In the game mode selection, there is a new option (If you have unlocked it) of "Negative Bombs" mode. This game mode has a different set of levels with some cells which are a lighter shade. They signify that if a bomb is present in that cell, it would count as a negative bomb. The clues give the number of normal positive bombs minus the negative bombs.
Regions now have regular positive circle elements, but now also negative square elements. As usual they compensate for revealed bombs. Regions with negative elements can be used in rules, but they occupy the equivalent of two regions. New regions with negative cells can be made by right clicking. Because now sometimes numbers become negative, negative numbers are available in the numbers box by holding Ctrl.
Good luck everyone and have fun scrambling your brain!