Mining or crafting by hand slowly decreases health. Running decreases health regeneration.

Automate the things and ride in cars! And keep some fish handy.

Update 2.0.0: Updated for use with Factorio 0.16. Even at default settings, this will decrease vanilla regeneration rates (the "in combat" delay is also reduced a bit, but the net result is still that it takes longer to heal). Many options now configurable.

Update
2.0.1/2.0.2: Updated for Factorio 0.17. Fixed crash on loading saves.
2.1.0: Altered default settings and fixed "stay in combat" calculations. Included health alert sounds (were removed from 0.17 vanilla and caused crashes).
2.1.1: Adjusted for prototype type change in 0.17.35, improved auto-cancel crafting.