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

Buckets of Tops

Reconstructing hadronically decaying top quarks is a key challenge at the LHC, affecting a long list of Higgs analyses and new physics searches. We propose a new method of collecting jets in buckets, corresponding to top quarks and initial state radiation. This method is particularly well suited for moderate transverse momenta of the top quark, closing the gap between top taggers and traditional top reconstruction. Applying it to searches for supersymmetric top squarks we illustrate the power of buckets.Comment: 14 pages, 7 figures, 5 table

Buckets of Higgs and Tops

We show that associated production of a Higgs with a top pair can be observed in purely hadronic decays. Reconstructing the top quarks in the form of jet buckets allows us to control QCD backgrounds as well as signal combinatorics. The background can be measured from side bands in the reconstructed Higgs mass. We back up our claims with a detailed study of the QCD event simulation, both for the signal and for the backgrounds.Comment: 16 pages, 7 figure

Large-System Analysis of Joint Channel and Data Estimation for MIMO DS-CDMA Systems

This paper presents a large-system analysis of the performance of joint channel estimation, multiuser detection, and per-user decoding (CE-MUDD) for randomly-spread multiple-input multiple-output (MIMO) direct-sequence code-division multiple-access (DS-CDMA) systems. A suboptimal receiver based on successive decoding in conjunction with linear minimum mean-squared error (LMMSE) channel estimation is investigated. The replica method, developed in statistical mechanics, is used to evaluate the performance in the large-system limit, where the number of users and the spreading factor tend to infinity while their ratio and the number of transmit and receive antennas are kept constant. The performance of the joint CE-MUDD based on LMMSE channel estimation is compared to the spectral efficiencies of several receivers based on one-shot LMMSE channel estimation, in which the decoded data symbols are not utilized to refine the initial channel estimates. The results imply that the use of joint CE-MUDD significantly reduces rate loss due to transmission of pilot signals, especially for multiple-antenna systems. As a result, joint CE-MUDD can provide significant performance gains, compared to the receivers based on one-shot channel estimation.Comment: The paper was resubmitted to IEEE Trans. Inf. Theor

An evaluation of the analytic continuation by duality technique

In Nucl. Phys. B391 (1993) 127, the value of the oblique correction parameter S for walking technicolor theories was estimated using a technique called Analytic Continuation by Duality (ACD). We apply the ACD technique to the perturbative vacuum polarization function and find that it fails to reproduce the well known result S=1/6\pi. This brings into question the reliability of the ACD technique and the ACD estimate of S.Comment: 8 pages, LaTeX, 1 postscript figure. Uses cite.sty, sprocl.sty, and epsfig.sty. Talk presented at the 1996 International Workshop on Perspectives of Strong Coupling Gauge Theories (SCGT'96), 13-16 Nov. 1996, Nagoy

Quantum-state tomography for spin-l systems

We show that the density matrix of a spin-l system can be described entirely in terms of the measurement statistics of projective spin measurements along a minimum of 4l+1 different spin directions. It is thus possible to represent the complete quantum statistics of any N-level system within the spherically symmetric three dimensional space defined by the spin vector. An explicit method for reconstructing the density matrix of a spin-1 system from the measurement statistics of five non-orthogonal spin directions is presented and the generalization to spin-l systems is discussed.Comment: 10 pages, including 2 tables, minor modifications in section II, final version for publication in Phys. Rev.