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The subject of this memoir is the spectrum of a Dirac-type operator on an odd-dimensional manifold M with boundary and, particularly, how this spectrum varies under an analytic perturbation of the operator. Two types of eigenfunctions are considered: first, those satisfying the ''global boundary conditions'' of Atiyah, Patodi, and Singer and second, those which extend to $L^2$ eigenfunctions on M with an infinite collar attached to its boundary. The unifying idea behind the analysis of these two types of spectra is the notion of certain ''eigenvalue-Lagrangians'' in the symplectic space $L^2(partial M)$, an idea due to Mrowka and Nicolaescu. By studying the dynamics of these Lagrangians, the authors are able to establish that those portions of the two types of spectra which pass through zero behave in essentially the same way (to first non-vanishing order). In certain cases, this leads to topological algorithms for computing spectral flow.
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