( Protons ( , ( ( along ( with neutrons ) ) ( , ( ( ( make up ) ( ( the nucleus ) ( of ( the atom ) ) ) ) . ) ) ) ) )
(ROOT (S (NP (NNS Protons)) (, ,) (ADVP (IN along) (PP (IN with) (NP (NNS neutrons)))) (, ,) (VP (VBP make) (PRT (RP up)) (NP (NP (DT the) (NN nucleus)) (PP (IN of) (NP (DT the) (NN atom))))) (. .)))
Protons, along with neutrons, make up the nucleus of the atom.
(ROOT (S (NP (NP (DT The) (NN atom)) (PP (IN in) (NP (DT a) (NN neutron)))) (VP (VBZ is) (VP (VBN found) (PP (IN in) (NP (DT the) (DT the) (NN nucleus))))) (. .)))