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.

Introduction

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?

Discussion

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.

One Month Post-Camp

What are the long term expected outcomes expected from TCM camp?

I had this excellent question posed to me shortly after I posted our experience, and the truth was, other than giving Dr. Li a better sense of James and his condition (in many ways, huge), I wasn't sure what, if any, the long term physical outcomes would be. We are only a month out, but I feel confident enough to give an update.

Hives

He simply hasn't had any. His last set of hives was at my mom's right before we went to see Dr. Li and, for a month, he has been hive free. This may seem like a small milestone but, considering he had his first hives at three years old, and now at 13, he has never been hive free for an entire month unless specifically medicated. After the first three years, most of his hive episodes were mild and self-resolving, but relentless. Once or twice a year, he would have head to toe hives that took a week to a month to resolve, with varying degrees of medications.

Our last day with Dr. Li, we told her, a bit shocked, that James hadn't had hives for the entire week. Dr. Li suggested that, based on other patients, this might be the starting point for being hive free for a month.

"Well," I said, "I'll take it a week at a time. Actually, I'll take it a day at a time."

That we are here, at the end of the month, with no hives, is astounding to me.

Sleep

Acupuncture made James tired and more calm, so sleep was not a problem in New York. Usually, he takes a melatonin at night to help him sleep. I had made it a goal this summer to eliminate any melatonin, slowly over the summer. We realized returning from New York, that he had not taken any melatonin while we were there. So, taking advantage of a two week break, an established sleep pattern, and the time change, we continued not giving it to him.

This has been a moderate success. He has had some days he has taken melatonin; he couldn't get to sleep as he's gotten used to the time difference. This has happened maybe once a week. He's had other days he's stayed up later than I would like, however, that was the case with melatonin. 

He has used melatonin for years, so being able to sleep regularly and without drama is huge progress.

(Not) Practically Perfect in Every Way

Any label making mistake could result in a life threatening reaction and I made not one, but two, last month alone. James is fine. My high rate of failure is unusual for me, but speaks to the heart of difficult for a lot of food allergic people.

I'm a human

Humans make mistakes. In a situation where a mistake can be life threatening, being imperfect leads to guilt. But, I'm still human.

Labeling sucks

1. According to FALCPA (Food Allergy Labeling and Consumer Protection Act), any food that contains the top eight allergens (tree nuts, peanuts, wheat, soy, fish, shellfish, milk, and eggs) must be clearly labeled as such, even in flavors, colors, spices. 

One of the labels I misread contained soy, completely my fault, and here's how: James can eat soy lecithin and soybean oil. You will find this in nearly every packaged food you buy. Because we were traveling, we bought him cookies we would not normally buy. I saw "contains soy" at the bottom, I scanned the label and saw the lecithin, and completely missed "soy flour" in the list. This was my fault completely for being complacent.

2. However, did you know that labels are not required to list if they item may have come into contact (ie "may contain") a top eight allergen? I became aware of this only a year after James had been diagnosed when he started having reactions to foods that were not labeled with cross contact warnings. At that point, I started contacting manufacturers to find out their labeling and cross contact policies.

3. Meat, poultry and eggs are covered by the USDA not FALCPA (not something I've had an issue with). There are no requirements covering alcohol (again, not something I've had a problem with). We have known a couple of people who had to avoid wheat in alcohol and it can be trickier than you might first think.

4. If you have an allergy outside of the top eight, you are on your own. This is a pdf of the labeling laws. If an ingredient is considered a spice or a flavor, it does not have to be listed. If it is present in incidental amount, it does not have to be listed. However, the FDA does not define what incidental amounts means.

You can follow (and support) efforts to get sesame listed on labels as another allergen here on Oh Ma Deehness! 

Complacency

Here we come to the final mistake I made. James has not had a major reaction for just over a year. He has barely had any minor reactions. And so, I have apparently relaxed my guard. Someone posted on Facebook that a vanilla ice cream was made separate from his allergens and, without doing my own research, I bought it. James complained he felt stuffy after eating it and he always felt stuffy after eating it. All I had to do was turn over the container to see that it had a may contain warning with all his allergens.

Teens and young adults are at the highest risk of fatal food induced anaphylaxis. I think part of this come from complacency. Teens and young adults are often diagnosed after a reaction in early childhood. Without a recent reaction, they may be less vigilant than someone recovering from a more recent reaction. I am grateful that I have been reminded about not being complacent with only a minor reaction.

   

Protocol Update

James's protocol has changed practical every month since October. Some months, the changes were minor, increasing dosages, adding one herb. Some months, much more significant. My most complete description of his protocol was in April with and update in June. At that point, I thought his protocol had stabilized somewhat because, although his protocol had changed a lot since his April update, there were no changes from May to June, only the second time since he had begun he had no changes at all. Little did I know that our visit in July would radically change his herbs once again.

To backtrack a little, he had a Prostaglandin D2 test, requested by Dr. Li, in June. The results were normal. Dr. Li was surprised. She was actually so certain that they would not be that when I said we had the test done, she completed my sentence by saying, "and the results were high." She then asked about a string of other tests, which we hadn't had done (she hadn't asked for them). And continued as if he had Mast Cell Activation Disorder. And, I think this is where we will stand. He will have no official diagnosis and if he stays reasonably stable (at this point, he is. He has improved considerably both under her care and since being diagnosed at all and cleaning his diet), I will not pursue further testing. If at some point his health slips, I know the direction to push in.

Current Protocol:

Put on two times a day, after bath and after shower. He is working up to complete coverage after bath, starting with just his legs. Right now, we use about six jars a month. The cream is IgE lowering, as can be seen in this abstract.          


Huang Lian and Niu Bang Zi

Both are bath herbs and he is working up to his full dose of two teaspoons of Huang Liang and two packets of Niu Bang Zi. He does this bath once a day.

He takes ten Mei Huang 4 twice a day. This is half the dose he was taking previously. Mei Huang 4 has some (not all) of the components of FAFH-2. 

He takes five Mu Lian tea two times a day.

He takes five Good Mood tea twice a day and this perhaps has been the most stable part of his protocol.

He takes six  Shi Zhen Tea 1A two times a day.

Finally, he takes six Shu Chuan Tea two times a day. This was the one I was happiest to add, as I know it is used, in part, to help with environmental allergies.

With additions and subtractions, our cost stayed steady this month at just over $1000.