Mavila9 Week 12

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User Page

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Assignment Page	Individual Journal Entry	Class Journal Entry
Week 1	Week 1 (User page)	Shared Journal Week 1
Week 2	Mavila9 Week 2	Shared Journal Week 2
Week 3	Gene Page Week 3	Shared Journal Week 3
Week 4	Journal Entry Page Week 4	Shared Journal Week 4
Week 5	RNAct Database Page Week 5	Shared Journal Week 5
Week 6	Journal Entry Page Week 6	Shared Journal Week 6
Week 7	Journal Entry Page Week 7	Shared Journal Week 7
Week 8	Journal Entry Page Week 8	Shared Journal Week 8
Week 9	Journal Entry Page Week 9	Shared Journal Week 9
Week 10	Journal Entry Page Week 10	Shared Journal Week 10
Week 11	Sulfiknights Team Page	Shared Journal Week 10
	Journal Entry Page Week 11
Week 12/13	Journal Entry Page Week 12	Shared Journal Week 11
Week 12/13	Sulfiknights DA Week 12/13	Shared Journal Week 12
N/A	Sulfiknights DA Week 14

Annotated Bibliography

Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98

1. The link to the abstract from PubMed.
   • https://www.ncbi.nlm.nih.gov/pubmed/10445758?report=abstract
2. The link to the full text of the article in PubMedCentral (if not available, write N/A).
   • N/A
3. The link to the full text of the article (HTML format) from the publisher web site.
   • The publisher website only provides the article as a PDF.
4. The link to the full PDF version of the article from the publisher web site.
   • https://watermark.silverchair.com/500098.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAl8wggJbBgkqhkiG9w0BBwagggJMMIICSAIBADCCAkEGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM8_pW__iD02HTM6m1AgEQgIICEiFWiVsdcTozKjN6UJplgjCe5_ZNofmm2vtpqhUw6YrmMV5l8Xg8H4wA5LGTzFOh5Dr0kRSNi5z2SCQ-QD5o1Y_itD1KdARt7RdUYThQWqVvQ12hLAnTvP1gcAN9FrffGv63ml5Jrc5G2MVIV6hLYH-L_aQMAFDW0Q-DY-2jAx1VjrmteH2IfjlIx-1mVPsX8a_qBOXON_z0xYBiX-qspMXUTIWrg6IBQJmKMP0LYwYq5LKYwYL8u_26ISQ87--_DrMOpsyH2TXxQv9aDkVdrx7geM9T40nviXIAONUzN8IG75f6TQTcYOQA9ZBElEpRfuX5mCes7KYirthp-lVYbFanmYBAhYtX7mkg2x9ApkfR1BQXYaf2uxYKqq6sUMfq6G32DahpBRwT0WFhGtXk1T6s8W9_NwjQCQ5SRKkJw1Pix1NwzCXNqZIPrWMp9mjZfVwvjI9HRo6cmLyvzH7JXpi0o3zPYkMNCN3NNJlRAM0CZWq9V50QbbF2yL6U3tRVXROQMS9TB_VEhSXqRLO5MCQ-TPBaaN-giQcRkAUSpZZIxjXLy7-qWCezHLqBL1MDLX4TL6tU82vtdD1Ow79RAhGd4VfR1b2rlhs5QZrsaqEKjD_Ws5c6RQ7vLTpdlKtSjy9QC-p2p7Ds0Wo4vXQZOhNQlSkHUzZ86iqK6lTb3e_-yJt857KgKkcsg8TPmXhU2PIv
5. Who owns the rights to the article?
   • The Society of Toxicology owns the rights to the article.
6. How is the article available to you?
   • LMU pays for a subscription to the journal.
7. Is the article available online-only or both in print and online?
   • The article is available both online and in print.
8. Who is the publisher of the journal?
   • The publisher is Oxford Academic, a non-profit scientific society that is part of the Open Access Publishers Association, and located in Oxford, England.
9. How Long has the journal been in operation? (e.g., browse the archive for the earliest article published)
   • The journal has been in operation since January 1981.
10. Are the articles in this journal peer-reviewed?
    • The articles in this journal are peer-reviewed.
11. Provide a link to the scientific advisory board/editorial board of the journal.
    • https://academic.oup.com/toxsci/pages/Editorial_Board
12. What is the journal impact factor? (Look to see if it is provided on the journal home page.)
    • 4.081
13. Is the article a review or primary research article?
    • This article is a primary research article.
14. Are the data associated with this article available? If so, provide a link to the dataset.
    • The dataset is not available.

Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/10.1186/s12934-015-0327-0

1. The link to the abstract from PubMed.
   • https://www.ncbi.nlm.nih.gov/pubmed/?term=Three-pathway+combination+for+glutathione+biosynthesis+in+Saccharomyces+cerevisiae
2. The link to the full text of the article in PubMedCentral (if not available, write N/A).
   • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574134/
3. The link to the full text of the article (HTML format) from the publisher web site.
   • https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-015-0327-0
4. The link to the full PDF version of the article from the publisher web site.
   • https://microbialcellfactories.biomedcentral.com/track/pdf/10.1186/s12934-015-0327-0
5. Who owns the rights to the article?
   • Tang et al. own the rights to the article.
6. How is the article available to you?
   • This article is open access.
7. Is the article available online-only or both in print and online?
   • The article is available online-only.
8. Who is the publisher of the journal?
   • The publisher is Biomed Central a Springer Nature, a for-profit scientific society that is part of the Open Access Publishers Association, and located in both London, England.
9. How long has the journal been in operation? (e.g., browse the archive for the earliest article published)
   • The journal has been in operation since 2000.
10. Are the articles in this journal peer-reviewed?
    • The articles in this journal are peer-reviewed.
11. Provide a link to the scientific advisory board/editorial board of the journal.
    • https://microbialcellfactories.biomedcentral.com/about/editorial-board
12. What is the journal impact factor? (Look to see if it is provided on the journal home page.)
    • 4.402 2-year impact factor and 4.669 impact factor.
13. Is the article a review or primary research article?
    • This article is a primary research article.
14. Are the data associated with this article available? If so, provide a link to the dataset.
    • The dataset is not available.

Database Searches

• You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science.

1. PubMed
   • What original keyword(s) did you use? How many results did you get?
     • I first searched "glutothione biosynthesis" and got 118,158 results.
   • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Next I added "in Saccharomyces cerevisiae" to the search and selected the "5-years" publication date restriction to narrow down the search and got 240 results.
2. Google Scholar
   • What original keyword(s) did you use? How many results did you get?
     • I searched "effects of metal on gene expression" and got about 1,880,000 results.
   • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • I next included "arsenic" and "regulation" to search "effects of arsenic on gene expression regulation" and for about 130,000 results.
3. Web of Science
   • What original keyword(s) did you use? How many results did you get?
     • I originally searched "gene expression arsenite response" and got 566 results.
   • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
     • Then I searched "in Saccharomyces cerevisiae" within the 566 results and added the "Open Access" filter to get 19 results.

• Use the advanced search functions for each of these three databases/tools and answer the following:

1. PubMed
   • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • The most useful search was the date range that is used to only see papers published within the last 5 years.
2. Google Scholar
   • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • I included a year range starting from 1995 until 2019 to the search because I new the first study to use the work microarray was in 1995 from a google search https://www.news-medical.net/life-sciences/History-of-Microarrays.aspx .
3. Web of Science
   • Which advanced search functions were most useful to narrow down the search? How many results did you get?
     • I found the "Open Access" filter the most useful to narrow down the search to results I could view which was about 19 publications.
4. Perform a prospective search on your article in the Web of Science and answer the following:

Satoh, R., Tanaka, A., Kita, A., Morita, T., Matsumura, Y., Umeda, N., ... & Sugiura, R. (2012). Role of the RNA-binding protein Nrd1 in stress granule formation and its implication in the stress response in fission yeast. PloS one, 7(1), e29683. https://doi.org/10.1371/journal.pone.0029683

1. • How many articles does this article cite?
     • 33 articles
   • How many articles cite this article?
     • 11 articles

Reflection

1. What impact does the choice of keywords have on your results?
   • The keywords allow the search engine to find other papers that have the keywords in either the title or content of the article. Also the order of the keywords are important when looking up expressions or particular organisms. In some cases, like that of yeast, the organism is referred to in its species name (S. cerevisiae) or common name (budding yeast, baker's yeast, etc.) so it would be important to try several searches with the different organism names.
2. What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?
   • The advantage of Pubmed is that there is a text availability filter, and the disadvantage is that filtering out articles that aren't fully available can remove some more informative articles out of your search. The advantage of Google Scholar is that it shows you just about every article on the internet, but this is also the downfall to Google Scholar because some of the results aren't related to the search terms. Finally, the advantage of Wed of Science is that it has extensive filter options that help narrow down the search. Wed of Science seemed to be the most complete search engine and I had trouble finding disadvantages, but I would say one is that the citation isn't as available as on Google Scholar.

Mavila9 (talk) 20:06, 18 November 2019 (PST)