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The ability to alter one’s emotional responses is central to overall well-being and to effectively meeting the demands of life. One of the chief symptoms of events such as trauma, that overwhelm our capacities to successfully handle and adapt to them, is a shift in our internal baseline reference such that there ensues a repetitive activation of the traumatic event. This can result in high vigilance and over-sensitivity to environmental signals which are reflected in inappropriate emotional responses and autonomic nervous system dynamics. In this article we discuss the perspective that one’s ability to self-regulate the quality of feeling and emotion of one’s moment-to-moment experience is intimately tied to our physiology, and the reciprocal interactions among physiological, cognitive, and emotional systems. These interactions form the basis of information processing networks in which communication between systems occurs through the generation and transmission of rhythms and patterns of activity. Our discussion emphasizes the communication pathways between the heart and brain, as well as how these are related to cognitive and emotional function and self-regulatory capacity. We discuss the hypothesis that selfinduced positive emotions increase the coherence in bodily processes, which is reflected in the pattern of the heart’s rhythm.This shift in the heart rhythm in turn plays an important role in facilitating higher cognitive functions, creating emotional stability and facilitating states of calm. Over time, this establishes a new inner-baseline reference, a type of implicit memory that organizes perception, feelings, and behavior. Without establishing a new baseline reference, people are at risk of getting "stuck" in familiar, yet unhealthy emotional and behavioral patterns and living their lives through the automatic filters of past familiar or traumatic experience.