( ( At first ) ( they ( ( ( found ( ( the ( top ( ( part or ) cranium ) ) ) ( of ( the skull ) ) ) ) ( in ( what ( appeared ( to ( be ( an ( altar room ) ) ) ) ) ) ) ) . ) ) )
(ROOT (S (PP (IN At) (NP (JJ first))) (NP (PRP they)) (VP (VBD found) (NP (NP (DT the) (JJ top) (NN part) (CC or) (NN cranium)) (PP (IN of) (NP (DT the) (NN skull)))) (PP (IN in) (SBAR (WHNP (WP what)) (S (VP (VBD appeared) (S (VP (TO to) (VP (VB be) (NP (DT an) (NN altar) (NN room)))))))))) (. .)))
At first they found the top part or cranium of the skull in what appeared to be an altar room.
(ROOT (S (NP (NP (DT The) (NN cranium)) (PRN (-LRB- -LRB-) (NP (NN skull)) (-RRB- -RRB-))) (VP (VBP protect) (S (-LRB- -LRB-) (NP (PRP s)) (-RRB- -RRB-) (NP (DT the) (NN brain)))) (. .)))
The cranium (skull) protect(s) the brain.