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High fecal cal protein generally means some kind of inflammation in the body and is usually caused by inflammatory bowel diseases like Crohn's or Ulcerative colitis.
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Yes, you can take these medicines and once the active phase is settled you can discontinue asking your treating doctor.
These lower the inflammatory cells and lessen the inflammation, long-term use can decrease immunity and you can read long-term side effects of prednisone on the web or in medical literature that comes with it.
Yes, that is correct.