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This would be called when a batsman is running two or more, but fails to make his ground and puts his bat in short at one of the turns.
Knocking a run off the score is signalled by touching one shoulder with the hand of the same arm.
We also have a penalty clause now for a batsman who runs deliberately short.
You may well ask why a batsman would want to do that, but he may well want to keep the strike.
If a good batsman is in and wants to protect a 'rabbit' at the other end, he might run two with one short in order to retain the strike, knowing that only one would be added to the score.
If he does that now, we can penalise him and no runs would count.
It's cheating really, but it very rarely happens.
I can't imagine any batsman giving that serious consideration, though of course it can happen by accident.