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All posts for the month March, 2020

Hi, everyone! For the idea, you can skip to the fourth paragraph.

Being bipolar, I usually work in fits and starts- nothing for a while, then all of a sudden a ton of ideas and inspiration come to me and I will have the energy to sit and work on them, and I can actually manage to get quite a lot done. My coworkers and former employers can tell you that I will go through times where I send spates of emails with new ideas, and these sometimes get passed over because, well, a brand new idea is a lot to deal with.

For my environmental studies, I had a couple of ideas in this current spate of productivity: to take some reports I had written a year ago or so and use them (the ideas in them, which are mine) to write methods/review articles describing the analyses I did and using the data I analyzed as an example of how to do it. I personally think the data, which dealt primarily with a tillage experiment, is worth publishing on its own but it would be impossible to make solid claims (too few data points), so I think that I’ll wind up presenting it in the context of being an example data set in a methods paper (on ecological network analysis, and another paper would focus on some more abstract ideas I have for looking at things such as functional redundancy in ecosystems using network data, and probably public datasets).

So that’s good. But I’m most proud of the idea I had today, which evolved over the course of the day as I thought about how to use existing data on the probiotic I studied in 2014, Lactobacillus johnsonii 456. I don’t know what stage clinical trials are at with this probiotic, but as the day progressed, I realized: this idea can be used for ANY CLINICAL TRIAL that is sufficiently advanced to have a large number of patients.

Here is the idea:

1. Clinical trial with lots of people: treatment, no treatment.

2. Take samples or use archived samples to determine if patients were infected with the virus. 

3. You now have four groups: treatment, no treatment, both with and without viral exposure.

4. Statistical analysis to determine if the treatment can reduce the probability of infection and/or reduce the probability of experiencing severe effects of viral infection.

So instead of starting a trial now and hoping that the drugs studied will work, and waiting 12-18 months for a result, we can take a look at everything that’s being studied now which is close to ending. The wide spread of the COVID-19 virus means that a lot of people enrolled in most trials could have been exposed, and it’s not unreasonable to assume that there may be enough to make statistical tests valid, assuming that we can assay patients for exposure to the virus adequately. It may be possible to use epidemiological data and the residence of each patient to determine the probability of when patients were likely to be exposed, if this is required in determining effects. It should be possible to track symptoms, especially for patients requiring hospitalization. And if patients are monitored from now on with this analysis in mind, if they do become ill they can be watched to see what happens.

It’s not ideal, but it is a potentially effective way to leverage a large amount of existing work to rapidly find treatments which can help protect (or alternately, increase risks) from COVID-19. Current efforts to contain the virus are not sustainable- and in the case of the USA, there simply is not enough medical equipment to be able to treat cases adequately. While the government struggles to find a response and states also are doing their best, the research community can step up, and see if their clinical trials can be used to assist in the race to find treatments, or identify additional at-risk groups which may not yet be considered.

[Note: I wrote two pieces, a short hypothesis paper- rejected from biorxiv for being a hypothesis, and rejected from mBio for not having enough supporting information- and a supplementary document with this trial idea plus some noodling where I pointed out the potential of the probiotic strain I studied to interact with genes in the human immune system. This last thing I tried to send to medrxiv and it was also rejected, because it was a proposal and not a research article. I’ve since revised my hypothesis though I haven’t revised the actual document, merely made notes. I lack the expertise required to finish some analysis requested by the mBio reviewers and resubmit, and I’ve been unable to find assistance, so essentially I am giving up. If more time goes by and I can’t find help, I may someday put it up on this website as a downloadable PDF, but it will probably never be taken seriously because of that.

I took out the saga of this process as well as some thoughts on how to use existing samples for studies relating to COVID-19 which, in hindsight, seem optimistic.]