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To examine whether skeletal adaptations to chronic non-weight-bearing exercise depend on the type of aquatic exercise (swimming or water polo) as well as on sex (men or women).This was a cross-sectional study at the Laboratory of Nutrition and Clinical Dietetics, Department of Nutrition and Dietetics, Harokopio University, Athens, Greece. A total of 43 water polo players, 26 swimmers, and 30 sedentary individuals, aged 17 to 34 years, were recruited (52 men, 47 women).Bone mineral content (BMC) and areal bone mineral density (aBMD) of the total body and of various subregions.Compared with controls, swimmers had lower leg and total aBMD (P < 0.05), whereas water polo players had lower leg but higher arm and trunk aBMD (all P < 0.05). Swimmers and water polo athletes differed at the arms (men only), trunk, and total body (all higher in water polo players, at P < 0.05). Bone adaptations to water polo playing were unaffected by sex. Female swimmers, but not male swimmers, had 13% higher arm BMC than controls (P < 0.05), whereas male swimmers, but not female swimmers, had 12% lower leg BMC than controls (P < 0.05).Athletes participating in long-term water polo playing and swimming have substantially different total and regional aBMD. The effect is not mediated by sex in water polo players; however, sex may mediate the differences between swimmers and controls. Whether the observed differences between athlete groups and sexes arise from different bone adaptations to activity or from other factors cannot be answered by the current data.Water polo playing may be preferable over swimming for maintaining bone health; both types of aquatic exercise at the elite level of participation, however, have unfavorable effects on the lower limb bones.