Computational Analysis Reveals a Critical Point Mutation in the N-Terminal Region of the Signaling Lymphocytic Activation Molecule Responsible for the Cross-Species Infection with Canine Distemper Virus

Infection of hosts by morbilliviruses is facilitated by the interaction between viral hemagglutinin (H-protein) and the signaling lymphocytic activation molecule (SLAM). Recently, the functional importance of the n-terminal region of human SLAM as a measles virus receptor was demonstrated. However, the functional roles of this region in the infection process by other morbilliviruses and host range determination remain unknown, partly because this region is highly flexible, which has hampered accurate structure determination of this region by X-ray crystallography. In this study, we analyzed the interaction between the H-protein from canine distemper virus (CDV-H) and SLAMs by a computational chemistry approach. Molecular dynamics simulations and fragment molecular orbital analysis demonstrated that the unique His28 in the N-terminal region of SLAM from Macaca is a key determinant that enables the formation of a stable interaction with CDV-H, providing a basis for CDV infection in Macaca. The computational chemistry approach presented should enable the determination of molecular interactions involving regions of proteins that are difficult to predict from crystal structures because of their high flexibility.     

Nonrelativistic limit in the energy space for nonlinear Klein-Gordon equations

We study the nonrelativistic limit of the Cauchy problem for the nonlinear Klein-Gordon equation and prove that any finite energy solution converges to the corresponding solution of the nonlinear Schr?dinger equation in the energy space, after the infinite oscillation in time is removed. We also derive the optimal rate of convergence in . Received: 13 July 2000 / Published online: 1 February 2002     

The kinetics of the light-induced defect creation in hydrogenated amorphous silicon – Stretched exponential relaxation

Our model for light-induced defect creation in hydrogenated amorphous silicon is applied to its kinetics, i.e., the growing curve of light-induced dangling bond density as a function of illumination time, which is fitted to a stretched exponential function. Two parameters β and τ involved in the function are estimated as functions of saturated dangling bond density in terms of our model. These are compared with two experimental results, i.e., our results obtained from ESR measurements and Shimakawa et al.’s results obtained from photoconductivity measurements. The saturated dangling bond density is also measured as a function of the generation rate of free carriers. The experimental results are compared with calculated results and discussed.     

Classical in-plane negative magnetoresistance and quantum positive magnetoresistance in undoped InSb thin films on GaAs (1 0 0) substrates

Magnetoresistance (MR) effects have been investigated in perpendicular and parallel magnetic fields at 300, 80 K and liquid He temperatures for undoped InSb thin films 0.1–2.3 μm thick grown on GaAs(1 0 0) substrates by MBE. At high temperatures, the intrinsic carriers show the parabolic negative MR observable only in magnetic fields parallel to the film. The skipping-orbit effect due to surface boundary scattering in the classical orbits in the plane vertical to the film has been argued to be responsible for the negative MR. At low temperatures (T=80 K), the transport is dominated by the two-dimensional (2D) electrons in the accumulation layers at the InSb/GaAs(1 0 0) hetero interface; MR is positive and shows a logarithmic increase with anisotropy between parallel and perpendicular field orientation, arising from the 2D weak anti-localization (WAL) that reflects the interplay between the spin-Zeeman effect and strong spin–orbit interaction caused by the asymmetric potential at the interface (Rashba term). The zero-field spin splitting energy of Δ₀13 meV, the electron effective mass of m^*0.10m₀ seven times of the band edge mass in bulk InSb and the effective g-factor of |g^*|15 in the accumulation layer have been inferred from fits of MR for the 0.1 μm thick film to the 2D WL theory.     

Compact directed acyclic word graphs for a sliding window

Suffix trees are a well-known and widely-studied data structure highly useful for string matching. The suffix tree of a string w can be constructed in O(n) time and space, where n denotes the length of w. Larsson achieved an efficient algorithm to maintain suffix trees for a sliding window. It contributes to prediction by partial matching (PPM) style statistical data compression scheme. Compact directed acyclic word graphs (CDAWGs) are a more space-economical data structure for indexing strings. In this paper we propose a linear-time algorithm to maintain CDAWGs for a sliding window.     

On K1 and K2 of Algebraic Surfaces

In this paper we study higher Chow groups of smooth, projective surfaces over a field k of characteristic zero, using some new Hodge theoretic methods which we develop for this purpose. In particular we investigate the subgroup of CH ^r+1 (X,r) with r = 1,2 consisting of cycles that are supported over a normal crossing divisor Z on X. In this case, the Hodge theory of the complement forms an interesting variation of mixed Hodge structures in any geometric deformation of the situation. Our main result is a structure theorem in the case where X is a very general hypersurface of degree d in projective 3-space for d sufficiently large and Z is a union of very general hypersurface sections of X. In this case we show that the subgroup of CH ^r+1 (X,r) we consider is generated by obvious cycles only arising from rational functions on X with poles along Z. This can be seen as a generalization of the Noether–Lefschetz theorem for r = 0. In the case r = 1 there is a similar generalization by Müller-Stach, but our result is more precise than it, since it is geometric and not only cohomological. The case r = 2 is entirely new and original in this paper. For small d, we construct some explicit examples for r = 1 and 2 where the corresponding higher Chow groups are indecomposable, i.e. not the image of certain products of lower order groups. In an appendix Alberto Collino constructs even more indecomposable examples in CH ³ (X,2) which move in a one-dimensional family on the surface X.Contribution to appendix.     

5-Aza-2′-deoxycytidine reactivates the CDH1 gene without influencing methylation of the entire CpG island or histone modification in a human cancer cell line

It is well-recognized that DNA methylation and histone modifications play critical roles in epigenetic regulation of gene activity through the alteration of chromatin structure. Recent studies have shown that in a subset of cancer cells, the silencing of the human E-cadherin (CDH1) gene is associated with hypermethylation of the CpG island. However, the associated molecular mechanism remains unclear. To understand the mechanism, we have investigated the alteration of CpG island methylation and histone modifications during the reactivation of the CDH1 gene by treatment with 5-aza-2′-deoxycytidine (5-aza-dC). Although the CDH1 gene expression was recovered by treatment with 5-aza-dC in a liver cancer cell line Li21, the methylation status of the entire CpG island and acetylation and methylation status of associated histones were not significantly altered. These results demonstrate that the silenced CDH1 gene can be reactivated without apparent alteration of histone modification or CpG island methylation.     

Stability of the steady state for the Falk model system of shape memory alloys

In this article a stability result for the Falk model system is proven. The Falk model system describes the martensitic phase transitions in shape memory alloys. In our setting, the steady state is a nonlocal elliptic problem. We show the dynamical stability for the linearized stable critical point of the corresponding functional. Copyright © 2007 John Wiley & Sons, Ltd.