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Fear is a very strong stressor, and the highly variable results of handling and transportation studies are likely to be due to different levels of psychological stress. Psychological stress is fear stress. Some examples are restraint, contact with people, or exposure to novelty. In many different animals, stimulation of the amygdala with an implanted electrode triggers a complex pattern of behavior and autonomic responses that resemble fear in humans. Both previous experience and genetic factors affecting temperament will interact in complex ways to determine how fearful an animal may become when it is handled or transported. Cattle trained and habituated to a squeeze chute may have baseline cortisol levels and be behaviorally calm, whereas extensively reared animals may have elevated cortisol levels in the same squeeze chute. The squeeze chute is perceived as neutral and non-threatening to one animal; to another animal, the novelty of it may trigger intense fear. Novelty is a strong stressor when an animal is suddenly confronted with it. To accurately assess an animal's reaction, a combination of behavioral and physiological measurements will provide the best overall measurement of animal discomfort.
Temple Grandin (1997) studied this question.