( And ( they ( ( are ( ( brain lesions ) ( in ( the ( brain stem ) ) ) ) ) . ) ) )
(ROOT (S (CC And) (NP (PRP they)) (VP (VBP are) (NP (NP (NN brain) (NNS lesions)) (PP (IN in) (NP (DT the) (NN brain) (NN stem))))) (. .)))
And they are brain lesions in the brain stem.
(ROOT (S (NP (DT The) (NN brain) (NN stem)) (VP (VBZ regulates) (NP (NP (DT the) (NN rate)) (PP (IN of) (NP (NN breathing))))) (. .)))