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A new intrinsic geometry based on a spectral analysis is used to motivate methods for aligning protein folds. The geometry is induced by the fact that a distance matrix can be scaled so that its eigenvalues are positive. We provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach and use it to motivate two(More)
A new linear programming model used to aid in the design of radiotherapy plans is introduced. This model incorporates elastic constraints, and when solved with a path following interior point method, produces favorable plans. A sound mathematical analysis shows how to interpret the solution, and hence, the treatment planner receives meaningful knowledge(More)
BACKGROUND Current United States (US) military doctrine emphasizes rapid evacuation of casualties to fixed medical facilities remote from the theater of war. To support this strategy, the Air Force has formed Critical Care Air Transport (CCAT) teams consisting of a physician, nurse, and respiratory therapist. STUDY OBJECTIVE To describe the(More)
We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem's intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst-case analysis of(More)
The data describing an asymptotic linear program rely on a single parameter , usually referred to as time, and unlike parametric linear programming, asymptotic linear programming is concerned with the steady state behavior as time increases to infinity. The fundamental result of this work shows that the optimal partition for an asymptotic linear program(More)
INTRODUCTION Cuff volume of an air-filled airway device varies inversely with ambient pressure at altitude. This may result in problems with ventilation, aspiration, and tissue ischemia in intubated patients transported by aircraft. We aimed to characterize cuff volume changes in airway devices as a function of altitude. METHODS Four inflatable airway(More)
Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows(More)