One-parameter extension of the Doi-Peliti formalism and relation with orthogonal polynomials

An extension of the Doi-Peliti formalism for stochastic chemical kinetics is proposed. Using the extension, path-integral expressions consistent with previous studies are obtained. In addition, the extended formalism is naturally connected to orthogonal polynomials. We show that two different orthogonal polynomials, i.e., Charlier polynomials and Hermite polynomials, can be used to express the Doi-Peliti formalism explicitly.Comment: 10 page

Doubly stochastic continuous-time hidden Markov approach for analyzing genome tiling arrays

Microarrays have been developed that tile the entire nonrepetitive genomes of many different organisms, allowing for the unbiased mapping of active transcription regions or protein binding sites across the entire genome. These tiling array experiments produce massive correlated data sets that have many experimental artifacts, presenting many challenges to researchers that require innovative analysis methods and efficient computational algorithms. This paper presents a doubly stochastic latent variable analysis method for transcript discovery and protein binding region localization using tiling array data. This model is unique in that it considers actual genomic distance between probes. Additionally, the model is designed to be robust to cross-hybridized and nonresponsive probes, which can often lead to false-positive results in microarray experiments. We apply our model to a transcript finding data set to illustrate the consistency of our method. Additionally, we apply our method to a spike-in experiment that can be used as a benchmark data set for researchers interested in developing and comparing future tiling array methods. The results indicate that our method is very powerful, accurate and can be used on a single sample and without control experiments, thus defraying some of the overhead cost of conducting experiments on tiling arrays.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS248 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Linear density response function in the projector-augmented wave method: Applications to solids, surfaces, and interfaces

We present an implementation of the linear density response function within the projector-augmented wave (PAW) method with applications to the linear optical and dielectric properties of both solids, surfaces, and interfaces. The response function is represented in plane waves while the single-particle eigenstates can be expanded on a real space grid or in atomic orbital basis for increased efficiency. The exchange-correlation kernel is treated at the level of the adiabatic local density approximation (ALDA) and crystal local field effects are included. The calculated static and dynamical dielectric functions of Si, C, SiC, AlP and GaAs compare well with previous calculations. While optical properties of semiconductors, in particular excitonic effects, are generally not well described by ALDA, we obtain excellent agreement with experiments for the surface loss function of the Mg(0001) surface with plasmon energies deviating by less than 0.2 eV. Finally, we apply the method to study the influence of substrates on the plasmon excitations in graphene. On SiC(0001), the long wavelength $\pi$ plasmons are significantly damped although their energies remain almost unaltered. On Al(111) the $\pi$ plasmon is completely quenched due to the coupling to the metal surface plasmon.Comment: 11 pages, 8 figures, articl

Double resonance in the infinite-range quantum Ising model

We study quantum resonance behavior of the infinite-range kinetic Ising model at zero temperature. Numerical integration of the time-dependent Schr\"odinger equation in the presence of an external magnetic field in the $z$ direction is performed at various transverse field strengths $g$. It is revealed that two resonance peaks occur when the energy gap matches the external driving frequency at two distinct values of $g$, one below and the other above the quantum phase transition. From the similar observations already made in classical systems with phase transitions, we propose that the double resonance peaks should be a generic feature of continuous transitions, for both quantum and classical many-body systems.Comment: 4 pages, 5 figure

Finite-volume Hamiltonian method for coupled channel interactions in lattice QCD

Within a multi-channel formulation of $\pi\pi$ scattering, we investigate the use of the finite-volume Hamiltonian approach to resolve scattering observables from lattice QCD spectra. The asymptotic matching of the well-known L\"uscher formalism encodes a unique finite-volume spectrum. Nevertheless, in many practical situations, such as coupled-channel systems, it is advantageous to interpolate isolated lattice spectra in order to extract physical scattering parameters. Here we study the use of the Hamiltonian framework as a parameterisation that can be fit directly to lattice spectra. We find that with a modest amount of lattice data, the scattering parameters can be reproduced rather well, with only a minor degree of model dependence.Comment: 25 pages, 16 figure

4p states and X-Ray Spectroscopy

The 4p states in transition metals and their compounds usually play minor roles on their physical quantities. Recent development of resonant x-ray scattering (RXS) at the K-edge of transition metals, however, casts light on the 4p states, because the signals on orbital and magnetic superlattice spots are brought about by the modulation in the 4p states. The 4p states are extending in solids and thereby sensitive to electronic states at neighboring sites. This characteristic determines the mechanism of RXS that the intensity on the orbital superlattice spots are mainly generated by the lattice distortion and those on magnetic superlattice spots by the coupling of the 4p states with the orbital polarization in the 3d states at neighboring sites. Taking up typical examples for orbital and magnetic RXS, we demonstrate these mechanisms on the basis of the band structure calculation. Finally, we study the MCD spectra at the K-edge, demonstrating that the same mechanism as the magnetic RXS is working.Comment: 9 pages, 9 figures, submitted to Physica Scripta (comment

A key to room-temperature ferromagnetism in Fe-doped ZnO: Cu

Successful synthesis of room-temperature ferromagnetic semiconductors, Zn$_{1-x}$Fe$_{x}$O, is reported. The essential ingredient in achieving room-temperature ferromagnetism in bulk Zn$_{1-x}$Fe$_{x}$O was found to be additional Cu doping. A transition temperature as high as 550 K was obtained in Zn$_{0.94}$Fe$_{0.05}$Cu$_{0.01}$O; the saturation magnetization at room temperature reached a value of $0.75 \mu_{\rm B}$ per Fe. Large magnetoresistance was also observed below $100$K.Comment: 11 pages, 4 figures; to appear in Appl. Phys. Let

Value-Added Meat: Measuring Past Successes and Predicting Future Winners

Livestock industries are significantly affected by changes in consumer behaviour. In order to add value to meat and livestock production, many firms and farms are supporting the development of new products – these products can differ by credence attribute, by degree of processing and by marketing strategies. The literature suggests that one of the most important determinants of success in product innovation is an understanding of the market the product is introduced into. In this report consumer preferences for meat products, by animal species including minor meats, and by type of processing are examined. Responses to economic variables such as price, advertising and income are identified as are responses to food safety and meat related health issues. Interesting results include the fact that income elasticities of demand for meat products purchased at grocery stores are negative in this study and that own and cross price elasticities for certain meats, across processing levels for example, show strong substitutions. Thus introducing new meat products may not result in increased sales by animal species but may only result in substitution of one meat type product for another product of the same meat type. Successful new product introductions or changes in product quality are shown, in this report, to be accompanied by significant marketing/advertising investment and, either by design or by serendipity, to have credence attributes in line with consumer's changing concerns. An example of this is the response in branded chicken sales, at the time of BSE in Canada, for a brand that could advertise itself as being 100% grain fed. Marketing strategies, such as working with the Health Check™ program of the Heart and Stroke Foundation of Canada are shown to have an impact on firm level sales (as well as on sales at the individual product level), a halo effect, that may be of importance in the firm's development of other value-added products. Significant heterogeneity exists in consumer behaviour and it is important to recognize this heterogeneity in the development of value-added meat products. Added to the consumer heterogeneity, in general, is the heterogeneity in responses by meat type. What works for one sector, such as poultry, could be problematic in other sectors given differences in economic interrelationships reported in this study.meat, consumer behavior, value-added, strategic behaviour, Consumer/Household Economics, Food Consumption/Nutrition/Food Safety, Livestock Production/Industries, Marketing, D12, Q18,

ELAV links paused Pol II to alternative polyadenylation in the Drosophila nervious system

Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes. A particularly dramatic form of APA occurs in the developing nervous system of flies and mammals, whereby various developmental genes undergo coordinate 3' UTR extension. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation sites, thereby fostering the formation of exceptionally long 3' UTRs. Here, we present evidence that paused Pol II promotes recruitment of ELAV to extended genes. Replacing promoters of extended genes with heterologous promoters blocks normal 3' extension in the nervous system, while extension-associated promoters can induce 3' extension in ectopic tissues expressing ELAV. Computational analyses suggest that promoter regions of extended genes tend to contain paused Pol II and associated cis-regulatory elements such as GAGA. ChIP-seq assays identify ELAV in the promoter regions of extended genes. Our study provides evidence for a regulatory link between promoter-proximal pausing and APA

Comparison of Magnetic Flux Distribution between a Coronal Hole and a Quiet Region

Employing Big Bear Solar Observatory (BBSO) deep magnetograms and H${\alpha}$ images in a quiet region and a coronal hole, observed on September 14 and 16, 2004, respectively, we have explored the magnetic flux emergence, disappearance and distribution in the two regions. The following results are obtained: (1) The evolution of magnetic flux in the quiet region is much faster than that in the coronal hole, as the flux appeared in the form of ephemeral regions in the quiet region is 4.3 times as large as that in the coronal hole, and the flux disappeared in the form of flux cancellation, 2.9 times as fast as in the coronal hole. (2) More magnetic elements with opposite polarities in the quiet region are connected by arch filaments, estimating from magnetograms and H${\alpha}$ images. (3) We measured the magnetic flux of about 1000 magnetic elements in each observing region. The flux distribution of network and intranetwork (IN) elements is similar in both polarities in the quiet region. For network fields in the coronal hole, the number of negative elements is much more than that of positive elements. However for the IN fields, the number of positive elements is much more than that of negative elements. (4) In the coronal hole, the fraction of negative flux change obviously with different threshold flux density. 73% of the magnetic fields with flux density larger than 2 Gauss is negative polarity, and 95% of the magnetic fields is negative, if we only measure the fields with their flux density larger than 20 Gauss. Our results display that in a coronal hole, stronger fields is occupied by one predominant polarity; however the majority of weaker fields, occupied by the other polarity