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  Reading and Writing About Immunology

This tool will help you

• evaluate immunology source material for intended audience, level of expertise of author(s), and reliability of information.
• select appropriate sources for gathering more information about immunology.
• read and understand primary immunology sources (research papers)
• write a review (critique) of an immunology research paper, explaining the main points of the paper and discussing its relationship to other information you have on the topic.
• write a literature review of an area of immunology beyond the textbook level, with appropriate citations.
• Write an immunology research proposal.

Reading About Immunology

Scientific sources are not just information that has something to do with science. There are several kinds of scientific papers, written for different audiences and written for different purposes. In order to get the most out of a source, it helps to determine why it was written and who the intended audience is before you start. If you do, you will know what sort of information to look for and how reliable the source will be.

Evaluating World Wide Web information

The web is a great source of information. It is available at any hour, from any computer with an Internet connection. The U of A has subscribed to on-line versions of dictionaries, encyclopedias, and journals that you can use for free if you follow the on-line instructions. Go on line to either the Arizona Health Sciences Library http://www.ahsl.arizona.edu/ or to SABIO http://www.library.arizona.edu/ to search for information sources. However, Internet sources are not interchangeable with published sources and come with their own rules:

• Check your assignment to see whether and how many web sources are allowed.
• Evaluate the source of the information. All web pages are not created equal, and anyone with the know-how and access to the technology can post a web page.
• Use the correct citation format for web material; an example can be found at http://www.library.arizona.edu/library/type1/tips/data/cite_cms.html Remember that web pages change, so include in your citation the date you accessed the material.
• Plagiarism is using, even with citation, eight or more words in a row directly from a source. Plagiarism is plagiarism, whether it is from an electronic or a print source. Faculty are pretty good at recognizing it, there are programs available to check student papers against web documents and against each other, your classmates may turn you in, and you will suffer consequences if caught - so don't plagiarize!!
• Electronic versions of journals ARE equivalent to the paper journal and include the print citation. Cite as you would for a print article, then say "available at" and give the url.

Evaluating print information

First, look at the source of the paper. Where was it published? Was it published in a magazine read by people who are not professional scientists? If so, the scientific jargon should be minimal and what is there should be explained. On the other hand, the information in the article will be simplified for its audience, so that you will not get a detailed explanation of all qualifications and exceptions to general statements. When you read an article written for a lay audience, check the scientific credentials of the author, since the article has not necessarily been screened by other experts in the field to make sure it is accurate. Scientific American and Discover are examples of reputable science magazines for lay people. The authors are generally highly regarded by others in their field and the articles are well-written and accurate. Articles written for general circulation magazines and newspapers are usually written by a science writer who is not directly involved in the work described; some of these articles are accurate and some are not. This is also true of books about science; anyone can write a book, so read critically!

If the information appears in a book written for other scientists or in a textbook, it is probably pretty well accepted in the field but will be a year or so older than the publication date of the book. Books written for scientists or students are more likely to be reviewed by other scientists for accuracy than books written for lay people.

If the article appears in a scientific journal, try to gauge its readership - is it written for scientists in many fields (Science and Nature), for scientists in several closely related fields (Cell), for scientists in one field (Journal of Immunology), for health professionals (New England Journal of Medicine), or for laboratory workers in industry (Biotechnology)? Professional journals publish several kinds of papers, but most are peer reviewed, which means other scientists in the field must agree that the paper contains accurate and important information and should be published, or solicited from recognized experts in the field by knowledgeable editors. The more diverse the intended readership, the less jargon may be used and the less specialized knowledge the author may expect you to have. A journal paper written for immunologists will require that you have extensive knowledge of the field to understand everything in the paper, but don't be discouraged - there will still be many things you can understand and learn from the paper!

Next, decide what kind of paper it is. Scientific papers are divided into research papers, review papers, news articles, and opinions/letters. Research papers are written to report original laboratory or clinical findings to other people in the field; they are primary sources. They are published in professional journals written for specialists and, if the findings are particularly important or have implications in other fields, in journals like Science and Nature. A list of publications containing immunology papers is at the end of this tutorial.

Review papers (literature reviews) summarize a great number of research findings in a particular area of research and list many references to other papers. They usually do not contain detailed experimental methods and results. They are written for people who may not do a particular kind of research but want to learn about it or people who may be entering a field and want to get up to speed quickly. Review papers are published in some specialty journals, in Science and Nature, and also in serials like Annual Review of Immunology or Current Topics in Immunology. Many science term papers are or contain literature reviews.

News articles summarize research papers or reports of scientific conferences. They are written by people trained in science but do not have all the details of the original paper or oral report and may or may not have references. Opinions and letters are written by scientists about science (or other scientists) and express their viewpoints; some of these provoke a lot of debate among scientists!

Finally, look at the title; what is the paper about? Does the title say, or is it designed to arouse your curiosity without giving you much information? A detailed title is usually found in a research or review paper, while a provocative title is more often found in a paper written for lay people or a news or opinion piece. You are now ready to read the paper.

Accessing research papers and review articles

If you want to find immunology information written for professionals, begin your search at the Arizona Health Sciences Library (AHSL) home page, http://www.ahsl.arizona.edu/. (SABIO is NOT helpful for finding technical papers.) Click on the link to MEDLINE on the left side of the home page, and then click on PubMed, a free search engine of the National Library of Medicine. (If you are accessing any library materials from off campus, check with a librarian for the required access codes). Once you are in PubMed, you can search by topic, author, or journal titles. PubMed will provide the citation, an abstract, and in some cases a link to the full text of the article.

If you get a citation but not the full text through PubMed, return to the AHSL home page and click on the link for Journals at the top of the page. On the Journals page under Electronic Journals, click on the first letter of the journal name and follow the links to the specific article you want. In general, most articles from the mid-1990s and later are available on line. Remember, even though you access the journal electronically, it is identical to the paper article and should be cited as such. Some journals (i.e. Nature Immunology) are only available in paper version in the AHSL.

Reading a research paper

A research paper will be the most technical scientific paper you read; it will also contain the most up-to-date information about a particular small slice of the field. Most research papers are written in the IMRAD format: Introduction, Materials and Methods, Results, and Discussion sections, preceded by an abstract and the list of authors with their affiliations and followed by acknowledgments and references.

Read the abstract or summary; all research papers should contain one or the other (usually at the beginning, but sometimes at the end). This part of the paper summarizes the most important findings in the paper and can help you decide whether you want to bother reading the whole paper. Electronic literature search results usually include abstracts.

Read the introduction. What specific scientific questions are addressed by the authors? What was known before the research was started? If you are fortunate, the authors will also explain some technical jargon and abbreviations here. You will find references to other sources all through the article, beginning here, which can provide additional information.

A research paper will next have a detailed materials and methods section (Cell and Immunity have theirs in small print at the end). The purpose of this section is to give readers enough information about how the research was done so they can repeat the experiments themselves. Initially, read only as much of this as you need to understand the results. You may not need to read much if you already understand what an ELISA measures or how cytotoxicity is analyzed. I skim the materials and methods to see what is included, and come back as I need more detailed information.

Read the results. If the papers is well written, each set of results will be preceded by a sentence or two saying why the particular experiment was done and an outline of the methods used. The data will be presented in a table or figure (graph), which should have a title or figure legend that identifies the purpose of the experiment or summarizes the findings. The authors will explain what the findings mean and mention other data they have but didn't show you. "Data not shown" saves precious journal pages for more exciting things. (Who wants to see the same thing in three different strains of mice or experiments where all data looked like the control?) The peer reviewers looked at this data to make sure it could be eliminated from the published paper.

Read the discussion. This is the authors' opportunity to tell you how this data fits or doesn't fit with what other researchers have found and, if there are differences, why they might have occurred. It is also the chance for the authors to discuss the important implications of the findings and perhaps present models to explain how the immune system works. The authors have the most latitude in writing this section, although the peer reviewers will keep them honest here, too.

Writing about Immunology

General rules

Scientific writing does not have to be complex. Good writing is simple and understandable, even if the topic is complex. The writing citations at the end of this tutorial offer excellent advice and examples of good scientific writing. There are a few conventions, some that are different from those used in English composition classes:

• Unless told otherwise, write in the third person: "Antigen was obtained from Sigma Pharmaceutical", not "I ordered the antigen from Sigma Pharmaceutical."
• Write descriptions of current work in research papers in the past tense; write of already published work in the present tense.
• If your paper is longer than a page, consider using subheadings, as I have in these tutorials. Subheadings will help you organize your information and will help the reader understand your writing.
• Plagiarism is using, even with citation, eight or more words in a row directly from a source. Plagiarism is plagiarism, whether it is from an electronic or a print source. Faculty are pretty good at recognizing it, there are programs available to check student work against web documents and against each other, your class mates may turn you in, and you will suffer consequences if caught - so don't plagiarize!!
• Use correct English grammar and punctuation.
• Watch for run-on sentences. If you can't read a sentence in one breath, make it shorter!
• Watch for sentence fragments; if you can't find a noun AND a verb, it's a fragment.
• Don't begin a sentence with a numeral; spell out the number instead.
• Don't start a sentence with"But"; to make a contrast with the previous sentence, use "However" or "On the other hand".
• Use fewer words whenever possible, as long as your meaning is clear.
• Use correct English spelling and word choice. The most commonly misused English words in student papers I read are shown below.
• Correctly spell and use technical terms and scientific names. The genus is capitalized, the species is not; both are italicized or underlined (Staphylococcus aureus). Spell out the genus the first time you use it and any time there might be confusion. Many biological terms are Latin; learn and use the correct singular and plural: bacterium, bacteria; coccus, cocci; genus, genera; medium, media.

Greek letters used in immunology (how to keyboard). If you don't have the proper symbols, spell out the name of the letter (a   or alpha, not a).

a alpha (symbol a)
b beta (symbol b)
d delta (symbol d)
e epsilon (symbol e)
f phi (symbol f)
g gamma (symbol g)
h eta (symbol h)
k kappa (symbol k)
l lambda (symbol l)
m mu (symbol m)
q theta (symbol q)
z zeta (symbol z)

Citing sources

Follow the Chicago manual of Style format when citing sources (this is different from what you learned when writing papers for English or social science classes). A good url for citation styles is http://www.library.arizona.edu/search/reference/citation-cms.html

Suppose you are writing about Legionella pneumophila and want to cite a recent review in ASM News.

Example

• In the body of the paper: Legionella pneumophila requires relatively high supplies of iron for survival inside the macrophage. (Viswanathan and Ciaciotto, 2001). [Include all authors if there are one or two. In the case of three or more authors, cite (Viswanathan et al., 2001) in the body of the paper and list all authors in the reference section.]
• In the Reference section at the end of the paper: Viswanathan, V. K. and N. P. Ciaciotto. Role of Iron acquisition in Legionella pneuphophila virulence. ASM News 67 (2001): 253-258. [Sources are listed in alphabetical order by the last name of the first author.]

Other rules about citations:

• Each statement or paragraph in your paper must have at least one citation to the source of that information. The only exceptions are information that has been generally accepted in the field for decades (The thymus is the site of T cell development) or your own thoughts. When in doubt, cite a source.
• The exact page on which the specific information is found is not included. The same citation is used each time you cite the same or different information from that source.
• If more than one source contains the information, cite source(s) most useful to the reader.
• Sources may be cited at the end of individual sentences in a paragraph if you used information from different sources, or at the end of the paragraph if all the information in that paragraph came from a single source.
• Multiple sources may be cited after a single sentence: (Viswanathan and Ciaciotto, 2001; Gebran et al., 1994).
• Long direct quotations from references should not be used; use your own words.
• If you find information in a review paper, cite the review; only cite the original research paper if you read that paper.

Writing a critique

After you have read a primary source several times, you may be asked to write a critique. A critique is a summary of a paper and a discussion of your reactions to it, like a movie or book review. However, unlike these reviews, a scientific critique is not written to criticize or praise the contents or the writing style of the paper, although you certainly can disagree with the authors' conclusions or opinions if you wish. You should also not hesitate to "give away" the ending (the principal conclusions of the paper).

When you write a critique,

• Be sure to include the complete citation to the paper.
• Your summary should include enough detail from the paper so that the reader knows you did read it and understand it. Include why the work was done, the basic findings, key materials and methods, and the author's conclusions.
• Do not string together long quotes from the paper; use your own words.
• Your reactions to the paper might include how the paper relates to lecture and text material, how the findings might affect clinical practice, comments on the experimental systems used, questions the work left unanswered, or your ideas for future work.

Writing a literature review

The purpose of a literature review is to summarize an area of immunology in more detail than would be found in a current textbook. A brief literature review is included in the introduction to a research paper to show how the experiments described in the paper fit with already published work. A literature review is also included in a proposal for funding new research (see below). When you review the literature, you may cite a few other reviews but should also read and cite the primary (research) literature. Many college term papers take the form of a literature review. Consult one or more of the sources below for examples.

Writing an immunology research proposal

A research proposal is designed to explain and justify a plan for learning more about the immune system (basic research) or influencing its function (clinical research, such as designing a vaccine against an infectious agent or an immunotherapy against cancer). The goal of the proposal is to get approval by experts in the field with a good enough score to receive funding to do the research or clinical study. Different funding agencies have slightly different formats for research proposals, but they generally contain the following elements:

• The Title should clearly state the purpose of the research; it may also state techniques that will be used in the research. Examples: "Function of IL-35 Elucidated Through the Use of Knock-out Mice" "Development of a Recombinant Vaccine Against the Human Immunodeficiency Virus".
• Biographical information tells the reader about the author(s) of the proposal; it is a condensed curriculum vitae containing information about formal post-high school education and training, professional positions, recent publications, and other research funding.
• A lay summary is a brief summary of the research proposal meant for a non-specialized audience.
• A background section is a review of the current state of knowledge in the research area. This is a brief literature review ; it should contain the most up-to-date information available and all information should be referenced to its source.
• The proposed research section describes the work that will be done and how the work will be evaluated. The proposed research should be divided into specific aims. Each specific aim is one clearly defined objective of the research. For each specific aim, describe the experimental protocol you will use to achieve that specific aim and how your results will be evaluated. Say what your expected results will be and what those results will mean; you can also address future directions the research might take based on your results.
• A reference section lists the sources you have cited in the text by number or author (see above).

For information about the proposal format used by the National Institutes of Health, see http://grants.nih.gov/grants/oer.htm

Sources

About writing

WWW sites

Chicago Manual of Style Examples available at http://www.library.arizona.edu/library/type1/tips/data/cite_cms.html
U of A Writing Center http://w3.arizona.edu/~uawc/
Purdue University Online Writing Lab (OWL) http://owl.english.purdue.edu/
Writing Guidelines for Engineering and Science Students:see section on Formal Reports http://fbox.vt.edu/eng/mech/writing/index.html

Full-text online books on scientific and technical writing through NetLibrary: (search on Sabio and look for record that says "[computer file]" or find NetLibrary in Databases list and search by title.)

Day, R. A. How to Write and Publish a Scientific Paper 4th edition, Oryx press, Phoenix, 1998.
Dear, P. R. The Literary Structure of Scientific Argument, University of Pennsylvania Press, 1991.
Moriarty. M. F. Writing Science Through Critical Thinking, Jones and Bartlett Publishers, Sudbury, MA, 1997.
Shelton, J. H. Handbook for Technical Writing, NTC Business Books, Lincolnwood, IL, 1994
Wilson, A. Handbook of Science Communication, Bristol, Philadelphia, 1998.

Print references

Hawkins, C. and M. Sorgi. Research: How to Plan, Speak, and Write About It Springer-Verlag. New York. 1985.
Moore, R. Writing to Learn Biology Saunders College Publishing, Fort Worth. 1992.
Penrose, A. M. and S. B. Katz. Writing in the Sciences. Exploring Conventions in Scientific Discourse. St. Martin's Press, New York, 1998

About immunology

Abbas, A. K., A. H. Lichtman, & J. S. Pober, Cellular and Molecular Immunology (2nd ed.),W. B. Saunders Co., Philadelphia, 1994.
Ader, R., D. L. Feltne, and N. Cohen, Psychoneuroimmunology, Academic Press, San Diego, 1990.
Bach, F. H., and H. Auchincloss, Jr., Transplantation Immunology, Wiley-Liss, New York, 1995.
Barclay, A. N., M. L. Birkeland, M. H. Brown, A. D. Beyers, S. J. Davis, C. Somoza, and A. F. Williams, The Leucocyte Antigen FactsBook, Academic Press, San Diego, 1992.
Benjamini, E. & S. Leskowitz, Immunology, A Short Course, Wiley Liss, New York, 2001.
Callard, R. and A. Gearing, The Cytokine FactsBook, Academic Press, San Diego, 1994.
Chapel, H. & M. Haeney, Essentials of Clinical Immunology (3rd ed.), Blackwell Scientific, Oxford, 1993.
Coleman, R. M., M. F. Lombard, & R. E. Sicard, Fundamental Immunology (2nd ed.), Wm. C. Brown Publishers, Dubuque, 1992.
Cooper, E. L. & E. Nisbet-Brown (eds.), Developmental Immunology, Oxford University Press, Cary, NC, 1993.
Cruse, J. M. and R. E. Lewis. Illustrated Dictionary of Immunology. CRC Press, Boca Raton, 1995
Decker, J. M. Introduction to Immunology (11th Hour Series), Blackwell Scientific, Malden, MA, 2000.
Goldsby, R. A., T. J. Kindt, and B. A. Osborne. Kuby Immunology (4th ed.), W. H. Freeman & Co., NY, 2000.
Janeway, C. A. Jr. P. Travers, M. Walport, and J. D. Capra, Immunobiology, The Immune System in Health and Disease (4th Edition), Garland Publishing, Hamden, CT., 1999.
Ogra, P. L., J. Mestecky, M. E. Lamm, W. Strober, J. R. McGhee, and J. Bienenstock, Handbook of Mucosal Immunology, Academic Press, San Diego, 1994.
Ollier, W. and D. P. M. Symmons, Autoimmunity, Bios Scientific Publishers, NY, 1992.
Parham, P. The Immune System. Garland Publishing, New York, 2000.
Paul, W. E., Fundamental Immunology (3rd ed.), Raven Press, New York, 1994.
Pigott, R. and C. Power, The Adhesion Molecule FactsBook, Academic Press, San Diego, 1993.
Roitt, I. M., J. Brostoff, D. K. Male, and A. Gray, Case Studies in Immunology, Mosby, Times-Mirror International Publishers Ltd., London, 1994.
Rosen, F. S., L. A. Steiner, and E. R. Unanue, Dictionary of Immunology, Stockton Press, NY, 1989 (Science Library reference room).
Silverstein, A. M., A History of Immunology, Academic Press, San Diego, 1989.
Stine, G. J., AIDS Update 2000, Prentice Hall, Engelwood Cliffs, NJ, 2000.

Serials which contain reviews on Immunology (go to http://www.ahsl.arizona.edu/journals/ejrnls/ and search for immunology to see which are available electronically)

Advances in Immunology
Annual Review of Biochemistry
Annual Review of Immunology
Annual Review of Medicine
Contemporary Topics in Immunology
Contemporary Topics in Molecular Biology
CRC Critical Review in Immunology
Current Opinion in Immunology
Immunology Reviews
Trends in Immunology (formerly Immunology Today)

Journals which contain papers on Immunology (go to http://www.ahsl.arizona.edu/journals/ejrnls/ and search for immunology to see which are available electronically)

Cell
Cellular Immunology
Clinical and Experimental Immunology
Developmental and Comparative Immunology
European Journal of Immunology
Human Immunology
Immunogenetics
Immunity
Immunology
Immunogenetics
Immunopharmacology
Infection and Immunity
International Immunology
Journal of Allergy and Clinical Immunology
Journal of Experimental Medicine
Journal of Immunological Methods
Journal of Immunology
Journal of Leukocyte Biology
Journal of Virology
Molecular Immunology
National Academy of Sciences (Proceedings)
Nature
Nature Immunology
Nature Medicine
New England Journal of Medicine
Science
Vaccine

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