With regard to the patent question, there are several possible answers depending on the underlying facts. If you...
are using software that is in the public domain prior to patent application it will not generally be protectable under the patent statute. If someone applies for registration before you license or begin using the software, it depends on the source from which you obtained the software, whether the underlying routines that are protected by the patent are contained in your software, etc.
In response to the last question, the short answer is no -- but that answer should not stop enterprises from considering the use of Linux and open source software; as with proprietary software, it's a matter of risk management. If you have any concerns, your IT department should consult with your in-house or outside counsel (assuming, of course, that you are large enough to have an IT department and in-house counsel). Lacking these resources, there are small consulting and law firms that can provide assistance.
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