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Regardless of the actual amount of sleep gotten daily, the body has an internal clock (the circadian cycle) where the eyes receive sunlight and transmit impulses to the pineal gland in the brain as to when to release hormones. One of these hormones linked to sleep regulation is melatonin, whose effects you are overriding when you are active or awake at night. The "bad" hormone you reference is probably cortisol, also called the "stress hormone." Many studies on late night workers have shown that the cumulative effects over months and years of night shift have a negative effect on overall health and longevity. For this reason it is recommended that night shifts be relegated to short (under six months) durations, especially in adults over 40 years old.

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