The protesters allege widespread institutional racism and discrimination at the university and have asked Duke to increase the minimum wage for all campus workers to $15 an hour.
They say the theft happened around 4 a.m. Sunday morning. The banners have been recovered but the flag was still missing as of Sunday afternoon.
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One of the students, junior Carolyn Yao, says was woken up by noises at her tent and then saw "someone in a gray shirt and baseball cap running in the distance."
After that she noticed the banners were gone. She said she found one banner at a bus stop and other in a trash can on the quad.
The students say the pride flag had been put up in response to a prior act of vandalism where earlier in the week a different pride flag had been cut down from a student's dorm window.
They claim these acts of theft and vandalism are part of a recent string of racist and homophobic acts at Duke, including a death threat against a freshman. The threat used a homophobic slur.