Here's an interesting cognitive study: A.H. Foss et al used fMRI (the brain scans in the scary tunnel that show blood flow) with exposure to various intervals based upon the Pythagoras ratios. Quick review of Pythagorean ratio rules: musical intervals can be described as ratios of the frequencies of the two pitches. Those ratios that are simplest (2:1, 3:2, 4:3, etc.) correspond with the intervals that Western civilization has judged as the most pleasant (octave, perfect fifth, perfect fourth), while the dissonant intervals of our culture (major seventh, minor second, tritone, etc.) have more complex ratios (243:128, 16:15, 45:32, etc.). The fMRI tests found that in trained musicians, five areas of the brain show activity with the interval performances, showing more activity as intervals progress from perfect consonances to imperfect consonances to dissonances. These five areas of the brain are the inferior frontal gyrus, superior temporal gyrus (location of the primary auditory cortex), medial frontal gyrus, inferior parietal lobule, and anterior cingulate (rational cognition). Nonmusicians (that horrible term used in music cognition to describe a population of listeners that have not had training in music) only had one area of their brain activated in the same consonance/dissonance pattern: the right inferior frontal gyrus.
I haven't yet had a chance to read the full article to see whether the intervals were actually played in just intonation, how many intervals were played, and how many participants were in the study (fMRI studies usually have smaller numbers due to the expense of MRI time). If the intervals were played in equal temperament, that would go against the whole ratio-rule interpretation.
AH Foss, EL Altschuler, and KH James. "Neural correlates of the Pythagorean ratio rules." Neuroreport 18, no. 15 (2007), 1521-1525.