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In this paper TCP performance are evaluated when high speed Ethernet over passive optical networks are interconnected by means of a core optical network based on the optical burst switching paradigm. The inter-working unit, or edge node, between these two networks is properly studied and discussed. A time-based assembly algorithm is here employed and it is analyzed and designed for operating with a EPON, characterized by some parameters such as the cycle time for managing the upstream transmissions. This hybrid network is evaluated through simulations by means of the ns2 simulation tool. It is shown that different assembly time values have to be used for different TCP congestion window values, for optimizing the TCP throughput. Also, longer assembly time values provide better fairness among TCP flows while the cycle time of the EPON has negligible impact on the end-to-end performance.