Recombination and Population Mosaic of a Multifunctional Viral Gene, Adeno-Associated Virus cap

Homologous recombination is a dominant force in evolution and results in genetic mosaics. To detect evidence of recombination events and assess the biological significance of genetic mosaics, genome sequences for various viral populations of reasonably large size are now available in the GenBank. We studied a multi-functional viral gene, the adeno-associated virus (AAV) cap gene, which codes for three capsid proteins, VP1, VP2 and VP3. VP1-3 share a common C-terminal domain corresponding to VP3, which forms the viral core structure, while the VP1 unique N-terminal part contains an enzymatic domain with phospholipase A2 activity. Our recombinant detection program (RecI) revealed five novel recombination events, four of which have their cross-over points in the N-terminal, VP1 and VP2 unique region. Comparison of phylogenetic trees for different cap gene regions confirmed discordant phylogenies for the recombinant sequences. Furthermore, differences in the phylogenetic tree structures for the VP1 unique (VP1u) region and the rest of cap highlighted the mosaic nature of cap gene in the AAV population: two dominant forms of VP1u sequences were identified and these forms are linked to diverse sequences in the rest of cap gene. This observation together with the finding of frequent recombination in the VP1 and 2 unique regions suggests that this region is a recombination hot spot. Recombination events in this region preserve protein blocks of distinctive functions and contribute to convergence in VP1u and divergence of the rest of cap. Additionally the possible biological significance of two dominant VP1u forms is inferred

Search for long-lived massive particles in extensive air showers

Air showers containing delayed sub-showers which may be produced by a long-lived massive particle have been investigated by using twelve detectors. Ten events have been selected out as the candidates. However, a definite conclusion cannot be reached at the present time

Finite temperature properties of the triangular lattice t-J model, applications to Nax_xCoO2_2

We present a finite temperature ($T$) study of the t-J model on the two-dimensional triangular lattice for the negative hopping $t$, as relevant for the electron-doped Na$_x$CoO$_2$ (NCO). To understand several aspects of this system, we study the $T$-dependent chemical potential, specific heat, magnetic susceptibility, and the dynamic Hall-coefficient across the entire doping range. We show systematically, how this simplest model for strongly correlated electrons describes a crossover as function of doping ($x$) from a Pauli-like weakly spin-correlated metal close to the band-limit (density $n=2$) to the Curie-Weiss metallic phase ($1.5<n<1.75$) with pronounced anti-ferromagnetic (AFM) correlations at low temperatures and Curie-Weiss type behavior in the high-temperature regime. Upon further reduction of the doping, a new energy scale, dominated by spin-interactions ($J$) emerges (apparent both in specific heat and susceptibility) and we identify an effective interaction $J_{eff}(x)$, valid across the entire doping range. This is distinct from Anderson's formula, as we choose here $t<0$, hence the opposite sign of the usual Nagaoka-ferromagnetic situation. This expression includes the subtle effect of weak kinetic AFM - as encountered in the infinitely correlated situation ($U=\infty$). By explicit computation of the Kubo-formulae, we address the question of practical relevance of the high-frequency expression for the Hall coefficient $R_H^*$. We hope to clarify some open questions concerning the applicability of the t-J model to real experimental situations through this study

Phase Coexistence Near a Morphotropic Phase Boundary in Sm-doped BiFeO3 Films

We have investigated heteroepitaxial films of Sm-doped BiFeO3 with a Sm-concentration near a morphotropic phase boundary. Our high-resolution synchrotron X-ray diffraction, carried out in a temperature range of 25C to 700C, reveals substantial phase coexistence as one changes temperature to crossover from a low-temperature PbZrO3-like phase to a high-temperature orthorhombic phase. We also examine changes due to strain for films greater or less than the critical thickness for misfit dislocation formation. Particularly, we note that thicker films exhibit a substantial volume collapse associated with the structural transition that is suppressed in strained thin films

Information criteria for efficient quantum state estimation

Recently several more efficient versions of quantum state tomography have been proposed, with the purpose of making tomography feasible even for many-qubit states. The number of state parameters to be estimated is reduced by tentatively introducing certain simplifying assumptions on the form of the quantum state, and subsequently using the data to rigorously verify these assumptions. The simplifying assumptions considered so far were (i) the state can be well approximated to be of low rank, or (ii) the state can be well approximated as a matrix product state. We add one more method in that same spirit: we allow in principle any model for the state, using any (small) number of parameters (which can, e.g., be chosen to have a clear physical meaning), and the data are used to verify the model. The proof that this method is valid cannot be as strict as in above-mentioned cases, but is based on well-established statistical methods that go under the name of "information criteria." We exploit here, in particular, the Akaike Information Criterion (AIC). We illustrate the method by simulating experiments on (noisy) Dicke states

High temperature expansion in supersymmetric matrix quantum mechanics

We formulate the high temperature expansion in supersymmetric matrix quantum mechanics with 4, 8 and 16 supercharges. The models can be obtained by dimensionally reducing N=1 U(N) super Yang-Mills theory in D=4,6,10 to 1 dimension, respectively. While the non-zero frequency modes become weakly coupled at high temperature, the zero modes remain strongly coupled. We find, however, that the integration over the zero modes that remains after integrating out all the non-zero modes perturbatively, reduces to the evaluation of connected Green's functions in the bosonic IKKT model. We perform Monte Carlo simulation to compute these Green's functions, which are then used to obtain the coefficients of the high temperature expansion for various quantities up to the next-leading order. Our results nicely reproduce the asymptotic behaviors of the recent simulation results at finite temperature. In particular, the fermionic matrices, which decouple at the leading order, give rise to substantial effects at the next-leading order, reflecting finite temperature behaviors qualitatively different from the corresponding models without fermions.Comment: 17 pages, 13 figures, (v2) some typos correcte

Magnetic-field enhanced aniferromagnetism in non-centrosymmetric heavy-fermion superconductor CePt3_3Si

The effect of magnetic field on the static and dynamic spin correlations in the non-centrosymmetric heavy-fermion superconductor CePt$_3$Si was investigated by neutron scattering. The application of a magnetic field B increases the antiferromagnetic (AFM) peak intensity. This increase depends strongly on the field direction: for B${\parallel}$[0 0 1] the intensity increases by a factor of 4.6 at a field of 6.6 T, which corresponds to more than a doubling of the AFM moment, while the moment increases by only 10 % for B${\parallel}$[1 0 0] at 5 T. This is in strong contrast to the inelastic response near the antiferromagnetic ordering vector, where no marked field variations are observed for B${\parallel}$[0 0 1] up to 3.8 T. The results reveal that the AFM state in CePt$_3$Si, which coexists with superconductivity, is distinctly different from other unconventional superconductors.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev.

Far-Ultraviolet and Far-Infrared Bivariate Luminosity Function of Galaxies: Complex Relation between Stellar and Dust Emission

Far-ultraviolet (FUV) and far-infrared (FIR) luminosity functions (LFs) of galaxies show a strong evolution from $z = 0$ to $z = 1$, but the FIR LF evolves much stronger than the FUV one. The FUV is dominantly radiated from newly formed short-lived OB stars, while the FIR is emitted by dust grains heated by the FUV radiation field. It is known that dust is always associated with star formation activity. Thus, both FUV and FIR are tightly related to the star formation in galaxies, but in a very complicated manner. In order to disentangle the relation between FUV and FIR emissions, we estimate the UV-IR bivariate LF (BLF) of galaxies with {\sl GALEX} and {\sl AKARI} All-Sky Survey datasets. Recently we invented a new mathematical method to construct the BLF with given marginals and prescribed correlation coefficient. This method makes use of a tool from mathematical statistics, so called "copula". The copula enables us to construct a bivariate distribution function from given marginal distributions with prescribed correlation and/or dependence structure. With this new formulation and FUV and FIR univariate LFs, we analyze various FUV and FIR data with {\sl GALEX}, {\sl Spitzer}, and {\sl AKARI} to estimate the UV-IR BLF. The obtained BLFs naturally explain the nonlinear complicated relation between FUV and FIR emission from star-forming galaxies. Though the faint-end of the BLF was not well constrained for high-$z$ samples, the estimated linear correlation coefficient $\rho$ was found to be very high, and is remarkably stable with redshifts (from 0.95 at $z = 0$ to 0.85 at $z = 1.0$). This implies the evolution of the UV-IR BLF is mainly due to the different evolution of the univariate LFs, and may not be controlled by the dependence structure.Comment: 10 pages, 7 figures, Earth, Planets and Space, in pres