Jeff,
First, some facts to help you understand me and the beast.
1) I have a deviated septum on my cluster side. That was caused by an assault in 1996.
2) 3 or 4 times a year since then I will blow a huge hard honker out of the left nasal cavity.
3) I have had numerous head traumas the last of which was also in 1996.
4) I've had allergy issues since very young. First starting with medication allergies beginning age 6, and then added food allergies in 1985, and again in 1989. Added pollens and other airborne pollutants in 1984, and new medication allergies in 1991. The airborne effect both my sinuses and my eyes.
But here is the kicker...well before I was officially DX with Clusters in 2004 or 2005, I can trace back in my medical records my first full on cycle to the spring of 1983.
Part of the roll the hypothalamus plays is in the fact that in Sufferers, the inferior posterior hypothalamus is malformed. Minimally, but the cells in this region are slightly larger and more dense than in a normal hypothalamus.
Science is not perfect, but knowing that this anomaly in the hypothalamus of cluster sufferers exists, is in itself a logical basis to show that the root of the condition lies there.
Now that being said, As you mentioned and can be found most anywhere the hypothalamus is the part of the brain that regulates many bodily functions. Those directly influenced in the Cluster pathogenesis are,
circadian rhythms,
body temperatures,
blood pressures,
and neurotransmitter production and action
If you read up more on this condition you will learn that there is a connection in this condition that is obviously and glaringly seasonal and clockwork.
Also, due to the fact that certain medications are effective we can know that there are certain neurotransmitters, (serotonin the main one) in the mix.
Most of us heat up and sweat like pigs during a hit. Some of us have natural high blood pressure to start with, and some, like myself, have naturally below normal blood pressures.
We know that during a hit, the blood vessels in our brains will swell to 10 or 20 times their normal size. This aggravates the trigeminal nerve, and is why the pain location can be traced along the branches of this nerve.
One of the three branches of this nerve directly effects the sinus cavity, and why many of us feel as if a large knitting needle heated to red hot is being jammed up our nostril, and why the nose runs or gets blocked. The nerves also branch to the upper and lower jaws, causing sever tooth and jaw pain. Do you know the numbers of people who have had their perfectly healthy teeth pulled needlessly because for them, their beast lived in those nerves?
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How, exactly, this process happens is yet to be discovered. But please, understand that there is more at work here than just a gooped up nose.