Week 12

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This journal entry is due on Thursday, April 11, at 12:01am PST.

Overview

  • To understand the role of journals and publishers in controlling and providing access to scholarly content.
  • To evaluate a journal article reliability, validity, accuracy, authority, and bias.
  • To prepare for the final project work by giving a journal club presentation, critically evaluating an article from the primary literature.

Grading for this assignment

  • Your individual journal entry with the outline of the journal club paper is worth a total of 10 points.
  • The journal club presentation on April 12 is worth a total of 45 points.
  • Instead of a class journal, you will create a team page with contributions from all members, worth 3 points. Each member of the team will receive the same grade for the team page.

Team Membership

The project roles are:

  • Team Name TBA
    • Project Manager: TBA
    • Quality Assurance: Hailey & Natalija
    • Data Analysis: Charlotte & Katie
    • Coder/Designer: Andrew & Dean

For this week, one member of the QA guild will join the Coder/Designers and one member will join the Data Analysts for the journal club presentation.

  • Charlotte, Katie, and Hailey will present on:
    • Sha, W., Martins, A. M., Laubenbacher, R., Mendes, P., & Shulaev, V. (2013). The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide. PloS one, 8(9), e74939. doi:10.1371/journal.pone.0074939
  • Andrew, Dean, and Natalija will present on:
    • Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., Danford, T. W., ... & Young, R. A. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99-104. doi: 10.1038/nature02800
      • Note that you should include supplementary figures 1-5 in your presentation.

Individual Journal Assignment

  • Invoke your personal template that you created for the Week 1 Assignment on your individual journal entry page. Your template should provide the following set of navigation links:
    • Link to your user page.
    • Links to the weekly Assignment pages.
    • Links to your weekly Individual Journal entry pages.
    • Links to the weekly Class Journal pages.
    • The category "Journal Entry".
  • Note that this week, we will add a new category, "Team Project". Please do not add this category to your individual templates because we want this category to be precisely used for the Team Project.
  • Include both the Acknowledgments and References section as specified by the Week 1 assignment.
  • The sections you need for this week's individual journal entry are Purpose, 10 definitions of terms, answers to the questions about your article, Data/files, Conclusion, Acknowledgments, and References (as specified by the Week 1 assignment).

Presentation Prep: Individual Journal Pages

In preparation for your journal club presentation, you will each individually complete the following assignment on your individual journal page.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
  2. Answer the following questions about your article. Your answers need to be in YOUR OWN WORDS, not copied straight from the article. It is not acceptable to copy another student's answers either. Even if you work together to understand the article, your individual entries need to be in your own words.
    1. What is the main result presented in this paper?
    2. What is the importance or significance of this work?
    3. What were the limitations in previous studies that led them to perform this work?
    4. How did they treat the yeast cells (what experiment were they doing?)
    5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
    6. What media did they grow them in? What temperature? What type of incubator? For how long?
    7. What controls did they use?
    8. How many replicates did they perform per treatment or timepoint?
    9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
    10. What mathematical/statistical method did they use to analyze the data?
    11. Are the data publicly available for download? From which web site?
    12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
      • What do the X and Y axes represent (if applicable)?
      • How were the measurements made?
      • What trends are shown by the plots and what conclusions can you draw from the data?
    13. How does this work compare with previous studies?
    14. What are the important implications of this work?
    15. What future directions should the authors take?
    16. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

Journal Club Presentation

Each team will prepare and give a 20-25 minute PowerPoint presentation for their paper in class on Thursday, April 12.

  • Please follow the Presentation Guidelines PowerPoint on Brightspace for how to format your slides.
  • You will need to prepare ~20 slides (assume 1 slide per minute of presentation).
  • You need to present the information that you answered for the questions above, but organized as a presentation. You will need the following:
    • Title slide with the complete reference to the article, presenter names, date and "BIOL 367".
    • Outline slide (list of key messages for the talk)
    • One or more introduction slides
    • A slide for each figure or table from the paper. Figures with multiple parts can/should be split between multiple slides.
    • A summary/conclusion slide that is a reflection of the outline.
    • Acknowledgments slide
    • References slide
  • Your PowerPoint slides must be uploaded to the wiki and linked to from your individual journal page and your team page by 12:01am on Thursday, April 12
    • You can update your slides before your presentation, but I will be grading the ones you upload by the deadline.
  • Your presentation (both the slides and the oral presentation) will be evaluated by the instructor using the Presentation Rubric.
  • Your presentation will also be evaluated by your fellow classmates (anonymously) who will answer the following questions:
    1. What is the speaker's take-home message (one short sentence)?
    2. What is the best thing about this presentation?
    3. What needs improvement?
    4. Please comment on the speaking style (language and delivery) of each presenter.
  • Although you may be working with different partners on this presentation than before, you are expected to take the feedback from your previous presentation into account when doing this one.

Evaluating the Meta Data of a Journal Article

Besides evaluating the content of the journal article itself, it is useful to evaluate the meta data about the article to assist in the determination of the article reliability, validity, accuracy, authority, and bias.

Assignment

  • For your assigned journal article, answer/provide the following on your individual journal entry.
    1. The complete bibliographic reference in the APA style (see this link), with DOI.
    2. The link to the abstract from PubMed (LMU-specific link.
    3. The link to the full text of the article in PubMedCentral (if not available, write N/A).
    4. The link to the full text of the article (HTML format) from the publisher web site.
    5. The link to the full PDF version of the article from the publisher web site.
    6. 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.
      • Additionally, is the article available under a Creative Commons license?
    7. How is the article available to you?
      • 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.
      • 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 here.
      • 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.
    8. 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.
    9. What organization is the publisher of the journal?
      • What type of organization is it?
        • Is the publisher for-profit or non-profit?
        • Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
        • Does the publisher belong to the Open Access Publishers Association?
      • What country is the journal published in?
    10. How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
    11. Are the articles in this journal peer-reviewed?
    12. Provide a link to the scientific advisory board/editorial board of the journal.
    13. What is the journal impact factor? (Look to see if it is provided on the journal home page. Alternately, it may be found through a Google Search.)
    14. On what date was the article submitted?
    15. On what date was the article accepted?
    16. Did the article undergo any revisions before acceptance?
    17. When was the article published?
    18. What is the approximate elapsed time between submission and publication?
    19. What are the institutions with which the authors are affiliated?
    20. Have the authors published other articles on this subject? (How will you find this out?) Hint:
    21. Is there a conflict of interest for any of the authors?
    22. Are the data associated with this article available? If so, provide a link to the dataset.
    23. Perform a prospective search on your article in the Web of Science and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
      • How many articles does this article cite?
      • How many articles cite this article?

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

  1. Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167
  2. PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
  3. PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
  4. Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
  5. Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
  6. Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article)
    • No Creative Commons license
  7. Article is not Open Access, but is freely available 2 months after publication, LMU did not pay for the article
  8. Availability: in print and online
  9. Publisher: American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA, published in the United States
  10. The journal begain in 1989
  11. Peer-reviewed articles: yes
  12. Editorial board.
  13. Impact factor: 3.512 (2017)
  14. Submitted March 1, 2004
  15. Accepted September 28, 2004
  16. Did the article undergo any revisions before acceptance? no/unknown
  17. Published October 13, 2004
  18. What is the approximate elapsed time between submission and publication? 6.5 months
  19. What are the institutions with which the authors are affiliated?
    • Biotechnology Research Institute, National Research Council of Canada; Department of Biochemistry, McGill University;Institute of Microbiology, Johann Wolfgang Goethe-University; Molecular Oncology Group, Royal Victoria Hospital
  20. Have the authors published other articles on this subject? (How will you find this out?) not too much
  21. Is there a conflict of interest for any of the authors?
  22. Data are not available (dead hyperlink)
  23. Web of Science
    • How many articles does this article cite? 73
    • How many articles cite this article? 131

Whole Team Journal Assignment: Creating a Team Wiki Page

Note that this work is postponed to the Week 13 assignment.

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team to kickstart your final projects.

  1. Select your team's Project Manager.
  2. Name your team and create your team home page on the wiki.
    • The name of your team home page should simply be the team name.
    • This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
  3. Create a link to your team's page on the course Main page.
  4. Create a template for your team with useful information and links that you will invoke on all pages that you will create for the project.
    • Include the category "Team Project" in your template.
      • However, please do not add this category to your own individual templates because we want them to precisely mark pages having to do with the Team Project.
  5. Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
  6. Each team member should reflect on the team's progress:
    1. What worked?
    2. What didn't work?
    3. What will I do next to fix what didn't work?
  7. Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.
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