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Daniel Pudil's goal gave the early initiative to Karel Bruckner's side, before Jan Koller struck 16 minutes from time to secure the points.
CNN: Czechs defeat Cyprus to finish top
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Germany's Borussia Dortmund remain in second, three points behind the Gunners after goals from Jan Koller, Tomas Rosicky and Marcio Amoroso saw them win 3-1 at PSV Eindhoven .
BBC: Zidane rescues Real
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Czech coach Karel Bruckner brought on giant striker Jan Koller, dropped to the bench after the win over the Swiss, but the country's all-time record scorer could not make the required impact.
CNN: Ronaldo puts Portugal into quarterfinals