Ito, who confirmed his resignation to The Post, notified members of the Media Lab of his departure in an email just after 3 p.m. Saturday.

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“I want to apologize again for my errors in judgment,” he wrote in the email provided to The Washington Post by a graduate student at the lab. “I have spent the last days and weeks listening to all of you and I want to thank you again for sharing your insights and perspectives with me, and allowing me [to] begin to try to make amends. After giving the matter a great deal of thought, I have chosen to resign as Director of the Media Lab and as a Professor and employee of the Institute, effective immediately.”

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In a letter to the university, MIT President L. Rafael Reif called the allegations “deeply disturbing,” adding that the school would hire a law firm to conduct an internal investigation into Epstein’s donations.

The Media Lab studies the application of technology to several fields, including medicine, agriculture, health, media, space exploration and artificial intelligence, according to its website. It has an annual operating budget of $80 million. Ito had served as its director since September 2011.

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The Epstein conflagration has swept up the Eastern Seaboard, first in the tony enclaves of Palm Beach, Fla., where the financier was known to party alongside Donald Trump, before moving on to New York, where Epstein allegedly ran a sex-trafficking ring from his Upper East Side mansion for years. Epstein died by suicide last month while in federal custody.

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Now, it has engulfed Cambridge.

According to the New Yorker’s Ronan Farrow, Epstein was listed as a “disqualified” donor in MIT’s database, and the Media Lab classified his donations as anonymous and kept his name off Ito’s calendar. In a September 2014 email obtained by Farrow, Ito asked Epstein to help fund a researcher, writing “Could you re-up/top-off with another $100K so we can extend his contract another year?”

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In a subsequent email with the subject line “Jeffrey Epstein money,” Farrow reports, Ito instructed his staff to “make sure this gets accounted for as anonymous.” Farrow writes that staff also raised objections to a 2015 visit from Epstein, according to Signe Swenson, a former employee at the lab who resigned in 2016.

These reports go beyond what Ito revealed last month.

On Aug. 15, five days after Epstein’s death, Ito disclosed in a blog post that the Lab had accepted money from the billionaire “through some of the foundations he controlled” and that the donations had been made with his knowledge and permission. Ito also disclosed that he allowed Epstein to “invest in several of my funds which invest in tech start-up companies outside of MIT.”

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Ito apologized for his dealings with Epstein but insisted that “in all of my interactions with Epstein, I was never involved in, never heard him talk about, and never saw any evidence of the horrific acts that he was accused of.”

Ito vowed to raise and donate funds equal to Epstein’s contribution to the Media Lab to nonprofits that combat sex trafficking.

MIT received about $800,000 over the course of 20 years from foundations that Epstein controlled, according to an Aug. 22 letter to the university from Reif, MIT’s president.

“All of those gifts went either to the MIT Media Lab or to Professor Seth Lloyd,” who teaches mechanical engineering and physics, Reif said. He also announced that an internal panel had been convened to look into the donations and to examine the university’s policies on such gifts.

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The New York Times later reported that Ito took about $1.7 million from Epstein over the past decade.

As a result of the disclosures, two researchers affiliated with the MIT Media Lab, Ethan Zuckerman and J. Nathan Matias, a visiting scholar, resigned in protest in late August, the New York Times reported.

At a meeting on Sept. 4, MIT Media Lab co-founder Nicholas Negroponte, an architect, appeared to defend the program’s initial decision to take Epstein’s money several years ago, the MIT Technology Review reported. After an outcry, Negroponte said that given what the public now knows about Epstein’s behavior, his money would and should not be accepted.

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Epstein had tried to use his money to ingratiate himself with the academic elite long before the first accusations against him became public in the mid-2000s. Epstein donated extensively to universities including MIT and Harvard, which has said it would not return a $6.5 million donation that the financier made in 2003, before he pleaded guilty in 2008 to charges of soliciting prostitution.

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After Epstein served a prison sentence he sought to rebuild his reputation, an effort that may have involved once again establishing his status among the scientific elite. In an Aug. 22 apology to Epstein’s victims, Lloyd, the MIT mechanical engineering and physics professor, called his decisions to accept grants from Epstein “professional as well as moral failings.”

While Ito maintained supporters after his initial disclosure, the new reports appear to have dealt him a blow.

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On Saturday, several organizations said Ito would step down from their boards. He resigned from the board of trustees of the American nonprofit Knight Foundation, spokesman Andrew Sherry confirmed, as well as the New York Times Co. board of directors, according to a company spokeswoman. The MacArthur Foundation announced he had stepped down from its board of directors as well.

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An August petition supporting Ito with over 200 signatures from friends and the MIT community has been updated to clarify that these signatures “should not be read as continued support of Joi staying on as Media Lab Director following the most recent revelations” in the New Yorker.

Before Ito’s resignations, prominent women in the media world such as Xeni Jardin had spoken out on social media against his ties to Epstein, and writer Anand Giridharadas announced he would leave the jury for the Media Lab’s Disobedience Award.

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Arwa Mboya, 25, a second-year graduate student at the Media Lab wrote a guest column in MIT’s student newspaper, the Tech, last Thursday, calling on Ito to resign.

“I feel vindicated, like I’m not crazy,” she said to The Post in the wake of Ito’s resignation. “I’m okay that it took a few weeks to happen. I thought he was wrong from the beginning.”