Kam Taghizadeh Week 10

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Purpose

  • The purpose of this assignment is to discover various search engines and the filters that they entail. Furthermore, we learned about the effect of keywords on the search results. By choosing various synonyms such as SARS-CoV-2 and Covid 19, we will see the different results that show up. Also, we will be choosing our journal club article this week.

Assignment

  1. Performed a search in Google Scholar
  2. Recorded the number of “hits” I found:158,000
  3. Recorded the top 10 papers, this time using APA format:
    • Tsatsakis, A., Petrakis, D., Nikolouzakis, T. K., Docea, A. O., Calina, D., Vinceti, M., ... & Hernández, A. F. (2020). COVID-19, an opportunity to reevaluate the correlation between long-term effects of anthropogenic pollutants on viral epidemic/pandemic events and prevalence. Food and Chemical Toxicology, 111418.
    • 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.
    • Morlacco, A., Motterle, G., & Zattoni, F. (2020). The multifaceted long-term effects of the COVID-19 pandemic on urology. Nature Reviews Urology, 1-3.
    • Fana, M., Pérez, S. T., & Fernández-Macías, E. (2020). Employment impact of Covid-19 crisis: from short term effects to long terms prospects. Journal of Industrial and Business Economics, 47(3), 391-410.
    • Fraser, E. (2020). Long term respiratory complications of covid-19.
    • Perkins, G. D., & Couper, K. (2020). COVID-19: long-term effects on the community response to cardiac arrest?. The Lancet Public Health.
    • Yoshikawa, H., Wuermli, A. J., Britto, P. R., Dreyer, B., Leckman, J. F., Lye, S. J., ... & Stein, A. (2020). Effects of the Global COVID-19 Pandemic on Early Childhood Development: Short-and Long-Term Risks and Mitigating Program and Policy Actions. The Journal of Pediatrics.
    • Ogen, Y. (2020). Assessing nitrogen dioxide (NO2) levels as a contributing factor to the coronavirus (COVID-19) fatality rate. Science of The Total Environment, 138605.
    • Mahase, E. (2020). Covid-19: What do we know about “long covid”?. bmj, 370.
    • Mattioli, A. V., Puviani, M. B., Nasi, M., & Farinetti, A. (2020). COVID-19 pandemic: the effects of quarantine on cardiovascular risk. European Journal of Clinical Nutrition, 1-4.
  4. Sorted my results by date (instead of relevance), and recorded the top 5 papers, using APA format:
    • Tsatsakis, A., Petrakis, D., Nikolouzakis, T. K., Docea, A. O., Calina, D., Vinceti, M., ... & Hernández, A. F. (2020). COVID-19, an opportunity to reevaluate the correlation between long-term effects of anthropogenic pollutants on viral epidemic/pandemic events and prevalence. Food and Chemical Toxicology, 111418.
    • Morlacco, A., Motterle, G., & Zattoni, F. (2020). The multifaceted long-term effects of the COVID-19 pandemic on urology. Nature Reviews Urology, 1-3.
    • 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.
    • Fraser, E. (2020). Long term respiratory complications of covid-19.
    • Fana, M., Pérez, S. T., & Fernández-Macías, E. (2020). Employment impact of Covid-19 crisis: from short term effects to long terms prospects. Journal of Industrial and Business Economics, 47(3), 391-410.
  5. Filtered my results using “Since 2019”, and recorded the top 5 papers, using APA format:
    • Tsatsakis, A., Petrakis, D., Nikolouzakis, T. K., Docea, A. O., Calina, D., Vinceti, M., ... & Hernández, A. F. (2020). COVID-19, an opportunity to reevaluate the correlation between long-term effects of anthropogenic pollutants on viral epidemic/pandemic events and prevalence. Food and Chemical Toxicology, 111418.
    • Morlacco, A., Motterle, G., & Zattoni, F. (2020). The multifaceted long-term effects of the COVID-19 pandemic on urology. Nature Reviews Urology, 1-3.
    • 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.
    • Perkins, G. D., & Couper, K. (2020). COVID-19: long-term effects on the community response to cardiac arrest?. The Lancet Public Health.
    • Fraser, E. (2020). Long term respiratory complications of covid-19.
  6. Filtered my results using “Since 2016”, and recorded the top 5 papers, using APA format:
    • 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.
    • Fana, M., Pérez, S. T., & Fernández-Macías, E. (2020). Employment impact of Covid-19 crisis: from short term effects to long terms prospects. Journal of Industrial and Business Economics, 47(3), 391-410.
    • Mahase, E. (2020). Covid-19: What do we know about “long covid”?. bmj, 370.
    • Mitrani, R. D., Dabas, N., & Goldberger, J. J. (2020). COVID-19 cardiac injury: implications for long-term surveillance and outcomes in survivors. Heart rhythm.
    • Ogen, Y. (2020). Assessing nitrogen dioxide (NO2) levels as a contributing factor to the coronavirus (COVID-19) fatality rate. Science of The Total Environment, 138605.
  7. 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
  8. Record the search terms that have now been assigned specifically to you: 2019-ncov and immunity
  9. Accessed the PubMed database by using the LMU-specific link. Performed an unrestricted search on my assigned keywords.
  10. Recorded the total number of hits: 3,500
  11. Recorded the top 10 papers (didn't need to do APA format for this):
    • 2019-nCoV (Wuhan virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness.
    • Advances in the research of mechanism and related immunotherapy on the cytokine storm induced by coronavirus disease 2019.
    • The possible of immunotherapy for COVID-19: A systematic review.
    • Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals.
    • A Review of SARS-CoV-2 and the Ongoing Clinical Trials.
    • Prevention and treatment of COVID-19 disease by controlled modulation of innate immunity.
    • The impact of nutrition on COVID-19 susceptibility and long-term consequences.
    • The many faces of the anti-COVID immune response.
    • Reducing mortality from 2019-nCoV: host-directed therapies should be an option.
    • The laboratory tests and host immunity of COVID-19 patients with different severity of illness.
  12. Perform a title/abstract search on your assigned keywords.
  13. Recorded the total number of hits:2,815
  14. Recorded the top 10 papers (didn't need to do APA format for this):
    • Overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses SARS-CoV, MERS-CoV, and 2019-nCoV.
    • 2019-nCoV (Wuhan virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness.
    • The possible of immunotherapy for COVID-19: A systematic review.
    • An overview of COVID-19.
    • A Review of SARS-CoV-2 and the Ongoing Clinical Trials.
    • Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.
    • The impact of nutrition on COVID-19 susceptibility and long-term consequences.
    • The many faces of the anti-COVID immune response.
    • Pre-existing immunity to SARS-CoV-2: the knowns and unknowns.
    • Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China.
  15. Added the word “Review” to any articles that are review articles that was listed in question 8.
  16. Picked an author that shows up in multiple citations (if there wasn't one, I just picked the last author from one of the papers)and performed an author search on the name.
  17. Do you find any new articles that you did not find before on PubMed?
  18. List up to 5 new articles that were found on the author name search: I picked the name Søreide, K.
    • Acute appendicitis: modern understanding of pathogenesis, diagnosis, and management.
    • The open abdomen in trauma and non-trauma patients: WSES guidelines.
    • Perforated peptic ulcer.
    • Splenic trauma: WSES classification and guidelines for adult and pediatric patients.
    • The management of intra-abdominal infections from a global perspective: 2017 WSES guidelines for management of intra-abdominal infections.

Accessed the Web of Science database. Performed an unrestricted search on my assigned keywords. Recorded the total number of hits: Record the top 10 papers (you don't need to use APA format for this):

    • 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
    • Diagnostics for SARS-CoV-2 detection: A comprehensive review of the FDA-EUA COVID-19 testing landscapes
    • A five-step risk management process for geriatric dental practice during SARS-CoV-2 pandemic
    • Potential Therapeutic Options for COVID-19: Current Status, Challenges, and Future Perspectives
    • Novel Coronavirus-2019 (2019-nCoV): Perspectives of emergence, prophylaxis and predicted treatment approaches
    • THE NOVEL CORONA VIRUS (nCoV2) SEEMS TO DEFY ALL LAWS OF VIROLOGY
    • Is There a Rationale for UsingBacillusCalmette-Guerin Vaccine in Coronavirus Infection?
    • Direct-RT-qPCR Detection of SARS-CoV-2 without RNA Extraction as Part of a COVID-19 Testing Strategy: From Sample to Result in One Hour
    • Low Humoral Immune Response and Ineffective Clearance of SARS-Cov-2 in a COVID-19 Patient With CLL During a 69-Day Follow-Up
    • Recent Understandings Toward Coronavirus Disease 2019 (COVID-19): From Bench to Bedside

We will now create a shared bibliography for the entire class

  1. Went through the search results that I have found and added articles to the class shared bibliography page.
  2. Only added articles that are unique (everyone will be adding to the page and we do not want redundant articles)
  3. I put the review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, I placed it in the other articles section.
  4. 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.
  5. Ideally, each student will contribute 2-3 unique articles.
  6. Now that we have our shared bibliography, each student will be assigned one article. Recorded the citation for my article in APA format:
    • Jeyanathan M, Afkhami S, Smaill F, Miller MS, Lichty BD, Xing Z. Immunological considerations for COVID-19 vaccine strategies. Nat Rev Immunol. 2020;20(10):615-632. doi:10.1038/s41577-020-00434-6
  7. In Web of Science, I searched for the specific article that I have been assigned.
  8. Recorded the number of cited references the article has:188
  9. Recorded how many articles have cited the article I have been assigned:1

Reflection on Search Engines

  1. What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
  2. Google Scholar: advantages
    • One advantage of google scholar is how straight forward it is, there is just one search bar and thousands of results will show up based on your keywords.
    • Another advantage is that it provides a citation feature, which makes it very easy when citing research papers
  3. Google Scholar: disadvantages
    • One disadvantage is that not all search results are actually "scholarly"
    • Another disadvantage is that it does not allow users to perform filtered searches
  4. PubMed: advantages
    • One advantage is that it is specific to medicine and health
    • Another advantage is that the sources are highly reliable
  5. Pubmed: disadvantages
    • One disadvantage is that one can't really tell if the results are the "best matched" or "most recent"
    • Another disadvantage is that the search bar is not that straight forward
  6. Web of Science: advantages
    • One advantage is how reliable all the sources are.
    • Another advantage is that its citation data is accurate.
  7. Web of Science: disadvantages
    • One disadvantage is that its user interface is kind of slow.
    • Another disadvantage is that it does not provide the citation like google scholar does.
  8. What impact does choice of keywords have on your results?
    • One's choice of keywords impacts the search results greatly, since they are the words that the search topic is about. If one were to search "pig" they would get articles regarding a pig, and if one were to search "covid" they would get articles regarding covid 19.

Conclusion

I have learned about the various search engines, and how keywords can impact search results. I have previously known about this, however I can see the impact of keywords more clearly after completing this assignment. For instance, the more specific one gets with these keywords, the less results will show up. Furthermore, I have learned how to search for reviewed articles, which will benefit me for my research projects.

Acknowledgements


Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Kam Taghizadeh (talk) 11:38, 12 November 2020 (PST)

References

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Links to Weekly Assignments

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