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From e http://eva.onegeek.org/pipermail/evangelion/2011-September/007052.html
During a panel, Miyamura was commented that at one point Anno came to her asked her something along the lines of 'If you were lying in bed but couldn't move and someone came up to the bed and did something [bad] in front of you, what would your response be?' (Please bear in mind that it's been 3 months since this panel and I didn't take notes. What I've quoted is very rough - it was only the general gist of what she said.) Miyamura replied to Anno - "kimochi warui". It was only as she was making this comment during the panel that she seemed to make the connection between Anno's question and the hospital/Shinji masturbation scene.
At the panel, out of personal interest I asked the two actresses about their interpretations of the ending of the TV series: did Shinji reject Complementation at the end or not? Tiffany Grant gave a reply along the lines that she felt much of the series was in Shinji's head and she referred to the fact that in the series, when he's listening to his SDAT player, he keeps cycling back between tracks 25 and 26. Miyamura Yuko replied that she remembered that as the series progressed the actors were wondering how the series was going to end. but she has no particular view on whether Shinji rejected Complementation or not.