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We propose a pilot-channel assisted modulation (PCAM) for pulse-based ultra-wideband systems that require accurate channel estimation for RAKE combining. The pilot channel is constructed with pulses that are orthogonal to the data-bearing pulses and each pilot pulse is transmitted together with a data pulse. PCAM parameters are designed to optimize the channel estimation and data detection performance jointly. Simulation results show that PCAM is able to provide desirable performance under channel time-variations and multi-user interference, without sacrificing the data rate.