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Heart rate variability (HRV) analysis provides noninvasive way for assessment of neural activity that control cardiovascular system. Contributions of sympathetic and parasympathetic autonomous nervous system that modulate instantaneous heart rate are studied by means of spectral analysis. The objective is to recover modulating signal spectrum from beat occurrence times. In this paper, properties of so called spectrum of counts with respect to artifact arising in practical application of this method are described. Specifically, spectral leakage and beat time detection precision are discussed. Phenomena are analyzed on theoretical basis of integral pulse frequency modulation (IPFM). Computer simulations and recommendations for artifact rejection are presented.