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. On Rev2 or later boards: there is a resistor that pulling the 8U2/16U2 HWB line to ground, making it easier to put into DFU mode.
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