Yaniv Maddahi Journal Week 10

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Purpose

  • The purpose of this lab is to explore search engines, different web-bases, and the effect keywords have on search results. We will be exploring search engines that are free as well as those that require subscriptions. Through our explorations we will be seeing the different results that appear with varying search engines and even the different results that appear with synonyms of words (such as SARS-CoV vs. COVID). We will also be finding our journal club article.

Assignment

The goal for this assignment is to create a class shared annotated bibliography of references for the next phase of the HIV research project where we will investigate the structure-function implications of mutations in the gp120 protein.

  1. Warm up exercise (announced in class).
  2. Perform a search in Google Scholar .
    1. Record the number of “hits” you found:
      • 483,000 results
    2. Record the top 10 papers, this time using APA format:
      • paper 1
        • Pfefferbaum, B., & North, C. S. (2020). Mental health and the Covid-19 pandemic. New England Journal of Medicine.
      • paper 2
        • Dashraath, P., Jeslyn, W. J. L., Karen, L. M. X., Min, L. L., Sarah, L., Biswas, A., ... & Lin, S. L. (2020). Coronavirus disease 2019 (COVID-19) pandemic and pregnancy. American journal of obstetrics and gynecology.
      • paper 3
        • Ranney, M. L., Griffeth, V., & Jha, A. K. (2020). Critical supply shortages—the need for ventilators and personal protective equipment during the Covid-19 pandemic. New England Journal of Medicine, 382(18), e41.
      • paper 4
        • Spinelli, A., & Pellino, G. (2020). COVID‐19 pandemic: perspectives on an unfolding crisis. The British journal of surgery.
      • paper 5
        • Hsiang, S., Allen, D., Annan-Phan, S., Bell, K., Bolliger, I., Chong, T., ... & Lau, P. (2020). The effect of large-scale anti-contagion policies on the COVID-19 pandemic. Nature, 584(7820), 262-267.
      • paper 6
        • Van Bavel, J. J., Baicker, K., Boggio, P. S., Capraro, V., Cichocka, A., Cikara, M., ... & Drury, J. (2020). Using social and behavioural science to support COVID-19 pandemic response. Nature Human Behaviour, 1-12.
      • paper 7
        • Søreide, K., Hallet, J., Matthews, J. B., Schnitzbauer, A. A., Line, P. D., Lai, P. B. S., ... & Teh, C. S. (2020). Immediate and long‐term impact of the COVID‐19 pandemic on delivery of surgical services. The British journal of surgery.
      • paper 8
        • Driggin, E., Madhavan, M. V., Bikdeli, B., Chuich, T., Laracy, J., Biondi-Zoccai, G., ... & Brodie, D. (2020). Cardiovascular considerations for patients, health care workers, and health systems during the COVID-19 pandemic. Journal of the American College of Cardiology, 75(18), 2352-2371.
      • paper 9
        • Collaborative, C. (2020). Global guidance for surgical care during the COVID‐19 pandemic. The British journal of surgery.
      • paper 10
        • Muniyappa, R., & Gubbi, S. (2020). COVID-19 pandemic, coronaviruses, and diabetes mellitus. American Journal of Physiology-Endocrinology and Metabolism, 318(5), E736-E741.
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • paper 1
      • Pilz, S. Letter to the Editor Re: Global perspective of COVID‐19 epidemiology for a full‐cycle pandemic. European Journal of Clinical Investigation, e13447.
    • paper 2
      • Brandão‐de‐Resende, C., Diniz‐Filho, A., de Almeida Brito, F., & Vasconcelos‐Santos, D. V. SARS‐CoV‐2 and COVID‐19 for the ophthalmologist. Clinical & Experimental Ophthalmology.
    • paper 3
      • Dong, J. Q. Technological Choices under Uncertainty: Does Organizational Aspiration Matter?. Strategic Management Journal.
    • paper 4
      • Abualfadl, E., Ismail, F., El Shereef, R. R., Hassan, E., Tharwat, S., Mohamed, E. F., ... & Noor, R. A. (2020). Impact of COVID-19 pandemic on rheumatoid arthritis from a Multi-Centre patient-reported questionnaire survey: influence of gender, rural–urban gap and north–south gradient. Rheumatology International, 1-9.
    • paper 5
      • Singla, T. (2020). The Impact of COVID-19 on Education System. CYBERNOMICS, 2(7), 13-16.
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • paper 1
      • Pfefferbaum, B., & North, C. S. (2020). Mental health and the Covid-19 pandemic. New England Journal of Medicine.
    • paper 2
      • Spinelli, A., & Pellino, G. (2020). COVID‐19 pandemic: perspectives on an unfolding crisis. The British journal of surgery.
    • paper 3
      • Watkins, J. (2020). Preventing a covid-19 pandemic.
    • paper 4
      • Collaborative, C. (2020). Global guidance for surgical care during the COVID‐19 pandemic. The British journal of surgery.
    • paper 5
      • Berman, J. D., & Ebisu, K. (2020). Changes in US air pollution during the COVID-19 pandemic. Science of the Total Environment, 739, 139864.
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • paper 1
      • Pfefferbaum, B., & North, C. S. (2020). Mental health and the Covid-19 pandemic. New England Journal of Medicine.
    • paper 2
      • Spinelli, A., & Pellino, G. (2020). COVID‐19 pandemic: perspectives on an unfolding crisis. The British journal of surgery.
    • paper 3
      • Watkins, J. (2020). Preventing a covid-19 pandemic.
    • paper 4
      • Collaborative, C. (2020). Global guidance for surgical care during the COVID‐19 pandemic. The British journal of surgery.
    • paper 5
      • Berman, J. D., & Ebisu, K. (2020). Changes in US air pollution during the COVID-19 pandemic. Science of the Total Environment, 739, 139864.
  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
  7. Record the search terms that have now been assigned specifically to you:
    • COVID 19 and Antibodies
  8. 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:
      • 3,355 results
    • Record the top 10 papers (you don't need to do APA format for this):
      1. paper 1
        • Towards treatment planning of COVID-19: Rationale and hypothesis for the use of multiple immunosuppressive agents: Anti-antibodies, immunoglobulins, and corticosteroids.
      2. paper 2
        • Perspectives on monoclonal antibody therapy as potential therapeutic intervention for Coronavirus disease-19 (COVID-19).
      3. paper 3
        • Antibodies in Infants Born to Mothers With COVID-19 Pneumonia.
      4. paper 4
        • Immune Response, Inflammation, and the Clinical Spectrum of COVID-19.
      5. paper 5
        • Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability.
      6. paper 6
        • Dynamics of anti-SARS-Cov-2 IgM and IgG antibodies among COVID-19 patients.
      7. paper 7
        • Diagnostic performance of COVID-19 serology assays.
      8. paper 8
        • Pandemic Preparedness: Developing Vaccines and Therapeutic Antibodies For COVID-19.
      9. paper 9
        • Treatment for emerging viruses: Convalescent plasma and COVID-19.
      10. paper 10
        • Convalescent plasma in Covid-19: Possible mechanisms of action.
  9. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits:
      • 24 results
    • Record the top 10 papers (you don't need to do APA format for this):
      1. paper 1
        • Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics.
      2. paper 2
        • Serological tests for COVID-19 antibodies: Limitations must be recognized.
      3. paper 3
        • COVID-19 antibodies on trial.
      4. paper 4
        • Seroprevalence of COVID-19 antibodies in the cleaning and oncological staff of a municipal clinic.
      5. paper 5
        • Test, test, test for COVID-19 antibodies: the importance of sensitivity, specificity and predictive powers.
      6. paper 6
        • Will plant-made biopharmaceuticals play a role in the fight against COVID-19?
      7. paper 7
        • Anesthesiologists' and Intensive Care Providers' Exposure to COVID-19 Infection in a New York City Academic Center: A Prospective Cohort Study Assessing Symptoms and COVID-19 Antibody Testing.
      8. paper 8
        • Diagnosing COVID-19 in the Emergency Department: A Scoping Review of Clinical Examinations, Laboratory Tests, Imaging Accuracy, and Biases.
      9. paper 9
        • Convalescent plasma, an apheresis research project targeting and motivating the fully recovered COVID 19 patients: A rousing message of clinical benefit to both donors and recipients alike.
      10. paper 10
        • Low risk of serological cross-reactivity between dengue and COVID-19.
  10. Add the word “Review” to any articles that are review articles that you listed in question 8.
  11. 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?
      • Convalescent plasma, an apheresis research project targeting and motivating the fully recovered COVID 19 patients: A rousing message of clinical benefit to both donors and recipients alike
    • List up to 5 new articles that were found on the author name search:
      • Author: Padoan, Andrea
      1. paper 1
        • Inflammation and Pancreatic Cancer: Focus on Metabolism, Cytokines, and Immunity.
      2. paper 2
        • Preanalytical challenges - time for solutions.
      3. paper 3
        • Decision Support and Patient Safety.
      4. paper 4
        • IgA-Ab response to spike glycoprotein of SARS-CoV-2 in patients with COVID-19: A longitudinal study.
      5. paper 5
        • Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics.
  12. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:
      • 1,446 Results
    • Record the top 10 papers (you don't need to use APA format for this):
      1. paper 1
        • Therapeutic Strategies of COVID-19: From Natural Compounds to Vaccine Trials
      2. paper 2
        • Survey of the current status of subclinical coronavirus disease 2019 (COVID-19)
      3. paper 3
        • First report of manic-like symptoms in a COVID-19 patient with no previous history of a psychiatric disorder
      4. paper 4
        • Corona-Like Illness: Did we get it before WHO Announcement of the Disease? A Cross-sectional Survey
      5. paper 5
        • Analysis of COVID-19 convalescent plasma for SARS-CoV-2 IgG using two commercial immunoassays
      6. paper 6
        • What can we learn from rapidly progressive interstitial lung disease related to anti-MDA5 dermatomyositis in the management of COVID-19?
      7. paper 7
        • Retrospective clinical evaluation of 4 lateral flow assays for the detection of SARS-CoV-2 IgG
      8. paper 8
        • SARS-CoV-2 IgG antibody responses in New York City
      9. paper 9
        • False-positive SARS-CoV-2 serology in 3 children with Kawasaki disease
      10. paper 10
        • Optimized Pseudotyping Conditions for the SARS-COV-2 Spike Glycoprotein

We will now create a shared bibliography for the entire class

  1. 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.

Now that we have our Shared Bibliography

shared bibliography

  1. each student will be assigned one article. Record the citation for your article in APA format:
    • Title: Immune Response, Inflammation, and the Clinical Spectrum of COVID-19
    • APA Citation: García, L. F. (2020). Immune response, inflammation, and the clinical spectrum of COVID-19. Frontiers in immunology, 11, 1441.
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
        • 138 cited references
      • How many articles have cited the article you have been assigned?
        • Cited 4 time

Reflection on Websites

  1. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
    • Google Scholar:
      • One advantage of google scholar is that out of all the other search engines it seems to pull from the most sources and produces the greatest number of results. Another advantage of google scholar is that it is incredibly easy to cite an article; by simply clicking on the double quotes.
    • Google Scholar: disadvantages
      • A disadvantage of google scholar is that it is not necessarily as finely curated for topics and so it may be harder to discover scientific journals of more prestigious institutions or those of higher credibility. Further, it does not have the same advanced search to be able to search by abstract or title as other search engines.
    • PubMed: advantages
      • One advantage of PubMed is that one can check search history and can log in and save searches and have emails regarding updates on the search results. Another advantage is being able to search by title/abstract or other criteria.
    • Pubmed: disadvantages
      • A disadvantage of PubMed is being able to cite, it is not as easy as other engines such as google scholar. Another disadvantage is the number of results; it appears to often times not produce the same number of hits as google scholar.
    • Web of Science: advantages
      • An advantage of Web of Science is the ability to save searches and be able to keep track of many articles without having them open. One can save a search or "favorite" it and thus keep track. Further, being a paid subscription, it produces more curated results that can often times be further advanced-searched to have more finite results.
    • Web of Science: disadvantages
      • A disadvantage of Web of Science is that it costs money, which while could be an advantage does also carry an aspect of not being accessible to the general public. Another disadvantage comes with its difficulty in ability to cite, not being as straight forward as google scholar. Lastly, similarly to PubMed, Web of Science does not seem to produce as many results as other engines such as google scholar.

What impact does choice of keywords have on your results?

  • In class we attempted using different synonyms in our searches such as SARS Cov vs COVID and we noticed that different results would appear. As time progresses, so do the terminology used to address certain topics. New words are developed as well as new names.

Conclusion

  1. In the process of this lab, I gained great insight into the different databases, how results vary between them, and the role of keywords in obtaining different results. I was most surprised by the way keywords can change results and how those vary even when representing the same topic or scenario. I also discovered what will be my journal club article for the following week.

Acknowledgements

  • I worked with my partner Kam Taghizadeh over Zoom during class hours to ask clarifying questions about the week's assignment.
  • I acknowledge my professor, Kam D. Dahlquist, Ph.D., with whom I met several times via zoom to discuss questions regarding the purpose and format.
  • I acknowledge my TA, Annika Dinulos, whom I contacted regarding a question for one of my assignments.
  • I copied and modified procedures from the Week 10 assignment page.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Yaniv Maddahi (talk) 13:23, 8 November 2020 (PST)


References

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Yaniv Maddahi Template

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