Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

Statistical distributions in the folding of elastic structures

The behaviour of elastic structures undergoing large deformations is the result of the competition between confining conditions, self-avoidance and elasticity. This combination of multiple phenomena creates a geometrical frustration that leads to complex fold patterns. By studying the case of a rod confined isotropically into a disk, we show that the emergence of the complexity is associated with a well defined underlying statistical measure that determines the energy distribution of sub-elements,``branches'', of the rod. This result suggests that branches act as the ``microscopic'' degrees of freedom laying the foundations for a statistical mechanical theory of this athermal and amorphous system

‘‘Lozenge’’ contour plots in scattering from polymer networks

We present a consistent explanation for the appearance of “lozenge” shapes in contour plots of the two dimensional scattering intensity from stretched polymer networks. By explicitly averaging over quenched variables in a tube model, we show that lozenge patterns arise as a result of chain material that is not directly deformed by the stretch. We obtain excellent agreement with experimental data

First Order Phase Transition of a Long Polymer Chain

We consider a model consisting of a self-avoiding polygon occupying a variable density of the sites of a square lattice. A fixed energy is associated with each $90^\circ$-bend of the polygon. We use a grand canonical ensemble, introducing parameters $\mu$ and $\beta$ to control average density and average (total) energy of the polygon, and show by Monte Carlo simulation that the model has a first order, nematic phase transition across a curve in the $\beta$-$\mu$ plane.Comment: 11 pages, 7 figure

Temperature suppression of Kelvin-wave turbulence in superfluids

Kelvin waves propagating on quantum vortices play a crucial role in the phenomenology of energy dissipation of superfluid turbulence. Previous theoretical studies have consistently focused on the zero-temperature limit of the statistical physics of Kelvin-wave turbulence. In this letter, we go beyond this athermal limit by introducing a small but finite temperature in the form of non-zero mutual friction dissipative force; A situation regularly encountered in actual experiments of superfluid turbulence. In this case we show that there exists a new typical length-scale separating a quasi-inertial range of Kelvin wave turbulence from a far dissipation range. The letter culminates with analytical predictions for the energy spectrum of the Kelvin-wave turbulence in both of these regimes

Dissipation in planar resonant planetary systems

Close-in planetary systems detected by the Kepler mission present an excess of periods ratio that are just slightly larger than some low order resonant values. This feature occurs naturally when resonant couples undergo dissipation that damps the eccentricities. However, the resonant angles appear to librate at the end of the migration process, which is often believed to be an evidence that the systems remain in resonance. Here we provide an analytical model for the dissipation in resonant planetary systems valid for low eccentricities. We confirm that dissipation accounts for an excess of pairs that lie just aside from the nominal periods ratios, as observed by the Kepler mission. In addition, by a global analysis of the phase space of the problem, we demonstrate that these final pairs are non-resonant. Indeed, the separatrices that exist in the resonant systems disappear with the dissipation, and remains only a circulation of the orbits around a single elliptical fixed point. Furthermore, the apparent libration of the resonant angles can be explained using the classical secular averaging method. We show that this artifact is only due to the severe damping of the amplitudes of the eigenmodes in the secular motion.Comment: 18 pages, 20 figures, accepted to A&

Polarization of thick polyvinylidene fluoride/trifluoroethylene copolymer films

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Anisotropic q-Gaussian velocity distributions in LambdaCDM halos

The velocity distribution function (VDF) of dark matter (DM) halos in $\Lambda$CDM dissipationless cosmological simulations, which must be non-separable in its radial and tangential components, is still poorly known. We present the first single-parameter, non-separable, anisotropic model for the VDF in $\Lambda$CDM halos, built from an isotropic $q$-Gaussian (Tsallis) VDF of the isotropic set of dimensionless spherical velocity components (after subtraction of streaming motions), normalized by the respective velocity dispersions. We test our VDF on 90 cluster-mass halos of a dissipationless cosmological simulation. Beyond the virial radius, $r_{\rm vir}$, our model VDF adequately reproduces that measured in the simulated halos, but no $q$-Gaussian model can adequately represent the VDF within $r_{\rm vir}$, as the speed distribution function is then flatter-topped than any $q$-Gaussian can allow. Nevertheless, our VDF fits significantly better the simulations than the commonly used Maxwellian (Gaussian) distribution, at virtually all radii within $5\,r_{\rm vir}$. Within 0.4 (1) $r_{\rm vir}$, the non-Gaussianity index $q$ is (roughly) linearly related to the slope of the density profile and also to the velocity anisotropy profile. We provide a parametrization of the modulation of $q$ with radius for both the median fits and the fit of the stacked halo. At radii of a few percent of $r_{\rm vir}$, corresponding to the Solar position in the Milky Way, our best-fit VDF, although fitting better the simulations than the Gaussian one, overproduces significantly the fraction of high velocity objects, indicating that one should not blindly use these $q$-Gaussian fits to make predictions on the direct detection rate of DM particles.Comment: This version consolidates the published version and the Erratum (changes in red