Physically-inspired Gaussian process models for post-transcriptional regulation in Drosophila

The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression patterns and levels. Since the post-transcriptional regulation of Drosophila depends on spatiotemporal interactions between mRNAs and gap proteins, proper physically-inspired stochastic models are required to study the link between both quantities. Previous research attempts have shown that using Gaussian processes (GPs) and differential equations lead to promising predictions when analysing regulatory networks. Here we aim at further investigating two types of physically-inspired GP models based on a reaction-diffusion equation where the main difference lies in where the prior is placed. While one of them has been studied previously using protein data only, the other is novel and yields a simple approach requiring only the differentiation of kernel functions. In contrast to other stochastic frameworks, discretising the spatial space is not required here. Both GP models are tested under different conditions depending on the availability of gap gene mRNA expression data. Finally, their performances are assessed on a high-resolution dataset describing the blastoderm stage of the early embryo of Drosophila melanogaster

Relativistic Two-stream Instability

We study the (local) propagation of plane waves in a relativistic, non-dissipative, two-fluid system, allowing for a relative velocity in the "background" configuration. The main aim is to analyze relativistic two-stream instability. This instability requires a relative flow -- either across an interface or when two or more fluids interpenetrate -- and can be triggered, for example, when one-dimensional plane-waves appear to be left-moving with respect to one fluid, but right-moving with respect to another. The dispersion relation of the two-fluid system is studied for different two-fluid equations of state: (i) the "free" (where there is no direct coupling between the fluid densities), (ii) coupled, and (iii) entrained (where the fluid momenta are linear combinations of the velocities) cases are considered in a frame-independent fashion (eg. no restriction to the rest-frame of either fluid). As a by-product of our analysis we determine the necessary conditions for a two-fluid system to be causal and absolutely stable and establish a new constraint on the entrainment.Comment: 15 pages, 2 eps-figure

Propagator of a Charged Particle with a Spin in Uniform Magnetic and Perpendicular Electric Fields

We construct an explicit solution of the Cauchy initial value problem for the time-dependent Schroedinger equation for a charged particle with a spin moving in a uniform magnetic field and a perpendicular electric field varying with time. The corresponding Green function (propagator) is given in terms of elementary functions and certain integrals of the fields with a characteristic function, which should be found as an analytic or numerical solution of the equation of motion for the classical oscillator with a time-dependent frequency. We discuss a particular solution of a related nonlinear Schroedinger equation and some special and limiting cases are outlined.Comment: 17 pages, no figure

Estimating ET using scintillometers and satellites in an irrigated vineyard in the Costa De Hermosillo, Sonora, Mexico

Observation techniques for surface energy balancecomponents on kilometer scale. Several methods have been proposed to estimate ET overlarge areas which combine Earth Observation Satellite datawith standard climate data. Here we use the Makkinkapproach where incoming solar radiation is obtained bycalculating exoatmospheric incoming solar radiation, usingvisible data from GOES West to estimate cloudiness and16-day composite MODIS Enhanced Vegetation Index data toestimate fractional vegetation cover. This methodology can beused operationally at a spatial resolution of 1 km2 butvalidation data are required at a similar spatial scale. LargeAperture Scintillometers transmit and receive near infraredradiation over distances of several kilometers and providemeasurements of the structure parameter for the refractiveindex of air which is related by Monin-Obukhov SimilarityTheory to the surface sensible heat flux (H), which requiresmeasurements of air temperature, pressure and wind speed.ET can then be obtained indirectly as the residual of theenergy balance, ET = Rn – G – H so that we need estimates ofNet Radiation (Rn) and Soil Heat Flux (G) as well. Ascintillometer (Scintec BLS-450) was installed over anirrigated vineyard with area of 72 hectares (1200m x 600m) inJune 6th 2009. Net Radiation was measured in the field andsoil heat flux was estimated using G = A * Rn, where theparameter A was obtained from 8-day composite MODIS LandSurface Temperature data. Comparison of ET derived fromsatellite and scintillometer for June 2009 showed considerablescatter with r2 = 0.81 and ETSAT = 1.12 * ETBLS. Thisapparent overestimation from the satellite-based ET is similarto that found in previous work. However, in these initialcalculations it was assumed that unstable conditions wouldprevail during the daytime but it appears that stableconditions often occur in the late afternoon. Secondly, theestimation of G needs to be carefully revised since this canhave a large effect on ET. These factors are being included inthe analysis of data over an entire growing season to assessthe seasonal behavior of the model

W=0 Pairing in (N,N)(N,N) Carbon Nanotubes away from Half Filling

We use the Hubbard Hamiltonian $H$ on the honeycomb lattice to represent the valence bands of carbon single-wall $(N,N)$ nanotubes. A detailed symmetry analysis shows that the model allows W=0 pairs which we define as two-body singlet eigenstates of $H$ with vanishing on-site repulsion. By means of a non-perturbative canonical transformation we calculate the effective interaction between the electrons of a W=0 pair added to the interacting ground state. We show that the dressed W=0 pair is a bound state for resonable parameter values away from half filling. Exact diagonalization results for the (1,1) nanotube confirm the expectations. For $(N,N)$ nanotubes of length $l$, the binding energy of the pair depends strongly on the filling and decreases towards a small but nonzero value as $l \to \infty$. We observe the existence of an optimal doping when the number of electrons per C atom is in the range 1.2$\div$1.3, and the binding energy is of the order of 0.1 $\div$ 1 meV.Comment: 16 pages, 6 figure

Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma

Neuroblastoma is a cancer of the developing sympathetic nervous system. It is diagnosed in 600–700 children per year in the United States and accounts for 12% of pediatric cancer deaths. Despite recent advances in our understanding of this malignancy's complex genetic architecture, the contribution of rare germline variants remains undefined. Here, we conducted a genome-wide analysis of large (>500 kb), rare (<1%) germline copy number variants (CNVs) in two independent, multi-ethnic cohorts totaling 5,585 children with neuroblastoma and 23,505 cancer-free control children. We identified a 550-kb deletion on chromosome 16p11.2 significantly enriched in neuroblastoma cases (0.39% of cases and 0.03% of controls; p = 3.34 × 10−9). Notably, this CNV corresponds to a known microdeletion syndrome that affects approximately one in 3,000 children and confers risk for diverse developmental phenotypes including autism spectrum disorder and other neurodevelopmental disorders. The CNV had a substantial impact on neuroblastoma risk, with an odds ratio of 13.9 (95% confidence interval = 5.8–33.4). The association remained significant when we restricted our analysis to individuals of European ancestry in order to mitigate potential confounding by population stratification (0.42% of cases and 0.03% of controls; p = 4.10 × 10−8). We used whole-genome sequencing (WGS) to validate the deletion in paired germline and tumor DNA from 12 cases. Finally, WGS of four parent-child trios revealed that the deletion primarily arose de novo without maternal or paternal bias. This finding expands the clinical phenotypes associated with 16p11.2 microdeletion syndrome to include cancer, and it suggests that disruption of the 16p11.2 region may dysregulate neurodevelopmental pathways that influence both neurological phenotypes and neuroblastoma

Signatures of Relativistic Neutrinos in CMB Anisotropy and Matter Clustering

We present a detailed analytical study of ultra-relativistic neutrinos in cosmological perturbation theory and of the observable signatures of inhomogeneities in the cosmic neutrino background. We note that a modification of perturbation variables that removes all the time derivatives of scalar gravitational potentials from the dynamical equations simplifies their solution notably. The used perturbations of particle number per coordinate, not proper, volume are generally constant on superhorizon scales. In real space an analytical analysis can be extended beyond fluids to neutrinos. The faster cosmological expansion due to the neutrino background changes the acoustic and damping angular scales of the cosmic microwave background (CMB). But we find that equivalent changes can be produced by varying other standard parameters, including the primordial helium abundance. The low-l integrated Sachs-Wolfe effect is also not sensitive to neutrinos. However, the gravity of neutrino perturbations suppresses the CMB acoustic peaks for the multipoles with l>~200 while it enhances the amplitude of matter fluctuations on these scales. In addition, the perturbations of relativistic neutrinos generate a *unique phase shift* of the CMB acoustic oscillations that for adiabatic initial conditions cannot be caused by any other standard physics. The origin of the shift is traced to neutrino free-streaming velocity exceeding the sound speed of the photon-baryon plasma. We find that from a high resolution, low noise instrument such as CMBPOL the effective number of light neutrino species can be determined with an accuracy of sigma(N_nu) = 0.05 to 0.09, depending on the constraints on the helium abundance.Comment: 38 pages, 7 figures. Version accepted for publication in PR

EPO does not promote interaction between the erythropoietin and beta-common receptors

A direct interaction between the erythropoietin (EPOR) and the beta-common (βc) receptors to form an Innate Repair Receptor (IRR) is controversial. On one hand, studies have shown a functional link between EPOR and βc receptor in tissue protection while others have shown no involvement of the βc receptor in tissue repair. To date there is no biophysical evidence to confirm a direct association of the two receptors either in vitro or in vivo. We investigated the existence of an interaction between the extracellular regions of EPOR and the βc receptor in silico and in vitro (either in the presence or absence of EPO or EPO-derived peptide ARA290). Although a possible interaction between EPOR and βc was suggested by our computational and genomic studies, our in vitro biophysical analysis demonstrates that the extracellular regions of the two receptors do not specifically associate. We also explored the involvement of the βc receptor gene (Csf2rb) under anaemic stress conditions and found no requirement for the βc receptor in mice. In light of these studies, we conclude that the extracellular regions of the EPOR and the βc receptor do not directly interact and that the IRR is not involved in anaemic stress.Karen S. Cheung Tung Shing, Sophie E. Broughton, Tracy L. Nero, Kevin Gillinder, Melissa D. Ilsley, Hayley Ramshaw, Angel F. Lopez, Michael D. W. Griffin, Michael W. Parker, Andrew C. Perkins, Urmi Dhaga

Late-time Entropy Production from Scalar Decay and Relic Neutrino Temperature

Entropy production from scalar decay in the era of low temperatures after neutrino decoupling will change the ratio of the relic neutrino temperature to the CMB temperature, and, hence, the value of N_eff, the effective number of neutrino species. Such scalar decay is relevant to reheating after thermal inflation, proposed to dilute massive particles, like the moduli and the gravitino, featuring in supersymmetric and string theories. The effect of such entropy production on the relic neutrino temperature ratio is calculated in a semi-analytic manner, and a recent lower bound on this ratio, obtained from the WMAP satellite and 2dF galaxy data, is used to set a lower bound of ~ 1.5 x 10^-23 Gev on the scalar decay constant, corresponding to a reheating temperature of about 3.3 Mev.Comment: 13 pages, to appear in PR