Dr. Simons and the school have their defenders: As word spread last week about The Times’s queries, two women on the faculty at the research center contacted The Times to say that he had been an outstanding leader who had promoted women, and that the accusations had been blown out of proportion.

Since the reduced suspension of Dr. Simons was announced last November, senior women on the faculty and, separately, junior women in the cardiology department had taken their concerns about his expected return in June 2015 to Dr. Salovey, the university president.

In a follow-up letter to the president, the senior women said the climate for women at the medical school had “substantially deteriorated under the current leadership.”

“We expressed concern about the lack of transparency or honesty in the communication announcing Dr. Simons’s leave, and particularly the absence of any suggestion that there had been wrongdoing,” the letter said, referring to their meeting. “The communication could easily have been interpreted as Dr. Simons being awarded a special academic leave relative to some important work.”