Mapping the domains of CD134 as a functional receptor for feline immunodeficiency virus (FIV)

The feline homologue of CD134 (fCD134) is the primary binding receptor for feline immunodeficiency virus (FIV), targeting the virus preferentially to activated CD4+ helper T cells. However, strains of FIV differ in their utilisation of CD134; the prototypic strain PPR, requires a minimal determinant in CRD1 of fCD134 to confer near optimal receptor function while strains such as GL8 require additional determinants in the CD134 CRD2. We map this determinant to a loop in CRD2 governing the interaction between the receptor and its ligand; substitution of amino acids S78N,S79Y,K80E restored full viral receptor activity to the CDR2 of human CD134 in the context of feline CD134 with tyrosine-79 appearing to be the critical residue for restoration of receptor function

Compressed sensing performance bounds under Poisson noise

This paper describes performance bounds for compressed sensing (CS) where the underlying sparse or compressible (sparsely approximable) signal is a vector of nonnegative intensities whose measurements are corrupted by Poisson noise. In this setting, standard CS techniques cannot be applied directly for several reasons. First, the usual signal-independent and/or bounded noise models do not apply to Poisson noise, which is non-additive and signal-dependent. Second, the CS matrices typically considered are not feasible in real optical systems because they do not adhere to important constraints, such as nonnegativity and photon flux preservation. Third, the typical $\ell_2$--$\ell_1$ minimization leads to overfitting in the high-intensity regions and oversmoothing in the low-intensity areas. In this paper, we describe how a feasible positivity- and flux-preserving sensing matrix can be constructed, and then analyze the performance of a CS reconstruction approach for Poisson data that minimizes an objective function consisting of a negative Poisson log likelihood term and a penalty term which measures signal sparsity. We show that, as the overall intensity of the underlying signal increases, an upper bound on the reconstruction error decays at an appropriate rate (depending on the compressibility of the signal), but that for a fixed signal intensity, the signal-dependent part of the error bound actually grows with the number of measurements or sensors. This surprising fact is both proved theoretically and justified based on physical intuition.Comment: 12 pages, 3 pdf figures; accepted for publication in IEEE Transactions on Signal Processin

A Fermi Fluid Description of the Half-Filled Landau Level

We present a many-body approach to calculate the ground state properties of a system of electrons in a half-filled Landau level. Our starting point is a simplified version of the recently proposed trial wave function where one includes the antisymmetrization operator to the bosonic Laughlin state. Using the classical plasma analogy, we calculate the pair-correlation function, the static structure function and the ground state energy in the thermodynamic limit. These results are in good agreement with the expected behavior at $\nu=\frac12$.Comment: 4 pages, REVTEX, and 4 .ps file

Ligand-based virtual screening using binary kernel discrimination

This paper discusses the use of a machine-learning technique called binary kernel discrimination (BKD) for virtual screening in drug- and pesticide-discovery programmes. BKD is compared with several other ligand-based tools for virtual screening in databases of 2D structures represented by fragment bit-strings, and is shown to provide an effective, and reasonably efficient, way of prioritising compounds for biological screening

Stability and effective masses of composite-fermions in the first and second Landau Level

We propose a measure of the stability of composite fermions (CF's) at even-denominator Landau-level filling fractions. Assuming Landau-level mixing effects are not strong, we show that the CF liquid at $\nu=2+1/2$ in the $n=1$ Landau level cannot exist and relate this to the absence of a hierarchy of incompressible states for filling fractions $2+1/3 < \nu < 2+2/3$. We find that a polarized CF liquid should exist at $\nu=2+1/4$. We also show that, for CF states, the variation with system size of the ground state energy of interacting electrons follows that for non-interacting particles in zero magnetic field. We use this to estimate the CF effective masses.Comment: 9 pages, Revtex, PSIZ-TP-940

Evaluation of a Bayesian inference network for ligand-based virtual screening

Background Bayesian inference networks enable the computation of the probability that an event will occur. They have been used previously to rank textual documents in order of decreasing relevance to a user-defined query. Here, we modify the approach to enable a Bayesian inference network to be used for chemical similarity searching, where a database is ranked in order of decreasing probability of bioactivity. Results Bayesian inference networks were implemented using two different types of network and four different types of belief function. Experiments with the MDDR and WOMBAT databases show that a Bayesian inference network can be used to provide effective ligand-based screening, especially when the active molecules being sought have a high degree of structural homogeneity; in such cases, the network substantially out-performs a conventional, Tanimoto-based similarity searching system. However, the effectiveness of the network is much less when structurally heterogeneous sets of actives are being sought. Conclusion A Bayesian inference network provides an interesting alternative to existing tools for ligand-based virtual screening

Effective mass of composite fermion: a phenomenological fit in with anomalous propagation of surface acoustic wave

We calculate the conductivity associated with the anomalous propagation of a surface acoustic wave above a two-dimensional electron gas at $\nu=1/2$. Murthy-Shankar's middle representation is adopted and a contribution to the response functions beyond the random phase approximation has been taken into account. We give a phenomenological fit for the effective mass of composite fermion in with the experimental data of the anomalous propagation of surface acoustic wave at $\nu=1/2$ and find the phenomenological value of the effective mass is several times larger than the theoretical value $m_{th}^*=6\epsilon/e^2l_{1/2}$ derived from the Hartree-Fock approximation. We compare our phenomenologically fitting composite fermion effective mass with those appeared in the measurements of the activation energy and the Shubnikov-de Haas effect and find that our result is fairly reasonable.Comment: 8 pages, 5 figures, the longer version of cond-mat/9801131 with crucial corrections, accepted for publication by PR