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Communication-Based Train Control (CBTC) system is an automated train control system using bidirectional train-ground communications to ensure the safe operation of rail vehicles. Handoff design has significant impacts on the train control performance in CBTC systems based on multi-input and multi-output (MIMO)-enabled WLANs. Most of previous works use traditional design criteria, such as network capacity and communication latency, in handoff designs. However, these designs do not necessarily benefit the train control performance. In this paper, we take an integrated design approach to jointly optimize handoff decisions and physical layer parameters to improve the train control performance in CBTC systems. We use linear quadratic cost for the train controller as the performance measure. The handoff decision and physical layer parameters adaptation problem is formulated as a stochastic control process. Simulation result shows that the proposed approach can significantly improve the control performance in CBTC systems.