JT Correy Journal Week 10

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Purpose

This week's assignment was intended to increase our understanding a proficiency with multiple different databases that are common to biology.

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
      • 17,900 for the keywords of "sars-cov-2 or covid-19 or 2019-ncov immune response"
    2. Record the top 10 papers, this time using APA format:
      • Lippi, G., Salvagno, G. L., Pegoraro, M., Militello, V., Caloi, C., Peretti, A., ... & Cascio, G. L. (2020). Assessment of immune response to SARS-CoV-2 with fully automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays. Clinical Chemistry and Laboratory Medicine (CCLM), 1(ahead-of-print).
      • Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020). Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses, 12(3), 254.
      • Prasad, K., Khatoon, F., Rashid, S., Ali, N., AlAsmari, A. F., Ahmed, M. Z., ... & Kumar, V. (2020). Targeting hub genes and pathways of innate immune response in COVID-19: a network biology perspective. International journal of biological macromolecules, 163, 1-8.
      • Prompetchara, E., Ketloy, C., & Palaga, T. (2020). Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol, 38(1), 1-9.
      • Ye, X., Xiao, X., Li, B., Zhu, W., Li, Y., Wu, J., ... & Huang, J. (2020). Low humoral immune response and ineffective clearance of SARS-Cov-2 in a COVID-19 patient with CLL during a 69-day follow-up. Frontiers in oncology, 10.
      • Ong, E. Z., Chan, Y. F. Z., Leong, W. Y., Lee, N. M. Y., Kalimuddin, S., Mohideen, S. M. H., ... & Low, J. G. H. (2020). A dynamic immune response shapes COVID-19 progression. Cell host & microbe.
      • Li, H., Liu, L., Zhang, D., Xu, J., Dai, H., Tang, N., ... & Cao, B. (2020). SARS-CoV-2 and viral sepsis: observations and hypotheses. The Lancet.
      • Bashyam, A. M., & Feldman, S. R. (2020). Should patients stop their biologic treatment during the COVID-19 pandemic. J Dermatolog Treat, 19, 1-2.
      • Cossarizza, A., De Biasi, S., Guaraldi, G., Girardis, M., Mussini, C., & Modena Covid‐19 Working Group. (2020). SARS‐CoV‐2, the virus that causes COVID‐19: cytometry and the new challenge for global health. Cytometry, 97(4), 340.
      • Tay, M. Z., Poh, C. M., Rénia, L., MacAry, P. A., & Ng, L. F. (2020). The trinity of COVID-19: immunity, inflammation and intervention. Nature Reviews Immunology, 1-12.
  3. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Banerjee, A. B., Singh, T. G., & Prashar, A. (2020). BCG vaccine, a ray of hope in treating Severe Acute Respiratory Syndrome (SARS). Infectious Disorders Drug Targets.
    • Urgessa, F. (2020). Biochemical, Hematological and Immunological Parameters among Covid19 Infected Patients. International Academic Journal of Applied Bio-Medical Sciences, 1(1).
    • Wu, Y., Ma, L., Zhuang, Z., Cai, S., Zhao, Z., Zhou, L., ... & Cui, J. (2020). Main protease of SARS-CoV-2 serves as a bifunctional molecule in restricting type I interferon antiviral signaling. Signal transduction and targeted therapy, 5(1), 1-3.
    • Caballero-Noguez, B., González-Yruegas, M. G., Ruiz-Rosas, R. A., & Caballero-Flores, J. D. (2020). Primer neonato nacido de madre con neumonía COVID-19 en el Instituto Mexicano del Seguro Social. Gaceta Médica de Bilbao, 117(2), 187-190.
    • Prachar, M., Justesen, S., Steen-Jensen, D. B., Thorgrimsen, S., Jurgons, E., Winther, O., & Bagger, F. O. (2020). Abstract PO-046: Assessment of COVID-19 vaccine candidates: Prediction and validation of 174 SARS-CoV-2 epitopes.
  4. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Lippi, G., Salvagno, G. L., Pegoraro, M., Militello, V., Caloi, C., Peretti, A., ... & Cascio, G. L. (2020). Assessment of immune response to SARS-CoV-2 with fully automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays. Clinical Chemistry and Laboratory Medicine (CCLM), 1(ahead-of-print).
    • Prompetchara, E., Ketloy, C., & Palaga, T. (2020). Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol, 38(1), 1-9.
    • Prasad, K., Khatoon, F., Rashid, S., Ali, N., AlAsmari, A. F., Ahmed, M. Z., ... & Kumar, V. (2020). Targeting hub genes and pathways of innate immune response in COVID-19: a network biology perspective. International journal of biological macromolecules, 163, 1-8.
    • Ong, E. Z., Chan, Y. F. Z., Leong, W. Y., Lee, N. M. Y., Kalimuddin, S., Mohideen, S. M. H., ... & Low, J. G. H. (2020). A dynamic immune response shapes COVID-19 progression. Cell host & microbe.
    • Bashyam, A. M., & Feldman, S. R. (2020). Should patients stop their biologic treatment during the COVID-19 pandemic. J Dermatolog Treat, 19, 1-2.
  5. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Lippi, G., Salvagno, G. L., Pegoraro, M., Militello, V., Caloi, C., Peretti, A., ... & Cascio, G. L. (2020). Assessment of immune response to SARS-CoV-2 with fully automated MAGLUMI 2019-nCoV IgG and IgM chemiluminescence immunoassays. Clinical Chemistry and Laboratory Medicine (CCLM), 1(ahead-of-print).
    • Prompetchara, E., Ketloy, C., & Palaga, T. (2020). Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pac J Allergy Immunol, 38(1), 1-9.
    • Prasad, K., Khatoon, F., Rashid, S., Ali, N., AlAsmari, A. F., Ahmed, M. Z., ... & Kumar, V. (2020). Targeting hub genes and pathways of innate immune response in COVID-19: a network biology perspective. International journal of biological macromolecules, 163, 1-8.
    • Ong, E. Z., Chan, Y. F. Z., Leong, W. Y., Lee, N. M. Y., Kalimuddin, S., Mohideen, S. M. H., ... & Low, J. G. H. (2020). A dynamic immune response shapes COVID-19 progression. Cell host & microbe.
    • Bashyam, A. M., & Feldman, S. R. (2020). Should patients stop their biologic treatment during the COVID-19 pandemic. J Dermatolog Treat, 19, 1-2.
  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 you:
      • COVID-19 and immune reaction
  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: 414
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Wiersinga, W. J., Rhodes, A., Cheng, A. C., Peacock, S. J., & Prescott, H. C. (2020). Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. JAMA, 324(8), 782–793. https://doi.org/10.1001/jama.2020.12839
      2. Le Bert, N., Tan, A. T., Kunasegaran, K., Tham, C., Hafezi, M., Chia, A., Chng, M., Lin, M., Tan, N., Linster, M., Chia, W. N., Chen, M. I., Wang, L. F., Ooi, E. E., Kalimuddin, S., Tambyah, P. A., Low, J. G., Tan, Y. J., & Bertoletti, A. (2020). SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584(7821), 457–462. https://doi.org/10.1038/s41586-020-2550-z
      3. Li, L., Zhang, W., Hu, Y., Tong, X., Zheng, S., Yang, J., Kong, Y., Ren, L., Wei, Q., Mei, H., Hu, C., Tao, C., Yang, R., Wang, J., Yu, Y., Guo, Y., Wu, X., Xu, Z., Zeng, L., Xiong, N., … Liu, Z. (2020). Effect of Convalescent Plasma Therapy on Time to Clinical Improvement in Patients With Severe and Life-threatening COVID-19: A Randomized Clinical Trial. JAMA, 324(5), 460–470. https://doi.org/10.1001/jama.2020.10044
      4. Grifoni, A., Weiskopf, D., Ramirez, S. I., Mateus, J., Dan, J. M., Moderbacher, C. R., Rawlings, S. A., Sutherland, A., Premkumar, L., Jadi, R. S., Marrama, D., de Silva, A. M., Frazier, A., Carlin, A. F., Greenbaum, J. A., Peters, B., Krammer, F., Smith, D. M., Crotty, S., & Sette, A. (2020). Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell, 181(7), 1489–1501.e15. https://doi.org/10.1016/j.cell.2020.05.015
      5. Iyer, M., Jayaramayya, K., Subramaniam, M. D., Lee, S. B., Dayem, A. A., Cho, S. G., & Vellingiri, B. (2020). COVID-19: an update on diagnostic and therapeutic approaches. BMB reports, 53(4), 191–205. https://doi.org/10.5483/BMBRep.2020.53.4.080
      6. Zhu FC, Li YH, Guan XH, Hou LH, Wang WJ, Li JX, Wu SP, Wang BS, Wang Z, Wang L, Jia SY, Jiang HD, Wang L, Jiang T, Hu Y, Gou JB, Xu SB, Xu JJ, Wang XW, Wang W, Chen W. Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet. 2020 Jun 13;395(10240):1845-1854. doi: 10.1016/S0140-6736(20)31208-3. Epub 2020 May 22. PMID: 32450106; PMCID: PMC7255193.
      7. Korakas, E., Ikonomidis, I., Kousathana, F., Balampanis, K., Kountouri, A., Raptis, A., Palaiodimou, L., Kokkinos, A., & Lambadiari, V. (2020). Obesity and COVID-19: immune and metabolic derangement as a possible link to adverse clinical outcomes. American journal of physiology. Endocrinology and metabolism, 319(1), E105–E109. https://doi.org/10.1152/ajpendo.00198.2020
      8. Jothimani, D., Venugopal, R., Abedin, M. F., Kaliamoorthy, I., & Rela, M. (2020). COVID-19 and the liver. Journal of hepatology, 73(5), 1231–1240. https://doi.org/10.1016/j.jhep.2020.06.006
      9. Balasubramanian, S., Rao, N. M., Goenka, A., Roderick, M., & Ramanan, A. V. (2020). Coronavirus Disease 2019 (COVID-19) in Children - What We Know So Far and What We Do Not. Indian pediatrics, 57(5), 435–442. https://doi.org/10.1007/s13312-020-1819-5
      10. Heneka, M. T., Golenbock, D., Latz, E., Morgan, D., & Brown, R. (2020). Immediate and long-term consequences of COVID-19 infections for the development of neurological disease. Alzheimer's research & therapy, 12(1), 69. https://doi.org/10.1186/s13195-020-00640-3
  8. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits: 19
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Iyer, M., Jayaramayya, K., Subramaniam, M. D., Lee, S. B., Dayem, A. A., Cho, S. G., & Vellingiri, B. (2020). COVID-19: an update on diagnostic and therapeutic approaches. BMB reports, 53(4), 191–205. https://doi.org/10.5483/BMBRep.2020.53.4.080
      2. Jothimani, D., Venugopal, R., Abedin, M. F., Kaliamoorthy, I., & Rela, M. (2020). COVID-19 and the liver. Journal of hepatology, 73(5), 1231–1240. https://doi.org/10.1016/j.jhep.2020.06.006
      3. Heneka, M. T., Golenbock, D., Latz, E., Morgan, D., & Brown, R. (2020). Immediate and long-term consequences of COVID-19 infections for the development of neurological disease. Alzheimer's research & therapy, 12(1), 69. https://doi.org/10.1186/s13195-020-00640-3
      4. Allegra, A., Di Gioacchino, M., Tonacci, A., Musolino, C., & Gangemi, S. (2020). Immunopathology of SARS-CoV-2 Infection: Immune Cells and Mediators, Prognostic Factors, and Immune-Therapeutic Implications. International journal of molecular sciences, 21(13), 4782. https://doi.org/10.3390/ijms21134782
      5. Coccheri S. (2020). COVID-19: The crucial role of blood coagulation and fibrinolysis. Internal and emergency medicine, 15(8), 1369–1373. https://doi.org/10.1007/s11739-020-02443-8
      6. Amiral, J., Vissac, A. M., & Seghatchian, J. (2020). Covid-19, induced activation of hemostasis, and immune reactions: Can an auto-immune reaction contribute to the delayed severe complications observed in some patients?. Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis, 59(3), 102804. https://doi.org/10.1016/j.transci.2020.102804#*# paper 7
      7. Elahi S. (2020). Neonatal and Children's Immune System and COVID-19: Biased Immune Tolerance versus Resistance Strategy. Journal of immunology (Baltimore, Md. : 1950), 205(8), 1990–1997. https://doi.org/10.4049/jimmunol.2000710
      8. Rahman, M. H., Akter, R., Behl, T., Chowdhury, M., Manirujjaman, M., Bulbul, I. J., Elshenawy, S. E., & Kamal, M. A. (2020). COVID-19 Outbreak and Emerging Management through Pharmaceutical Therapeutic Strategy. Current pharmaceutical design, 10.2174/1381612826666200713174140. Advance online publication. https://doi.org/10.2174/1381612826666200713174140
      9. Li, K., Hao, Z., Zhao, X., Du, J., & Zhou, Y. (2020). SARS-CoV-2 infection-induced immune responses: Friends or foes?. Scandinavian journal of immunology, 92(2), e12895. https://doi.org/10.1111/sji.12895
  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?
    • List up to 5 new articles that were found on the author name search:
      1. Jothimani, D., Venugopal, R., Abedin, M. F., Kaliamoorthy, I., & Rela, M. (2020). COVID-19 and the liver. Journal of hepatology, 73(5), 1231–1240. https://doi.org/10.1016/j.jhep.2020.06.006
      2. Jothimani, D., Govil, S., & Rela, M. (2016). Management of post liver transplantation recurrent hepatitis C infection with directly acting antiviral drugs: a review. Hepatology international, 10(5), 749–761. https://doi.org/10.1007/s12072-016-9744-3
      3. Jothimani, D., Chandy, G. M., & Conjeevaram, H. (2013). A new era in the treatment of chronic hepatitis C infection. Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology, 32(2), 71–79. https://doi.org/10.1007/s12664-012-0254-5
      4. Jothimani, D., Cramp, M. E., Mitchell, J. D., & Cross, T. J. (2011). Treatment of autoimmune hepatitis: a review of current and evolving therapies. Journal of gastroenterology and hepatology, 26(4), 619–627. https://doi.org/10.1111/j.1440-1746.2010.06579.x
      5. Anand, A. C., Nandi, B., Acharya, S. K., Arora, A., Babu, S., Batra, Y., Chawla, Y. K., Chowdhury, A., Chaoudhuri, A., Eapen, E. C., Devarbhavi, H., Dhiman, R., Datta Gupta, S., Duseja, A., Jothimani, D., Kapoor, D., Kar, P., Khuroo, M. S., Kumar, A., Madan, K., … INASL Task-Force on Acute Liver Failure (2020). Indian National Association for the Study of the Liver Consensus Statement on Acute Liver Failure (Part 1): Epidemiology, Pathogenesis, Presentation and Prognosis. Journal of clinical and experimental hepatology, 10(4), 339–376. https://doi.org/10.1016/j.jceh.2020.04.012
  11. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits: 14
    • Record the top 10 papers (you don't need to use APA format for this):
      1. BCG is a Good Immunotherapeutic Agent for Viral and Autoimmune Diseases: Is it a New Weapon against Coronavirus (COVID-19)?
      2. Behavioral immune system linked to responses to the threat of COVID-19
      3. COVID-19 and the liver
      4. Invited Review: The spectrum of neuropathology in COVID-19
      5. Neonatal and Children's Immune System and COVID-19: Biased Immune Tolerance versus Resistance Strategy
      6. Comparison of Efficacy of Dexamethasone and Methylprednisolone in Improving PaO2/FiO2 Ratio Among COVID-19 Patients
      7. Understanding the structure and dynamics of anti-inflammatory corticosteroid dexamethasone by solid state NMR spectroscopy
      8. Approaching coronavirus disease 2019: Mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2
      9. Infection as a Stroke Risk Factor and Determinant of Outcome After Stroke
      10. The potential role of the carotid body in COVID-19
  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.
  13. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format: Kampf, G., Todt, D., Pfaender, S., & Steinmann, E. (2020). Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents. Journal of Hospital Infection, 104(3), 246-251. https://www.journalofhospitalinfection.com/article/S0195-6701(20)30046-3/pdf
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
        • The article cited 41 different references.
      • How many articles have cited the article you have been assigned?
        • This article has been cited by 81 other articles on Web of Science
  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 by far the most search results of any of the three search engines. If you are looking for a specific article Google scholar is useful because if the quantity of articles it has, your article is likely to be in the engine.
    • Google Scholar: disadvantages
      • Google scholar is much harder to find good articles and filter your searches. Articles in the other databases usually have to have a certain standard of credibility (usually based on the journal they were published in). It is also hard to filter the search results from Google Scholar based on anything other than date of publication.
    • PubMed: advantages
      • Pubmed is useful because it free and more well put together than Google scholar. You can customize your search much better and the results are able to be sorted in more ways.
    • Pubmed: disadvantages
      • Pubmed is pretty solid all around, the major disadvantage is that there are not as many articles as Google scholar has.
    • Web of Science: advantages
      • Web of Science has a great user interface that is by far the most customizable and accurate of the three databases.
    • Web of Science: disadvantages
      • Just like Pubmed, the only major disadvantage is that there are not as mony articles as Google scholar.
  15. What impact does choice of keywords have on your results?
    • The importance of keywords varies from database to database. Web of Science is great because you can make sure that the keywords occur in the title or abstract and not just in the actual article. This is beneficial because Google scholar you give you an article that has the keyword at least once even if it is not super related. keyword is a great way to start finding articles if you do not know exactly what you are looking for. By searching for a keyword you get a general idea of the literature about a given topic and you can then get more specific from there.
  16. 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.
    • In the Coastal Ecology and Conservation Lab we are currently working on a systematic review of seagrass articles in southern Los Angeles. To collect all the relevant articles we used Web of Science, so I was already pretty familiar with that database. But I did learn a lot about PubMed since I have never used that before. I have also used Google Scholar a lot in the past. Overall, I didn't learn too much this week but I definitely picked up in little things here and there and also became more proficient with the engines.

Acknowledgements

  • Taylor Makela
    • Yaniv and I worked as homework partners for this week. We communicated and worked together both at the end of the week 10 lab and throughout the week to create our research project and assignment pages.
  • Dr. Dahlquist
    • Dr. Dahlquist served as a coach for how to begin our pages. She also instructed the class and provided us with the guiding homework document.
  • I copied and modified the protocol shown on the Week 10 page of our class OpenWetWare.

Jcorrey (talk) 18:03, 11 November 2020 (PST)

References



JT Correy Template

BIOL368/F20

JT Correy Template

Weekly Assignments

Individual Journal Pages

Class Journal Pages

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