Systemic Brain Function of Human Physiology
Neural top–down control of physiology concerns the direct regulation by the brain of physiological functions (in addition to smooth muscle and glandular ones). Cellular functions include the immune system’s production of T-lymphocytes and antibodies, and nonimmune related homeostatic functions such as liver gluconeogenesis, sodium reabsorption, osmoregulation, and brown adipose tissue nonshivering thermogenesis. This regulation occurs through the sympathetic and parasympathetic system (the autonomic nervous system), and their direct innervation of body organs and tissues that starts in the brainstem. There is also a noninnervation hormonal control through the hypothalamus and pituitary (HPA). These lower brain areas are under control of cerebral cortex ones. Such cortical regulation differs between its left and right sides. Pavlovian conditioning shows that brain control over basic cell level physiological function can be learned.
Higher brain.
Cerebral cortex.
Sympathetic and parasympathetic nervous systems and the hypothalamus are regulated by the higher brain. Through them, the higher cerebral cortex areas can control the immune system, and the body’s homeostatic and stress physiology. Areas doing this include the insular cortex, the orbital, and the medial prefrontal cortices. These cerebral areas also control smooth muscle and glandular physiological processes through the sympathetic and parasympathetic nervous system including blood circulation, urogenital, gastrointestinal functions, pancreatic gut secretions, respiration, coughing, vomiting, piloerection, pupil dilation, lacrimation and salivation.
Lateralization.
The sympathetic nervous system is predominantly controlled by the right side of the brain (focused upon the insular cortex), while the left side predominantly controls the parasympathetic nervous system. The cerebral cortex in rodents shows lateral specialization in its regulation of immunity with immunosuppression being controlled by the right hemisphere, and immunopotention by the left one. Humans show similar lateral specialized control of the immune system from the evidence of strokes, surgery to control epilepsy, and the application of TMS.
Brainstem.
The higher brain top down control of physiology is mediated by the sympathetic and parasympathetic nervous systems in the brainstem, and the hypothalamus. The sympathetic nervous system arises in brainstem nuclei that project down into intermediolateral columns of thoracolumbar spinal cord neurons in spinal segments T1–L2. The parasympathetic nervous system in the motor nuclei of cranial nerves III, VII, IX, (control over the pupil and salivary glands) and X (vagus –many functions including immunity) and sacral spinal segments (gastrointestinal and urogenital systems). Another control occurs through top down control by the medial areas of the prefrontal cortex. upon the hypothalamus which has a nonnerve control of the body through hormonal secretions of the pituitary.
Immunity.
The brain controls immunity both indirectly through HPA glucocorticoid secretions from the pituitary, and by various direct innervations.
Metabolism.
The liver receives both sympathetic and parasympathetic nervous system innervation. 
Conditioning.
The brains of animals can anticipatorily learn to control cell level physiology such as immunity through Pavlovian conditioning. In this conditioning, a neutral stimulus saccharin is paired in a drink with an agent, cyclophosphamide, that produces an unconditioned response (immunosuppression). After learning this pairing, the taste of saccharin by itself through neural top down control created immunosuppression, as a new conditioned response. This work was originally done on rats, however, the same conditioning can also occur in humans. The conditioned response happens in the brain with the ventromedial nucleus of the hypothalamus providing the output pathway to the immune system, the amygdala, the input of visceral information, and the insular cortex acquires and creates the conditioned response. 
The production of different components of the immune system can be controlled as conditioned responses: 
Nonimmune functions can also be conditioned:
References.
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