Lurbinah Week 8

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Lizzy Urbina

Template:lurbinah

Assignments


Weekly Assigments

Class Journal Assigments

Purpose

To learn about the uses and tools of different engine search, and learn about copy rights and profits, and different data bases to access different articles.

Assignment

  1. Perform a search in Google Scholar .
    1. Record the number of “hits” you found: 37,700
    2. Record the top 10 papers, this time using APA format:
      • Pancera, M., Zhou, T., Druz, A. et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 514, 455–461 (2014). https://doi.org/10.1038/nature13808
      • White, T. A., Bartesaghi, A., Borgnia, M. J., Meyerson, J. R., de la Cruz, M. J., Bess, J. W., Nandwani, R., Hoxie, J. A., Lifson, J. D., Milne, J. L., & Subramaniam, S. (2010). Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS pathogens, 6(12), e1001249. https://doi.org/10.1371/journal.ppat.1001249
      • Milich, L., Margolin, B. H., & Swanstrom, R. (1997). Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein. Virology, 239(1), 108-118.
      • Stewart-Jones, G. B., Soto, C., Lemmin, T., Chuang, G. Y., Druz, A., Kong, R., ... & Bylund, T. (2016). Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell, 165(4), 813-826.
      • Merk, A., & Subramaniam, S. (2013). HIV-1 envelope glycoprotein structure. Current opinion in structural biology, 23(2), 268-276.
      • Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I. S., Crooks, E. T., Gorman, J., ... & Soto, C. (2015). Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature structural & molecular biology, 22(7), 522.
      • Curlin, M. E., Zioni, R., Hawes, S. E., Liu, Y., Deng, W., Gottlieb, G. S., ... & Mullins, J. I. (2010). HIV-1 envelope subregion length variation during disease progression. PLoS pathogens, 6(12).
      • Mao, Y., Wang, L., Gu, C., Herschhorn, A., Xiang, S. H., Haim, H., ... & Sodroski, J. (2012). Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nature structural & molecular biology, 19(9), 893.
      • Gao, F., Yue, L., Craig, S., Thornton, C. L., Robertson, D. L., McCUTCHAN, F. E., ... & WHO NETWORK FOR HIV ISOLATION AND CHARACTERIZATION. (1994). Genetic variation of HIV type 1 in four World Health Organization-sponsored vaccine evaluation sites: generation of functional envelope (glycoprotein 160) clones representative of sequence subtypes A, B, C, and E. AIDS research and human retroviruses, 10(11), 1359-1368.
      • Kwong, P. D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (2000). Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure, 8(12), 1329-1339.
  2. Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Paesano, L., Marmiroli, M., Bianchi, M. G., White, J. C., Bussolati, O., Zappettini, A., ... & Marmiroli, N. (2020). Differences in toxicity, mitochondrial function and miRNome in human cells exposed in vitro to Cd as CdS quantum dots or ionic Cd. Journal of Hazardous Materials, 122430.
    • Yang, D., Zhang, W., Zhang, H., Zhang, F., Chen, L., Ma, L., ... & Tran, P. H. Progress, opportunity, and perspective on exosome isolation–efforts for efficient exosome-based theranostics.
    • Oliveira Silva Martins, D., de Andrade Santos, I., Moraes de Oliveira, D., Riquena Grosche, V., & Carolina Gomes Jardim, A. (2020). Antivirals against Chikungunya Virus: Is the Solution in Nature?. Viruses, 12(3), 272.
    • Bhimma, R. 12 HIV-Related Kidney Diseases. HIV Infection in Children and Adolescents, 143.
    • Madusanka, R. K., Theruka, M. N., Liyanage, D. S., Sirisena, D. M. K. P., & Lee, J. (2020). Role of rockfish (Sebastes schlegelii) glutaredoxin 1 in innate immunity, and alleviation of cellular oxidative stress: Insights into localization, molecular characteristics, transcription, and function. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, 110432.
  3. Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Chuang, G. Y., Zhou, J., Acharya, P., Rawi, R., Shen, C. H., Sheng, Z., ... & Doria-Rose, N. A. (2019). Structural survey of broadly neutralizing antibodies targeting the HIV-1 Env trimer delineates epitope categories and characteristics of recognition. Structure, 27(1), 196-206.
    • Kumar, S., Sarkar, A., Pugach, P., Sanders, R. W., Moore, J. P., Ward, A. B., & Wilson, I. A. (2019). Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Nature communications, 10(1), 1-10.
    • Whitaker, N., Hickey, J. M., Kaur, K., Xiong, J., Sawant, N., Cupo, A., ... & Sanders, R. W. (2019). Developability assessment of physicochemical properties and stability profiles of HIV-1 BG505 SOSIP. 664 and BG505 SOSIP. v4. 1-GT1. 1 gp140 envelope glycoprotein trimers as candidate vaccine antigens. Journal of pharmaceutical sciences, 108(7), 2264-2277.
    • Palmer, J., & Poon, A. F. (2019). Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution, 5(2), vez022.
    • Trinh, H. V., Gohain, N., Pham, P. T., Hamlin, C., Song, H., Sanders-Buell, E., ... & Robb, M. L. (2019). Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort. Cells, 8(4), 365.
  4. Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Munro, J. B., & Lee, K. K. (2018). Probing structural variation and dynamics in the HIV-1 Env fusion glycoprotein. Current HIV research, 16(1), 5-12.
    • Chuang, G. Y., Zhou, J., Acharya, P., Rawi, R., Shen, C. H., Sheng, Z., ... & Doria-Rose, N. A. (2019). Structural survey of broadly neutralizing antibodies targeting the HIV-1 Env trimer delineates epitope categories and characteristics of recognition. Structure, 27(1), 196-206.
    • Stewart-Jones, G. B., Soto, C., Lemmin, T., Chuang, G. Y., Druz, A., Kong, R., ... & Bylund, T. (2016). Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell, 165(4), 813-826.
    • Chuang, G. Y., Zhou, J., Rawi, R., Shen, C. H., Sheng, Z., West, A. P., ... & Louder, M. K. (2018). Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates. BioRxiv, 312579.
    • Meyer, B. (2018). The role of HIV-1 subtype B Envelope transmission motifs in subtype C variant infectivity (Doctoral dissertation, University of Cape Town).
  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:
    • mutations gp120
    • HIV gp120
    • Structure-function mutation gp120
    • structure and function of 120
    • Structure of gp10
    • gp120
    • gp120 structure and function
    • gp120 structure function
    • mutation in the gp120 protein
    • HIV-1 gp120 protein
    • gp120 mutation structure
    • mutation in gp120
    • HIV gp120 mutation
    • HIV gp120 function
    • Record the search terms that have now been assigned specifically to you:
      • HIV-1 env structure variation
  6. 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:82
    • Record the top 10 papers (you don't need to do APA format for this):
      1. Selective transmission of some HIV-1 subtype C variants might depend on Envelope stimulating endritic cells to secrete IL-10.
      2. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization.
      3. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort.
      4. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies.
      5. Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition
      6. NGS combined with phylogenetic analysis to detect HIV-1 dual infection in Romanian people who inject drugs.
      7. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120.
      8. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein.
      9. Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.
      10. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates.
  7. Perform a title/abstract search on your assigned keywords.
    • Record the total number of hits:0
      1. zero results where shown with this filter
  8. Add the word “Review” to any articles that are review articles that you listed in question 8.
  9. 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? yes
    • List up to 5 new articles that were found on the author name search:
      1. Structural insights into key sites of vulnerability on HIV-1 Env and influenza HA.
      2. Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin.
      3. Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262.
      4. Interaction between the hemagglutinin-neuraminidase and fusion glycoproteins of human parainfluenza virus type III regulates viral growth in vivo.
      5. Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains.
  10. Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
    • Record the total number of hits:51
    • Record the top 10 papers (you don't need to use APA format for this):
      1. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization
      2. Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer
      3. Humoral Response to the HIV-1 Envelope V2 Region in a Thai Early Acute Infection Cohort
      4. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies
      5. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120
      6. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Gly- coprotein
      7. Insights into the molecular mechanism underlying CD4-dependency and neutralization sensitivity of HIV-1: a comparative molecular dynamics study on gp120s from isolates with different phenotypes
      8. Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring
      9. Determinants of HIV-1 CD4-Independent Brain Adaptation
      10. Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike
  11. 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.
  12. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:
    • Pancera, M., Zhou, T., Druz, A. et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 514, 455–461 (2014). https://doi.org/10.1038/nature13808
    • In Web of Science, search for the specific article that you have been assigned.
      • How many cited references does that article have?
        • 127
      • How many articles have cited the article you have been assigned?
        • 416
  13. 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
      • this search engine is free.
      • It is very simple to find the citations for each article.
    • Google Scholar: disadvantages
      • There are not many search variation
      • The articles shown are based on the text, and therefore more options are shown that might not be entirely related to the search.
    • PubMed: advantages
      • there is a lot of search variability
      • It is restricted to the science community
    • Pubmed: disadvantages
      • Does not have citations ready to use
      • Some of the articles in its data base are not free.
    • Web of Science: advantages
      • selective with what articles in adds to its platform
      • Add a new tool that allows to see the times an article has been cited since it was published, and it allows to save citation
    • Web of Science: disadvantages
      • Not as good for key word search
      • It is not free
  14. What impact does choice of keywords have on your results?
    • In general it reduces or expands the amount of articles available. In Google scholars key word play a very impotant role in reducing thousands of articles, likewise PubMed and Web of science reduce teh amount of articles, but since these search engines are more specefic it helps to specify the search to a few articles.
  15. Now we will begin to evaluate your assigned article in three areas availability, the journal, and the article metadata. Again, provide a citation for the article in APA format, this time including the DOI. For the following questions, for information that is not available, answer n/a).
    1. Provide a link to the abstract of the article on PubMed
    2. Provide a link to the full text of the article in PubMed Central
    3. Provide a link to the full text of the article (HTML format) from the publisher website.
    4. Provide a link to the full PDF version of the article from the publisher website.
    5. Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.
      • Macmillan Publishers Limited
    6. How is the article available to you:
      • online via PubMEd, Publishers page, PubMed Central, Google Scholar, and nature journal.
      • Is the article available “open access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
        • Yes
      • If the article is not “open access” is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here
      • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop
      • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
    7. Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
      • Both
  16. Evaluating the source--the journal
    1. Who is the publisher of the journal?
      • Nature
    2. Is the publisher for-profit or non-profit?
      • Profit
    3. Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
      • It a profit scientific society with a research option
    4. Does the publisher belong to the Open Access Publishers Association?
      • It gives an open acces option to their scientists
    5. What country is the journal published in?
      • Great Britain
    6. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
      • Since November 1869
    7. Are articles in this journal peer-reviewed?
      • Yes
    8. Provide a link to the scientific advisory board/editorial board of the journal.
    9. What is the journal impact factor (look to see if it is provided on the journal home page; often you can also find it through a Google search)?
      • 2018= 43.07 5 year= 45.819
  17. Evaluating the source--the article
    1. Is the article a review or primary research article?
      • Primary Research Article
    2. On what date was the article submitted?
      • 04 June 2014
    3. On what date was the article accepted?
      • 01 September 2014
    4. Did the article undergo any revisions before acceptance?
      • Yes
    5. When was the article published?
      • 08 October 2014
    6. What is the approximate elapsed time between submission and publication?
      • about 3 months
    7. What are the institutions with which the authors are affiliated?
      • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, 20892, Maryland, USA,
    8. Have the authors published other articles on this subject? (How will you find this out?)
      • Yes search for authors name in pubmed, web of science, and google scholar
    9. Is there a conflict of interest for any of the authors?
      • The authors declare no competing financial interests.
    10. Read the abstract. Write 1-2 sentences about the relevance of this article to understanding the structure-function relationship of mutations in the HIV-1 gp120 protein.
      • The structure at 3.5-Å resolution for an HIV-1-Env trimer shows the prefusion conformation of gp41, useful for immune evasion and immune recognition.
    11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
      • I don't think we should use this article for journal club because it works with gp41 and we are currently working with gp120.
    12. Copy your 1-2 sentence statement about the relevance and the recommendation (plus justification) and paste into the class shared bibliography as a bullet point underneath your assigned paper.

Conclusion

This assigment was very useful to know how key words can affect different search engines and how to properly use keywords in each specific search engine. I knew about pubmed and google scholar and how to manage my way around it. Web of science and some of the features learned in pubmed were completely new to me. Additionally, I did not fully undertand the copy rights and who get profit from the articles as much as I do after doing this assigment. Overall, it has given me a better sense of how the publishing world works.

Acknowledgments

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

Lurbinah (talk) 23:29, 25 March 2020 (PDT)

References

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