Thanks so much for all the replies and prayers. I have been meaning to update. First of all, his rheumatologist has been consulting with a specialist from Duke and one other doctor at a conference he attended in another state. He asked the speaker specifically about my dad's case, and both experts confirmed that the treatment he was doing was the same thing they'd recommend. A couple of weeks ago, when moving to another hospital might have been an option, he refused to go, and I think this the best we could hope for until he is well enough to travel.
A couple of days ago he had an EEG, MRI, lumbar puncture, and several other tests, some of which are cultures and haven't come back yet. They found that the swelling in his brain (encephalitis) is probably due to the same virus that causes shingles. He had shingles a year or so ago, but it had long since cleared up. They also found (with the EEG I think?) that there was brain activity, but it was slow. They told us he was initiating his breaths and that the respirator was just helping him. The rheumatologist says his Wegener's seems to be under control from the three rituxan treatments, and his lungs are clearing up. They put him on IV antivirals and we have been waiting and waiting for him to improve. Then this morning I got a call from my mom that he opened his eyes and looked at her! We are hopeful, but are trying not to get too excited. It will definitely be a long, difficult road to recovery for him and we've been told to expect baby steps. Tonight I am going to watch The Sound of Music TV special with him and my mom. He never would have missed that :-)
Thanks so much for the support and info you all offer here. It makes a huge difference and can be life-saving! I will try to update again soon.
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