An Expansion Term In Hamilton's Equations

For any given spacetime the choice of time coordinate is undetermined. A particular choice is the absolute time associated with a preferred vector field. Using the absolute time Hamilton's equations are $- (\delta H_{c})/(\delta q)=\dot{\pi}+\Theta\pi,$+ (\delta H_{c})/(\delta \pi)=\dot{q}$, where$\Theta = V^{a}_{.;a}$is the expansion of the vector field. Thus there is a hitherto unnoticed term in the expansion of the preferred vector field. Hamilton's equations can be used to describe fluid motion. In this case the absolute time is the time associated with the fluid's co-moving vector. As measured by this absolute time the expansion term is present. Similarly in cosmology, each observer has a co-moving vector and Hamilton's equations again have an expansion term. It is necessary to include the expansion term to quantize systems such as the above by the canonical method of replacing Dirac brackets by commutators. Hamilton's equations in this form do not have a corresponding sympletic form. Replacing the expansion by a particle number$N\equiv exp(-\int\Theta d \ta)$and introducing the particle numbers conjugate momentum$\pi^{N}$the standard sympletic form can be recovered with two extra fields N and$\pi^N$. Briefly the possibility of a non-standard sympletic form and the further possibility of there being a non-zero Finsler curvature corresponding to this are looked at.Comment: 10 page

Parallel approach to sliding window sums

Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure

On the Orbital Period of the Intermediate Polar 1WGA J1958.2+3232

Recently, Norton et al. 2002, on the basis of multiwavelength photometry of 1WGA J1958.2+3232, argued that the -1 day alias of the strongest peak in the power spectrum is the true orbital period of the system, casting doubts on the period estimated by Zharikov et al. 2001. We re-analyzed this system using our photometric and spectroscopic data along with the data kindly provided by Andy Norton and confirm our previous finding. After refining our analysis we find that the true orbital period of this binary system is 4.35h.Comment: 4 pages, 5 figures, Accepted for publication in A&A Letter

Investigating the Effect of Stratospheric Radiation on Seed Germination and Growth

Three seed types: bean (Phaseolus vulgaris), corn (Zea mays) and radish (Raphanus sativus) were flown in a high altitude weather balloon into the mid-stratosphere to investigate the effects of high altitude radiation on germination success and seedling growth. After recovering and planting the seeds, the bean seeds showed lower germination success with exposure to high altitude radiation, and consequently stunted seedling growth. Cord and radish seeds experienced a statistically significant positive effect on germination success form radiation exposure compared to control seeds, but negative effect on seedling growth. Overall, the field experiments presented here support laboratory studies that show radiation exposure on vegetable seeds has a mixed effect on the germination success and negative effect on seedling growth on investigated seed types

Stability of Negative Image Equilibria in Spike-Timing Dependent Plasticity

We investigate the stability of negative image equilibria in mean synaptic weight dynamics governed by spike-timing dependent plasticity (STDP). The neural architecture of the model is based on the electrosensory lateral line lobe (ELL) of mormyrid electric fish, which forms a negative image of the reafferent signal from the fish's own electric discharge to optimize detection of external electric fields. We derive a necessary and sufficient condition for stability, for arbitrary postsynaptic potential functions and arbitrary learning rules. We then apply the general result to several examples of biological interest.Comment: 13 pages, revtex4; uses packages: graphicx, subfigure; 9 figures, 16 subfigure

The String Deviation Equation

The relative motion of many particles can be described by the geodesic deviation equation. This can be derived from the second covariant variation of the point particle's action. It is shown that the second covariant variation of the string action leads to a string deviation equation.Comment: 18 pages, some small changes, no tables or diagrams, LaTex2

Getting More out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/ outcome models in the UK’s largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors’ own group) who work in text processing for biomedicine and other areas. GATE is available online ,1. under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis

Theory Support for the Excited Baryon Program at the Jlab 12 GeV Upgrade

This document outlines major directions in theoretical support for the measurement of nucleon resonance transition form factors at the JLab 12 GeV upgrade with the CLAS12 detector. Using single and double meson production, prominent resonances in the mass range up to 2 GeV will be studied in the range of photon virtuality $Q^2$ up to 12 GeV$^2$ where quark degrees of freedom are expected to dominate. High level theoretical analysis of these data will open up opportunities to understand how the interactions of dressed quarks create the ground and excited nucleon states and how these interactions emerge from QCD. The paper reviews the current status and the prospects of QCD based model approaches that relate phenomenological information on transition form factors to the non-perturbative strong interaction mechanisms, that are responsible for resonance formation.Comment: 52 pages, 19 figures, White Paper of the Electromagnetic N-N* Transition Form Factor Workshop at Jefferson Lab, October 13-15, 2008, Newport News, VA, US