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In USSR jews could go to other universities too (though they were low profile and i think had quotas too, just higher). I don't understand how it justifies the discrimination.

While it's not as extreme as the the situation described in the article, it's still racism. A restaurant isn't allowed to discriminate based on race, why is a university?

"Don't go to Moscow State University, go to Moscow Institute of Oil and Gas. They have an Applied Math program too!"

You are implying racism just as the article.

He wanted to study "pure" maths, not applied:

"Moscow had many schools, but there was only one place to study pure math: Moscow State University, known by its Russian abbreviation MGU, Moskovskiy Gosudarstvenny Universitet. Its famous Mekh-Mat, the Department of Mechanics and Mathematics, was the flagship mathematics program of the USSR. Since I wanted to study pure math, I had no choice but to apply there."

Ok, let's say the option was between 2 pure math schools, where one was much better than the other. My point still stands.