Getting started with case reports

A case report is the perfect starting point for a resident new to scholarly publishing. It is easy to write, requires little creativity (after all it is just a documentation of a patient that came to meet the doctor) and though has limited impact, has good educational value. More than anything else, it lowers the barrier to scientific writing.

There is a catch though – case reports are the low hanging fruits. Accordingly there is quite a bit of competition there – lot of people want to write, very few publishers want to publish. This has created a vacuum which has been fulfilled by speciality case report journals. These journals publish only case reports and therefore have a much higher acceptance rate – somewhere in the range of 30 to 70 %. The increased demand also causes a situation where publishers may resort to questionable practices. In fact, almost half the journals are found to be dubious.

How to identify the genuine journals?

The trick is to find those case report journals which are PubMed Indexed. Only one PubMed Indexed journal(published by Baishideng group) is known to indulge in questionable practices[Refer to the Excel file linked at the end of the article]. So a case report journal that is PubMed Indexed is highly likely to be genuine. For example, my first publication was a case report in BMJ case reports.  BMJ case reports has a decent acceptance rate, but in order to submit one of the authors or the institution must have subscription. Individual subscription costs around 185 GBP (around Rs.15000), but just one subscription in a department is more than enough. Be sure to check if your institution has subscription – in which case, you can contact the librarian to get the submission access code. BMJ case reports doesn’t have an impact factor as such (many case report only journals don’t.). However you can use the scimagojr 2 year citations per article as a reasonable proxy.

Of course, case reports are also published by journals that publish other stuff like reviews and original articles. However the acceptance rate is likely to be lower in these journals. If you are confident of your material, it is best to try in a general journal first before trying a case reports only journal. When in doubt, ask an expert.

A master list of case reports only journals can be accessed in Excel format here. Sadly I couldn’t get a master list of submission fees – if you have details on that, do let me know. If you found this post useful, please share with your friends.

Further reading

New journals for publishing medical case reports


Aaplot: Easy way to draw annotated scatterplot in Stata

The standard way to draw scatter plot with a linear fit in Stata is quite simple. Even then you will have to use the built in graph editor for polishing it or making it publication ready.

Let me illustrate that with the auto dataset that ships with Stata. We will draw a scatter plot of mpg(miles per gallon) and the price of the cars. We will also draw a line of best fit and a confidence interval.

sysuse auto
twoway scatter mpg price || liftci mpg price

Now this is the unedited resulting graph.


As you can see, it needs labelling of the axis, line equation etc. Its not a lot of work, but still there is a way to make this easier.

Aaplot is a user written ado file, contributed by Nicholas Cox.

Install it like this

ssc install aaplot

Now you can draw the same thing with additional details with a single command.

aaplot mpg price,addplot(lfitci mpg price)


(Unlike R, you don’t need to load the addons separately in Stata! How cool is that :-))


Scientific publishing: Online platforms for writing

The early computers didn’t have a pretty user interface. They were geared towards the nerds and hobbyists – that was until Steve Jobs laid his eyes on the  GUI(Graphical user interface) developed in Palo Alto Research center by Xerox. The rest as they say is history.
Fast forward a few years. A Stanford computer scientist,Donald Knuth developed an entire document preparation system. It was robust and it was immediately lapped up by the Mathematics community : for it was a great way to format equations beautifully. This system was later made a little more friendly by Leslie Lamport and was called \LaTeX
It had many advantages

  • It delinked content and formatting
  • It could be scripted /automated with macros
  • It was just plain text with markup – thus making version control easy
  • It could output to a variety of formats that could be viewed from practically any device
  • It was free and open source

Unfortunately \LaTeX was and still is a little hard to learn. Consequently the life sciences community heavily uses WSIWYG(What you see is what you get) programs like MS Word for scientific writing.

\LaTeXneeded a front end –

  • one that is easy to use
  • does not require any installation (or at least opensource and cross platform)
  • has an easy way to add tables,figures and citations(which are not so easy to do if you use LaTeX and a customized citation style)

LyX was the first step – but it requires a local \LaTeX installation. Then came the likes of Overleaf and ShareLaTeX. They were both online, thus freeing the user from the need to install anything locally. Unfortunately they still very much retain the \LaTeX flavor and are thus not suitable for the average doctor. Then came Authorea – it had a freemium model, it was online, it was easy to use and almost felt like the long battle to develop an unintimidating face for \LaTeX had succeeded.It has a few templates for life science journals, but the operating word here is few.
I had thought that the whole process was complete. You could write papers online, collaboratively with anyone from anywhere and produce camera ready pdfs !
Well, it turns out life isn’t that simple. Enter the publisher. Each publisher has specific formatting guidelines for clarity, uniqueness and for good design. So most life science publishers prefer to receive the manuscript in MS Word format and wouldn’t want to touch your tex files. (There are of course, some exceptions). This formatting of everything as per inhouse style(including citations) keeps the journal unique and is unlikely to be solved anytime soon. As I said before,LaTeX has a nice front end, it could be scripted and automated. So what if, we could have a web app that can help do everything Authorea does and generate a journal specific pdf at the click of a button? It would solve the problem for the authors as well as the publishers!
Typeset  is one such tool. It is online, free (currently in beta), incredibly easy to use( text,tables,images and citations), can be versioned and can generate a pdf as per the journal requirements at the click of a button! I haven’t been this excited about the possibilities of an academic software in a longtime. I will outline some in the next post. For now, feel free to check out Typeset

Here’s a comparison of these web apps

Feature Overleaf Sharelatex Authorea Typeset
Free option
LaTeX usage
Version control ✔ (premium account only)
For those who don’t know LaTeX
Journal Specific Styles ✔ ( only few for medical journals) ✔ (4500+ journals)
Reproducible research(text+data+code)
Social Tools(comments,chat)

Bonus: If you have a Mac and would prefer an installed app with similar functionality, check out Manuscripts app.

Note: Of course, the most popular and straightforward online option is google doc, but I guess you are already quite proficient in its use.

Titulus Insipidus

The first thing we read when we see an academic article is its ‘title’. The attention span of readers has been going down steadily, not because the academic content has somehow taken a downward tumble – but because the other digital content we consume has become more and more catchy. It isn’t uncommon to find people skimming through articles and learning as much as they can from the title. Thus more than anything else, it is the title that should deserve maximum attention while writing an article. Unfortunately this doesn’t always happen.

Take any speciality/general academic journal and go through the titles of articles published in any journal and you are apt to find the symptoms of ‘Titulus Insipidus’ – the malady of bland and boring titles . [checked one item off my bucket list. I always wanted to coin a term ;-)]. One might wonder why a researcher would deliberately choose a boring title when a more interesting title is possible.

Why does this happen?

There are perhaps a few reasons why this might happen

  • Title may not be a conscious choice – the writer defaults to the first idea that strikes him/her. This happens more often than we might think

  • Disciplinary conventions
    Certain disciplines are more rigid in following conventions and the young researcher often learns the tricks of the trade by mimicking the articles in the most popular journal of his field. This encourages conformity and discourages experimenting with stylistic choices.
    The idea that offbeat titles are just a gimmick and a way to sell poor content

  • SEO :Experienced writers are well aware of the need for search engine optimization. This is just a fancy way of saying that your article should be easy to find. As Google’s PageRank algorithm is one of the world’s most closely guarded secrets, any recipe for such search engine optimization is only an educated guess. However in a recent paper, the authors argued that since longer titles and abstract are more search engine friendly and have more ‘hooks’ for the computer, they tend to show up in a search query in the first page or so.Since most people don’t go beyond the first page of search results for their information needs, this creates a situation where writing long and stodgy prose is actually advantageous! This unintentional, but perverse system of discentives might dissuade one from sticking to simple titles.

To give an example, “Aggressive serpentine movement in a controlled aviation environment: A descriptive study” is more likely to be noticed and cited than ‘Snakes on a plane’!. However for regular readers of a journal, the click rates may be higher for the latter.

Assesment of catchiness – learning from dating apps

The essential question is then – how to manage the tradeoff? Should the title be informative or interesting? How does one decide which article is interesting? I chanced upon a recent web app called Papr in R/Shiny by JT Leek. The idea is similar to the dating apps like Tinder. The web app collects information on whether the title is exciting and correct by directly asking the users. A random selection of articles is used. You can even download your likes.By analyzing the characteristics of the likes, one can get an idea of what works and what doesn’t. Sadly this is for bioArxiv not PubMed. (Making one for pubmed will be my personal project for Feb 2017)

Some tips

Disclaimer: Your mileage might vary depending on a lot of factors.

Here are some tips and tricks you can use while titling your next article. I believe these are more important for case reports or small research studies. Titling is neither a science nor an art. It is actually a craft. Hence it can be learnt by anyone who is willing to learn.

  1. Remember that titles signal intent. It can be serious, engaging, challenging or even frivolous. Ask yourself if the title adequately captures your intent.
  2. Get away from your comfort zone – if you have been using a colon in all your published work, get rid of it. Think of a way to say the same thing without a colon. A question, a claim or an unexpected term can be used.
  3. Breach the boundaries of your discipline. Just for the heck of it, visit a hard science journal – mathematics, physics or chemistry. I promise that you won’t regret those two minutes.
  4. Impose a Twitter like character limit on yourself. Don’t use more words than is absolutely necessary.
  5. Take the first title that comes to your mind. Promise yourself that you won’t use it. Actively think of alternatives. If the alternatives all seem to be bad choices, then(and only then) use the original title.
  6. Visit your favorite journal. Scan the page for titles you like. Pause and ponder – why did you like a particular title? What was so interesting about it?
  7. Identify the titles that didn’t interest you in the same journal. Attempt an improvement onf those titles.
  8. Cut yourself some slack – there is sometimes no option but to fall back on the predictable and time-tested approaches. Bide for your time – after all in the larger scheme of things, titles are but, only a small piece of the puzzle. Your academic reputation is far more important and for that no amount of intellectual circus with titling will help. Focus on the science and the good things will follow . Acche din will come soon 😉

Feel free to give your comments and suggestions below.

Additional reading

  1. Kpaka S, Krou-danho N, Lingani S, et al. Relation between online “ hit counts ” and subsequent citations : prospective study of research papers in the BMJ. 2004;318(September):3-4.

2. Weinberger CJ, Evans JA, Allesina S, et al. Ten Simple (Empirical) Rules for Writing Science. PLOS Comput Biol. 2015;11(4):e1004205. doi:10.1371/journal.pcbi.1004205.

3. Letchford A, Preis T, Moat HS. The advantage of simple paper abstracts. J Informetr. 2016;10(1):1-8. doi:10.1016/j.joi.2015.11.001.