Courtney L. Merriam Week 5

Purpose

The purpose of this experiment was to select information that provides relevant evidence for my topic and to use databases to find scholarly professional information. Also to understand how to differentiate between source types.

Annotated Bibliography for HIV Evolution Project

• Mayr, L. M., & Zolla-Pazner, S. (2015). Antibodies Targeting the Envelope of HIV-1. Microbiol Spectr, 3(1), AID-0025-2014. doi:10.1128/microbiolspec.AID-0025-2014
  1. Who owns the right to the article and what is is the availability?
     • Does the journal or the author own the copyright?
       • The Journal: American Society for Microbiology.
     • Is this article “Open Access” upon publication under a Creative Commons license?
       • No
     • Is this article available for free after a certain period of time has elapsed?
       • No
     • Is this article only available behind a paywall?
       • Yes
  2. What organization is the publisher of the article?
     • American Society for Microbiology
     • What type of organization is it?
       • Scientific society
  3. Is this article available in print or online only?
     • Online Only
  4. Has LMU paid a subscription or other fee for your access to this article?
     • Yes
  5. Write 2-3 sentences about why this article is relevant to your project.
     • This article explores the relationship antibodies produced by the human body have with the HIV virus, and how certain antibodies require a significant amount of time to elevate the effectiveness of their capabilities. This article is relevant to my project because it further expands my understanding of the nuances of the immune response to the HIV virus, and the various ways the HIV virus conversely responds and challenges the immune system.
  6. How many articles does this article cite?
     • 116
  7. How many articles cite this article?
     • 3
• Immonen, T. T. (12/2015). PLoS computational biology: Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus population. Public Library of Science. doi:10.1371/journal.pcbi.1004625
  1. Who owns the right to the article and what is is the availability?
     • Does the journal or the author own the copyright?
       • CC0 Copy Right
     • Is this article “Open Access” upon publication under a Creative Commons license?
       • Yes
  2. What organization is the publisher of the article?
     • PLoS computational biology
     • What type of organization is it?
       • A Peer-Reviewed Open-Access Journal
  3. Is this article available in print or online only?
     • Online Only
  4. Has LMU paid a subscription or other fee for your access to this article?
     • No
  5. Write 2-3 sentences about why this article is relevant to your project.
     • This article expands on new evidence that shielded HIV variants released from latent cells may have the capacity to compete against better adapted HIV viral variants that have so far mutated in response to counter the host's immune response. This is yet another mechanism by which HIV infects its host, and is therefore relevant to my understanding and development of my project.
  6. How many articles does this article cite?
     • 56
  7. How many articles cite this article?
     • 1
• Rademeyer, C. C. (07/2016). PLoS pathogens: Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition: Implications for active and passive immunization. Public Library of Science. doi:10.1371/journal.ppat.1005742
  1. Who owns the right to the article and what is is the availability?
     • Does the journal or the author own the copyright?
       • CC0 Copy Right
     • Is this article “Open Access” upon publication under a Creative Commons license?
       • Yes
  2. What organization is the publisher of the article?
     • PLoS pathogens
     • What type of organization is it?
       • A Peer-Reviewed Open-Access Journal
  3. Is this article available in print or online only?
     • Online Only
  4. Has LMU paid a subscription or other fee for your access to this article?
     • No
  5. Write 2-3 sentences about why this article is relevant to your project.
     • This article explains how vaccine and immunization trials are being implemented in epidemic areas in southern Africa, and more specifically, how increased understanding can help determine the implications of viral diversity on antibody recognition. Many of these articles are on similar topics and ways of exploring how the diversity of the HIV variants leads to the difficulty the body has neutralizing it.
  6. How many articles does this article cite?
     • 72
  7. How many articles cite this article?
     • Could not be found because of time issue
• Rinaldo, C. C. (09/1995). Journal of virology: High levels of anti-human immunodeficiency virus type 1 (HIV-1) memory cytotoxic T-lymphocyte activity and low viral load are associated with lack of disease in HIV-1-infected long-term nonprogressors. American Society for Microbiology.
  1. Who owns the right to the article and what is is the availability?
     • Does the journal or the author own the copyright?
       • American Society for Microbiology
     • Is this article “Open Access” upon publication under a Creative Commons license?
       • No
     • Is this article available for free after a certain period of time has elapsed?
       • No?
     • Is this article only available behind a paywall?
       • Yes
  2. What organization is the publisher of the article?
     • American Society for Microbiology
     • What type of organization is it?
       • Scientific society
  3. Is this article available in print or online only?
     • Print
  4. Has LMU paid a subscription or other fee for your access to this article?
     • Yes
  5. Write 2-3 sentences about why this article is relevant to your project.
     • This article develops research based around the discovery that lack of disease within long-term nonprogressors is closely linked with the low copy number of HIV DNA and RNA. Since my project is based around examining the copy numbers of the viruses and not necessarily the decline of CD4 cells, this article can shed more light on the relevance of copy number over CD4 decline.
  6. How many articles does this article cite?
     • 42
  7. How many articles cite this article?
     • 469

1. What original keywords did you use?
   • HIV-1 virus diversity and divergence
2. How many results did you get?
   • PubMed: 111
   • Google Scholar: 22,900
   • Web of Science: 124
3. Which terms in which combinations were most useful to narrow down the search?
   • diversity divergence HIV-1
4. How many results did you get after narrowing the search?
   • PubMed: 65
   • Google Scholar: 16,400
   • Web of Science: 79
5. Which advance search functions were most useful to narrow down the search? How many results did you get?
   • PubMed: 48
     • Adding the topic to also include envelope diversity
   • Google Scholar: 22,600
     • Having the exact phrase HIV 1 and having at lease one of the terms diversity or divergence
   • Web of Science: 33
     • Changing the time frame of publication

Data and Files

1. Antibodies Targeting the Envelope of HIV-1³
2. Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition: Implications for active and passive immunization⁴
3. High levels of anti-human immunodeficiency virus type 1 (HIV-1) memory cytotoxic T-lymphocyte activity and low viral load are associated with lack of disease in HIV-1-infected long-term nonprogressors⁵
4. Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus population¹

Conclusion

what was your main finding for today's work; briefly summarize the progress you made towards your research question? The development of this bibliography helped me gather valuable resources that will enable me to amplify my understanding of the relationship between HIV progression and HIV viral copy number. Additionally, I now have a better command of how to access the scientific journal's essential to furthering my understanding in any area of research. I was able to work towards my research question because I now have a better comprehension of the material as well as more resources to utilize later.

Acknowledgments

I collaborated with Avery Vernon-Moore and Kam D. Dahlquist in class on this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. Courtney L. Merriam 13:42, 28 September 2016 (EDT):

References

1 Immonen, T. T. (12/2015). PLoS computational biology: Recombination enhances HIV-1 envelope diversity by facilitating the survival of latent genomic fragments in the plasma virus population. Public Library of Science. doi:10.1371/journal.pcbi.1004625

2 Markham, R.B., Wang, W.C., Weinstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. dos: 10.1073/pnas.95.21.12568

3 Mayr, L. M., & Zolla-Pazner, S. (2015). Antibodies Targeting the Envelope of HIV-1. Microbiol Spectr, 3(1), AID-0025-2014. doi:10.1128/microbiolspec.AID-0025-2014

4 Rademeyer, C. C. (07/2016). PLoS pathogens: Features of recently transmitted HIV-1 clade C viruses that impact antibody recognition: Implications for active and passive immunization. Public Library of Science. doi:10.1371/journal.ppat.1005742

5 Rinaldo, C. C. (09/1995). Journal of virology: High levels of anti-human immunodeficiency virus type 1 (HIV-1) memory cytotoxic T-lymphocyte activity and low viral load are associated with lack of disease in HIV-1-infected long-term nonprogressors. American Society for Microbiology.

Useful Links

Courtney L. Merriam

Clas Page: Bioinformatics Laboratory

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