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Just looking at the anchor text in your back link profile alone gives clues to why it's hard to rank - http://moz.com/researchtools/ose/anchors?page=1&site=http%3A%2F%2Fwww.mesocare.org%2F - that is, the anchors are mainly commercial keywords that one would try to rank for - this is exactly the site of link building that is not working as much, and will even get you penalized in extreme cases. You have links on such pages as this: http://blogs.creighton.edu/klb89788/2012/08/31/hello-world/ and this http://wsn.eecs.berkeley.edu/?p=56 etc etc - which are not going to help and will likely only hurt the site in rankings. Unfortunately this will take quite a bit of effort and work to overcome. You'll really have to show Google over time (6-12 months at least) some more quality signals - not only links but user metrics etc as well.

Hello Keri. Thank you so much for your reply. I thought I may have been asking too early in the day as I am in New York. Thanks so much your reply and just as you said the index had rolled out later that day and I habe seen the increases I expected. Looking forward to the next update.