Statistical Time Series Models of Pilot Control with Applications to Instrument Discrimination

A general description of the methodology used in obtaining the transfer function models and verification of model fidelity, frequency domain plots of the modeled transfer functions, numerical results obtained from an analysis of poles and zeroes obtained from z plane to s-plane conversions of the transfer functions, and the results of a study on the sequential introduction of other variables, both exogenous and endogenous into the loop are contained

Gauge Invariance and the Pauli-Villars Regulator in Lorentz- and CPT-Violating Electrodynamics

We examine the nonperturbative structure of the radiatively induced Chern-Simons term in a Lorentz- and CPT-violating modification of QED. Although the coefficient of the induced Chern-Simons term is in general undetermined, the nonperturbative theory appears to generate a definite value. However, the CPT-even radiative corrections in this same formulation of the theory generally break gauge invariance. We show that gauge invariance may yet be preserved through the use of a Pauli-Villars regulator, and, contrary to earlier expectations, this regulator does not necessarily give rise to a vanishing Chern-Simons term. Instead, two possible values of the Chern-Simons coefficient are allowed, one zero and one nonzero. This formulation of the theory therefore allows the coefficient to vanish naturally, in agreement with experimental observations.Comment: 8 page

Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009

Statistical Mechanics and Lorentz Violation

The theory of statistical mechanics is studied in the presence of Lorentz-violating background fields. The analysis is performed using the Standard-Model Extension (SME) together with a Jaynesian formulation of statistical inference. Conventional laws of thermodynamics are obtained in the presence of a perturbed hamiltonian that contains the Lorentz violating terms. As an example, properties of the nonrelativistic ideal gas are calculated in detail. To lowest order in Lorentz violation, the scalar thermodynamic variables are only corrected by a rotationally invariant combination of parameters that mimics a (frame dependent) effective mass. Spin couplings can induce a temperature independent polarization in the classical gas that is not present in the conventional case. Precision measurements in the residual expectation values of the magnetic moment of Fermi gases in the limit of high temperature may provide interesting limits on these parameters.Comment: 7 pages, revte

Asymptotically Universal Crossover in Perturbation Theory with a Field Cutoff

We discuss the crossover between the small and large field cutoff (denoted x_{max}) limits of the perturbative coefficients for a simple integral and the anharmonic oscillator. We show that in the limit where the order k of the perturbative coefficient a_k(x_{max}) becomes large and for x_{max} in the crossover region, a_k(x_{max}) is proportional to the integral from -infinity to x_{max} of e^{-A(x-x_0(k))^2}dx. The constant A and the function x_0(k) are determined empirically and compared with exact (for the integral) and approximate (for the anharmonic oscillator) calculations. We discuss how this approach could be relevant for the question of interpolation between renormalization group fixed points.Comment: 15 pages, 11 figs., improved and expanded version of hep-th/050304

NCBI BLAST: a better web interface

Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified search forms, improved navigation, a list of recent BLAST results, saved search strategies and a documentation directory. Here, we describe the BLAST web application's new features, explain design decisions and outline plans for future improvement

Correction, improvement and model verification of CARE 3, version 3

An independent verification of the CARE 3 mathematical model and computer code was conducted and reported in NASA Contractor Report 166096, Review and Verification of CARE 3 Mathematical Model and Code: Interim Report. The study uncovered some implementation errors that were corrected and are reported in this document. The corrected CARE 3 program is called version 4. Thus the document, correction. improvement, and model verification of CARE 3, version 3 was written in April 1984. It is being published now as it has been determined to contain a more accurate representation of CARE 3 than the preceding document of April 1983. This edition supercedes NASA-CR-166122 entitled, 'Correction and Improvement of CARE 3,' version 3, April 1983

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

An Alternative Model of Amino Acid Replacement

The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment. We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.Comment: Minor improvements. Added figure and reference