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There is still controversy about the prognostic value of motor evoked potentials (MEPs) in the assessment of hemiplegia. The aims of this study are to determine the relationship between functional and electrophysiological recovery and thus the value of MEP as a prognostic indicator of clinical outcome in acute ischemic stroke.Seventeen healthy subjects and 38 stroke patients were included in this study. Functional recovery was assessed with the Modified Canadian Neurological Scale (MCNS), the Barthel Activities of Daily Living Index (BI), and the Rankin scale. Transcranial magnetic stimulation was used to determine the change in central motor conduction time (CMCT). Stroke outcome was assessed at the end of 2 weeks. One-way ANOVA with post hoc comparisons using the Scheffé procedure as well as t tests were used to assess the significance of the results in this study.Unpaired t test showed significantly higher mean scores of the MCNS (2P=0.001), BI (2P=0.002), and Rankin scale (P<0.001) at day 14 in the group of patients with recordable MEP at day 1. A better clinical improvement with a higher mean score of the MCNS (2P<0.001), BI (2P<0.001), and the Rankin scale (2P<0.001) was also observed in the patients in whom the CMCT improved.These data show that there is a close relationship between clinical and electrophysiological improvement and that MEP is a useful prognostic indicator of clinical outcome.