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In the current paper,under the transverse Ricci flow on a totally geodesic Riemannian foliation, we prove two types of differential Harnack inequalities (Li-Yau gradient estimate) for the positive solutions of the heat equation associated with the time dependent horizontal Laplacian operators. We also get a time dependent version of the generalized curvature dimension inequality. As a consequence of aforementioned results, we also get parabolic Harnack inequalities and heat kernel upper bounds.

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