Boyce (2004) (analyses / notes) that animals kept in captivity suffer from many aliments.
notes - comments or makes reference to - notes that
analyses - in depth investigation - analyse something / analyse ~~that~~
It is clear that Lam and Wong (2009) (confuse / imagine / dispute) animals used as food (the / that / with) animals which are primarily used as pets.
confuse something with something else
Smith et al. (2010) (discover / investigate) that free range cattle live better lives than those kept inside.
discover - discover a fact / a finding
investigate - detailed analysis of something / investigate ~~that~~
Some academics (estimate / point out) that meat is unhealthy, but Wong’s (2009) paper (refutes / investigates / notes) this claim.
point out - express or draw attention to the fact that meat is unhealthy. Nothing is being estimated here.

refute - argue against or disagree with this point
This paper (investigates / mentions) the effects of organic food on minor illnesses and (decides / concludes) that further research be conducted as a matter of urgency.
investigates - detailed analysis of the effects as opposed to mentions - makes a casual reference to them

concludes - sums up the ultimate results of the research / final analysis of the findings that further research is required. No decision is made here.