This guide explains several common issues noted by our editors at each stage of the publishing process. Avoiding/addressing these kinds of mistakes before submitting will make things easier for you in that you will get less extraneous comments and more high-level feedback on your science.
Common mistakes seen in initial submissions
- Senior author missing. All manuscripts at JEI are required to have a senior author. This individual should be listed last in the order of authors to acknowledge their contribution. Typically the senior (last) author is the individual who mentored the students throughout the experiment and writing process for the manuscript.
- Formatted for publication already. Manuscripts should not be formatted for publication like you see for published manuscripts on our website. Our proofing editors will do this once scientific review and copy editing has been completed.
- Typical formatting issues we see with initial submissions include:
- i. Using two-column formatting instead of single column
- ii. Placing figures directly into the manuscript text or providing indications of where figures should be placed
- Please see our Manuscript Format & Content page for formatting guidelines for your initial submission.
- Inclusion of previously published figures. Figures that have been previously published cannot be used in your manuscript unless you have written permission from the author of the figure and the place of previous publication due to copyright reasons. If you feel that a previously published figure is absolutely essential to your manuscript please contact our editorial team where we will work with you to determine if it is necessary and appropriate steps to take.
- Manuscript written like a lab report. One of the hardest things is transforming your work from a standard lab report format into a polished manuscript for publication! Our review process is aimed at helping our student authors with this, but here are some tips and tricks to help get you started:
- Look at previously published manuscripts at JEI.
- i. We have hundreds of manuscripts online that you can look through! You can search by topic to find manuscripts related to your field of research as you’ll see that there are slight differences between different fields.
- Follow our manuscript content guide to help ensure each section has the appropriate content.
- i. Take a look at our resources available on our submit home page. We’ve tried to provide as many educational guides to help out our student authors as possible.
- 1. If you still have questions or think we’ve missed something, e-mail us: firstname.lastname@example.org.
Common mistakes seen in scientific review
- Lack of or inappropriate use of statistics. Statistics is a very complicated field, and even professional researchers struggle to apply the proper statistical tests to their data. JEI also recognizes that access to professional statistical software can be a limitation for many students, but there are some statistical tests that can be run in Excel or even calculated by hand. Statistical analysis is a very important tool in science because results of this analysis indicates the probability that the data observed happened by chance (a low probability or p-value indicates a “significant” result). Most JEI studies include experiments following one of these patterns, in order of complexity:
- Comparing two groups (control and treatment) by a single dependent variable. This is a simple analysis requiring only a t-test.
- Comparing three or more groups by a single dependent variable.
- i. Straightforward method: Ideally, this kind of data would be analyzed using a one-way ANOVA. If the ANOVA is significant, this can be followed by post hoc tests (Tukey and Dunnett’s tests are the most common) to look for differences between specific groups.
- ii. Alternative method: If statistical software is a limitation, an ANOVA may be difficult, so you can alternatively analyze this type of data with t-tests. However, there is an important caveat: if you use multiple t-tests to compare related data, you increase the probability that you will find a statistically significant result among your comparisons by chance. Thus, a correction for multiple comparisons, such as a Bonferroni correction, is necessary. This correction basically reduces the alpha level or the threshold for a significant p-value.
- Comparing multiple groups by multiple dependent variables. This is somewhat complicated, but the best way to analyze this kind of data is by a multivariate ANOVA, again with post hoc tests. This will also indicate whether there are interaction effects between two variables (whether the effect of one variable is impacted by another variable).
- Gene vs. protein nomenclature. Efforts have been made to standardize naming conventions for genes and proteins across different species so that they follow the same general format. Our editors will help verify that everything is correct, but these basics will help get you started.
- Genes are italicized. Whenever you write out a gene name (i.e. BRCA2) it should be italicized to denote that you are talking about the gene and not the protein.
- i. This formatting also means that you don’t have to say “the BRCA2 gene” because the italics already tell your readers that it’s a gene.
- Proteins have no special formatting. Proteins don’t need any special formatting. You simply just write it out like BRCA2.
- Different species have different capitalization standards.
- i. Human
- 1. For genes and proteins in humans every letter is capitalized in both the protein and gene names.
- 2. Gene: BRCA2
- 3. Protein: BRCA2
- ii. Mouse, Rat, Zebrafish
- 1. Only the first letter is capitalized.
- 2. Gene: Brca2
- 3. Protein: Brca2
- Species nomenclature. As with genes and proteins the scientific community has standardized the ways in which we write out the scientific names for organisms. When we talk about an organism, let’s say the common house mouse, we would first introduce it as Mus musculus. In this case you can see that both the genus and species names are italicized and the genus starts with a capital letter regardless if it starts a sentence. You only have to type out this full name the first time. After that you can simply just write “M. musculus” and it will be understood what you are referring back to.
Common mistakes seen in copy editing
- Manuscript submitted as a pdf. JEI editors use the Track Changes tool in Word to provide edits to authors. Converting a pdf into a Word document leads to very messy formatting (inconsistent line breaks, spacing, etc), so if we get pdf submissions, we have to ask the authors to provide an original Word document, delaying the manuscript’s progress.
- Tables labeled as figures. Many authors submit tables as images and refer to them as figures. However, tables (numbers organized in columns and rows) should be placed at the end of the Word document with the figure and table captions, and these should be editable in Word, not just pasted images of a table copied from another application. This allows the editors to edit and make comments on them. Tables should also be labeled as Table 1, Table 2, etc., which is a separate numbering system from the figures. Similar to figures, however, tables should also have a descriptive caption explaining what is shown and defining any abbreviations used in the table.
- Figures and captions. Almost every manuscript that comes through copy editing receives suggestions for improving their figures and tables. This guide on making figures and tables for publication covers the major concerns.
- Passive voice/tense used outside of the methods section. Passive voice or tense (e.g. The experiment was done at the school.) tends to be wordy and at times difficult to understand, in part because it can hide the subject of the sentence, so JEI and many academic journals prefer the use of active voice (e.g. We did the experiment at the school.). The methods section is the only component of the manuscript where passive voice is acceptable.
- Use of present tense to describe results. Everything that you did for your study was done in the past, and anything you did and any observations you drew should be written in past tense. The same goes for describing studies from the literature.
- Improper acronym usage. Acronyms and abbreviations are useful tools for making your writing more concise, but to use them, please follow these guidelines:
- Spell out the entire word/phrase the first time the term is used followed by the abbreviation in parentheses. Example: “We used nuclear magnetic resonance (NMR) spectroscopy to validate our compound synthesis.”
- Once you define an acronym or abbreviation, use the abbreviation consistently throughout the rest of the manuscript unless use of the abbreviation would cause confusion.
- Use of first-person singular (I, me). The only time first-person singular is acceptable in scientific writing is if a single author did the work and wrote the paper, and this is very rare. Every JEI manuscript should have at least two authors, so even if you personally did the experiments, everything should be explained in terms of “we”.
- References. The individual references in the references section should be formatted according to MLA8, and Purdue’s Formatting and Style Guide is a nice resource for this. However, contrary to MLA format but consistent with scientific literature, the list should be numbered in the order in which the references appear in the text, and in-text citations should be the reference number in parentheses at the end of the sentence.
Common mistakes in proof submissions
- Figures need to be high resolution. At least 1000x1000 pixel resolution is ideal for publication of figures. This problem comes up most often with images of graphs exported from Excel. The default size for a chart in Excel is too small to yield high enough resolution when exported as a picture, but there is an easy fix for this: simply enlarge the image before saving it as an image file (JPEG, PNG, or TIFF). To check whether the resolution is high enough, right click on the image file and check the file info or properties.
- Figures or notes about figure placement throughout the manuscript. Part of what the proofing editors do is position figures with their captions logically within the manuscript. We generally try to put figures on the same page as the first reference to the figure in the text, but this is not always possible. Please do not put notes indicating where you would like your figures placed as these have to be deleted for the final proof.
- Submitting manuscript as a pdf. Proofing editors need to be able to edit the document to format and move components around, which is not possible with a pdf, so please submit a Word document. As with copy editing, submitting a pdf will result in a delay of your manuscript’s progress!
- Formatting equations. The Insert Equation feature in Word produces very nice-looking equations that can easily be transferred to the proof so please use this for any equations. However, do not use this function to insert Greek letters or other symbols in the main body of the text as Word has a convenient Insert Symbol function that better integrates such symbols into the font formatting of the text.