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Gauge invariance of scalar perturbations is studied together with the associated equations of motion. Extending methods developed in the framework of hamiltonian General Relativity, the Hamilton-Jacobi equation is investigated into the details in Loop Quantum Cosmology. The gauge-invariant observables are built and their equations of motions are reviewed both in Hamiltonian and Lagrangian approaches. This method is applied to scalar perturbations with either holonomy or inverse-volume corrections.

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