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.     

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.     

Re-hardening of hadron transverse mass spectra in relativistic heavy-ion collisions

We analyze the spectra of pions and protons in heavy-ion collisions at relativistic energies from 2 A GeV to 65+65 A GeV by using a jet-implemented hadron-string cascade model. In this energy region, hadron transverse mass spectra first show softening until SPS energies, and re-hardening may emerge at RHIC energies. Since hadronic matter is expected to show only softening at higher energy densities, this re-hardening of spectra can be interpreted as a good signature of the quark-gluon plasma formation     

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.     

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.     

PEO-based composite lithium polymer electrolyte, PEO-BaTiO3-Li(C2F5SO2)2N

Polyethylene oxide (PEO) based polymer electrolytes with BaTiO₃ as filler and Li(C₂F₅SO₂)₂N as salt have been examined in lithium polymer batteries. The aluminum disolution potential in PEO-Li(C₂F₅SO₂)₂N was estimated to be 4.1 V vs. Li/Li⁺ at 80 °C, which was compared to that of 3.8 V vs. Li/Li⁺ in PEO-Li(CF₃SO₂)₂N. The electrical conductivity of the system was measured as a function of O/Li ratio. The highest conductivity was observed in O/Li=8. The conductivity was 1.65×10⁻³ S/cm at 80 °C and 1.5×10⁻⁵ S/cm at 25 °C. The interfacial resistance of Li/polymer electrolyte/Li annealed at 80 °C for 15 days was lower than 100 Ωcm². Paper presented at the 8th EuroConference on Ionics, Carvoeiro, Algarve, Portugal, Sept. 16 – 22, 2001.     

A Simple Chaotic Circuit with Impulsive Switch Depending on Time and State

This paper presents a simple chaotic circuit consisting of two capacitors, one linear two-port VCCS and one time-state-controlled impulsive switch. The impulsive switch causes rich chaotic and periodic behavior. The circuit dynamics can be simplified into a one-dimensional return map that is piecewise linear and piecewise monotone. Using the return map, we clarify parameter conditions for existence of chaotic and periodic attractors and coexistence state of attractors.