Let me share some of what we've gathered, keeping in mind that we really didn't know what to expect because everything was on the table.
The youngest child to join this phase was five months, and we accepted children through age twelve (although I suspect at least one parent had a 14 year old and just fudged to get in - who am I to judge?). The diagnosis were varied, but included multiple forms of cerebral palsy, developmental delay, various combinations of hyper spastic and hypotonic symptoms, brain bleeds, sensory processing, microcephalic, CVI, seizures, and chromosomal abnormalities. (This list is off the top of my head - everything is in a database format - computer geek, remember?) Although we initially believed the deficiency issues were going to be mainly caused by prematurity, we did accept children with traumatic birth issue related diagnosis, because why not? 
After the sensory processing thing happened, we ended up with an autism subset. They saw the same 4 out 5 relief of sensory issues, but no other benefit was reported by them.
We recorded birth data where available (most had it, but we also had some adopted children where the data was not available - one of the microcephalic children who saw an increase in skull size was FET), including gestational age, birth weight, some basic data from the mother (preemie herself/absorption issues like Crohns), GMAC level, medications being taken, and other supplements being taken. Once they started the protocol we recorded starting weight/height, and quantities of micronutrients taken.
Every two weeks parents reported changes (or lack of) in eight categories: bowels (this was generally one of the first signs of a positive response to the protocol, and usually occurred within ten days - also, this population is known for its chronic constipation issues), appetite (most didn't like to eat, but between days 14-21 began eating as if they were teenage boys), weight/height, strength/tone, cognitive, speech/communication, sensory and energy. We tracked everyone for a minimum of six months to a year.
Keep in mind we didn't know what to expect. One of the "traumatic birth" babies gained weight and started crawling. Another had no change. We couldn't control for diet, and there was no control group - bluntly, the control group is all of the other people who weren't trying this.
The dramatic changes were completely outside the realm of expected. Core strength does NOT improve in two months, with children who had never been able to hold up their own heads doing so - except we had kids who did exactly that. Clonus doesn't ever go away - except it did. Microcephalic children do not see an increase in skull size at age 8 - except they did. And GMAC level does not generally change after age four - except it did A LOT. (One kid told his mom he didn't want to use his walker when going across a snowy parking lot, so the mom said okay, at which point the kid Picked It Up and RAN across the parking lot!) Chronic failure to thrive in 74% of my kids was gone within 90 days, and jokes were made about how the Project didn't cover new clothing or the increase in your grocery bills.
The changes were not normal development based on the diagnosis. Even more surprising, the children continued to see improvement even during these periods of high growth.
Some of it made no sense - the "worse side" seemed to get better first in several children; one girl had a headache and slept for three days, then started using the left side of her body normally. (Her brain hemorrhage was on the right side of her brain.) Measuring in a quantifiable way changes in speech/communication has been giving ME a headache (I have 117 pages of raw data reports on that topic alone!), and cognitive was one we were very skeptical about reporting. (Multiple children were diagnosed ADD/ADHD and were reported as "calmer, better able to focus" which made me wonder if they were really undiagnosed sensory kids.) But the parents were the judges, and since they could back everything up with data from their medical and therapeutic support teams, we recorded it.
When children went off the supplement, some saw regression in strength/tone, and sensory came back within 48 hours. As soon as they went back on, the benefits returned. Several parents began scheduling "breaks" because there seemed to be a "dramatic visible change" when they restarted.
There also seemed to be a personality component - children with siblings or who were "risk takers" reported improvements in a dramatic fashion (see parking lot story). Another child got out of a wheelchair and walked up a flight of stairs at a playground to go down a slide. One of my "risk averse" children crawled across the living room on her own, while one mother called me in shock to explain her son had gotten out of bed and was beating on the television. He was five, and had been carried out of bed his entire life; his mother had to child proof because he was officially mobile after six weeks!
Not every child saw these types of changes. We recorded data about those children, too, because this puzzle is one that has a lot of pieces to it. Pediasure and Ensure do not have the trace minerals necessary for health - were some of the changes because their bodies were finally getting what they needed? Zinc deficiency is associated with a lack of appetite - correcting for that meant they started eating, which meant they started getting more of what they needed in their food supply. Is it "brain repair" or simply building muscles? I don't have all of the answers, and my list of questions just gets longer.
The goal was to generate enough data to see if there was justification for further investigation. I am convinced we did that. If we can't get the formal studies done, I will put it all on the web, and let parents decide for themselves.
In the meantime, I have a bunch of data, and really no one interested in looking at it. I am an anal retentive geek, and these parents were/are awesome.
If you want to see it, I will be happy to share. Parent summary reports through February 2012 are on the web page at the link in my sig line.
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