pathogenesis. The Journal of allergy and clinical immunology, 146(1), 18–22.
    • In Web of Science, searched for the specific article that I have been assigned.
      • How many cited references does that article have?
        • The article has 30 References.
      • How many articles have cited the article you have been assigned?
        • The article was cited by 6 other articles.
  9. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Named two advantages and disadvantages for each.
    • Google Scholar: advantages
      1. A lot of search results for any topic.
      2. Easy to narrow the search results.
    • Google Scholar: disadvantages
      1. Too many results for any topic.
      2. Completely different results for a very similar query.
    • PubMed: advantages
      1. Able to search the query for titles with specific phrases.
      2. Gives narrow, more useful results.
    • Pubmed: disadvantages
      1. Doesn't have an easy citation tool like google scholar.
      2. Interface isn't as easy as google scholar.
    • Web of Science: advantages
      1. Easy to see the article's citations and how many times it was cited by other articles.
      2. Easy to search for authors.
    • Web of Science: disadvantages
      1. Doesnt have as many results for the query.
      2. Advanced searches seem a little bit more complicated.
  10. Answered: what impact does choice of keywords have on your results?
    • As we saw in class, switching out a single word for its synonym produced a variety of other results. The choice of the keyword is important because the article you need might not show up if one does not enter the precise worlds. The databases also yield different results depending on the database that was chosen.

Scientific Conclusion

  • In this lab we learned about how to word specificity and database choice determine the articles that you come across. With any search query, in many of these databases, there are hundreds of not thousands of search results. In databases, like google scholar, a change in a phrase to a similar phrase can yield many different results. Databases like PubMed and web of science can help narrow results and provide more relevant articles. Understanding how to navigate databases is prudent for biologists as finding reliable relevant articles can help understand concepts that were previously misunderstood.

Acknowledgments

  1. Copied questions and procedures from the BIOL368/F20 Week 10 Page.
  2. Worked with my partner Anna Horvath on understanding the assignment.
  3. Copied the list of assigned keywords from the Class Bibliography page
  4. Worked and Cited sources from Google Scholar, Web of Science, and Pubmed.
  5. Looked for information from the article COVID-19: Unanswered questions on immune response and pathogenesis.

References

  1. OpenWetWare. (2020). BIOL368/F20:Week 10. Retrieved November 11, 2020, from https://openwetware.org/wiki/BIOL368/F20:Week_10.
  2. Google Scholar (2020). Articles. Retrieved from https://scholar.google.com/.
  3. National Library of Medicine and National Center for Biotechnology Information (2020). PubMed, Retrieved from https://pubmed.ncbi.nlm.nih.gov/.
  4. Web of Science (2020). Web of Science Core Collection, retrieved from http://apps.webofknowledge.com.electra.lmu.edu/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=8EzEsFjgNfcuNFcY7wi&preferencesSaved=.
  5. Maggi, E., Canonica, G. W., & Moretta, L. (2020). COVID-19: Unanswered questions on immune response and pathogenesis. The Journal of allergy and clinical immunology, 146(1), 18–22, Retrieved from DOI: 10.1016/j.jaci.2020.05.001.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source"Nathan R. Beshai (talk) 23:55, 11 November 2020 (PST)

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