At several points during the meeting, demonstrators in the audience were heard yelling over board members as they were speaking.
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After a final warning, the board asked officers from the California Highway Patrol to remove the students from the room.
"I hereby request the appropriate police officer make a declaration of unlawful assembly and clear the room," said one of the Board of Regents.
This comes after UC Merced students set up an encampment on Sunday ahead of the three-day board of regents meeting on campus.
Over the last four days, the crowd has grown significantly larger, and so has the tension.
During Tuesday's meeting, the board of regents told protesters their call to divest from companies and institutions that support Israel was a complex issue that would require selling $32 billion of investments.
"I don't think that's a very complex issue. I think that corporate greed might be a complex issue and maybe they might be having to reckon with themselves in some type of way. But personally, I don't think that that is a very complex issue, and I don't think any of the people here think it's a complex issue," said protester Nooruline Irshad.
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Irshad graduated from UC Merced over the weekend but she said she is staying on campus to make her voice heard.
She says that the growing police presence has become a concern for protesters.
A video shared with Action News shows police dining across the street in the early morning hours on Wednesday.
"We weren't seeing police presence in this way, this tangible way in a way that personally felt like intimidation to me," said Irshad.
"Our police presence is consistent with the security measures that other campuses that have held a regents meeting," said Sam Yniguez, director of communications for UC Merced.
Yniguez says the police presence was not to intimidate protesters.
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The college said the student encampment is deemed an unlawful, according to UC Merced policy.
"We don't have Issue with the crowd or the size you know as long as it's peaceful we want people to see this as a reflection of UC Merced being a place where different voices are different opinions can be heard in a safe environment," said Yniguez.
Both UC Merced and the student protesters have been meeting over the last few days.
Student organizers said they plan to meet with school officials on negotiating their demands.
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