Taylor Makela Journal Week 10

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Taylor Makela Week 10

Purpose

The purpose of this assignment is to gain experience working with the following research databases: Google Scholar, PubMed, and Web of Science. This exercise serves to explain the different features of each databases, and to start collecting scientific articles that can be used for our future research project.

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).

Google Scholar

  1. Perform a search in Google Scholar .
    1. Record the number of “hits” you found: 79,000
    2. Record the top 10 papers, this time using APA format:
      • Lu, C. W., Liu, X. F., & Jia, Z. F. (2020). 2019-nCoV transmission through the ocular surface must not be ignored. Lancet (London, England), 395(10224), e39.
      • Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., ... & Seilmaier, M. (2020). Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New England Journal of Medicine, 382(10), 970-971.
      • Peng, X., Xu, X., Li, Y., Cheng, L., Zhou, X., & Ren, B. (2020). Transmission routes of 2019-nCoV and controls in dental practice. International Journal of Oral Science, 12(1), 1-6.
      • Riou, J., & Althaus, C. L. (2020). Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Eurosurveillance, 25(4), 2000058.
      • Wang, X., Pan, Z., & Cheng, Z. (2020). Association between 2019-nCoV transmission and N95 respirator use. medRxiv.
      • Haider, N., Yavlinsky, A., Simons, D., Osman, A. Y., Ntoumi, F., Zumla, A., & Kock, R. (2020). Passengers' destinations from China: low risk of novel coronavirus (2019-nCoV) transmission into Africa and South America. Epidemiology & Infection, 148.
      • Ji, W., Wang, W., Zhao, X., Zai, J., & Li, X. (2020). Cross‐species transmission of the newly identified coronavirus 2019‐nCoV. Journal of medical virology, 92(4), 433-440.
      • Carlos, W. G., Dela Cruz, C. S., Cao, B., Pasnick, S., & Jamil, S. (2020). Novel Wuhan (2019-nCoV) Coronavirus. Am J Respir Crit Care Med, P7-P8.
      • Tang, B., Bragazzi, N. L., Li, Q., Tang, S., Xiao, Y., & Wu, J. (2020). An updated estimation of the risk of transmission of the novel coronavirus (2019-nCov). Infectious disease modelling, 5, 248-255.
      • Tang, B., Wang, X., Li, Q., Bragazzi, N. L., Tang, S., Xiao, Y., & Wu, J. (2020). Estimation of the transmission risk of the 2019-nCoV and its implication for public health interventions. Journal of clinical medicine, 9(2), 462.
  2. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Verma, M., & Soni, A. NOVEL CORONAVIRUS (2019-NC0V) OUTBREAK: THINGS YOU NEED TO KNOW.
    • Sohrabpour, S., Heidari, F., Karimi, E., Ansari, R., Tajdini, A., & Heidari, F. Subacute Thyroiditis in COVID-19 Patients. European Thyroid Journal, 1-3.
    • Ceyhan, S., & Uzuntarla, Y. Akademik Personelin COVID-19’a Yönelik Bilgi, Tutum ve Davranışlarının Belirlenmesi.
    • Mattar, S., Martinez-Bravo, C., Rivero, R., Contreras, H., Faccini_Martinez, A., Guzman, C., ... & Gonzalez, M. (2020). Epidemiological and viral features of a cohort of SARS-CoV-2 symptomatic and asymptomatic individuals in an area of the Colombian Caribbean.
    • de Babaçulândia, P. (2020). Plano de enfrentamento Coronavírus-COVID-19.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Lu, C. W., Liu, X. F., & Jia, Z. F. (2020). 2019-nCoV transmission through the ocular surface must not be ignored. Lancet (London, England), 395(10224), e39.
    • Wang, X., Pan, Z., & Cheng, Z. (2020). Association between 2019-nCoV transmission and N95 respirator use. medRxiv.
    • Peng, X., Xu, X., Li, Y., Cheng, L., Zhou, X., & Ren, B. (2020). Transmission routes of 2019-nCoV and controls in dental practice. International Journal of Oral Science, 12(1), 1-6.
    • Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., ... & Seilmaier, M. (2020). Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New England Journal of Medicine, 382(10), 970-971.
    • Riou, J., & Althaus, C. L. (2020). Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Eurosurveillance, 25(4), 2000058.
  4. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Lu, C. W., Liu, X. F., & Jia, Z. F. (2020). 2019-nCoV transmission through the ocular surface must not be ignored. Lancet (London, England), 395(10224), e39.
    • Wang, X., Pan, Z., & Cheng, Z. (2020). Association between 2019-nCoV transmission and N95 respirator use. medRxiv.
    • Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., ... & Seilmaier, M. (2020). Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New England Journal of Medicine, 382(10), 970-971.
    • Peng, X., Xu, X., Li, Y., Cheng, L., Zhou, X., & Ren, B. (2020). Transmission routes of 2019-nCoV and controls in dental practice. International Journal of Oral Science, 12(1), 1-6.
    • Riou, J., & Althaus, C. L. (2020). Pattern of early human-to-human transmission of Wuhan 2019 novel coronavirus (2019-nCoV), December 2019 to January 2020. Eurosurveillance, 25(4), 2000058.
  5. 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 and immune response: 241,000
    • COVID-19 and antibodies: 62,900
    • COVID-19 and immunity: 77,500
    • COVID-19 and immune reaction: 104,000
    • SARS-CoV-2 and immune response: 48,800
    • SARS-CoV-2 and antibodies: 48,200
    • SARS-CoV-2 and immunity: 57,000
    • SARS-CoV-2 and immune reaction: 97,700
    • 2019-nCoV and immune response: 25,600
    • 2019-nCoV and antibodies: 17,400
    • 2019-nCoV and immunity: 24,500
    • 2019-nCoV and immune reaction: 15,500
    • Record the search terms that have now been assigned specifically to you:
      • SARS-CoV-2 and immune response

PubMed

  1. Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords. (SARS-CoV-2 and immune response)
    • Record the total number of hits: 2,008
    • Record the top 10 papers (you don't need to do APA format for this):
      1. 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 COVID-19. Allergy. 2020 Jul;75(7):1564-1581. doi: 10.1111/all.14364. PMID: 32396996; PMCID: PMC7272948.
      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.
      3. Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, Marrama D, de Silva AM, Frazier A, Carlin AF, Greenbaum JA, Peters B, Krammer F, Smith DM, Crotty S, Sette A. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell. 2020 Jun 25;181(7):1489-1501.e15. doi: 10.1016/j.cell.2020.05.015. Epub 2020 May 20. PMID: 32473127; PMCID: PMC7237901.
      4. Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell. 2020 May 28;181(5):1036-1045.e9. doi: 10.1016/j.cell.2020.04.026. Epub 2020 May 15. PMID: 32416070; PMCID: PMC7227586.
      5. Liang Y, Wang ML, Chien CS, Yarmishyn AA, Yang YP, Lai WY, Luo YH, Lin YT, Chen YJ, Chang PC, Chiou SH. Highlight of Immune Pathogenic Response and Hematopathologic Effect in SARS-CoV, MERS-CoV, and SARS-Cov-2 Infection. Front Immunol. 2020 May 12;11:1022. doi: 10.3389/fimmu.2020.01022. PMID: 32574260; PMCID: PMC7236801.
      6. 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.
      7. Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host Microbe. 2020 Apr 8;27(4):671-680.e2. doi: 10.1016/j.chom.2020.03.002. Epub 2020 Mar 16. PMID: 32183941; PMCID: PMC7142693.
      8. Ovsyannikova IG, Haralambieva IH, Crooke SN, Poland GA, Kennedy RB. The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity. Immunol Rev. 2020 Jul;296(1):205-219. doi: 10.1111/imr.12897. Epub 2020 Jul 13. PMID: 32658335; PMCID: PMC7404857.
      9. 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.
      10. Folegatti PM, Ewer KJ, Aley PK, Angus B, Becker S, Belij-Rammerstorfer S, Bellamy D, Bibi S, Bittaye M, Clutterbuck EA, Dold C, Faust SN, Finn A, Flaxman AL, Hallis B, Heath P, Jenkin D, Lazarus R, Makinson R, Minassian AM, Pollock KM, Ramasamy M, Robinson H, Snape M, Tarrant R, Voysey M, Green C, Douglas AD, Hill AVS, Lambe T, Gilbert SC, Pollard AJ; Oxford COVID Vaccine Trial Group. Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet. 2020 Aug 15;396(10249):467-478. doi: 10.1016/S0140-6736(20)31604-4. Epub 2020 Jul 20. Erratum in: Lancet. 2020 Aug 15;396(10249):466. PMID: 32702298; PMCID: PMC7445431.
  2. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 853
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Nakra NA, Blumberg DA, Herrera-Guerra A, Lakshminrusimha S. Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management. Children (Basel). 2020 Jul 1;7(7):69. doi: 10.3390/children7070069. PMID: 32630212; PMCID: PMC7401880. Review
      2. Runfeng L, Yunlong H, Jicheng H, Weiqi P, Qinhai M, Yongxia S, Chufang L, Jin Z, Zhenhua J, Haiming J, Kui Z, Shuxiang H, Jun D, Xiaobo L, Xiaotao H, Lin W, Nanshan Z, Zifeng Y. Lianhuaqingwen exerts anti-viral and anti-inflammatory activity against novel coronavirus (SARS-CoV-2). Pharmacol Res. 2020 Jun;156:104761. doi: 10.1016/j.phrs.2020.104761. Epub 2020 Mar 20. PMID: 32205232; PMCID: PMC7102548.
      3. Cleary SJ, Pitchford SC, Amison RT, Carrington R, Robaina Cabrera CL, Magnen M, Looney MR, Gray E, Page CP. Animal models of mechanisms of SARS-CoV-2 infection and COVID-19 pathology. Br J Pharmacol. 2020 Nov;177(21):4851-4865. doi: 10.1111/bph.15143. Epub 2020 Jul 19. PMID: 32462701; PMCID: PMC7283621.
      4. Kellam P, Barclay W. The dynamics of humoral immune responses following SARS-CoV-2 infection and the potential for reinfection. J Gen Virol. 2020 Aug;101(8):791-797. doi: 10.1099/jgv.0.001439. PMID: 32430094.
      5. Sa Ribero M, Jouvenet N, Dreux M, Nisole S. Interplay between SARS-CoV-2 and the type I interferon response. PLoS Pathog. 2020 Jul 29;16(7):e1008737. doi: 10.1371/journal.ppat.1008737. PMID: 32726355; PMCID: PMC7390284.
      6. Ovsyannikova IG, Haralambieva IH, Crooke SN, Poland GA, Kennedy RB. The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity. Immunol Rev. 2020 Jul;296(1):205-219. doi: 10.1111/imr.12897. Epub 2020 Jul 13. PMID: 32658335; PMCID: PMC7404857. Review
      7. 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.
      8. Liang Y, Wang ML, Chien CS, Yarmishyn AA, Yang YP, Lai WY, Luo YH, Lin YT, Chen YJ, Chang PC, Chiou SH. Highlight of Immune Pathogenic Response and Hematopathologic Effect in SARS-CoV, MERS-CoV, and SARS-Cov-2 Infection. Front Immunol. 2020 May 12;11:1022. doi: 10.3389/fimmu.2020.01022. PMID: 32574260; PMCID: PMC7236801. Review
      9. 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.
      10. Shah VK, Firmal P, Alam A, Ganguly D, Chattopadhyay S. Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past. Front Immunol. 2020 Aug 7;11:1949. doi: 10.3389/fimmu.2020.01949. PMID: 32849654; PMCID: PMC7426442. Review
  3. Add the word “Review” to any articles that are review articles that you listed in question 8.
  4. 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?
      1. Yes, in addition to the article I found in question 8, I found 3 other results.
    • List up to 5 new articles that were found on the author name search:
      1. Nakra NA, Awasthi S, Lakshminrusimha S, Kalra V. Visual Diagnosis: An Extremely Preterm Neonate with Gray Plaques on the Back. Neoreviews. 2019 May;20(5):e302-e305. doi: 10.1542/neo.20-5-e302. PMID: 31261084.
      2. Nakra NA, Madan RP, Buckley N, Huber AM, Freiermuth JL, Espinoza L, Walsh J, Parikh UM, Penrose KJ, Keller MJ, Herold BC. Loss of Innate Host Defense Following Unprotected Vaginal Sex. J Infect Dis. 2016 Mar 1;213(5):840-7. doi: 10.1093/infdis/jiv488. Epub 2015 Oct 13. PMID: 26464206; PMCID: PMC4747617.
      3. Dove ML, Jaggi P, Kelleman M, Abuali M, Ang JY, Ballan W, Basu SK, Campbell MJ, Chikkabyrappa SM, Choueiter NF, Clouser KN, Corwin D, Edwards A, Gertz SJ, Ghassemzadeh R, Jarrah RJ, Katz SE, Knutson SM, Kuebler JD, Lighter J, Mikesell C, Mongkolrattanothai K, Morton T, Nakra NA, Olivero R, Osborne CM, Panesar LE, Parsons S, Patel RM, Schuette J, Thacker D, Tremoulet AH, Vidwan NK, Oster ME. Multisystem Inflammatory Syndrome in Children: Survey of Protocols for Early Hospital Evaluation and Management. J Pediatr. 2020 Oct 16:S0022-3476(20)31293-2. doi: 10.1016/j.jpeds.2020.10.026. Epub ahead of print. PMID: 33075369; PMCID: PMC7566788.

Web of Science

  1. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 1,001
    • Record the top 10 papers (you don't need to use APA format for this):
      1. Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19) [1]
      2. Peripheral blood CD4+cell counts but not CD3+and CD8+cell counts are reduced in SARS-CoV-2 infection [2]
      3. BCG is a Good Immunotherapeutic Agent for Viral and Autoimmune Diseases: Is it a New Weapon against Coronavirus (COVID-19)? [3]
      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 [4]
      5. SARS-CoV-2 IgG antibody responses in New York City [5]
      6. Immunological features of coronavirus disease 2019 in patients with cancer [6]
      7. Safety assessment of drug combinations used in COVID-19 treatment: in silico toxicogenomic data-mining approach [7]
      8. 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 [8]
      9. Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach [9]
      10. Phillyrin (KD-1) exerts anti-viral and anti-inflammatory activities against novel coronavirus (SARS-CoV-2) and human coronavirus 229E (HCoV-229E) by suppressing the nuclear factor kappa B (NF-kappa B) signaling pathway [10]
  2. 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.
  3. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format: Ovsyannikova IG, Haralambieva IH, Crooke SN, Poland GA, Kennedy RB. The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity. Immunol Rev. 2020 Jul;296(1):205-219. doi: 10.1111/imr.12897. Epub 2020 Jul 13. PMID: 32658335; PMCID: PMC7404857. https://pubmed.ncbi.nlm.nih.gov/32658335/
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have? 166
      • How many articles have cited the article you have been assigned? 2

Comparing the 3 Databases

  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 Advantages: Provides the greatest number of results, is very user friendly, and has an easy way to cite the resulting articles
    • Google Scholar Disadvantages: Does not have specific advanced search options and the results from each search are not always directly related to the search
    • PubMed Advantages: Has many advanced search options and is user friendly
    • Pubmed Disadvantages: Does not always provide many search results, and does not provide readily available citations
    • Web of Science Advantages: Has many different search options such as advanced search, author search, structure search, and more. Web of Science also provides much more specific results compared to Google Scholar.
    • Web of Science Disadvantages: This search engine requires a paid subscription, and does not provide an easy way to cite articles.
  2. What impact does choice of keywords have on your results?
  3. For your Conclusion section, write a short reflection about what you learned by doing this exercise. Include in your answer what you knew previously about searching the biological literature, and what you learned that was new today.

Conclusion

Overall, this exercise taught me a lot about searching for biological research. Prior to completing this exercise, I was familiar with Google Scholar and would often use this database for completing academic research. Since completing this exercise, I learned a lot about the PubMed and Web of Science databases. Before this assignment, I was somewhat familiar with PubMed, but I since learned how to properly use the site and all of its useful features. Additionally, before this assignment, I had not been exposed to the Web of Science database, but I now feel comfortable working with the database and using its features. As a whole, I feel that now that I have completed this assignment, I now have the tools that I need to conduct proper biological research.

Acknowledgements

  • I acknowledge my homework partner JT, who I consulted on zoom regarding syntax, formatting, and content questions.
  • I acknowledge that I copied and modified the protocol shown on the Week 10 assignment page for this course.

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

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