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http://www.runnersworld.com/article/...-0-246,00.html
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Sideaches
The best way to cure a sideache while running--is to try something else for awhile
Many beginners suffer sideaches, or stomach cramps, when they run. This can be because of a number of reasons.
DIET: One cause of sideaches is eating too soon, or too much, before you run. It takes three to four hours to digest a large meal. If you have undigested food--or too much fluid--in your stomach, your stomach muscles may cramp. Some people may be allergic to certain foods, which may cause problems. Adjusting your diet may help.
MUSCLE WEAKNESS: When you begin running, you quickly discover the weakest part of your body. That body part begins to hurt. It may be your legs, your arms or your stomach muscles--causing a sideache. Your body is telling you to slow down. Pay attention, gradually strengthen your stomach muscles, and the sideaches eventually should go away.
MEDICAL CONDITION: A sideache could signal appendicitis, a kidney infection, even a heart problem. We're not trying to be alarmist, but if you continually experience sideaches while running, you may want to get a medical evaluation.
Once you experience a sideache, regardless of its cause, how do you alleviate it? The best way to cure a sideache, while running, is to do something different. Here are some common remedies:
BREATHING: Changing breathing pattern is often the best strategy for curing a sideache. Shift from 2/2 to 3/3 or some other pattern. Try belly breathing: using your stomach muscles instead of your lung muscles. (Pregnant women learn belly breathing by lying on the ground and moving a book placed on their bellies up and down.)
CHANGE OF PACE: Slow down. Speed up. Slowing down may work best, since one of the reasons for the sideache may be that you are pushing too hard. The sideache is a message from the body telling you to slow down. Any change in your rhythm may help relieve the problem.
MASSAGE: Act as your own massage therapist. While continuing to run, massage the aching area. Pinching may help. Swing your arms forward, backwards and in circles. If runners around you think you're crazy, that's all right. Tell them you have a sideache. Everybody gets sideaches.