Writing a scientific publication

You should cite this article if you use its information in other circumstances. An example of citing this article is:
Ronny Gunnarsson. Writing a scientific publication [in Science Network TV]. Available at: http://science-network.tv/writing-a-publication/. Accessed July 28, 2017.

It is likely that others will find your project interesting and perhaps also important. Should it be an oral or written presentation? In most cases it should be both. There are different types of publications and they can be grouped as belonging to one or more groups / types of publications.
Click to expand and see the most common publication types

  • Article – Review
    A review article in a journal. Often a meta analysis or review of research previously published by others. Summary of the current state of understanding on a subject published after examination of research previously published by others.
  • Article – Book review
    Reviews are reviews of books in a journal or daily magazine. Refers to an article in a scientific, or other type of journal.
  • Article – Peer reviewed scientific (often also labelled as Journal Article)
    Refers to a peer-reviewed article in a scientific journal, often presenting original scientific work.
  • Article – Other scientific
    Refers to a written note or article in a scientific journal. E.g. letter to editor, historical description, comment in a scientific journal, supplement in a scientific journal or other non-original contribution, meta-analysis or systematic literature review.
  • Article – Other
    Refers to an article published in a non-scientific journal.
  • Book
    Book or eBook with one author.
  • Book with editor
    Book with several authors of separate chapters joined together by one or more editors.
  • Book Chapter
    Chapter in an edited book. Authors of chapters can be others than the editor (s).
  • Doctoral Thesis
    Refers to approved doctoral thesis.
  • Masters Thesis
    Refers to approved thesis for a Masters by research degree.
  • Honours Thesis
    Refers to approved thesis for an Honours by research degree.
  • Conference Poster
    Non-peer reviewed posters.
  • Conference Paper – Peer reviewed
    Peer reviewed conference paper. Published in a conference proceeding.
  • Conference Paper – Other
    Other non peer reviewed conference papers published in conference proceeding.
  • Research and development from the field of arts
    Report from research and development from the field of arts. May be published in media other than text.
  • Report
    Publication as part of a series. E.g. essays, compositions, guidelines etc. papers.
  • Other
    Publications where all other available publication types are not suitable.

The best way to make your findings easily accessible is to submit them to a scientific journal. This journal has routines to ensure your publication is indexed in the right publication and citation databases. The rest of this page focus on writing a manuscript of the type Article – Peer reviewed scientific for publication in a peer reviewed scientific journal.

Copyright

Scientific journals are usually produced by Publishing companies (publishers). Sometimes non-profit organisations have scientific journals. However, it is quite common that they don’t do all the work. They may pay a publisher to do a lot of the practical work. Scientific journals do not want manuscripts published elsewhere. They want the publication in their journal to be a unique publication not found elsewhere. Thus, when you submit your work you must state that this material is not published or submitted for publication elsewhere. In case your manuscript, after proper review, is accepted for publication many publishers require you to sign over the copyright for an accepted manuscript to them before publication. This is common procedure and nothing unusual. After doing this you are no longer the copyright holder. This means that you must obtain permission from the publisher if you wish to include your published papers in a thesis. This also poses a (manageable) problem when writing a thesis. This also poses a (manageable) problem if you want to present results in a conference ahead of publication.

Finding the right journal for submission

The best way to make your findings easily accessible is to submit them to a scientific journal. This journal has routines to ensure your publication is indexed in the right publication and citation databases. There are different pathways to find the best journal for submission:

  1. Write your manuscript as you want first (following guidelines given further down on this page). Once you are finished have a look at your own reference list in your manuscript. You cite journals in your reference list because they have published other studies relevant to your study. Hence, they are likely to be interested in your research. Have a look at the journals found in your own reference list. Which journals do you cite most often. What is their impact factor? Decide which one you want to try first. Make minor adjustments to your manuscript to tailor it to this journal.
  2. Find the journals in your topic with the highest impact factor before your manuscript is written and tailor your writing according to these author instructions.

I would recommend option A in most situations. This will give you a short list of 3-5 possible journals. If it gets rejected by the first then you already have an idea of where to send it next. Before finally deciding check that the journal you aim to submit to…

Journal Impact factor

In the good old days each institution subscribed on a very limited amount of journals printed in hard copies. Publications in other journals were read much less, if at all. Manual search in databases could be done and a specific publication could be ordered. However, this was a costly and tedious process. Thus, getting your publication in a journal with many subscribers was essential. If successful then your publication was much more likely to be read and hence cited.

Impact factor is one method to estimate how many citations a publication in a journal will get as an average. Impact factor usually only consider citations within a specific time frame. Some topics will have their peak number of citations within this time frame while others may have it outside. Thus, the impact factor will get publications in some topics a much higher rating than within other topics. However, this may not reflect the relative importance of a publication or a journal within its topic.

In some disciplines 10 citations would be a lot, in others 100. Thus, there is s strong criticism against the relevance of impact factors as a means to rank journals. Read more about this criticism of impact factor on Wikipedia. Furthermore, one consequence of today’s availability of online databases and online access is that few institutions subscribe on hard copies of scientific journals. They rather subscribe on all journals online produced by a number of publishing companies. This makes the impact of a single publication more interesting than the impact of a journal. This does not mean that journal impact factors are completely uninteresting, just that their relative importance for choosing journal is declining and it should not be the sole ground for choosing journal.

Content of your manuscript and author instructions

Overall layout

The purpose of a manuscript for submission to a scientific journal is not to look good but to convey the information in a standardized way. Hence, a manuscript for submission should not have a nice graphical layout. This is something the journal adds on after the manuscript is accepted. They have their own methods to address this. Any graphical stuff added before just makes their job more difficult. This means that most journals don’t want you to put tables into the text. Some journals want you to put a placeholder (a kind of notation) describing where you would prefer a table. They still want you to have a table either as a separate page later in the manuscript or, as a completely separate file. The desired layout of your manuscript is for most journals:

  1. Title page
  2. Abstract / Summary
  3. Introduction / Background
  4. Methods
  5. Results
  6. Discussion
  7. Acknowledgements
  8. References / Bibliography
  9. Tables
  10. Figures (Most journals wants all figures after all tables – even if you refer to figures before tables)

All scientific journals have author instructions. Study them carefully and follow them. Some journals may want you to submit without a title page. Some journals want the tables and figures as the last part of the manuscript. Other journals want you to upload tables and figures as separate files. Some journals may want the acknowledgement in another place. All text should be written with 1.5 or 2 in line spacing. Most journals prefer a font size of 12. Common limitations in allowed total number of Words (excluding abstract, references and tables) are 1,500-3,500. However, this varies depending on journal and type of manuscript so you need to check author instructions for the particular journal you aim to submit to.

Learn how to get a new page by inserting a page break (in Word for Windows usually pressing Ctrl+Enter). You should never “push” text to a new page by just pressing enter a number of times creating lots of empty paragraphs. This will create later problems with layout.

Title page

Most journals want this page to contain the title, author names, author affiliations, name and contact information to corresponding author. Some journals also want it to state word count, number of tables and figures. The title page is a separate page. Some journals prefer it to be the first page of the document. Other journals want it as a separate file.

Abstract

Some journals prefer a structured abstract with subheadings while others preferred an unstructured abstract. The allowed number of words in an abstract varies greatly depending on journal. References are normally never used in the abstract. The abstract is usually also a separate page coming after the title page but before the introduction. Hence, the introduction starts on a new page.

Paragraphs in Introduction-Background

  1. Begin with describing the topic and why it is an important topic. You may want to mention prevalence or costs associated with this topic.
  2. The rationale for a project is always to solve a problem. In this paragraph describe the unresolved problem associated with the topic. The problem may be (a few examples):
    -We do not have a good treatment option for Dengue fever
    -We have a high incidence of postoperative infections
    -We have insufficient information to identify high risk patients
  3. Once you have defined the topic and the associated problem then you need to state what others have done to solve the problem. This paragraph is a very short summary of publications describing studies focusing on the problem you just described. In rare situations you (and your advisors) may find that to your knowledge none has tried to solve the problem. If that is the case state that this rather than just not addressing previous publications in the topic.
  4. In the previous paragraphs you have described the topic, the remaining problem and what others have made to try and solve the problem. If others did solve the problem completely then there would not be a need for a new project. Thus, you need to describe, in light of what others already have made, what remains to be solved. This is the rationale for your project.
  5. State in a general form what you want to achieve in your project. What do you aim for? What is the objective? This aim must link up closely to the rationale you concluded in the previous paragraph.
  6. If your project is evaluated using quantitative methods (statistics) then you must clarify your aim in answerable research questions or hypotheses that you can confirm or reject. Primary research questions are those questions you perceive as most important and where you have made an appropriate sample size calculation. Other research questions are secondary research questions. If you plan a purely qualitative project where no part involves statistics then it is common to refrain from describing specific research questions or hypothesis.

Paragraphs in Methods

  1. A brief description of the setting and ethics approval (if relevant).
  2. Detailed description of how participants were chosen. Inclusion criteria should be specified. Once participants are included are there specific criteria for later exclusion?
  3. In randomized controlled trials describe how participants were allocated to different groups. How was randomization done.
  4. In studies comparing treatments describe the different treatments given in enough detail so a reader can replicate this.
  5. Describe what kind of data was collected for analysis. This section should be detailed. Established well known questionnaires do not need to be described in detail. A reference is enough.
  6. Describe sample size calculations (if relevant)
  7. Describe how analysis of collected data was done.

Paragraphs in Results

In a study using quantitative approach (statistics):

  1. Start with describing how many participants were invited and how many actually did that in the end. This can sometimes be a very short sentence referring to a figure. State reasons for non-participation. Investigate if those declining participation differs from those that did participate.
  2. Describe the actual outcome directly related to your specified research questions. It can often be done by referring to one or several tables. Do not interpret the findings here. Thus, the text belonging to this section can often be rather short.
  3. If you have any unexpected or unusual findings not related to your specified research questions describe them.

In a study using qualitative approach:

  1. Describe the informants (can sometimes be done by referring to a table).
  2. Describe the findings this section tends to be long with lots of quotes from interviews. Findings are in some publications presented without an interpretation. However, it is common in qualitative research to jointly present the result and the interpretation of it.

Paragraphs in Discussions

  1. Begin with a short summary of your main findings (results). This summary should be short (1-3 sentences).
  2. Describe strength and weaknesses with this study
  3. Comment your own results and compare it with results from previous studies.
  4. Your conclusions about the application and relevance of your results and a sentence describing the specific need for future research.
Are you making a stand?

Are you making a stand?

Your manuscript should have avoided appraisals up until the discussion-section. The discussion is the right place to include an appraisal of your own or others results. An appraisal adds a subjective element which is perfectly OK in the discussion as long as it is clear what is an appraisal and what is a scientific finding. Don’t be afraid to make a stand for what you believe in!

Acknowledgements

Thank staff and participants for their contribution (not co-authors). When it comes to staff be specific on what they did that you want to thank them for.

References / Bibliography

There are two main systems for presenting references; Harvard and Vancouver. Each journal tends to have its own variation of any of these. This means that the reference list and the annotations in the text are specific to a journal. Follow author instructions regarding reference style carefully. A good software for managing references will save you a lot of time. The importance of these software cannot be overestimated.

Tables

The decision to put information in a table or purely in the text (usually under the heading Results) depends on the amount of information. Small amounts of information should be described solely in text. The more information you can arrange into a table the better. However, there is an upper limit where tables tends to be too big and difficult to grasp. Always carefully consider if all information is necessary. The problem of information overload tends to be more common than the problem of providing too little information (although the latter exists as well). Also consider the number of tables you want to have. Few journals would accept more than five tables. In most manuscripts you can often do well with 1-3 tables. A few things to consider:

More information about tables is found on another page: Descriptive statistics using tables.

Figures

There are two types of figures. One type is presenting an image of something that would take many words to describe. It can be a picture of a patient or a cell. It can also be a figure explaining relations between different events. The other type of figure presents your own data, often in the form of a diagram. The latter is only suitable if the amount of information is limited. If you present own data comparing more than five groups then a figure quickly becomes cluttered. Thus, a figure is only suitable for presenting own data if the amount of information is very limited. If you want to present more information then I recommend you consider using a table instead.

All journals were printed in hard copies in the past. Printing in color was expensive so figures were mostly in black and white. Today all journals are published online. However, a fair share of them are still also printing hard copies. Most of these journals charge extra if you want to include figures in color. Another aspect to consider is color blindness. Five to eight percent of the male population have difficulty in differing between red and green. Thus, think carefully if you really need colors. More information about figures is found on another page: Descriptive statistics using figures.

Examples of formatting a manuscript

Below are examples showing how a manuscript can be formatted with an initial title page, increased line spacing and the order of the different sections. Observe that tables and figures are placed after text and references.

A few tips when using Word or similar software

  • Tables and figures should each start on a new page. Don’t “push over” to the next page by pressing the enter key thus creating a lot of empty paragraphs. Instead insert a “page break”. On a windows machine you get a page break by pressing Ctrl+Enter. The reason for using this command is that it looks the same on every computer. If you use the method of simply pressing enter multiple times it means that the start of a new page will change as soon as you change anything in the manuscript located before this. Secondly, different computers may display the same font slightly different and this may affect where the transition to the next page takes place. Using Ctrl+Enter eliminates these problems.
  • Use the same font size in all tables. Some large tables require landscape orientation while the text and most tables are presented in portrait orientation. This is solved by inserting a “section break”. You find this function in Word’s “Page Layout” tab. Click on “Breaks”. You can then set that this following section should have landscape orientation while the first section has portrait orientation. You can also create a third section returning to portrait orientation.
  • Use the spelling function in Word. It does not solve all problems but may save you from some simple and embarrassing ones. Ensure you mark all text with the correct language before using the spelling function. Please note that there are more than one version of English. In what country is the head office for the journal located?

In what order should I write the different sections?

There are different opinions and no given truth. I can describe how I usually write a manuscript based on a quantitative study using statistics:

  1. Start with creating the tables in results and fill them with information. In case figures are needed then I make them after the tables.
  2. I write the Results section once the tables and figures are finished. The results section refers to the tables or figures just created.
  3. Once the Results section is finished I would proceed with the Discussion.
  4. After I have written a discussion around my results I usually proceed to write the introduction.
  5. I usually write the methods section last. The methods are of course established a long time ago when the study protocol was written so it is quite simple to take the text from there (tweaking it according to space and author instructions).

Introduction and methods are usually more or less already written in previous project proposals or grant applications. The new challenge, once the results are analysed, is to write them up and discuss them. I usually start with the new challenge because I find that more interesting.

Academic writing

“Everything should be as simple as it is, but not simpler.”
Albert Einstein
1879 – 1955
Theoretical physicist and philosopher

Academic writing sound a bit boring but is actually quite simple. It is about writing as simple and straight forward as possible. For every paragraph, every sentence and finally every word question if it is needed. The shorter the better. It is more common for an inexperienced researcher to write too long rather than too short. There are also a few details that needs to be considered:

  • Every sentence must pass “the breathing test”. It means that you must be able to read the whole sentence without breathing in between. If you can’t do that you need to split the sentence. (this might be a good argument to quit smoking… 🙂
  • Avoid starting sentences with acronyms or numerals. The best option is often to try and rephrase the sentence so it does not start with an acronym or a numerical. If that can’t be done case spell out the acronym / numbers at the beginning of the sentence. .
  • (Under construction)

Using a translator or a language editor

English is the most common language used in scientific peer-reviewed publications. This pose a problem for authors whose native language is something other than English. Using a translator to do a complete translation or a language editor to polish your own text written in English is highly recommended. However, bear in mind that the translator / language editor might be very good in English but may not fully understand the scientific text and this pose a risk for misunderstandings. Most of the work done by a translator / language editor is very good but a minor part usually ends up being wrong due to misunderstandings. Hence, it is important that you carefully check the text after it has been with the translator. If possible discuss tricky parts directly with the translator.  Failing to check for misunderstandings after the manuscript has been with the translator / language editor may turn out to be fatal.

After submission – Rejection

Most journals reject 50-98% of submitted manuscripts. Even good manuscripts get rejected because some journals get more good manuscripts than they possibly can publish. In case this happens follow these steps:

Depressed?

Depressed?

  1. Look at a video describing your feelings (always good to take a short moment acknowledging that this was a disappointment. However, don’t get stuck here!)
  2. Realize that a better approach to rejection is needed.
  3. Read Rejection improves eventual impact of manuscripts. This manuscript is just so true! Rejection will force you to work a bit further with your manuscript and it will get better.
  4. Quite often your manuscript is not actually rejected. You are given lots of (perhaps harsh negative comments) but somewhere in the response encouraged to submit a revised manuscript. These offers often contain much comments and at first glance may appear as a harsh rejection. Find out if the response you got actually is a final rejection or just a long list of suggestions for improvements with an encourage to resubmit a revised manuscript. The latter is a half acceptance. Please read further advice below.
  5. If the editor wants a revised versions submit that (see advise below). Otherwise consider if the manuscript has something to say that is worth publishing. If yes find another journal and submit a revised version. It is very common that manuscripts need to be submitted to several journals before they are finally accepted for submission.

If you submit a revised version to the same journal ensure you submit a detailed author response / comment detailing your response to the raised criticism. This is usually done by citing referee and give a rather detailed response to each comment from the referee. Remember that some of reviewers comments may be very good improving the manuscript while other comments might be based on a misunderstanding and should not be followed. However, the latter can’t be ignored with silence, you still need to comment on these in a polite manner. You need to make some argument if you don’t follow some of the reviewers comments. Some more transparent journals (such as the BMC-series) publish all versions of the manuscript, all reviewers comments (with names) and all author responses. See some of these examples of referee statements and author responses / comments (read Author comments in the examples below):

After submission – Checking a proof and answering questions if accepted

Admin staff starts to work on your raw manuscript after it is finally accepted. Suddenly you get an e-mail with something like: “Please check the proof and return the corrections to me by email or fax within 3 working days of receipt of this notification.”. It is common that they also pose a few specific questions. The notification usually contains a direct link or other instructions so you can access their proof that is usually in the form of a PDF file. There are a few things you need to do urgently:

  • You need to carefully compare their preliminary pdf with the latest version of the manuscript you submitted (be 100% sure you compare with the correct latest manuscript). Check all sentences and all figures in all tables. Also check all figures. I have several times experienced that admin staff (with no understanding of the topic or research methodology) try to improve the language, most often quite successfully, but may sometimes by mistake alter the meaning so it becomes completely wrong. I have also experienced that they have swapped figures in a table to figures that were completely wrong (probably from another manuscript they were working on in parallel). Hence, don’t forget to check tables and figures as well. All this needs to be done thoroughly because publication will pore a bucket of concrete on text, tables and figures. It can only be adjusted by publishing an amendment stating that the original publication contains errors and this is a tedious process.
  • The admin staff often also pose several legitimate questions asking for your clarification. Answer these carefully.

Don’t fall for the temptation to ignore this request because it will likely result in a few annoying errors being published or maybe that your manuscript does not get published.

Plagiarism – a gateway to hell?

Presenting others ideas as if they were your own is plagiarism and everybody understands this. Some people do it because they think it helps their career and that they can get away with it. They are double wrong. Not putting in enough effort to come up with your own ideas means that you miss out on the development and refining of your thinking that would make you a unique expert. Secondly, you are very unlikely to get away with it. Universities and journals use advanced software that compares your text with pretty much everything written, including student submissions. Copying text and then make minor changes does not fool this type of software. There are other more or less advanced ways to trick this type of software but these tricks are also known to Universities and journals and they can check for it. I recommend you have a look at this Norwegian video from University of Bergen UiB brilliantly expressing all this:

Reusing your own ideas presented previously may constitute “self-plagiarism”. The best way to avoid problems is to clearly refer to previous sources whether that is yourself or someone else.

General advice on academic publication

Nick Hopwood gives an overview of concepts you need to consider when you plan to submit a manuscript for publication.

Ten ways to ensure your work is never published, or worse, cited

Nick Hopwood talks about barriers towards getting published and cited.

Recommended information – reading

You should cite this article if you use its information in other circumstances. An example of citing this article is:
Ronny Gunnarsson. Writing a scientific publication [in Science Network TV]. Available at: http://science-network.tv/writing-a-publication/. Accessed July 28, 2017.

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