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Cognitive radio (CR) is an innovative technique to improve the utilization of radio frequency spectrum, in which different users compete for limited resources. Non-contiguous orthogonal frequency division multiplexing (NC-OFDM) is regarded as a well-matched technology for CR systems. In these systems, one of the major concerns is the fairness of resource allocation among secondary users. In this paper, a concept of fairness index threshold is defined, which achieves a better tradeoff between the system capacity and fairness. And for reducing the complexity of the solving process, we exploit the particle swarm optimization (PSO) algorithm to allocate power. At the end of the paper, simulation results show that the proposed algorithm makes good performances in both fairness and system capacity.