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Using non relativistic effective Lagrangian techniques, we analyze the hadronic decay of the pi+pi- atom and the strong energy-level shift of pionic hydrogen in the ground state. We derive general formulae for the width and level shift, valid at next-to-leading order in isospin breaking. The result is expressed in terms of hadronic threshold amplitudes that include isospin-breaking effects. In order to extract isospin symmetric scattering lengths from the data, we invoke chiral perturbation theory, that allows one to relate the scattering lengths to the threshold amplitudes.

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