Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

<b>BACKGROUND:</b> MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs are involved in regulating developmental programs of parasitic nematodes is currently unknown. Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question. <b>RESULTS:</b> The small RNAs from larval and adult stages of two parasitic species, Brugia pahangi and Haemonchus contortus, were identified using deep-sequencing and bioinformatic approaches. Comparative analysis to known miRNA sequences reveals that the majority of these miRNAs are novel. Some novel miRNAs are abundantly expressed and display developmental regulation, suggesting important functional roles. Despite the lack of conservation in the miRNA repertoire, genomic positioning of certain miRNAs within or close to specific coding genes is remarkably conserved across diverse species, indicating selection for these associations. Endogenous small-interfering RNAs and Piwi-interacting (pi)RNAs, which regulate gene and transposon expression, were also identified. piRNAs are expressed in adult stage H. contortus, supporting a conserved role in germline maintenance in some parasitic nematodes. <b>CONCLUSIONS:</b> This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention

Fourier Based Three Phase Power Metering System

The increased application of higher frequency nonlinear loads, such as electronic fluorescent ballasts and higher speed adjustable drives, has resulted in the need to monitor the higher power system harmonics which were largely ignored in earlier power monitors. Addressing this need requires a meter with substantially higher sample rate and greater computational power. This paper describes a zero-blind, three-phase, three-element power meter that samples three voltages and four currents at 256 points per cycle. The instrument relies on the FFT to compute real and reactive power at each harmonic and reports total real, reactive, and distortion power on each phase. The innovative design is based on a multiprocessor chip which incorporates a DSP for acquisition and point metering, a CISC processor for floating point summary data, and a RISC processor for interface to support communications with the host PC. The paper concludes with a system evaluation on highly distorted industrial power system waveforms

Stretching and folding versus cutting and shuffling: An illustrated perspective on mixing and deformations of continua

We compare and contrast two types of deformations inspired by mixing applications -- one from the mixing of fluids (stretching and folding), the other from the mixing of granular matter (cutting and shuffling). The connection between mechanics and dynamical systems is discussed in the context of the kinematics of deformation, emphasizing the equivalence between stretches and Lyapunov exponents. The stretching and folding motion exemplified by the baker's map is shown to give rise to a dynamical system with a positive Lyapunov exponent, the hallmark of chaotic mixing. On the other hand, cutting and shuffling does not stretch. When an interval exchange transformation is used as the basis for cutting and shuffling, we establish that all of the map's Lyapunov exponents are zero. Mixing, as quantified by the interfacial area per unit volume, is shown to be exponentially fast when there is stretching and folding, but linear when there is only cutting and shuffling. We also discuss how a simple computational approach can discern stretching in discrete data.Comment: REVTeX 4.1, 9 pages, 3 figures; v2 corrects some misprints. The following article appeared in the American Journal of Physics and may be found at http://ajp.aapt.org/resource/1/ajpias/v79/i4/p359_s1 . Copyright 2011 American Association of Physics Teachers. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the AAP

Trace Complexity of Chaotic Reversible Cellular Automata

Delvenne, K\r{u}rka and Blondel have defined new notions of computational complexity for arbitrary symbolic systems, and shown examples of effective systems that are computationally universal in this sense. The notion is defined in terms of the trace function of the system, and aims to capture its dynamics. We present a Devaney-chaotic reversible cellular automaton that is universal in their sense, answering a question that they explicitly left open. We also discuss some implications and limitations of the construction.Comment: 12 pages + 1 page appendix, 4 figures. Accepted to Reversible Computation 2014 (proceedings published by Springer

Bifurcations in the Space of Exponential Maps

This article investigates the parameter space of the exponential family $z\mapsto \exp(z)+\kappa$. We prove that the boundary (in \C) of every hyperbolic component is a Jordan arc, as conjectured by Eremenko and Lyubich as well as Baker and Rippon. In fact, we prove the stronger statement that the exponential bifurcation locus is connected in \C, which is an analog of Douady and Hubbard's celebrated theorem that the Mandelbrot set is connected. We show furthermore that $\infty$ is not accessible through any nonhyperbolic ("queer") stable component. The main part of the argument consists of demonstrating a general "Squeezing Lemma", which controls the structure of parameter space near infinity. We also prove a second conjecture of Eremenko and Lyubich concerning bifurcation trees of hyperbolic components.Comment: 29 pages, 3 figures. The main change in the new version is the introduction of Theorem 1.1 on the connectivity of the bifurcation locus, which follows from the results of the original version but was not explicitly stated. Also, some small revisions have been made and references update

Hash Functions Using Chaotic Iterations

International audienceIn this paper, a novel formulation of discrete chaotic iterations in the field of dynamical systems is given. Their topological properties are studied: it is mathematically proven that, under some conditions, these iterations have a chaotic behavior as defined by Devaney. This chaotic behavior allows us to propose a way to generate new hash functions. An illustrative example is detailed in order to show how to use our theoretical study in practice

Cutting and Shuffling a Line Segment: Mixing by Interval Exchange Transformations

We present a computational study of finite-time mixing of a line segment by cutting and shuffling. A family of one-dimensional interval exchange transformations is constructed as a model system in which to study these types of mixing processes. Illustrative examples of the mixing behaviors, including pathological cases that violate the assumptions of the known governing theorems and lead to poor mixing, are shown. Since the mathematical theory applies as the number of iterations of the map goes to infinity, we introduce practical measures of mixing (the percent unmixed and the number of intermaterial interfaces) that can be computed over given (finite) numbers of iterations. We find that good mixing can be achieved after a finite number of iterations of a one-dimensional cutting and shuffling map, even though such a map cannot be considered chaotic in the usual sense and/or it may not fulfill the conditions of the ergodic theorems for interval exchange transformations. Specifically, good shuffling can occur with only six or seven intervals of roughly the same length, as long as the rearrangement order is an irreducible permutation. This study has implications for a number of mixing processes in which discontinuities arise either by construction or due to the underlying physics.Comment: 21 pages, 10 figures, ws-ijbc class; accepted for publication in International Journal of Bifurcation and Chao

Reversible skew laurent polynomial rings and deformations of poisson automorphisms

A skew Laurent polynomial ring S = R[x(+/- 1); alpha] is reversible if it has a reversing automorphism, that is, an automorphism theta of period 2 that transposes x and x(-1) and restricts to an automorphism gamma of R with gamma = gamma(-1). We study invariants for reversing automorphisms and apply our methods to determine the rings of invariants of reversing automorphisms of the two most familiar examples of simple skew Laurent polynomial rings, namely a localization of the enveloping algebra of the two-dimensional non-abelian solvable Lie algebra and the coordinate ring of the quantum torus, both of which are deformations of Poisson algebras over the base field F. Their reversing automorphisms are deformations of Poisson automorphisms of those Poisson algebras. In each case, the ring of invariants of the Poisson automorphism is the coordinate ring B of a surface in F-3 and the ring of invariants S-theta of the reversing automorphism is a deformation of B and is a factor of a deformation of F[x(1), x(2), x(3)] for a Poisson bracket determined by the appropriate surface

Calculations of Neutron Reflectivity in the eV Energy Range from Mirrors made of Heavy Nuclei with Neutron-Nucleus Resonances

We evaluate the reflectivity of neutron mirrors composed of certain heavy nuclei which possess strong neutron-nucleus resonances in the eV energy range. We show that the reflectivity of such a mirror for some nuclei can in principle be high enough near energies corresponding to compound neutron-nucleus resonances to be of interest for certain scientific applications in non-destructive evaluation of subsurface material composition and in the theory of neutron optics beyond the kinematic limit.Comment: 18 pages, 5 figures, 1 tabl