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The thyroid gland releases thyroid hormones, thyroxine (T4) and triiodothyronine (T3). Some target organs can also convert T4 to T3 intracellularly. The primary function of thyroid hormones is in regulating metabolic rate, but are also important for normal neural development and can also affect reproduction (though the mechanism for this is unknown). TSH, or thyroid stimulating hormone, is produced in the pituitary, and is under the regulation of thyroid releasing hormone (TRH) produced by the hypothalamus. TSH tells the thyroid to produce T3 and T4. TRH tells the pituitary to produce TSH, and T3 and T4 (mostly T4 crosses the blood-brain barrier) signals the hypothalamus to not produce quite so much TRH (negative feedback in simple terms).
The parathyroid glands are small glands located on the thyroid gland. They produce parathyroid hormone and calcitonin. One of the best known functions of the parathyroids is in calcium regulation.
Usually lean muscle mass refers to the mass of skeletal muscle excluding fat...at least as far as I know. I don't know if the term is used differently in other contexts.
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