Module 6: Methods sections in scientific papers
Compiler: Prof Willie van Heerden
1. General aspects pertaining to the Methods section
· The precise name of this section varies between different journals. It may be called Materials and Methods, Method or Methodology.
· This section is the easiest to write and should generally be done first.
· The purpose of this section is to present your experimental design or describe how the study was performed. It should contain sufficient information for the reader to duplicate the experiment exactly and to replicate your work. It is always a good idea to look at other related papers that have been published in the journal you are preparing the manuscript for to get some idea of the format required for this (and other sections).
· It is not necessary to describe a method in detail if it has been published before. It will help the reader to give a short description of the cited methodology. If the reader needs more information, it can be obtained from the cited reference(s). Any change to the published method should be described in detail and identified as a modification/change to the published method.
o Example: “Sections for flow cytometric analysis were prepared according to the modified Hedley method (6)”….followed by a short description of the modified Hedley method. (It is good practice to refer to the original article where the method was published and not to later articles using the same method)
· Detailed information about the methods should be given if it has not been described before. Only the essential aspects needed to repeat the experiment should be included. Aspects such as the racial and sexual profile of humans in a study always carry some form of sensitivity and should not be mentioned if it has no specific bearing on the results of the study. It is however important to mention it in certain instances, especially when epidemiological studies are performed.
o An Example of how to effectively forward only essential information allowing the reader to duplicate the experiment: “Antigen enhancement was performed by microwave heating of the sections in a microwave pressure cooker in citric acid buffer (pH 6). Slides were subsequently cooled for 20 min and then washed three times in phosphate buffer and treated with hydrogen peroxide for 5 min at 37 °C to reduce endogenous peroxidase activity”.
Compare it with the following tedious paragraph that describes exactly the same laboratory technique but which contains unnecessary detail, much of which is common knowledge to personnel who use this technique:
“Antigen enhancement was performed by immersing sections in a 10 mM citric acid solution buffered to pH 6 with 1 M sodium hydroxide in a suitable Tissue-Tek staining dish. The slides were put into a microwave pressure cooker, the lid sealed and the sections were micro waved for three minutes. After the pressure in the microwave had returned to 0 psi the Tissue-Tek staining dish with slides were removed and subsequently cooled for 20 min at room temperature by immersing the staining dish in cold water. The slides were washed in phosphate buffered saline and treated with a 3% aqueous hydrogen peroxide solution for 5 min at 37 °C on a heating plate to reduce endogenous peroxidase activity.”
· The methodology section should be written in past tense as it described the work you have already done. This is in contrast to the Methodology section of a research protocol where techniques to be used in the proposed project are described. These grammatical changes should be remembered when copying information directly from the protocol document and pasting it into the manuscript or dissertation/thesis in preparation.
· There is a tendency towards the use of the first person and active voice in scientific writing. Writing in passive voice is supportive of objectivity and together with writing in the third person place the emphasis on the experiment and less on the person performing the study. It should be compulsory in the Methodology section to use the third person and passive voice.
o Example: Do not say “I have plotted the DNA histograms of at least 10 000 cells,” but rather “DNA histograms of at least 10 000 cells were plotted.”
· The method should not be written as a laboratory manual or in a prescriptive manner.
o Example: Do not write “Incubate the sections with the antibody for 60 min at room temperature,” but rather “The sections were incubated with the antibody for 60 min at room temperature.”
· The metric system should be used for all measurements, time of day should be described using a 24-hour clock and temperatures should be given in centigrade. Standard abbreviations should be used where possible.
o Example: Write: “The cDNA was amplified using RT- PCR with an annealing cycle at 50 0C for 1 min” instead of “The complimentary deoxyribonucleic acid was amplified using reverse transcriptase polymerase chain reaction with an annealing cycle at 50 degree centigrade for 1 minute.”
· Instruments, chemicals and specialised apparatus that were used, especially those not commonly found in most laboratories, should be listed and their vendor name supplied.
o Example: ”Sample purity was further enhanced with the PALM® Microlaser System (P.A.L.M. Microlaser Technologies AG, Bernried, Germany), which allowed the non-contact harvesting of individually selected cells.”
· The results should correspond directly with the methods described in this section of the manuscript. It is therefore important to ensure that methods are described for all the experimental results reported in the study.
· Be careful not to include any results in this section or to justify/discuss your methodology. The latter forms part of the Discussion section.
2. Structure of the Methods section
· Consult the “Guidelines to authors” section of each journal (as well as related publications in the targeted journal) regarding the preferred format of the Methodology section. Many journals prefer the use of subheadings to indicate the subsections such as “Sample Collection” and then “Methods” etc.
· The information supplied should be in paragraph format and not a list of steps.
· Whatever the guidelines given by the journal, it is always important that the order of the methods described should follow the exact sequence of the experiment performed.
· The first paragraph or subsection should be a clear and concise description of the material studied such as which patients were included, how they were selected, the exclusion criteria if any; did the selection process involve randomization and if so, how was it randomized?
· Description of for example the laboratory experiments or clinical procedures performed on the study subjects follows. This should be in sufficient detail for other scientists to repeat your work and verify your findings. Subheadings (if allowed in the author guidelines) should be used if different techniques or experiments are performed on the study material.
· Flow diagrams or table formats can be used to help simplify description of the methods used in certain studies.
· Describe how data were summarized and the data analysis techniques used. The specific statistical test used and the reason for choosing it should be mentioned.
o Example: “The factors evaluated were related to the nodal status in 2X2 contingency tables. The Chi square with Yates correction and Fischer’s exact tests were used for the analysis of the categorical data. Correlations with a p<0.05 were considered statistically significant.”
3. Ethical aspects of the study
· Ethics approval is an important aspect of the majority of scientific studies. This is applicable for all studies involving humans and animals. The ethics approval number and the specific committee that granted the ethics approval should be supplied. This can be done in a single sentence or paragraph.
o Example: Patients attending the antiretroviral clinic at the Pretoria Academic Hospital for initiation of antiretroviral treatment were screened for the presence of oral lesions by an oral pathologist. All mucosal abnormalities and infections were recorded. Patient consent, as approved by the Ethics Committee of the University of Pretoria (EC 234/10) was obtained.
· If the study is of a clinical nature and involves patients directly, various ethics issues should be addressed. The way of obtaining informed consent (verbal versus written) and if the patients could opt out of participation in the study, how patient anonymity was ensured throughout the study, if the patients experienced discomfort or embarrassment and in the case of children participating in the study, how procedures were explained to both the child and the parent/ guardian should be described. Consent forms for children under the age of 18 years should be created and also alluded to in this section. The editor/readers should be assured that patients and their families were treated with dignity and respect.
· Similar questions about care and treatment during the duration of the project should be addressed if animals were used in the experiments. If termination of the animals involved is part of the study, the exact method thereof should be described. This is especially pertinent for primates.
4. Checklist
· Section is written in past tense, in passive voice and in third person.
· Methods are included for all results described later in the manuscript.
· Methods are described in the correct and exactly the same sequence as performed during the study.
5. Common mistakes
· Results are reported in this section.
· Problems encountered during the project are alluded to in this section.
· Tedious descriptions of aspects that were either published before or for which acknowledged/ internationally accepted abbreviations could have been used.
· Description of aspects of the methods that does not necessarily relate to the results. This happens regularly when the author prepares more than one manuscript on different aspects of the Master or PhD study but copies the Methodology from the thesis/ dissertation and pastes it directly into the Methodology section of the manuscript.