Academia

Solving the attribution problem in research

Imagine you have a name like me -Karthik. This is quite common in Tamilnadu and perhaps even in South India. Luckily since we don’t use surnames and rather father’s name as the last name in our state, each name is more likely to be unique. (Unless you have a family history of common names 😀). If I had been in the North and have a surname like Aggarwal or Gupta, it becomes signinficantly more difficulty to identify me as a unique individual even after knowing both first name and last name. In normal circumstances,this wouldn’t be a problem. However when you start publishing, this causes unwanted issues. In database terms, one way to uniquely identify an observation is to use composite fields -the combination of two fields,such as first name and last name. The strength of the composite field depends on the uniqueness of the combination. As I said before, this first name last name combo doesn’t work well in places where the surname is very common. There is perhaps a north south difference even in this.

Why is this a problem?

For individual faculty/researcher

You may have to use your name with title of publication or affiliation to retrieve your publications. This is cumbersome and can lead to under or over counting.

For the institute/ university

It is very hard to improve something we can’t measure. So an institute might want to track the research productivity of its faculty and researchers. One way is to have an aggregate of publications at the level of institute,department and individual. This would be automatically updated and a report can be produced quarterly. This helps us visualise the trends in publication and see when and where we need to buckle up and improve.
All of this requires identifying the publications and correctly attributing them to the respective authors. If there is a problem or error in indetification or attribution, then the whole exercise will be a waste of time.
A software called Researgence uses an approach of searching for all possible combinations of the relevant fields. This isn’t free, but can be used by universities and institutes to track their research output. As you can imagine this is computationally intensive and needs manual verification.
So we need some way to uniquely identify individuals and their contributions.
How can we simplify this process?
By following the same method that is used to uniquely identify inviduals – by assigning a unique id( for example a number or alphanumeric code) to every researcher. That will solve the problem of attribution.
Two services are available which help in this regard. If you are an academic, go over to both of these and sign up. Both are free to use.

  1. ResearcherID
  2. ORCID

From your next publication, you can let the journal known your ResearcherID or ORCID during submission itself. And it won’t matter how common your name is.

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Insanely simple data collection

Problem: You want to collect data quickly using your mobile phone, but you have neither the resources nor the expertise to design a solution from scratch
Solution: EpiCollect

EpiCollect is a free data collection app developed at the Imperial College of London. In my opinion, it is the simplest way to collect data on a mobile, without writing a single line of code. It is so simple that you can make a fully functional data collection form in under 3 minutes! It even allows you to take the patient’s photo or read a bar code.

epicollect

How to make a simple data collection form?

The steps are

  1. Go to EpiCollect website
  2. Login with your Google account
  3. Create a project
  4. Make a web form using the drag and drop form builder
  5. Set the access to your project to be private and visibility to be “visible”
  6. Download EpiCollect app to your phone
  7. Login and search for your project
  8. Start entering data
  9. Export to CSV(or JSON if you want) [ you can also view it on the web]

What is so exciting about EpiCollect?

  1. It is free for everyone – unlike REDCap you don’t need an institutional email id
  2. It allows flawless data collection using a mobile app – even offline
  3. It allows some special fields for data collection – like photos,audio,video, barcode – useful for qualitative research as well
  4. It allows geotagging – useful for field research
  5. It allows advanced data collection – data validation(even allowing regex – regular expressions),branching and jumps
  6. You can add multiple users to your project – for example, a multi-department registry

I want to know more. What can I do?

Go to the EpiCollect website and you will have all the information you need. I can guarantee that you will find the process very easy – even if you are a luddite. Just give it a spin.(Be sure to use the latest version-EpiCollect 5).

Note: You can do some other advanced stuff with this. For example, MicroReact (which uses EpiCollect allows researchers to track epidemics in real time)

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

Online workflow for writing articles

It has become increasingly common for people to collaborate on writing projects. The tools that enable such collaboration have improved over the years too and currently allow for a completely online workflow. Unfortunately many residents and early career researchers don’t take advantage of the recent developments. In this post, I will outline a completely online workflow for writing articles
This way, you could work with any number of people on the same project and all of you could have access to the same digital library from which you can cite. You might wonder that the functionality of team library has been available for quite some now in popular reference management software like Zotero. However , without going through a few hoops, you can’t get Zotero to work seamlessly with Google docs.
Of late, I am increasingly using Google docs for my document preparation needs. Sure it isn’t MS Word, but few people need the full power of MS Word for their routine documents. The ‘portability’ of a Google docs document is particularly attractive to me since I have computers running different operating systems.
Here’s my completely online workflow. Every component of the workflow is free.(as in free beer).

workflow

The advantages of this online workflow includes

  • No need to install any software
  • You always get the latest and greatest version
  • OS/device independent
  • Collaboration is easy and seamless

The F1000 workspace also has a desktop client and  and you can start working even if you already have a pdf collection. It also has  a word add in, if you prefer to write in MS Word.Try it out for your next article. You will be pleasantly surprised.

5 Rupees medicines and diabetes

 

Story time.
Once upon a time, there lived a conman. He decided to make some quick buck. He sold 1000 lottery tickets, each at a price of  $ 5. The bumper prize was $1000. So you could buy a ticket for 5 and if you are lucky , get $1000. He marketed it, saying if you lost, you just lost 5 $. But think of what you will get if you win – $1000. 200 times your initial investment. Or an insane profit of close to 20000%. There was  a mad rush to buy the lottery. The numbers on the ticket were 8 digits long and were alphanumeric. It was a clever ploy. Had he numbered the tickets sequentially from 1 to 1000, people would easily remember that. His alphanumeric system precluded that possibility. A few days later, the results were released. Photos were flashed of the winner getting a cheque.Many who had bought the tickets were disappointed. But they went about their lives as usual. After all, the loss was tiny. One of the guys who lost it was a little suspicious. No one he knew had won the prize. He decided to dig deeper. When he confronted the conman with questions, he was told to prove his theory in court ( a legal battle that would ruin him financially) or take his $5 as refund. The poor guy got his $ 5, while the conman made  $ 4995. No one actually won the lottery.

Recently I was asked by a patient about the  effectiveness and side effects of two drugs  called BGR -34 and IME-9. I must admit I hadn’t heard of those drugs.As an allopathic doctor and an endocrinologist, the name sounded odd to me. Such names are reminiscent of  candidate molecules being tested. Nevertheless I decided to dig deeper and find out more.

BGR -34 is an ayurvedic medicine developed jointly by National Botanical Research Institute (NBRI) and Central Institute for Medicinal and Aromatic Plant (CIMAP) — both funded by government. BGR 34 stands for Blood Glucose Regulator with 34 active phyto ingredients. The NBRI website unfortunately doesn’t give much details. The drug is touted as having 67 % ‘success rate’ based on animal studies. No human data are available. The senior principal scientist AK Rawat has said, “The drug has extracts from four plants mentioned in Ayurveda and that makes it safe”. I have no idea how that will make a drug safe ! Tell me if you do.

IME 9 stands for Insulin Management Expert. It’s  developed by another government body called CCRAS (Central Council for Research in Ayurvedic Sciences). This one doesn’t have much information listed either.
I decided to check for any publications on BGR 34 and IME 9. Unfortunately I coudn’t find one. Next I proceeded to the AIMIL pharmaceuticals page( the company that is licensed for manufacturing and marketing this drug). When I tried to see the products page, it told me helpfully that I was not authorized to view that page and that I should login! Why should I login to view a company’s drug landing page? I ve never had to ‘login’ to see the details of any drug in the past!

aimil

Even more brazenly, the privately owned entity has used DRDO logo in its website to give itself an ‘official’ veneer. In an event attended by Dr Man Mohan Singh and JP Nadda, the company has also been awarded the AYUSH company of the year!

aimil2

So I turned to the mother of all search engines, Google for help. There were a few blog posts. One of them had lamented that the drug had actually increased the blood glucose in his mother ! Now the ridiculousness of checking blog posts for evidence of efficacy is an injury. To watch youtube videos on the same topic is insult to that injury. Nevertheless, I did that too. The comments on the YouTube videos were mostly negative[There are tools to make formal ‘Sentiment Analysis’, though I haven’t done here]. Yet one common thread was the feeling that native medicines were side effect free. How many more years will it take for people to understand that there is no such thing as a drug without side effects? (Paracelsus said this thousands of years back)

All drugs are poisons. Only dose makes the difference.

                                                                   – Paracelsus

Curiously these drugs are marketed as 5 rupee medicines for diabetes. Metformin and sulphonylureas, the two most commonly used diabetes medications with a huge evidence base, cost much less than 5 rupees. Yet no one had ever marketed them as 5 rupee wonder drugs! There’s  even a Facebook page for this drug with a rating of 4.5 ! Ever seen Facebook pages for drugs before? Me neither. It is available in Amazon, Ebay and Snapdeal, not to mention some less well known online retailers.
Just like we can’t accept anecdotal evidence for the efficacy as valid, we can’t accept anecdotal evidence for the lack of efficacy as valid too. As much as I would hate it, I was forced to say that this drug’s efficacy was ‘unknown’.More importantly the safety was questionable too.
We have no data at all.So who is tasked with regulating this market? Why is our tax money used to fund such projects incompletely? What prevents them from testing the drugs? How are they made to trend in pill selling apps like 1 mg? Why are they marketed as government approved drugs? Why are these drugs marketed to patients directly?Too many questions , too few answers.
At the end of the day, diabetes is as much a disease of behaviour as it is of beta cells. The lure of a cheap drug without side effects with no need for any pesky life style changes , becomes irresistible to the common man. Thus clever marketing always works (just like it works for pharma on doctors). Direct to consumer marketing must be banned, regardless of the system of medicine practiced. For the simple reason that the patient isn’t qualified to make an informed choice. Otherwise we will always have the lottery tickets and dubious drugs.

Science shouldn’t be sacrificed at the altar of business.

Further reading
http://https://www.ayurtimes.com/bgr-34-for-diabetes/

www.aimilpharmaceuticals.com

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
Online
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.

Virtual Journal Club – a first experience

The journal club is one of the most rewarding experiences of postgraduate training. Almost every department has a journal club, in which the interesting and important articles are discussed. The scope of this discussion though is limited to the department. For instance, if a paper is presented in the Medicine department of a college, only those in Dept of Medicine of that college benefit.

For a long time, there was no way to improve the “scope” of any presentations. With the advent of web, though this has changed dramatically. It is possible today to have a presentation that can be done across the country via the web. This results in greater participation and a cross pollination of ideas.

Several portals can be thought of

Portal Pros Cons
WhatsApp Easy to use Difficult to search
Does not approximate a real presentation
Difficult to index and catalogue
Screencast Approximates a “real” presentation
Allows people from different timezones to contribute to discussion
Technical complexity Time consuming Doesn’t allow direct interaction
Webinar Closest to a real presentation Technical complexity
May require additional person
Forum Content can be indexed and catalogued
Allows people from different timezones to contribute More permanent
Access control
Technically most complex
Hosting and managing expenses
Telemedicine Official
Best twoway interactivity
Requires institutional setup
Expensive
Facebook Group Same as WhatsApp, but no limit on number of members Same as WhatsApp

The idea of a journal club for early career Endocrinologists was mooted in the FRENDOS WhatsApp group. Since the idea was fairly new, we wanted to try out a few different approaches before settling on one. Indeed I am not even sure if we should settle on one – as variety adds spice.

So I made a YouTube presentation yesterday – the first virtual journal club in Indian Endocrine setting. The article is from JAMA. You can access the original article here.

You can access the original journal club here. The original video had weak audio. So I have enhanced the volume and the upgraded link can be accessed by clicking the image below.

presentation

The presentation can be downloaded from here.

We had more than a hundred attendees – a number that is virtually impossible in traditional journal club settings. Indeed this will work for any presentation. Eventually we ended up using the audio-video platform of YouTube and the ease of use of WhatsApp to make the first virtual journal club.

It turns out, making a screencast is a rather enjoyable process. It does require a presentation, but most residents already make one anyway. The technical bottleneck is the familiarity with software for making a screencast and a decent quality audio input (a 30$ headphone is more than enough).

The following are the minimum requirements

  1. Presentation – made in LaTeX beamer. Of course it can be made in PowerPoint or any tool of your choice
  2. A headphone / mic – to record audio
  3. Screen recording software – Camtasia Studio for Windows is a premium all in one package for this. If you re on linux, you can get the same functionality by installing Vokoscreen or SimpleScreenRecorder. Post recording , the video can be edited with Pitivi(if you prefer GNOME desktop environment like me) or KDenLive(if you use KDE as the desktop environment)
  4. Audio Editing – Audacity, an open source software for enhancing audio. This is extremely useful for removing noise and amplifying the voice.
  5. YouTube account – for uploading the video. You can use any of the other video uploading sites as well.

As you can see, the whole toolchain can be completely free and opensource. A screencast can thus be produced and shared at absolutely zero cost. We did the discussions after watching the video on WhatsApp. Since a YouTube link can be shared with anyone, the potential reach can be theoretically very high.

We will be experimenting with other portals soon and hopefully improve next time. If you feel the paper /presentation is useful, please share with your PGs,juniors or friends.