Matrix-Assisted Refolding, Purification and Activity Assessment Using a `Form Invariant' Assay for Matrix Metalloproteinase 2 (MMP2)

Matrix metalloproteinases expression is used as biomarker for various cancers and associated malignancies. Since these proteinases can cleave many intracellular proteins, overexpression tends to be toxic; hence, a challenge to purify them. To overcome these limitations, we designed a protocol where full length pro-MMP2 enzyme was overexpressed in E. coli as inclusion bodies and purified using 6xHis affinity chromatography under denaturing conditions. In one step, the enzyme was purified and refolded directly on the affinity matrix under redox conditions to obtain a bioactive protein. The pro-MMP2 protein was characterized by mass spectrometry, CD spectroscopy, zymography and activity analysis using a simple in-house developed `form invariant' assay, which reports the total MMP2 activity independent of its various forms. The methodology yielded higher yields of bioactive protein compared to other strategies reported till date, and we anticipate that using the protocol, other toxic proteins can also be overexpressed and purified from E. coli and subsequently refolded into active form using a one step renaturation protocol.

Lower bounds on Ricci flow invariant curvatures and geometric applications

We consider Ricci flow invariant cones C in the space of curvature operators lying between the cones ``nonnegative Ricci curvature'' and ``nonnegative curvature operator''. Assuming some mild control on the scalar curvature of the Ricci flow, we show that if a solution to the Ricci flow has its curvature operator which satisfies R + epsilon I is an element of C at the initial time, then it satisfies R + epsilon I is an element of C on some time interval depending only on the scalar curvature control. This allows us to link Gromov-Hausdorff convergence and Ricci flow convergence when the limit is smooth and R + I is an element of C along the sequence of initial conditions. Another application is a stability result for manifolds whose curvature operator is almost in C. Finally, we study the case where C is contained in the cone of operators whose sectional curvature is nonnegative. This allows us to weaken the assumptions of the previously mentioned applications. In particular, we construct a Ricci flow for a class of (not too) singular Alexandrov spaces.

NON-COERCIVE RICCI FLOW INVARIANT CURVATURE CONES

This note is a study of nonnegativity conditions on curvature preserved by the Ricci flow. We focus on a specific class of curvature conditions which we call non-coercive: These are the conditions for which nonnegative curvature and vanishing scalar curvature does not imply flatness. We show, in dimensions greater than 4, that if a Ricci flow invariant nonnegativity condition is satisfied by all Einstein curvature operators with nonnegative scalar curvature, then this condition is just the nonnegativity of scalar curvature. As a corollary, we obtain that a Ricci flow invariant curvature condition, which is stronger than a nonnegative scalar curvature, cannot be strictly satisfied by curvature operators (other than multiples of the identity) of compact Einstein symmetric spaces. We also investigate conditions which are satisfied by all conformally flat manifolds with nonnegative scalar curvature.

Exact Phase Retrieval in Principal Shift-Invariant Spaces

We address the problem of phase retrieval from Fourier transform magnitude spectrum for continuous-time signals that lie in a shift-invariant space spanned by integer shifts of a generator kernel. The phase retrieval problem for such signals is formulated as one of reconstructing the combining coefficients in the shift-invariant basis expansion. We develop sufficient conditions on the coefficients and the bases to guarantee exact phase retrieval, by which we mean reconstruction up to a global phase factor. We present a new class of discrete-domain signals that are not necessarily minimum-phase, but allow for exact phase retrieval from their Fourier magnitude spectra. We also establish Hilbert transform relations between log-magnitude and phase spectra for this class of discrete signals. It turns out that the corresponding continuous-domain counterparts need not satisfy a Hilbert transform relation; notwithstanding, the continuous-domain signals can be reconstructed from their Fourier magnitude spectra. We validate the reconstruction guarantees through simulations for some important classes of signals such as bandlimited signals and piecewise-smooth signals. We also present an application of the proposed phase retrieval technique for artifact-free signal reconstruction in frequency-domain optical-coherence tomography (FDOCT).

Action of Hopf on the twisted modular Hecke operator

Let Gamma subset of SL2(Z) be a principal congruence subgroup. For each sigma is an element of SL2(Z), we introduce the collection A(sigma)(Gamma) of modular Hecke operators twisted by sigma. Then, A(sigma)(Gamma) is a right A(Gamma)-module, where A(Gamma) is the modular Hecke algebra introduced by Connes and Moscovici. Using the action of a Hopf algebra h(0) on A(sigma)(Gamma), we define reduced Rankin-Cohen brackets on A(sigma)(Gamma). Moreover A(sigma)(Gamma) carries an action of H 1, where H 1 is the Hopf algebra of foliations of codimension 1. Finally, we consider operators between the levels A(sigma)(Gamma), sigma is an element of SL2(Z). We show that the action of these operators can be expressed in terms of a Hopf algebra h(Z).

Coarse-to-fine vision-based localization by indexing scale-invariant features

This paper presents a novel coarse-to-fine global localization approach inspired by object recognition and text retrieval techniques. Harris-Laplace interest points characterized by scale-invariant transformation feature descriptors are used as natural landmarks. They are indexed into two databases: a location vector space model (LVSM) and a location database. The localization process consists of two stages: coarse localization and fine localization. Coarse localization from the LVSM is fast, but not accurate enough, whereas localization from the location database using a voting algorithm is relatively slow, but more accurate. The integration of coarse and fine stages makes fast and reliable localization possible. If necessary, the localization result can be verified by epipolar geometry between the representative view in the database and the view to be localized. In addition, the localization system recovers the position of the camera by essential matrix decomposition. The localization system has been tested in indoor and outdoor environments. The results show that our approach is efficient and reliable. © 2006 IEEE.

Image-based localization and pose recovery using scale invariant features

In this paper, we propose a vision based mobile robot localization strategy. Local scale-invariant features are used as natural landmarks in unstructured and unmodified environment. The local characteristics of the features we use prove to be robust to occlusion and outliers. In addition, the invariance of the features to viewpoint change makes them suitable landmarks for mobile robot localization. Scale-invariant features detected in the first exploration are indexed into a location database. Indexing and voting allow efficient recognition of global localization. The localization result is verified by epipolar geometry between the representative view in database and the view to be localized, thus the probability of false localization will be decreased. The localization system can recover the pose of the camera mounted on the robot by essential matrix decomposition. Then the position of the robot can be computed easily. Both calibrated and un-calibrated cases are discussed and relative position estimation based on calibrated camera turns out to be the better choice. Experimental results show that our approach is effective and reliable in the case of illumination changes, similarity transformations and extraneous features. © 2004 IEEE.

Rotation Numbers Of Invariant Manifolds Around Unstable Periodic Orbits For The Diamagnetic Kepler Problem

In this paper, a method to construct topological template in terms of symbolic dynamics for the diamagnetic Kepler problem is proposed. To confirm the topological template, rotation numbers of invariant manifolds around unstable periodic orbits in a phase space are taken as an object of comparison. The rotation numbers are determined from the definition and connected with symbolic sequences encoding the periodic orbits in a reduced Poincare section. Only symbolic codes with inverse ordering in the forward mapping can contribute to the rotation of invariant manifolds around the periodic orbits. By using symbolic ordering, the reduced Poincare section is constricted along stable manifolds and a topological template, which preserves the ordering of forward sequences and can be used to extract the rotation numbers, is established. The rotation numbers computed from the topological template are the same as those computed from their original definition.

Hopf bifurcation in wakes behind a rotating and translating circular cylinder

A low-dimensional Galerkin method, initiated by Noack and Eckelmann [Physica D 56, 151 (1992)], for the prediction of the flow field around a stationary two-dimensional circular cylinder in a uniform stream at low Reynolds number is generalized to the case of a rotating and translating cylinder. The Hopf bifurcation describing the transition from steady to time-periodic solution is investigated. A curve indicating the transitional boundary is given in the two-dimensional parameter plane of Reynolds number Re and rotating parameter alpha. Our results show that rotation may delay the onset of vortex street and decrease the vortex-shedding frequency. (C) 1996 American Institute of Physics.