Often used by parents to soothe children's minor injuries, conveying tenderness and care. When the little boy bumped his head, his father kissed it better.
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Emotional Relief
The phrase suggests that affection can provide emotional relief, not just physical healing. Her grandmother kissed the stuffed animal better, making her smile again.
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Metaphorical Use
Can be used metaphorically to describe someone's attempt to fix a non-physical problem. He tried to kiss her worries better by assuring her everything would be fine.