Shivum Desai Journal Week 5

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Shivum Desai Bioinformatics 08/03/2016 Template:Shivum A Desai

Bibliography Citations

1. PRIMARY: Margolick, J. B., Apuzzo, L., Singer, J., Wong, H., Lee, T., Gallant, J. E., . . . Conway, B. (2015). A Randomized Trial of Time-Limited Antiretroviral Therapy in Acute/Early HIV Infection. PLOS ONE, 10(11). doi:10.1371/journal.pone.0143259

a. Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26600459
b. PMC: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658016/
c. Publisher Full Text: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143259
d. PDF: http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0143259.PDF
e. Who owns right to the article and what is the availability:
i. The author owns the rights to this article
ii. It is open access under a creative commons license
iii. It is currently free
iv. It is not behind a paywall
f. What organization is the publisher of the article?
i. It was published by the journal PLOS ONE which is a nonprofit publisher.
g. This article is available online only.
h. No subscription necessary because this is an open access journal.
i. This article described a study which involved the testing of a new antiviral treatment on a group of test patients who had HIV and the results showed that no matter the progression stage at which the patient was, the virus was no affected by the treatment. This is due to the constant mutation of the virus which is thus related to the Markham article.

2. PRIMARY: Garrett, N. J., Werner, L., Naicker, N., Naranbhai, V., Sibeko, S., Samsunder, N., . . . Abdool-Karim, S. S. (2015, January 1). HIV Disease Progression in Seroconvertors from the CAPRISA 004 Tenofovir Gel Pre-exposure Prophylaxis Trial. JAIDS Journal of Acquired Immune Deficiency Syndromes, 68(1), 55-61. doi:10.1097/qai.0000000000000367

a. Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25247433
b. PMC: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262710/
c. Publisher Full Text: http://journals.lww.com/jaids/Fulltext/2015/01010/HIV_Disease_Progression_in_Seroconvertors_from_the.9.aspx\
d. PDF: http://pdfs.journals.lww.com/jaids/2015/01010/HIV_Disease_Progression_in_Seroconvertors_from_the.9.pdf?token=method%7CExpireAbsolute;source%7CJournals;ttl%7C1475015409752;payload%7CmY8D3u1TCCsNvP5E421JYK6N6XICDamxByyYpaNzk7FKjTaa1Yz22MivkHZqjGP4kdS2v0J76WGAnHACH69s21Csk0OpQi3YbjEMdSoz2UhVybFqQxA7lKwSUlA502zQZr96TQRwhVlocEp/sJ586aVbcBFlltKNKo+tbuMfL73hiPqJliudqs17cHeLcLbV/CqjlP3IO0jGHlHQtJWcICDdAyGJMnpi6RlbEJaRheGeh5z5uvqz3FLHgPKVXJzd2/tJWbBypN0UA6UOYazuUXAarKdyrmvKNeltLAJcUos=;hash%7CPg8IhiYppdx20DDN4+KWlw==
e. Who owns right to the article and what is the availability:
i. The journal owns the rights to this article
ii. This is a free article on the journal’s website.
iii. It is not behind a paywall because it is free
f. What organization is the publisher of the article?
i. Journal of Acquired Immune Deficiency Syndromes. Non profit medical journal.
g. This article is print only.
h. No subscription necessary because it is a free article from the publisher.
i. This article is relevant to my project because patients CD4 counts and viral loads were watched over a minimum of two years to observe their disease progression in the presence of tenofovir gel. The relevance is that this article studied and provides data that is similar to the Markham paper, especially because similar factors were observed and the tenofovir ended up not having an impact on the CD4 counts. Thus, data in regards to CD4 counts were unaltered by any extracellular forces.

3. PRIMARY: Xu, C., Shen, T., Zheng, J., Tu, J., Zhang, W., & Lu, F. (2012, November 24). Higher dN/dS ratios in the HCV core gene, but not in the E1/HVR1 gene, are associated with human immunodeficiency virus-associated immunosuppression. Arch Virol Archives of Virology, 157(11), 2153-2162. doi:10.1007/s00705-012-1390-z

a. Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=higher+dn%2Fds+ratios+in+the+hcv+core+gene
b. PMC: not available
c. Publisher full text: http://link.springer.com/article/10.1007%2Fs00705-012-1390-z
d. PDF: http://download.springer.com/static/pdf/746/art%253A10.1007%252Fs00705-012-1390-z.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs00705-012-1390-z&token2=exp=1475018429~acl=%2Fstatic%2Fpdf%2F746%2Fart%25253A10.1007%25252Fs00705-012-1390-z.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Farticle%252F10.1007%252Fs00705-012-1390-z*~hmac=dd5efcf2dcb7f0b93ff4acf7d5abb770e0df5a29a4c9dd0542ea2b883b7f828c
e. Who owns right to the article and what is the availability:
i. The journal owns the rights to the article
ii. This journal is not open access nor is it available for free after a period of time
iii. It is only available behind a paywall of $200 for a subscription.
f. What organization is the publisher of the article?
i. Archives of Virology, nonprofit journal.
g. This article is both available in print and online.
h. LMU has a subscription to this journal.
i. This article contains a test and analysis of dN/ds ratios of a HCV core gene and its association with HIV immunosuppression. It is relevant to my study because it is testing to see whether the dN/ds ratios of the HCV core gene will show the reason why this gene is associated HIV suppression. However, just as I am trying to find out if this method or counting CD4 cells is better, this experiment concluded that the ratio of dN/dS is actually more influenced by the host CD4 t cell immunity. This is contrary to my scientific hypothesis which is that the point mutations in the HIV retrovirus are responsible for lack of immunosuppression.

4. REVIEW: Wang, B. (2013, December 24). Viral Factors in Non-Progression. Frontiers in Immunology, 4. doi:10.3389/fimmu.2013.00355

a. Abstract: https://www.ncbi.nlm.nih.gov/pubmed/24400003
b. PMC: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871964/
c. Publisher Website: http://journal.frontiersin.org/article/10.3389/fimmu.2013.00355/full
d. PDF:
e. Who owns right to the article and what is the availability:
i. The author owns the rights to this article
ii. This article is open access.
iii. It is currently free and is not behind a paywall.
f. Frontiers in Immunology is the online publisher. Non profit journal
g. This journal is online only
h. LMU does not have a subscription to this journal .
i. This article shines light on the factors that could prevent progression of an HIV virus in a human. This is interesting and related to my research because my project is specifically involved with nonprogessor that hav HIV and this sheds some critical information on my project. The genetic reasons behind this situation also relate to the reason why there is a difference between people who are rapid progressers and moderate progressors.

Database Questions

PubMed

What original keyword(s) did you use? How many results did you get?
I used key words like HIV (307,555 results), HIV dN/dS ratio (20 results), and HIV suppression (6,945 results).
Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
In fact, I did not have to narrow my search terms. I simply used those three terms and went though hundreds of different papers at a time.
Which advanced search functions were most useful to narrow down the search? How many results did you get?
I used the "Review" and "5 years" under publication date, to narrow my search. I got 300 results for the HIV suppression search terms, 8220 when I inputted the term HIV. Lastly, I did not receive any results after narrowing using the term "HIV dN/dS ratio".

GoogleScholar

What original keyword(s) did you use? How many results did you get?
I used the same key words as I did in pubmed but this time i received very different results. I received 2,390 results for "HIV dN/dS ratios", 2,170,000 for "HIV", and 485,000 results for "HIV suppression".
Which terms in which combinations were most useful to narrow down the search?
I changed my terminology to "HIV mutation suppression"(131,000 results), "dN/dS ratios" (11,600 results and then used the find option on my mac to find the word HIV), and lastly I used HIV again instead of narrowing that search more.
Which advanced search functions were most useful to narrow down the search? How many results did you get?
For "dN/dS ratios" I narrowed the range to 2011-2015 and got 5,810 results. Then for "HIV mutation suppression" i received 17,900 results within the same time frame. Lastly, for "HIV" i received 600,000 results after narrowing.

Web of Science

What original keyword(s) did you use? How many results did you get?
Once again I used the same terms initially. For "HIV" I received 10,000 results. Then 79 results for "HIV mutation suppression" and 35 results for "dN/dS ratios".
Which terms in which combinations were most useful to narrow down the search?How many results did you get after narrowing the search?
I actually used the same terms for this database because I narrowed on the other databases and received good results.
Which advanced search functions were most useful to narrow down the search? How many results did you get?
For "dN/dS ratios" I received 187 results after refining to the last five years. The 262 results for "HIV mutation suppression" and 95,149 results for "HIV"
Perform a prospective search on the Markham et al. (1998) article and answer the following:
How many articles does the Markham et al. (1998) article cite?
51 citations in the web of science collection
How many articles cite the Markham et al. (1998) article?
74 articles cite the Markham article.

HIV Evolution Project-Current Progress

Purpose

The purpose of this investigation is to finalize our scientific question and purpose as well as establish a general outline of methods that will be used to obtain data and results.

Hypothesis

It is hypothesized that a comparison between dN/dS values will reveal a correlation between non-synonymous mutations and subjects that are rapid progressors. It is also hypothesized that a larger theta value will be more common with those subjects considered rapid progressors because of their higher level of genetic diversity.

Methods

  • First begin to rank subjects based on dN/dS ratios.
  • Then a method of establishing cut offs for "non progressor", "rapid progressors", and "moderate progressors" will be designed for orginzational purposes.
  • This information will then be run through a series of tests that will results in s values and then subsequently theta values in order to determine the level of genetic diversity amongst those populations.
  • The next step will be to input the theta values into the Biology Workbench program to generate data trees that will show the genetic similarity and diversity amongst the three progressor groups.
  • After this is done, the theta values will be run through a Chi-squared test in order to show the statiscal significant difference between the three groups of progressors.
  • All data will be organized into tables.
  • We will then begin work on power point.

Data and Files

No files

Scientific Conclusion

Todays work concluded in the establishment of a plan of action/scientific method on how to approach this research expeirment and most importantly, how to incorporate steps into our scientific method which will help to prove the purpose of this experiment.

References

Pubmed. (January 1996). Retrieved October 3, 2016.

Web of Science. (1990). Retrieved October 3, 2016.

Google Scholar. (November 20, 2004). Retrieved October 3, 2016.

Useful Links

Acknowledgments

I would like to thank Dr. Dahlquist for her help on this experiment. I would also like to thank Zachary T. Goldstein who was my partner in this experiment and on our HIV experiment for our week 6 presentations. I would also like to thank PubMed, Web of Science, and Google Scholar for their resources and help in researching scholarly papers. Lastly, while I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Shivum A Desai 20:20, 3 October 2016 (EDT):