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Midfielder Yossi Benayoun and forwards Gael Kakuta and Salomon Kalou suffered problems in Chelsea's 4-3 loss.
BBC: Chelsea manager Carlo Ancelotti concerned by injuries
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Gael Kakuta missed the crucial spot kick as Rovers won the shoot-out 4-3.
BBC: Blackburn 3-3 Chelsea
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Ancelotti selected a young side and the match finished 3-3 after extra-time before 18-year-old Gael Kakuta missed his spot kick in the quarter-final tie.
BBC: Chelsea boss Carlo Ancelotti defends cup team selection
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Football's governing body handed out a ban until 2011 after they found the Blues guilty of inducing Gael Kakuta to break his contract with Lens in 2007.
BBC: Transfer embargo hope for Chelsea
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Chelsea were found guilty by Fifa of inducing Gael Kakuta to break his contract with Lens in 2007 but the club have vowed to "mount the strongest appeal possible".
BBC: Chelsea chief Kenyon leaves role
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It meant an opportunity for 18-year-old Gael Kakuta, at the centre of the transfer ban briefly imposed on Chelsea earlier this season after his move from Lens, while Joe Cole also started.
BBC: Sport - Football - Chelsea 2-2 Apoel Nicosia
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In addition, Chelsea were recently found guilty by Fifa of inducing Gael Kakuta to break his contract with Lens in 2007 when he was 16 which has opened up the debate on the tapping up of young talent.
BBC: Clubs agree to 'home-grown' quota
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In recent seasons, Chelsea have reduced the lavish spending that characterised the early years of Abramovich's reign, an approach that has seen greater first-team opportunities for some of their academy players, including forward Gael Kakuta, defender Jeffrey Bruma and midfielder Josh McEachran.
BBC: Frank Arnesen resigns as Chelsea sporting director
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Chelsea even had the luxury of bringing on youngsters Gael Kakuta and Joshua McEachran as they comfortably closed out the game and deliver an early sign of their determination to end their Champions League jinx and win the competition for the first time.
BBC: MSK Zilina 1-4 Chelsea