Square brackets in quotes are usually used to indicate that a minor alteration has been made in order to make it more readable (e.g. to fit into the context that the quote is placed in) but that does not alter the intended meaning of the quote.
In your example, it probably means that the original quote had a capital letter, but has been re-written to fit its place in the middle of a sentence.
Another example would be if I wanted to quote your question. I could write
"[BirdMars] come[s] upon a lot of quotes in academic papers [...]"
to maintain the spirit of your quote while clarifying who the pronoun "I" refers to. The ellipsis in square brackets indicates that this is not the full quote.