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

Lorentz Violation and Synchrotron Radiation

We consider the radiation emitted by an ultrarelativistic charged particle moving in a magnetic field, in the presence of an additional Lorentz-violating interaction. In contrast with prior work, we treat a form of Lorentz violation that is represented by a renormalizable operator. Neglecting the radiative reaction force, the particle's trajectory can be determined exactly. The resulting orbit is generally noncircular and does not lie in the place perpendicular to the magnetic field. We do not consider any Lorentz violation in the electromagnetic sector, so the radiation from the accelerated charge can be determined by standard means, and the radiation spectrum will exhibit a Lorentz-violating directional dependence. Using data on emission from the Crab nebula, we can set a bound on a particular combination of Lorentz-violating coefficients at the $6\times10^{-20}$ level.Comment: 14 page

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

Synchrotron and Inverse Compton Constraints on Lorentz Violations for Electrons

We present a method for constraining Lorentz violation in the electron sector, based on observations of the photons emitted by high-energy astrophysical sources. The most important Lorentz-violating operators at the relevant energies are parameterized by a tensor c^{nu mu) with nine independent components. If c is nonvanishing, then there may be either a maximum electron velocity less than the speed of light or a maximum energy for subluminal electrons; both these quantities will generally depend on the direction of an electron's motion. From synchrotron radiation, we may infer a lower bound on the maximum velocity, and from inverse Compton emission, a lower bound on the maximum subluminal energy. With observational data for both these types of emission from multiple celestial sources, we may then place bounds on all nine of the coefficients that make up c. The most stringent bound, on a certain combination of the coefficients, is at the 6 x 10^(-20) level, and bounds on the coefficients individually range from the 7 x 10^(-15) level to the 2 x 10^(-17) level. For most of the coefficients, these are the most precise bounds available, and with newly available data, we can already improve over previous bounds obtained by the same methods.Comment: 28 page

Velocity in Lorentz-Violating Fermion Theories

We consider the role of the velocity in Lorentz-violating fermionic quantum theory, especially emphasizing the nonrelativistic regime. Information about the velocity will be important for the kinematical analysis of scattering and other problems. Working within the minimal standard model extension, we derive new expressions for the velocity. We find that generic momentum and spin eigenstates may not have well-defined velocities. We also demonstrate how several different techniques may be used to shed light on different aspects of the problem. A relativistic operator analysis allows us to study the behavior of the Lorentz-violating Zitterbewegung. Alternatively, by studying the time evolution of Gaussian wave packets, we find that there are Lorentz-violating modifications to the wave packet spreading and the spin structure of the wave function.Comment: 24 page

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

HMMER web server: interactive sequence similarity searching

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them

Time Required for a Sphere to Fall Through a Funnel

We experimentally test a recently proposed theory of the behavior of a single frictional, inelastic, spherical particle falling under gravity through a symmetric funnel. We find that, while many qualitative results of the theory are supported by the data, the quantitative behavior of a real sphere falling through a real funnel differs from the predictions. The behavior above a 45◦ funnel angle, the duration, and the dependence of the duration on the initial horizontal position all show significant deviations from the predicted results. In particular, for drop positions near the gap, the duration of the fall is often significantly less than predicted for 50◦ and 60◦ funnel angles; and at a 60◦ funnel angle, where the data best matches the model, the R 2 goodness of fit is only 0.27. The fit can be significantly improved for 60◦ funnel angle by relaxing the most stringent approximation of the theory, which asserts that the transition from slipping to rolling is governed by a single constant parameter, β, independent of impact speed and angle. We conclude that, although the theory captures most of the key features of the dynamics of a ball falling through a funnel, it does not do so with quantitative accuracy, indicating that for commonly encountered balls and drop heights, a more realistic model of particle collisions is required

Simplified amino acid alphabets based on deviation of conditional probability from random background

The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional probability from random background, a scheme for reduction of amino acid alphabet is proposed. It is observed that evident discrepancy exists between reduced alphabets obtained from raw data of the Miyazawa-Jernigan's and BLOSUM's residue pair counts. Taking homologous sequence database SCOP40 as a test set, we detect homology with the obtained coarse-grained substitution matrices. It is verified that the reduced alphabets obtained well preserve information contained in the original 20-letter alphabet.Comment: 9 pages,3figure

Generational differences in loneliness and its psychological and sociodemographic predictors:An exploratory and confirmatory machine learning study

BACKGROUND: Loneliness is a growing public health issue in the developed world. Among older adults, loneliness is a particular challenge, as the older segment of the population is growing and loneliness is comorbid with many mental as well as physical health issues. Comorbidity and common cause factors make identifying the antecedents of loneliness difficult, however, contemporary machine learning techniques are positioned to tackle this problem. METHODS: This study analyzed four cohorts of older individuals, split into two age groups – 45–69 and 70–79 – to examine which common psychological and sociodemographic are associated with loneliness at different ages. Gradient boosted modeling, a machine learning technique, and regression models were used to identify and replicate associations with loneliness. RESULTS: In all cohorts, higher emotional stability was associated with lower loneliness. In the older group, social circumstances such as living alone were also associated with higher loneliness. In the younger group, extraversion's association with lower loneliness was the only other confirmed relationship. CONCLUSIONS: Different individual and social factors might underlie loneliness differences in distinct age groups. Machine learning methods have the potential to unveil novel associations between psychological and social variables, particularly interactions, and mental health outcomes