Monday, August 24, 2015

How I Read a Scientific Paper

"A research problem is not solved by apparatus; it is solved in a man's head." Charles F. Kettering

I'm using a case report from Dr. Li as an example, because it's openly available on-line. The analysis is slightly different than it would be for other research papers, because it is a case report. Instead of asking a question and doing an experiment, they are retrospectively reporting on patients. Where possible, I've included what I would do differently with a different type of study.

Print it

You may not want to print it, but I do recommend having on a device you can take notes on. Highlight and look up all the words you don't know. This may be a lot. That's okay. You can't understand the paper without the work.

Identify the Authors

In this case, I was already familiar, so there was no need. But, if you are not, find out where the authors are from and, for that matter, what journal is publishing the paper. Not all sources are equally valid. Reading a scientific paper can be a commitment. Make sure you are reading something worth your time. 

Skip the Abstract

Often, all I have access to is the abstract. When possible, try to leave the abstract to the end so you don't become biased.


This paper doesn't have one. If it did, read and decide, 'what is the question being asked.' Also, ask yourself, "does there seem to be an agenda here?'

My summary of the case report: 

Although the case report doesn't have an introduction, there is still an implied question: "Does TCM work for FSFA (frequent, severe food induced anaphylaxis) patients?" I do think there is something of an agenda. By design with case reports, supportive cases will be selected (this is the purpose of a case report).

Summarize briefly the background

My summary of the case report: 

Treatments are needed for those with FSFA (severe food-induced anaphylaxis) as avoidance is not working. TCM has been studied for treating food allergies, both in mice and in Phase I clinical trials. This study looks at the success of the treatment of three children with FSFA.

Summarize the Approach

My summary of the case report: 

The investigators will present data showing that TCM helped three FSFA patients.

Read the Methods 

Take your time with this, so you truly understand what the researchers are doing. I find a mind map helpful at this point.

My summary of the case report:

If you click on the mind map, it will be larger and easier to read.

Case Presentation (usually the results section)

Write a paragraph or two to explain the results. A lot of information is buried in the charts and graphs. It can be difficult to understand. Again, wrestle with it a bit because the charts and graphs are the visual summary of all the words.

My summary of the case report (you can see these are notes and largely informal):

Case 1:

13 yo milk allergic patient who had >100 reactions in the 2 years before starting TCM, 50 of which required epinephrine. She had frequent and severe reactions, from inhalation, contact, and trace ingestion, impacting her QOL. She used all 4 TCM remedies described, as well as acupuncture and Fructus Arctii Lappae. She has 16 reported allergic reactions in year 1, 6 requiring epinephrine. She had 4 reported reactions in year 2, 1 requiring epinephrine. In the first 6 months of her 3rd year, she has had no reactions. 

Case 2:

16 yo tree nut allergic patient, diagnosed at 13 yo, who had 30 severe reactions in the 2 years before starting TCM (requiring 34 epinephrine doses). She reacted from contact, inhalation, and trace ingestion. QOL so impacted she developed anxiety/depression. She followed the same protocol as patient 1 (not clear to me: also Fructus Arctii Lappae? acupuncture/acupressure?). She had only 2 mild allergic reactions in year one and passed a tree nut challenge at the end of the year. Treatment was discontinued. E-mail communication continued for 6 more months and patient 2 was able to continue eating tree nuts.

Case 3:

9 yo peanut/tree nut allergic patient, diagnosed at 7 yo, who developed more food allergies after diagnosis. He had approximately 400 reactions in the 2 years before starting TCM, 5 of which required epinephrine. He reacted from inhalation, contact, and trace ingestion. His QOL was impacted; he had chronic stomach pains, headaches, and a sleep disorder. He received the same herbs as Patients 1 & 2, but in decreased amounts due to his age. He also had monthly acupuncture. Patient 3 started in June 2013, so there is only 7 months of data. In the first 7 months, he had 13 allergic reactions, 1 of which required epinephrine. His stomach discomfort, headaches, and sleep disorder resolved.

A summary of the results section would look much different if this was not a case study. Here are some things to look for: how big is the study? do I understand the statistics, graphs, and lingo (do you know what a p value is, or the purpose of an error bar? There are certainly more examples. These are results I found simply by googling and you can understand the text more with a basic understanding of the numbers behind it). Do the researchers answer the question they set out to answer?


What does the researcher think their paper shows? Do you agree? Do they find fault with their study? Do you? What is the next step they propose? Do you agree?

My summary of the case report:

What the researcher thinks: These three cases represent three cases of extremely severe food allergies. The food allergies were improved using TCM. The compliance, based on the self-reporting, of these three cases to the protocol was excellent in contrast to a previous, broader study.

Faults in they find: # of cases, relying on memory and knowledge of parents for reporting.

Next Step they propose: clinical studies, ramdomized trials, as well as testing the individual treatments to see if each of the 3 were required.

My thoughts: I would additionally like to see longer term studies. Having a reporting system would minimize reporting errors.

Return to the Abstract

Now, return to the abstract. Does is match with what is written in the paper?

My summary of the case report:

Yes, it matches

Rabbit Trails

Were there any papers cited in the article that you wanted to follow up with?

My summary of the case report:

I was particularly interested in this statement: "In, addition, acupuncture has been reported to reduce wheal size following allergen skin tests and to reduce basophil activation in individuals with atopic dermatitis [24,25]."

Secondly, I wanted to follow up on this: "A recent large cohort study reported that although 80.7% of food allergy reactions were triggered by ingestion, 12.9% were triggered by skin contact, and 1.2% by inhalation [6]."

And finally, I want to look into a couple papers on MCAD: "Both primary and idopathic MCAD usually have no objective evidence of food specific IgE allergy by ImmunoCAP® and percutaneous testing, which distinguishes them from IgE-mediated hypersensitivity reactions, a form of secondary MCAD [36, 37]."

So, this one paper leads to five more to look up.

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