Academic Grades and Motivation in High School Science Classrooms Among Male and Female Students: Associations with Teachers' Characteristics, Beliefs, and Practices, the chapter by Schmidt and Shumow describes what we learned about gender differences by observing high school science classes and interviewing the teachers.
Encouraging Girls in Math and Science is a downloadable practical guide that offers suggestions on helping girls succeed and persist in science. It was written for by Halpern, D, Aronson, J., Reimer, N. Simpkins, S., Star, J. & Wentzel, K., (2007).
There is a Doing What Works webpage with more materials and links supporting the ideas presented in the guide.
Thought Activity is a worksheet for identifying how students are alike and how they are different and is available as a downloadable pdf.