Celebration Thread! Biogen is going to the FDA with Aducan.

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J11
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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Above is from page 19 of https://investors.biogen.com/static-fil ... eedc3a8fed

It is quite amazing what happens to the numbers when you have different views.
Here they include the Post-PV4 treatment. The focus has been been on the ITT on the left, what happens with Post-PV4 on the right?
A fairly large shift. Now we have 0.53 in Emerge to -30% reduction relative to placebo and -0.48 in Engage to -27%.
The placebo change is very similar for the Post-PV4 in both. The n's for both are fairly large.
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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Tau 1.GIF
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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https://investors.biogen.com/static-fil ... eedc3a8fed page 14

In this figure what I find intriguing is the possibility that perhaps in future trials they might be able to use imaging to test for the particular tau lesion that each patient has. Each of the patients in the placebo and aducan arms have different patterns of tau deposition. Merely testing with standardized tests probably would not find the specific progression (or not) for each of the patients.
It would be fascinating if one could take for example the bottom patient in the placebo and say well we see that there is quite a built up of tau in the brain image in what appears to be the left (our left) hippocampus let's find a specific cognitive test that can test for that .

I'm not clear whether that is possible or not, though if it were then it could add a great deal of power to the cognitive testing. There are stereotypical patterns of AD progression that possibly could be leveraged by creating highly focused testing items for these specific deficits. Personalized cognitive progression testing!
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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Code 1.GIF
Code 2.GIF
Code 3.GIF
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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I have been meaning to get back to the alpha beta idea mentioned earlier in the thread and now I finally have.
This is the rough code that seems to make sense to me, though it might not be the "official" approach.

What does the above code mean?

First we start off with the placebo x<-AllPlacebo1$V2
Then run through the code in the first chunk (down to fit.params).
This fits the data (shifted over by 5 because gamma distributions have to have x above 0)
for the placebo to gamma distribution. The fit.params gives us the shape and rate for a gamma.
We then generate 275 random variables with the shape and rate of the placebo (take out the 5 we added in and
move around the "1.55" until we find a count = ~60 for the 10,000 runs. What this means is that .6% of the times
our placebo will be as extreme as 1.55. (On the actual first run it was <= 1.55, not >=. For the placebo 1.55 CDRsb is
on the bottom tail.). I am using 0.6% here because I suspect that they might have used a 2 two tailed test. They put half the
alpha on the low extreme and half on the high extreme. Better safe than sorry. (Not entirely sure, though whether
this completely makes sense.)

So, this is great. This is what I understand to be alpha, type 1 error. The FDA does not want to approve drugs that are
not effective; it does not want to make an alpha error. For two-sided alpha of 1.2%, 0.6% is for the bottom tail.

Now, we start at the top and run through the code a second time.
x<-AllHigh1$V2 +5
This time the fit.params match is what is shown in the third chunk of code.
shape = 10.38 and rate =1.58 and >=1.55 is correct as given.

We run through 10,000 iterations and this time the count = ~ 5700.
What does this mean?
What I think this is now is beta.

First we found the rejection region boundary for alpha for 0.6% at 1.55 using the placebo distribution.
This was the alpha that was reported for 302 high dose.

Now we have pivoted to the treatment distribution and with the same rejection boundary found beta.
Here our beta turns out to be ~57%.

This makes more sense than my previous numbers that forced the rejection region to always be at the mean of
the treatment. This would imply that beta would always have to be almost exactly ~50%.

This is only a first run at finding the numbers. One problem is that the gamma distribution doesn't fit the empirical
distribution all that well. With only 2 parameters to work with it can only do so much. Apparently there is a way
to sample from an empirical distribution, though I am unsure how this is done.

What does the above actually mean?
My interpretation is that there is a fairly low chance of risking the type 1 error (approve aducan when you shouldn't).
~1% when only considering the 302 high dose top-line results for CDRsb.

Yet, there is a fairly substantial chance of risking the type 2 error (not approve aducan when you should have-- i.e., you should accept the alternative hypothesis.) ~~~57% (very uncertainly) when considering the 302 high dose. This is what the dementia community should be mostly focused on. I am very unclear whether beta was ever reported in the Briefing Document.

The length used was 251 for AllHigh1 and 209 for AllPlacebo. (There are many different subsets that I have used. I would also like to see the numbers for the 14 dosers.)

I am very glad that I can post code to the thread because when you run R code things before you know it you have no idea what you just did. What I have posted above gives me an archived record of what I did; allowing me to revisit this anytime in the future.

Also good to know that I included R libraries

library(ggplot2)
library(MASS)

Also maybe
library(latticeExtra)
library(lattice)
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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My current understanding of aducan is that it is effective.

The 22% reduction in decline reported from the topline of Emerge is a large understatement of its true effect. When you consider the patients who received maximal high doses, the effect for both Emerge and Engage moves to 30%. As also seen in the Briefing Document when propensity matched placebos are included for comparison the difference expands yet further to ~40%. Considering the influence of even one marginal dose to this difference, it does not seem overly optimistic that the maximal benefit might exceed 50% (relative to placebo).

This is a large benefit and would offer substantial clinical benefit for many of the readers of this thread (and others) who have relatives approaching or actively experiencing symptomatic dementia. I am fully aware of the terrifying aspect of caregiving for someone with progressive cognitive impairment and then profound dementia. Given the evidence in favor of aducan I am unable to comprehend how there could be opposing opinion regarding aducan approval. However, surprisingly, there is: There is a lot of opposing opinion.

For starters, only one (of 11) members of the FDA advisory panel voted in favor of the question of whether Emerge provided convincing evidence of aducan's efficacy. This was notwithstanding a 1.2% p-value topline for high dose for CDRsb, 4.93% for MMSE (admittedly this was under somewhat mysterious circumstances), 0.97% for ADAS-COG, and 0.06% for ADCS-ADL. ADAS-cog is an objective measure of cognitive ability. It was mentioned (somewhere) that there was a concern that it was only subjective measures (which might be more open to bias) that demonstrated aducan effects. In addition, the issues related to ARIA were prospectively known so various measures were included to try to avoid distortions that this could cause.

The smallish size of the treatment effect is related to the population of patients chosen. As has been mentioned on several occasions on this thread, it is surprising how many of the placebo did not progress over 18 months; some even improved. Despite this, the high dose treatment arm of Emerge was still able to achieve a significant result.

The panel's vote on Emerge is not easy to reconcile.

{0.4 CDRsb slowing over 18 months}
"Panelists questioned whether this amount of slowing would be meaningful, especially given the cost and side effects of the treatment. On a voice vote, only one of the 11 panelists found the evidence from EMERGE convincing; eight rejected it, two were uncertain." https://www.alzforum.org/news/research- ... rchers-say

Yet, when you read the aducan comments on the below FDA page, there is a majority negative opinion. Perhaps the future of this type of online regulatory democracy could include more threads similar to the one I have posted to this forum (i.e., this thread). The problem is not so much that I disagree or agree with many of the opinions expressed; it is more that there is insufficient basis to form a quantitative opinion on the comments as given. Evidently, this thread is excessively and monotonously prolix, however, hopefully after all the posts the issues surrounding aducan have been sufficiently explored. (Fortunately, more explication will likely continue.) It would also be helpful to have the url where Biogen provides comprehensive answers to the concerns raised. I am not sure whether my suggestions have always been entirely on track. It continues to be a memorable complaint from the aducan advisory meeting that it was claimed that the clock was talked down without clear enough answers being offered. The planet has been locked down for almost a year now due to COVID; answers that should satisfy the most critical observer should be achievable.

I think it was a big missed opportunity that the APOE 4 forum did not submit a collective statement to the FDA outlining our position. Yet, of course "our position" might be too presumptuous a characterization; I am sure that a range of opinion might be expressed in any such comment. Even still the fundamentally important aspect would be to go through the process of interpreting the research surrounding aducan. From what I can see, the more that this research is actually carefully considered, the more positive one might be about aducan's efficacy.

Also below there is an article that provides yet another assessment of aducan.

https://beta.regulations.gov/document/F ... 24/comment
https://www.karger.com/Article/Pdf/511506
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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During this Yuletide it is an especially fitting to update the story of Jesus.
For whatever reason, Biblical sources have provided no backstory on Jesus's grandmother.
However, recently uncovered archival evidence has discovered that his grandmother, an epsilon 44, was coping with severe Alzheimer's dementia at the time of his birth. So, in some sense the story of the manger can be understood as also describing his grandma's heroic struggle against a neurodegenerative illness. The magic of the season can be reimagined as a celebration of the love and joy that our dementing elders shine out into the world as they help us focus on what is of true meaning to us; namely providing devoted care to those in true need.

Best Wishes at this special time of the year.
Joy, peace and goodwill to all.
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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J11 wrote:...

Best Wishes at this special time of the year.
Joy, peace and goodwill to all.
Thank you J11 for your kind wishes, and for seeking always to shine light into the world through your explication of research. Best wishes for you also for peace, joy and hope during this season of unanswered questions and long nights. .
4/4 and still an optimist!
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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J11 wrote:The magic of the season can be reimagined as a celebration of the love and joy that our dementing elders shine out into the world as they help us focus on what is of true meaning to us; namely providing devoted care to those in true need.

Best Wishes at this special time of the year.
Joy, peace and goodwill to all.
Thank you , J11, for your tireless dedication to this thread and for this post. As someone who found tremendous emotional healing with my mother as her dementia was progressing, I really appreciate your highlighting the love and joy that those with AD can bring into the world. That is important to remember. While I would not in a million years have wished dementia on my mother, I also recognize that without the changes it brought, she and I might not have had the opportunity to reach out to each other on another level from that which had defined our troubled relationship. It was a gift to both of us that we were able to finally show each other the love that had always been there.

Sending best wishes,
Floramaria
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IFM/ Bredesen Training in Reversing Cognitive Decline (March 2017)
ReCODE 2.0 Health Coach with Apollo Health
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Re: Celebration Thread! Biogen is going to the FDA with Aducan.

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NF52 and floramaria thank you for your replies.
This is a time of year that allows all of us to refocus on what should be at the center of our life, though often is not.

This special season provides us the opportunity to speak about the often difficult truths of living with dementing parents. floramaria, speaking about these troubled relationships is so fundamentally important for achieving personal growth and emotional healing. People can spend years in psychotherapy and never get around to honestly speaking to their emotional experiences. It is always the things that we never allow ourselves to say that are so important to say. This is a magical time of year in which people are closest to being able to speak of the unspoken things. No matter what one's opinion of psychotherapy might be, clearly never admitting and bringing the truth into conscious introspection can not be healthy. Families that have coped with dementing illness typically have a great deal of turmoil that needs to be acknowledged.

Even with all this turmoil there is still a great deal of love and caring that develops as the illness progresses. On one of our trips to a medical clinic with our loved one, one of the nurses told me how blessed I was to have dementia in my life. At the time our loved one was in the moderate stage of AD which was by far the most difficult time for caregiving; it was unbelievable. It went all night, throwing bundles of clothes in heaps, throwing clothes out the windows; an overwhelming energy. This carried on for months. I did not feel blessed; I felt completely exhausted.

Yet, the nurse was totally correct. After we weathered this phase, a deep sense of calm emerged. There was state of flow that continued for years. There was no disjointed time segments; life was one single experience. The cacophony of modern life disappeared.

When modern life did intrude it was more to reinforce our lifestyle than to dissuade it. Others in our community who were not blessed with dementia strangely had lives that were surprisingly even more disordered than our own. Marriages collapsed because love was found not to be the optimal strategy to maximize short-term rational self-interests: The irrationality of rationality. The pursuit of material and goals was secondary to long-term personal relationships.

Dementia is largely the opposite. It is the rationality of irrationality. On the surface there does not appear to be any upside to caregiving in dementing illness. A home-care doctor that stopped by was nearly speechless when viewing our home care arrangement. The doctor could hardly believe that a home could be so much like an ICU from what we were told often in professional care environments bed sores never got better; they would go necrotic, cause enormous amounts of pain and then have severe medical implications. For us it was not much of a problem. It only required changing the bandages every few days and then the sores would rapidly heal. the main problem that caused these sores was the g-tube unexpectedly popping open.

The few problems that we had were amply repaid by the unexpected appearance of many gifts: foremost among them was the endless flow -- a deep connection with an eternal time that stretched to the horizon and beyond. It did not feel as if time was segmented into intervals, time felt to be a single non-interrupted unit; we could look forward to tomorrow and tomorrow and when it arrived it was what we had expected, what we planned for, what we were ready for and not something of an awkward mystery-- why should your life be playing an awkward actor trying to understand the mystery of life?

Along with many others in the dementia community we have a substantial backlog of the unspoken (even to ourselves) that could be profitably disclosed as an exercise in mental hygiene. One of the more notable such examples would be our loved ones kleptomania. The NPI scale does not appear to have a kleptomania behavior check box, though this would probably be one we would want to write-in as it was one of the more troubling aspects of dementia care for us. We have a whole room full of glasses and dentures. What are you supposed to do with other people's dentures? They don't fit. It is truly remarkable how unhelpful these items are. Who wants a 5 foot pink bunny anyways? Even more remarkable was that apparently our loved one was arrested, fingerprinted and charged for these indiscretions.

actus reus? mens rea? Was mens? Criminalizing severe mental illness de-legitimizes the criminal justice system. How does criminalizing dementing illness possibly make sense? Own goal. We did the best that we could to return everything that we could, though it was relentless. Admittedly, when this behavior was disclosed to me in confidence with the interpretation that this was some great shame on us, I thought of this in exactly the opposite way. How much sicker could a society be that criminalizes neurodegenerative illness and then offers this up to us as a Scarlet letter? This would probably be a good topic for Alzheimer Associations to formulate a policy position on.
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