The Mega 2560 can be powered via the USB connection or with an external power supply. If more than 500 mA is applied to the USB port, the fuse will automatically break the connection until the short or overload is removed. Although most computers provide their own internal protection, the fuse provides an extra layer of protection. The Mega 2560 has a resettable polyfuse that protects your computer's USB ports from shorts and overcurrent. See this user-contributed tutorial for more information. Or you can use the ISP header with an external programmer (overwriting the DFU bootloader). You can then use Atmel's FLIP software (Windows) or the DFU programmer (Mac OS X and Linux) to load a new firmware.
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