- Title and authors
- Materials and Methods
- Database and software versions
- Real-time PCR
- Regression analysis
- Results: including experimental design
Is Abstract a summary of the whole paper?
In a poorly prepared manuscript, important information is sometimes missing in Abstract. The structure of my ideal Abstract is as follows (2). See Abstract の書き方.
- General introduction. 1 - 2 sentences.
- Specific introduction, or detailed background. 1 - 2 sentences.
- One sentence clearly stating the general problem being assessed by this paper.
- One sentence summarising the main results of this paper. Started with a phrase like
Here we show...
- Result 1, result 2, result 3,... If experiments are organized very well, not many explanatory sentences should be needed.
- One or two sentences to put the results into a general context. Should be closely related to the aforementioned problem.
- Two to three sentences to provide a broader perspective.
I think that
Introduction is not a review
Do not describe unnecessary details, which are not related to the contents of the paper, like a review.
Materials and Methods
In this section, authors are requested to provide
Database and software versions
Many biological databases, as well as analyzing softwares, are frequently updated recently. Using different version of database and software results in different results. It is necessary to describe the version in M&M section to ensure reproducibility (4).
- The authors have used MEGA 7.0 for the phylogenetic analysis. Currently, MEGA 10.0
with advanced functionsis available. I would recommend to revise the phylogenetic analysis using the latest version.
Author guideline package of some journals provide useful information about immunohistochemistry (4).
- Provide the origin (e.g. human, rat, zebrafigh) and sequence of immunogen for antibody.
- If commercial antibodies were used, provide the name of company, immunized species, and monoclonal/polyclonal.
- Characterization information such as western blot, radioimmunoassay and ELISA should be included. This is because it is difficult to find non-specific bindings in immunohistochemistry.
- Negative controls: pre-adsorption with the original antigen, and/or incubation with secondary antibody only.
- If transfected cells are used, two negative controls are required. Non-transfected cells stained with primary and secondary antibodies, and transfected cells stained with secondary antibody only.
To be updated. See minimum information for the publication of real-time quantitative PCR experiments guidelines for now.
If the paper performs regression analyses, check the following points.
- Is the selection of function (linear, exponential, logarithmic etc) appropriate? Computers can calculate how their data fit to the specific function, but authors determine functions to calculate.
- Are the coefficient of determination and statistic results shown?
Results: including experimental design
Time- and concentration-dependency?
If the paper examines the effect of some reagents on animals or cells,
A good example is the right Figure (1). If you have only one timepoint, for example 1 h, you would conclude that "Bcl-2 protein expression was significantly increased".
However, if you have only the 12 h result, you should conclude in the other way; "Bcl-2 was decreased". Analyzing limited timepoints generally have a risk to miss important results.
- Scale, X and Y labels are OK?
- Error bar, SD or SE? N is mentioned in legend?
If the value is normalized, the data should be carefully checked.
Pointing out statistical mistakes is often difficult because reviewers should know well about statistics. I hope that this page helps Japanese people to learn statistics.
- Duncan's multiple-range test is now widely criticized because of its poor control over type I error. The *** test is a better option.
Figure legend is getting longer and longer nowadays. Many papers mention results in figure legends. Alothough there are many styles, in my opinion, the optimum length of legend is
You might want to point out this if the paper does not include the following information:
- Number of samples (N)
- Meaning of error bars. Standard error or standard deviation.
- Meaning of asterisks. Typically P < 0.05.
- Abbreviations used in Figures
Cui et al. 2012a.Propofol prevents autophagic cell death following oxygen and glucose deprivation in PC12 cells and cerebral ischemia-reperfusion injury in rats. PLoS ONE 7, e35324.
- How to construct a Nature summary paragraph. Link.
- Obokata et al. 2014. Essential technical tips for STAP cell conversion culture from somatic cells. Protocol Exchange. doi:10.1038/protex.2014.008
- Author information pack. General and Comparative Endocrinology.