In some cases like the word vice, the negative connotation stems from a direct definition of the word(vice means wicked, but another definition is 'a substitute for' so 'vice president'). In other cases, word may be used in a culture to identify a group or individual that is portrayed negatively, thus modifying the inherent definition of the word to better portray how society thinks of the word.
Yes, the context influences meaning, so it's true.
I think it is because personification is the attribution of a personal nature or human characteristics to something nonhuman, or the representation of an abstract quality in human form.
The correct sentence is:
Individuals who study the brain understand more about how we learn and think.
"who study the brain" is a relative clause which begins with the relative pronoun "who". It refers to the subject of the sentence "individulas".
