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Data files for Experimental Analysis Review

Seed density from Paquette, A., E. Laliberté, A. Bouchard, S. de Blois, P. Legendre, and J. Brisson (2007) Lac Croche Understory Vegetaion Data Set (1998–2006), Ecology 88:3209.

Species presence/altitude data from Table 5 of Lobo, J.M. and G. Halffter (2000) Biogeographical and Ecological Factors Affecting the Altitudinal Variation of Mountainous Communities of Coprophagous Beetles (Coleoptera: Scarabaeoidea): a Comparative Study, Annals of the Entomological Society of America 93:115-126.

Review of reporting the results of statistical tests (excerpted from the BSCI 111a lab manual)

In the scientific literature, there are standardized ways of reporting the results of statistical tests.  The following items should always be included in reporting the results of a test: the calculated value of the statistic (which varies depending on the test - for example in a t-test the calculated value of t would be reported), the number of degrees of freedom (i.e. df) if appropriate for the test, and an indication of the value of P.  In some cases, the actual value of P as calculated by statistical software is reported.  In other cases, symbols are used to indicate that a particular quantity in a table is significant at a certain P level.  For example, an asterisk (*) is often used to indicate that P<0.05 and two asterisks (**) is often used to indicate that P<0.01.  "NS" is used to indicate "not significant".  When such symbols are used in a table, it is expected that a key will explain the symbols.  Other quantities are included as appropriate. 

Specific examples for tests we have used

t-test of means or paired t-test:  t=0.709, df=26, P=0.485 (state if one or two-tailed)

chi-squared contingency test (by computer):  χ²=7.4, df=1, P=0.007

chi-squared goodness of fit test (by hand):  χ²=8.95, df=2, P<0.05  or  χ²=4.21, df=2, NS

regression:  slope= -7.25 mW/h, N=15, R²=0.894, P=0.029   The slope should be expressed with the correct units.  Alternatively, the entire equation of best fit can be stated rather than just the slope.

ANOVA: The results are typically reported in the form of a table with a row for each source of variability (the experimental factor(s) and the error term) and the totals. 

Source	Degrees of freedom	Sum of squares	Mean square	F ratio	P
Soap	1	4704500	4704500	7.1	0.0164
Triclosan	1	264500	264500	0.40	0.536
Error	17	11280500	663559
Total	19	16249500

Note: since it is possible to calculate some values in the table from others, sometimes the totals or the mean square may be omitted. 

Immunology basics

Definitions
An antibody is a protein produced by cells of the immune system that specifically recognizes and binds to a protein or carbohydrate that is recognized as "foreign". An antigen is any substance (protein or carbohydrate) that stimulates the production of a specific antibody or antibodies by the immune system.

Antibodies are composed of two light chains and two heavy chains.  Binding sites recognize specific antigens.

The chains are held together by disulfide bonds.  For Molecular Models of Antibodies (CHIME) see: http://www.umass.edu/microbio/chime/antibody/

Both the heavy and light chains have regions that do not vary among antibody types.  However, the differences among the variable regions determine the isotype of the antibody.

Here are some examples of important isotypes:

• IgA: prevents entry by inhibiting binding of micro-organisms to mucosal surfaces. Related to food allergies.
• IgE: "normal" function seems to be in anti-parasite defense, produces typical allergy such hay fever
• IgG: the major circulating antibody which enters tissues freely, and participates in diverse immune events.
• IgM: forms large insoluble complexes which are readily cleared from the blood, e.g. blood types A and B, micro-organisms

For more information about the different classes of antibodies (IgA, IgD, IgE, IgG, and IgM):
 http://www.nutramed.com/immunology/antibodies.htm
 

 Antibody semantics: