Formatting APS Journal Articles :: Main Text
The Materials and Methods section is where the authors provide their readers with detailed instructions or descriptions as to how the experiments were carried out. The purpose of this is to allow others to be able to repeat the investigations of the study. In terms of formatting, you are responsible for making sure that the headers are correctly placed and that the section has been correctly coded. In addition, this is a very good time to make that the authors have included information that APS requires, such as Institutional Review Board or Animal Care and Use Committee approval and/or statements showing that informed consent was obtained from human subjects. In addition, this gives you an opportunity to review the text and identify any idiosyncrasies of the manuscript. You may also want to review the statistical analysis of the paper and query the author if they do not follow our statistic style.
This section can be titled as Materials and Methods, Methods, or Experimental Procedures. This is a level 1 header.
In the proofs, this section is in a slightly smaller font size. This is coded using the «smt» code.
Right before the «h1» code of the Materials and Methods section, type «smt» to code for the reduced font size.
APS is very firm in regard to making sure that proper humane treatment of animals has been followed in the course of a study. This means that animals were not subjected to unnecessary procedures or pain, that they were given proper access to antibiotics, food, and water, and that they were anesthetized before any surgery was performed on them. This included studies in which cells or tissues were isolated from living animals by the authors. In the same manner, APS also requires that human subjects/patients received detailed information about the experiments in which they participated, that they consented to any procedures, and that they gave permission for certain data to be shared (informed consent).
In all studies using animals or human subjects, the authors must provide a statement detailing that they obtained proper approval for the study by a medical oversight board (which is usually associated with their institution). Cells or tissues obtained from already deceased animals (like pig arteries from an abattoir) and cell lines provided as a gift from an individual or obtained from a company (like the American Type Culture Collection) cannot provide informed consent, and their care is not covered by any particular guidelines. Therefore, no such statement is necessary. However, in the case of embryonic stem cells or fetal cells and tissues, the authors must provide their source (these are particularly dicey political topics).
The approval statement is usually found somewhere in the Materials and Methods section, most often in the first few paragraphs. If you do not see such a statement, you must query the author. The following text is an example of such a query, and it can be placed automatically using the AU function in ABRA in the Toolkit (listed as Animal or Human Research):
APS Journal policy requires that a statement of protocol approval be included in the Methods section of all papers involving animal or human research (see http://www.the-aps.org/publications/i4a/prep_manuscript.htm#humans_animals). Were your protocols submitted to, and approved by, an independent review committee? Please provide us with the appropriate statement about the review and approval of your study by an independent committee (Institutional Review Board, Institutional Animal Care and Use Committee, or equivalent). Alternatively, if you have been granted a license from your government or institutional office to conduct the animal or human research described in your study, please provide a statement to this effect.
Approval of procedures in foreign countries. Some countries do not require approval from an oversight committee for scientific research. APS, however, still requires the study to have conformed to basic care principles. In this situation, APS accepts approval of the study by an equivalent body or governmental approval (as stated in the above template query).
Let me set your mind at ease on this topic: you are not required to have any knowledge of statistics or review the statistical analysis of the material presented in the paper. There are no math tests here. Instead, as you look in the Materials and Methods section, make a note of whether the author specifically states that they are analyzing their results based on standard error (SE) or standard deviation (SD) from the mean (or average). APS has instituted guidelines for the presentation of such results. If the author presents their results as means ± SE, with values as x ± y (where x and y are numbers), then everything is fine and you don't have to worry about anything. However, if the author states that the results are means ± SD, with values as x ± y, then this is technically (statistically) incorrect: they should be stated as means (SD), with values of x (y). It is not your responsibility to change this in the text as you copy edit it. What you should do is to query the author, and the following is a sample query using the AU function in ABRA in the Toolkit (listed as Standard Deviation):
In this manuscript, you provide standard deviation (SD) values. Please refer to the "Guidelines for reporting statistics in journals published by the American Physiological Society," by Dr. Curran-Everett and Dr. Dale Benos (APS Publications Committee Chair), which describe preferences for presentation of SD values in APS journals (http://physiolgenomics.physiology.org/cgi/content/full/18/3/249). If you feel that changes should be made to the presentation of the SD values in this manuscript (text, figures, or tables) to comply with the guidelines, please alter the proofs as needed.
Please note that authors may choose not to comply with the guidelines. This is their choice, and their paper should not be altered.