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Macrakis is also the author of numerous articles, both scholarly and popular. While a graduate student at Harvard she found that the Rockefeller Foundation funded science in Nazi Germany; that work was covered in the "Frankfurter Allgemeine Zeitung". ("Frankfurter Allgemeine Zeitung", 29 October 1986). Her most widely read popular magazine article is"The Case of Agent Gorbachev," published in "American Scientist".