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After the processes of digestion and absorption, large amounts of materials remain undigested. These materials, largely consisting of plant fibres, dead bacteria, etc., are passed into the rectum and are eventually thrown out of the body through the anus. The undigested waste matter is called faeces. The brown colour of the faeces is due to the presence of bile pigments.

If the residue of a meal remains in the body longer than 36-48 hours, the condition is called constipation. In this condition, defecation takes place at prolonged intervals, irregularly or inadequately. Constipation is due to a number of reasons of which the most important are: 
  1. decreased colon motility,
  2. a diet containing too little fluid,
  3. too much absorption of water by the colon resulting in dry faecal matter.
Vomiting is a protective reflex that makes it possible to eject harmful or irritating substances from the stomach. The act of vomiting is coordinated by the vomiting centre, located in the medulla of the brain. Vomiting is generally preceded by increased salivation and nausea.

Diarrhoea is characterised by frequent defecation. The faecal matter usually contains high fluid material. Greater intestinal motility which results in less time for digested food to be absorbed, is an important cause for diarrhoea. The irritation of the intestinal wall by disease causing bacteria also results in increased intestinal motility leading to diarrhoea.

A peptic ulcer is an erosion of the lining of the digestive tract as a result of the action of the enzyme pepsin. Pepsin digestion of the gastric mucosa starts when the acid content of the gastric juice increases. Normally the high concentration of HCl and proteolytic enzymes does not harm the stomach epithelium as a layer of mucus secreted by the goblet cells protects it. The mucus being highly alkaline neutralizes the HCl. However, in some people such protective mechanism is not enough to prevent HCl and enzymes causing damage to the stomach epithelium.

Neural and Hormonal Regulation of Digestive Juices
The digestion of food materials involves the action of various digestive juices secreted by different regions of the alimentary canal and accessory glands. There should be proper coordination and control of these secretions for their proper digestive function. The secretion of digestive juices and enzymes is under the control of the nervous and hormonal systems.

Neural Control
The secretion of saliva from the salivary glands is controlled by the nervous system by way of conditioned reflex. The mere talk, sight or smell of good food makes one's mouth water. This happenes by the stimulation of the vagus nerve. The secretions, in this case, are produced in advance. The presence of food in the digestive tract also serves as a stimulus for the secretion of digestive juices.

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