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

Dielectric Behavior of Nonspherical Cell Suspensions

Recent experiments revealed that the dielectric dispersion spectrum of fission yeast cells in a suspension was mainly composed of two sub-dispersions. The low-frequency sub-dispersion depended on the cell length, whereas the high-frequency one was independent of it. The cell shape effect was qualitatively simulated by an ellipsoidal cell model. However, the comparison between theory and experiment was far from being satisfactory. In an attempt to close up the gap between theory and experiment, we considered the more realistic cells of spherocylinders, i.e., circular cylinders with two hemispherical caps at both ends. We have formulated a Green function formalism for calculating the spectral representation of cells of finite length. The Green function can be reduced because of the azimuthal symmetry of the cell. This simplification enables us to calculate the dispersion spectrum and hence access the effect of cell structure on the dielectric behavior of cell suspensions.Comment: Preliminary results have been reported in the 2001 March Meeting of the American Physical Society. Accepted for publications in J. Phys.: Condens. Matte

Cosmological Three-Point Function: Testing The Halo Model Against Simulations

We perform detailed comparison of the semi-analytic halo model predictions with measurements in numerical simulations of the two and three point correlation functions (3PCF), as well as power spectrum and bispectrum. We discuss the accuracy and self-consistency of the halo model description of gravitational clustering in the non-linear regime and constrain halo model parameters. We exploit the recently proposed multipole expansion of three point statistics that expresses rotation invariance in the most natural way. This not only offers technical advantages by reducing the integrals required for the halo model predictions, but amounts to a convenient way of compressing the information contained in the 3PCF. We find that, with an appropriate choice of the halo boundary and mass function cut-off, halo model predictions are in good agreement with the bispectrum measured in numerical simulations. However, the halo model predicts less than the observed configuration dependence of the 3PCF on ~ Mpc scales. This effect is mainly due to quadrupole moment deficit, possibly related to the assumption of spherical halo geometry. Our analysis shows that using its harmonic decomposition, the full configuration dependence of the 3PCF in the non-linear regime can be compressed into just a few numbers, the lowest multipoles. Moreover, these multipoles are closely related to the highest signal to noise eigenmodes of the 3PCF. Therefore this estimator may simplify future analyses aimed at constraining cosmological and halo model parameters from observational data.Comment: Minor corrections. Accepted for publication by Ap

Proton Sea Quark Flavour Asymmetry and Roper Resonance

We study the proton and the Roper resonance together with the meson cloud model, by constructing a Hamiltonian matrix and solving the eigenvalue equation. The proton sea quark flavour asymmetry and some properties of the Roper resonance are thus reproduced in one scheme

Magnetic Evolution and Temperature Variation in a Coronal Hole

We have explored the magnetic flux evolution and temperature variation in a coronal-hole region, using Big Bear Solar Observatory (BBSO) deep magnetograms and {\it SOHO}/EIT images observed from 2005 October 10 to 14. For comparison, we also investigated a neighboring quiet region of the Sun. The coronal hole evolved from its mature stage to its disappearance during the observing period. We have obtained the following results: (1) When the coronal hole was well developed on October 10, about 60 % of the magnetic flux was positive. The EUV brightness was 420 counts pixel$^{-1}$, and the coronal temperature, estimated from the line ratio of the EIT 195 {\AA} and 171 {\AA} images, was 1.07 MK. (2) On October 14, when the coronal hole had almost disappeared, 51 % of the magnetic flux was positive, the EUV radiance was 530 counts pixel$^{-1}$, and the temperature was 1.10 MK. (3) In the neighboring quiet region, the fraction of positive flux varied between 0.49 and 0.47. The EUV brightness displayed an irregular variation, with a mean value of 870 counts pixel$^{-1}$. The temperature was almost constant at 1.11 MK during the five-day observation. Our results demonstrate that in a coronal hole less imbalance of the magnetic flux in opposite polarities leads to stronger EUV brightness and higher coronal temperatures

Proton radiography to improve proton radiotherapy: Simulation study at different proton beam energies

To improve the quality of cancer treatment with protons, a translation of X-ray Computed Tomography (CT) images into a map of the proton stopping powers needs to be more accurate. Proton stopping powers determined from CT images have systematic uncertainties in the calculated proton range in a patient of typically 3-4\% and even up to 10\% in region containing bone~\cite{USchneider1995,USchneider1996,WSchneider2000,GCirrone2007,HPaganetti2012,TPlautz2014,GLandry2013,JSchuemann2014}. As a consequence, part of a tumor may receive no dose, or a very high dose can be delivered in healthy ti\-ssues and organs at risks~(e.g. brain stem)~\cite{ACKnopf2013}. A transmission radiograph of high-energy protons measuring proton stopping powers directly will allow to reduce these uncertainties, and thus improve the quality of treatment. The best way to obtain a sufficiently accurate radiograph is by tracking individual protons traversing the phantom (patient)~\cite{GCirrone2007,TPlautz2014,VSipala2013}. In our simulations we have used an ideal position sensitive detectors measuring a single proton before and after a phantom, while the residual energy of a proton was detected by a BaF$_{2}$ crystal. To obtain transmission radiographs, diffe\-rent phantom materials have been irradiated with a 3x3~cm$^{2}$ scattered proton beam, with various beam energies. The simulations were done using the Geant4 simulation package~\cite{SAgostinelli2003}. In this study we focus on the simulations of the energy loss radiographs for various proton beam energies that are clinically available in proton radiotherapy.Comment: 6 pages, 6 figures, Presented at Jagiellonian Symposium on Fundamental and Applied Subatomic Physics, 7-12 June, 2015, Krak\'ow, Polan

Strange meson-nucleon states in the quark potential model

The quark potential model and resonating group method are used to investigate the $\bar{K}N$ bound states and/or resonances. The model potential consists of the t-channel and s-channel one-gluon exchange potentials and the confining potential with incorporating the QCD renormalization correction and the spin-orbital suppression effect in it. It was shown in our previous work that by considering the color octet contribution, use of this model to investigate the $KN$ low energy elastic scattering leads to the results which are in pretty good agreement with the experimental data. In this paper, the same model and method are employed to calculate the masses of the $\bar{K}N$ bound systems. For this purpose, the resonating group equation is transformed into a standard Schr\"odinger equation in which a nonlocal effective $\bar{K}N$ interaction potential is included. Solving the Schr\"odinger equation by the variational method, we are able to reproduce the masses of some currently concerned $\bar{K}N$ states and get a view that these states possibly exist as $\bar{K}N$ molecular states. For the $KN$ system, the same calculation gives no support to the existence of the resonance $\Theta ^{+}(1540)$ which was announced recently.Comment: 15 pages, 4 figure

Modeling study on the validity of a possibly simplified representation of proteins

The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones. A large ground state gap for the native structure shows the thermodynamic stability of the reduced sequences. The general validity of such a five-letter reduction is further studied via the correlation between the reduced sequences and the original ones. As a comparison, a reduction with two letters is found not to reproduce the native structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure

Pattern-recalling processes in quantum Hopfield networks far from saturation

As a mathematical model of associative memories, the Hopfield model was now well-established and a lot of studies to reveal the pattern-recalling process have been done from various different approaches. As well-known, a single neuron is itself an uncertain, noisy unit with a finite unnegligible error in the input-output relation. To model the situation artificially, a kind of 'heat bath' that surrounds neurons is introduced. The heat bath, which is a source of noise, is specified by the 'temperature'. Several studies concerning the pattern-recalling processes of the Hopfield model governed by the Glauber-dynamics at finite temperature were already reported. However, we might extend the 'thermal noise' to the quantum-mechanical variant. In this paper, in terms of the stochastic process of quantum-mechanical Markov chain Monte Carlo method (the quantum MCMC), we analytically derive macroscopically deterministic equations of order parameters such as 'overlap' in a quantum-mechanical variant of the Hopfield neural networks (let us call "quantum Hopfield model" or "quantum Hopfield networks"). For the case in which non-extensive number $p$ of patterns are embedded via asymmetric Hebbian connections, namely, $p/N \to 0$ for the number of neuron $N \to \infty$ ('far from saturation'), we evaluate the recalling processes for one of the built-in patterns under the influence of quantum-mechanical noise.Comment: 10 pages, 3 figures, using jpconf.cls, Proc. of Statphys-Kolkata VI