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Extensive empirical work indicates that the exhaust emission and fuel efficiency of modern common-rail diesel engines characterise strong resilience to biodiesel fuels when the engines are operating in conventional high temperature combustion cycles. However, as the engine cycles approach the low temperature combustion (LTC) mode, which could be implemented by the heavy use of exhaust gas recirculation (EGR) or the homogeneous charge compression ignition (HCCI) type of combustion, the engine performance start to differ between the use of conventional and biodiesel fuels. Therefore, a set of fuel injection strategies were compared empirically under independently controlled EGR, intake boost, and exhaust backpressure in order to improve the neat biodiesel engine cycles.