Inference for reaction networks using the Linear Noise Approximation

We consider inference for the reaction rates in discretely observed networks such as those found in models for systems biology, population ecology and epidemics. Most such networks are neither slow enough nor small enough for inference via the true state-dependent Markov jump process to be feasible. Typically, inference is conducted by approximating the dynamics through an ordinary differential equation (ODE), or a stochastic differential equation (SDE). The former ignores the stochasticity in the true model, and can lead to inaccurate inferences. The latter is more accurate but is harder to implement as the transition density of the SDE model is generally unknown. The Linear Noise Approximation (LNA) is a first order Taylor expansion of the approximating SDE about a deterministic solution and can be viewed as a compromise between the ODE and SDE models. It is a stochastic model, but discrete time transition probabilities for the LNA are available through the solution of a series of ordinary differential equations. We describe how a restarting LNA can be efficiently used to perform inference for a general class of reaction networks; evaluate the accuracy of such an approach; and show how and when this approach is either statistically or computationally more efficient than ODE or SDE methods. We apply the LNA to analyse Google Flu Trends data from the North and South Islands of New Zealand, and are able to obtain more accurate short-term forecasts of new flu cases than another recently proposed method, although at a greater computational cost

Quantum Separability of Thermal Spin One Boson Systems

Using the temperature Green's function approach we investigate entanglement between two non-interacting spin 1 bosons in thermal equilibrium. We show that, contrary to the fermion case, the entanglement is absent in the spin density matrix. Separability is demonstrated using the Peres-Horodecki criterion for massless particles such as photons in black body radiation. For massive particles, we show that the density matrix can be decomposed with separable states.Comment: References & comments related to AQFT added. no figure, revtex4, to be published in Phys. Lett.

Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds

A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical mastitis to be mapped to a small interval (<1 cM) between the markers BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9

Constraints on decaying Dark Matter from XMM-Newton observations of M31

We derive constraints on parameters of the radiatively decaying Dark Matter (DM) particles, using XMM-Newton EPIC spectra of the Andromeda galaxy (M31). Using the observations of the outer (5'-13') parts of M31 we improve the existing constraints. For the case of sterile neutrino DM, combining our constraints with the latest computation of abundances of sterile neutrino in the Dodelson-Widrow (DW) scenario, we obtain the lower mass limit m_s < 4 keV, which is stronger than the previous one m_s < 6 kev, obtained recently by Asaka et al. (2007) [hep-ph/0612182]. Comparing this limit with the most recent results on Lyman-alpha forest analysis of Viel et al. (2007) [arXiv:0709.0131] (m_s > 5.6 kev), we argue that the scenario in which all the DM is produced via DW mechanism is ruled out. We discuss however other production mechanisms and note that the sterile neutrino remains a viable candidate of Dark Matter, either warm or cold.Comment: 13 pages, 12 figure

Constraining DM properties with SPI

Using the high-resolution spectrometer SPI on board the International Gamma-Ray Astrophysics Laboratory (INTEGRAL), we search for a spectral line produced by a dark matter(DM) particle with a mass in the range 40keV < M_DM < 14MeV, decaying in the DM halo of the Milky Way. To distinguish the DM decay line from numerous instrumental lines found in the SPI background spectrum, we study the dependence of the intensity of the line signal on the offset of the SPI pointing from the direction toward the Galactic Centre. After a critical analysis of the uncertainties of the DM density profile in the inner Galaxy, we find that the intensity of the DM decay line should decrease by at least a factor of 3 when the offset from the Galactic Centre increases from 0 to 180 degrees. We find that such a pronounced variation of the line flux across the sky is not observed for any line, detected with a significance higher than 3 sigma in the SPI background spectrum. Possible DM decay origin is not ruled out only for the unidentified spectral lines, having low (~3 sigma) significance or coinciding in position with the instrumental ones. In the energy interval from 20 keV to 7 MeV, we derive restrictions on the DM decay line flux, implied by the (non-)detection of the DM decay line. For a particular DM candidate, the sterile neutrino of mass MDM, we derive a bound on the mixing angle.Comment: Minor changes; v.2 - Final version appeared in MNRA

Genetic and environmental influences on human height from infancy through adulthood at different levels of parental education

Genetic factors explain a major proportion of human height variation, but differences in mean stature have also been found between socio-economic categories suggesting a possible effect of environment. By utilizing a classical twin design which allows decomposing the variation of height into genetic and environmental components, we tested the hypothesis that environmental variation in height is greater in offspring of lower educated parents. Twin data from 29 cohorts including 65,978 complete twin pairs with information on height at ages 1 to 69 years and on parental education were pooled allowing the analyses at different ages and in three geographic-cultural regions (Europe, North America and Australia, and East Asia). Parental education mostly showed a positive association with offspring height, with significant associations in mid-childhood and from adolescence onwards. In variance decomposition modeling, the genetic and environmental variance components of height did not show a consistent relation to parental education. A random-effects meta-regression analysis of the aggregate-level data showed a trend towards greater shared environmental variation of height in low parental education families. In conclusion, in our very large dataset from twin cohorts around the globe, these results provide only weak evidence for the study hypothesis.Peer reviewe