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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, 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, 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. 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 crystal. To obtain transmission radiographs, diffe\-rent phantom
materials have been irradiated with a 3x3~cm 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 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 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 bound systems.
For this purpose, the resonating group equation is transformed into a standard
Schr\"odinger equation in which a nonlocal effective interaction
potential is included. Solving the Schr\"odinger equation by the variational
method, we are able to reproduce the masses of some currently concerned
states and get a view that these states possibly exist as
molecular states. For the system, the same calculation gives no support to
the existence of the resonance 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 of
patterns are embedded via asymmetric Hebbian connections, namely,
for the number of neuron ('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
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