Vis-SPLIT: Interactive Hierarchical Modeling for mRNA Expression Classification

We propose an interactive visual analytics tool, Vis-SPLIT, for partitioning a population of individuals into groups with similar gene signatures. Vis-SPLIT allows users to interactively explore a dataset and exploit visual separations to build a classification model for specific cancers. The visualization components reveal gene expression and correlation to assist specific partitioning decisions, while also providing overviews for the decision model and clustered genetic signatures. We demonstrate the effectiveness of our framework through a case study and evaluate its usability with domain experts. Our results show that Vis-SPLIT can classify patients based on their genetic signatures to effectively gain insights into RNA sequencing data, as compared to an existing classification system.Comment: To be published in IEEE Visualization and Visual Analytics (VIS), 202

On the twist-2 contributions to polarized structure functions and new sum rules

The twist-2 contributions to the polarized structure functions in deep inelastic lepton--hadron scattering are calculated including the exchange of weak bosons and using both the operator product expansion and the covariant parton model. A new relation between two structure functions leading to a sequence of new sum rules is found. The light quark mass corrections to the structure functions are derived in lowest order QCD.Comment: 15 pages Latex, inclding five eps-figures, all compressed by uufile substituting the ps-file available befor

Polarized deep inelastic scattering at high energies and parity violating structure functions

A comprehensive analysis of deep inelastic scattering of polarized charged leptons on polarized nucleons is presented; weak interaction contributions, both in neutral and charged current processes, are taken into account and the parity violating polarized nucleon structure functions are studied. Possible ways of their measurements and their interpretations in the parton model are discussed.Comment: (slightly modified version, includes a few new references and corrects few misprints for publication), 14 pages in TeX (needs harvmac) no figure, DFTT 80/9

A Census of Baryons and Dark Matter in an Isolated, Milky Way-sized Elliptical Galaxy

We present a study of the dark and luminous matter in the isolated elliptical galaxy NGC720, based on deep X-ray observations made with Chandra and Suzaku. The gas is reliably measured to ~R2500, allowing us to place good constraints on the enclosed mass and baryon fraction (fb) within this radius (M2500=1.6e12+/-0.2e12 Msun, fb(2500)=0.10+/-0.01; systematic errors are <~20%). The data indicate that the hot gas is close to hydrostatic, which is supported by good agreement with a kinematical analysis of the dwarf satellite galaxies. We confirm a dark matter (DM) halo at ~20-sigma. Assuming an NFW DM profile, our physical model for the gas distribution enables us to obtain meaningful constraints at scales larger than R2500, revealing that most of the baryons are in the hot gas. We find that fb within Rvir is consistent with the Cosmological value, confirming theoretical predictions that a ~Milky Way-mass (Mvir=3.1e12+/-0.4e12 Msun) galaxy can sustain a massive, quasi-hydrostatic gas halo. While fb is higher than the cold baryon fraction typically measured in similar-mass spiral galaxies, both the gas fraction (fg) and fb in NGC720 are consistent with an extrapolation of the trends with mass seen in massive galaxy groups and clusters. After correcting for fg, the entropy profile is close to the self-similar prediction of gravitational structure formation simulations, as observed in galaxy clusters. Finally, we find a strong heavy metal abundance gradient in the ISM similar to those observed in massive galaxy groups.Comment: 23 pages, 13 figures, 4 tables. Accepted for publication in the Astrophysical Journal. Minor modifications to match accepted version. Conclusions unchange

On the Twist 2 and Twist 3 Contributions to the Spin-dependent Electroweak Structure Functions

The twist 2 and twist 3 contributions of the polarized deep-inelastic structure functions are calculated both for neutral and charged current interactions using the operator product expansion in lowest order in QCD. The relations between the different structure functions are determined. New integral relations are derived between the twist 2 contributions of the structure functions $g_3(x,Q^2)$ and $g_5(x,Q^2)$ and between combinations of the twist 3 contributions to the structure functions $g_2(x,Q^2)$ and $g_3(x,Q^2)$. The sum rules for polarized deep inelastic scattering are discussed in detail.Comment: 24 pages plain Latex, some typographical errors correcte

Ram pressure stripping in elliptical galaxies: I. the impact of the interstellar medium turbulence

Elliptical galaxies contain X-ray emitting gas that is subject to continuous ram pressure stripping over timescales comparable to cluster ages. The gas in these galaxies is not in perfect hydrostatic equilibrium. Supernova feedback, stellar winds, or active galactic nuclei (AGN) feedback can significantly perturb the interstellar medium (ISM). Using hydrodynamical simulations, we investigate the effect of subsonic turbulence in the hot ISM on the ram pressure stripping process in early-type galaxies. We find that galaxies with more turbulent ISM produce longer, wider, and more smoothly distributed tails of the stripped ISM than those characterised by weaker ISM turbulence. Our main conclusion is that even very weak internal turbulence, at the level of <15% of the average ISM sound speed, can significantly accelerate the gas removal from galaxies via ram pressure stripping. The magnitude of this effect increases sharply with the strength of turbulence. As most of the gas stripping takes place near the boundary between the ISM and the intraclustermedium (ICM), the boost in the ISM stripping rate is due to the "random walk" of the ISM from the central regions of the galactic potential well to larger distances, where the ram pressure is able to permanently remove the gas from galaxies. The ICM can be temporarily trapped inside the galactic potential well due to the mixing of the turbulent ISM with the ICM. The galaxies with more turbulent ISM, yet still characterised by very weak turbulence, can hold larger amounts of the ICM. [Abridged]Comment: 12 pages, 11 figures, 2 tables; accepted for publication in MNRA

Transcriptional regulation of the IGF signaling pathway by amino acids and insulin-like growth factors during myogenesis in Atlantic salmon

The insulin-like growth factor signalling pathway is an important regulator of skeletal muscle growth. We examined the mRNA expression of components of the insulin-like growth factor (IGF) signalling pathway as well as Fibroblast Growth Factor 2 (FGF2) during maturation of myotubes in primary cell cultures isolated from fast myotomal muscle of Atlantic salmon (Salmo salar). The transcriptional regulation of IGFs and IGFBP expression by amino acids and insulin-like growth factors was also investigated. Proliferation of cells was 15% d(-1) at days 2 and 3 of the culture, increasing to 66% d(-1) at day 6. Three clusters of elevated gene expression were observed during the maturation of the culture associated with mono-nucleic cells (IGFBP5.1 and 5.2, IGFBP-6, IGFBP-rP1, IGFBP-2.2 and IGF-II), the initial proliferation phase (IGF-I, IGFBP-4, FGF2 and IGF-IRb) and terminal differentiation and myotube production (IGF2R, IGF-IRa). In cells starved of amino acids and serum for 72 h, IGF-I mRNA decreased 10-fold which was reversed by amino acid replacement. Addition of IGF-I and amino acids to starved cells resulted in an 18-fold increase in IGF-I mRNA indicating synergistic effects and the activation of additional pathway(s) leading to IGF-I production via a positive feedback mechanism. IGF-II, IGFBP-5.1 and IGFBP-5.2 expression was unchanged in starved cells, but increased with amino acid replacement. Synergistic increases in expression of IGFBP5.2 and IGFBP-4, but not IGFBP5.1 were observed with addition of IGF-I, IGF-II or insulin and amino acids to the medium. IGF-I and IGF-II directly stimulated IGFBP-6 expression, but not when amino acids were present. These findings indicate that amino acids alone are sufficient to stimulate myogenesis in myoblasts and that IGF-I production is controlled by both endocrine and paracrine pathways. A model depicting the transcriptional regulation of the IGF pathway in Atlantic salmon muscle following feeding is proposed.Publisher PDFPeer reviewe

RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences

Motivation: RNA secondary structure plays an important role in the function of many RNAs, and structural features are often key to their interaction with other cellular components. Thus, there has been considerable interest in the prediction of secondary structures for RNA families. In this article, we present a new global structural alignment algorithm, RNAG, to predict consensus secondary structures for unaligned sequences. It uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in convergence time. This algorithm iteratively samples from the conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure). Not surprisingly, there is considerable uncertainly in the high-dimensional space of this difficult problem, which has so far received limited attention in this field. We show how the samples drawn from this algorithm can be used to more fully characterize the posterior space and to assess the uncertainty of predictions

Abundance ratios in the hot ISM of elliptical galaxies

To constrain the recipes put forth to solve the theoretical Fe discrepancy in the hot interstellar medium of elliptical galaxies and at the same time explain the [alpha/Fe] ratios. In order to do so we use the latest theoretical nucleosynthetic yields, we incorporate the dust, we explore differing SNIa progenitor scenarios by means of a self-consistent chemical evolution model which reproduces the properties of the stellar populations in elliptical galaxies. Models with Fe-only dust and/or a lower effective SNIa rate achieve a better agreement with the observed Fe abundance. However, a suitable modification to the SNIa yield with respect to the standard W7 model is needed to fully match the abundance ratio pattern. The 2D explosion model C-DDT by Maeda et al. (2010) is a promising candidate for reproducing the [Fe/H] and the [alpha/Fe] ratios. (A&A format)Comment: 11 pages, 4 figures, to appear on A&