A significant problem is the prevention of organic residue build-up in the mechanical heart valves.  Similar build-up occurs in natural blood vessels, in fact being a most often cause for heart stroke: should a large enough particle detach from such plaque, it may move with the blood flow and clog a smaller blood vessel, damaging some tissue by starving them of oxygen. 

Another challenge is to integrate the implanted components with the surrounding body tissues, and to avoid a response from the patient's immune system.
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