Abnormal immune responses can trigger a range of autoimmune diseases, in which an individual’s immune system is attacking normal tissues in the body. Well-known examples of autoimmune diseases are type 1 diabetes mellitus, lupus, and multiple sclerosis.

Ideally, one would like to harness the immune system to attack abnormal substances or tissues like cancer, while sparing the normal (unaffected) tissue. Many tumor cells produce antigens (proteins) that theoretically ought to trigger an immune response: that is, one’s immune system ought to recognize cancer cells as somehow foreign or abnormal, and thereafter eliminate these cells from the body. The field of cancer immunotherapy is actively pursuing this study.

Tumor antigens may also be useful for diagnostic tests; high levels of tumor antigens could be taken as markers or indicators of cancer. In this assignment, you will be examining levels of tumor-associated antigens (TAAs) as determined from immunoassays (i.e., biochemical tests that measure the concentrations of the tumor-associated antigens in serum samples).

• Download the Excel file MHA610_assignment_3_data.xls, and open it.
• The spreadsheet contains data on 250 individuals: 90 normal individuals from San Diego (the controls), and 160 individuals from Korea and China, all of whom were diagnosed with hepatocellular carcinoma (HCC).
  • Serum samples were taken from the controls and from the cases at time of diagnosis of HCC. Levels of a panel of 12 tumor-associated antigens (TAAs) were assessed via immunoassays in all individuals;
    • The levels are given in the columns with headings Ab14, HCC1, IMP1, KOC, MDM2, NPM1, P16, P53, P90, RaIA, and Survivin. (These are the designations of the 12 TAAs, all of which were thought to be potentially predictive of cancer.)
• The underlying question is whether we can effectively discriminate between the cases and controls on the basis of the levels of these TAAs. This is sometimes termed a classification problem in the statistics and biostatistics literature: we wish to classify individuals as normal or cancer patients on the basis of their TAA levels.
• We will examine these data in Statdisk. Use the MHA610_Week 3_Assignment_Data.CSV file to upload this information into Statdisk.
  • If you choose the latter option, Start Statdisk, then choose File>Open and select the .csv file you created (unless you changed the name, it ought to be MHA610_assignment_3_data.csv)
  • Check the box that specifies the data contains column titles or headers, select Comma separated for how the data are delimited, click finish, and the dataset will have been successfully imported into Statdisk.
  • NOTE: you may want to read through the remainder of the assignment first, before proceeding with this step. This may save you some work afterwards!
• Note that Statdisk operates on columns of data, and that both cases and controls are contained in each column of TAA levels. It will be necessary to separate the cases and controls for further analyses. This can be accomplished either by copying within Statdisk or by reverting to the original Excel workbook, copying in Excel, exporting as a .csv file, and then importing into Statdisk. (Don’t say you weren’t warned!)
• Explain if you would characterize any or all of the TAA levels as approximately normally distributed for the controls and for the cases.
  • Provide plots and statistics in support of your conclusions.
• Explain if any of the TAAs are useful for discriminating between the cases and controls.
  • Provide plots and statistics in support of your conclusions.
• All writing assignments should be at least 250-500 words in APA format supported by scholarly sources.

BONUS. In the above, we pooled all cases together.  Summarize whether you think this is legitimate or whether the levels of any of the TAAs appear to differ significantly between the cases from China and the cases from Korea. Provide evidence in support of your conclusion.

Objective: Write a 3-4 page college-level paper in APA format, in which you analyze one scientific, peer-reviewed article in the discipline of psychology and discuss how the results of the study may benefit the surrounding community and/or society as a whole.

CRITERIA FOR JOURNAL ARTICLE CRITIQUE

TOPIC
Article topics must be selected from topics within the discipline of psychology.
More information on topic selection/assignment will be provided by your instructor.

SOURCE
The journal article…
must be current.
must come from professional, scientific journals.
must be a research article (MUST HAVE SECTIONS LABELED “METHODS”, “RESULTS” & “DISCUSSION”)

GUIDELINES
Specific guidelines are listed on the next page.
Any further details will be provided by your instructor.

FORMAT
You must use APA format. The format directions can be found on the following web site: http://owl.english.purdue.edu/owl/resource/560/01/
APA format requirements include a cover page, reference page, in-text citations, etc.
PLAGIARISM WILL NOT BE TOLERATED. All information must be stated in your own words.

STRUCTURE OF JOURNAL ARTICLE CRITIQUE

Introduction (PURPOSE: to educate the reader on the topic/concept)
will define topic and other key terms
will include symptoms, statistics of occurrence and current information in the field
Main body (PURPOSE: to explain the research conducted in the article)
will state what you found in the journal article
HYPOTHESIS or PURPOSE:
What were the researchers trying to discover (i.e. what was the hypothesis or purpose)?
This is usually found at the beginning of the article. Usually the hypothesis or statement of a problem appears at the end of the review of the literature, most often in the last or next to last paragraph. The words that indicate that it is a hypothesis are, “We will examine. . .” or “Our hypothesis is . . .” In a statement of a problem, the researcher may say, “We plan to see if a relationship…,” “We proposed to observe…,” or “The problem we proposed to study…” (You must use your own words—do NOT use quotes).
METHODOLOGY:
How was the research conducted (research design or type of study)?
Is the research descriptive (case study, naturalistic observation, laboratory observations, surveys, tests), correlation, experimental, or developmental? For more information on research methods, refer to chapter 1 of your text.
When and where the research was conducted?
How long did the study take?
Who were the participants? (number [N], age, sex, criteria to be a part of study)?
RESULTS/DISCUSSION:
What did the researchers actually find in relation to their hypothesis/purpose?
ARTICLE MAY STATE: The researchers found that . . .
What limitations did the researchers reveal?
Summary/conclusion (PURPOSE: to show critical thinking in regards to the research)
How does the information in the article integrate with information from class discussion, the text, and/or other information in the discipline?
TIP: It is a good idea to use the subject index in your text to look up the topic in your text.
What is your opinion of the research findings?
EXAMPLE: was this research well done or not and why?
Why is this topic/research important? (relevance/benefits to community and/or society)
EXAMPLE: A conclusion to a study that suggests a new therapy/treatment for children with ADHD might help the child struggling to perform successfully in school, which then improves her confidence, her relationship with her parents, siblings, and classmates. Write about the implications of this new treatment.
In what ways does this topic relate to your own personal experience and how is your experience in agreement or disagreement with the outcome of this study?
How has your opinion of this topic changed since your review of the study?

REFERENCE PAGE – you will only reference the article you read for the assignment. That means that you will only have 1 reference.

Header with running head (in proper format) and page number.
“Reference” at the top, center of the page.
The reference should be formatted according to the instructions provided in the links above.