Modeling dependent gene expression

In this paper we propose a Bayesian approach for inference about dependence of high throughput gene expression. Our goals are to use prior knowledge about pathways to anchor inference about dependence among genes; to account for this dependence while making inferences about differences in mean expression across phenotypes; and to explore differences in the dependence itself across phenotypes. Useful features of the proposed approach are a model-based parsimonious representation of expression as an ordinal outcome, a novel and flexible representation of prior information on the nature of dependencies, and the use of a coherent probability model over both the structure and strength of the dependencies of interest. We evaluate our approach through simulations and in the analysis of data on expression of genes in the Complement and Coagulation Cascade pathway in ovarian cancer.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS525 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Sedimentology and facies analysis of ancient sand ridges: Jurassic Rogn Formation, Trøndelag Platform, offshore Norway

Sand ridges represent a common type of sedimentary bedform of modern shelves seldom used as analogues to interpret isolated marine sandbodies recognised in the subsurface. Lack of extended literature on outcrop and subsurface examples limits the possibility for their recognition and seems one of the reason behind this underrepresentation. The Draugen discovery made in the early 80's represents an unicum in the Trøndelag Platform, offshore Norway. After more than 30 years the Froan Basin and Frøya High area are still underexplored and the Late Jurassic Rogn Fm play not well understood. Predicting reservoir distribution, and its internal architecture and properties requires the understanding of factors controlling sedimentation (e.g. palaeocirculation, depositional processes). North-south elongated sandbodies pertaining to the Rogn Formation are recognised in the Froan Basin and Frøya High encased within thick shaly deposits. Sandbodies develop above a ravinement or flooding surface (i.e. Callovian Unconformity) of regional extent where local depressions occur with a non-erosional concave-up top. Depressions representing the depositional loci for the accumulation of sand and development of the ridge. The presence of eastward and westward dipping reflections within the sandbodies allows identifying their large-scale architectures. Sediments form coarsening-upward vertical units characterised by a shaly base evolving upwards to medium- and coarse-grained sand forming tabular and trough cross strata. Locally, a fining upward trend characterised by plane-parallel stratification and coarse-grained massive layers is recognised. Sediments results well organised and sorted, which positively affects final porosity and permeability with values up to 30% and 6 Darcy, respectively - typical values for many sand ridges. Accordingly, sand ridges encased within thick shaly deposits can form stratigraphic traps with the potential for large hydrocarbon accumulations. The aim of the present study is to help the understanding of distribution, and internal architectures and properties of the Rogn Fm in the Trøndelag Platform

Scaling and correlations in the dynamics of forest-fire occurrence

Forest-fire waiting times, defined as the time between successive events above a certain size in a given region, are calculated for Italy. The probability densities of the waiting times are found to verify a scaling law, despite that fact that the distribution of fire sizes is not a power law. The meaning of such behavior in terms of the possible self-similarity of the process in a nonstationary system is discussed. We find that the scaling law arises as a consequence of the stationarity of fire sizes and the existence of a non-trivial ``instantaneous'' scaling law, sustained by the correlations of the process.Comment: Not a long paper, but many figures (but no large size in kb

Evolution of superconductivity by oxygen annealing in FeTe0.8S0.2

Oxygen annealing dramatically improved the superconducting properties of solid-state-reacted FeTe0.8S0.2, which showed only a broad onset of superconducting transition just after the synthesis. The zero resistivity appeared and reached 8.5 K by the oxygen annealing at 200\degree C. The superconducting volume fraction was also enhanced from 0 to almost 100%. The lattice constants were compressed by the oxygen annealing, indicating that the evolution of bulk superconductivity in FeTe0.8S0.2 was correlated to the shrinkage of lattice.Comment: 13 pages, 6 figure

Anomalous diffusion in the dynamics of complex processes

Anomalous diffusion, process in which the mean-squared displacement of system states is a non-linear function of time, is usually identified in real stochastic processes by comparing experimental and theoretical displacements at relatively small time intervals. This paper proposes an interpolation expression for the identification of anomalous diffusion in complex signals for the cases when the dynamics of the system under study reaches a steady state (large time intervals). This interpolation expression uses the chaotic difference moment (transient structural function) of the second order as an average characteristic of displacements. A general procedure for identifying anomalous diffusion and calculating its parameters in real stochastic signals, which includes the removal of the regular (low-frequency) components from the source signal and the fitting of the chaotic part of the experimental difference moment of the second order to the interpolation expression, is presented. The procedure was applied to the analysis of the dynamics of magnetoencephalograms, blinking fluorescence of quantum dots, and X-ray emission from accreting objects. For all three applications, the interpolation was able to adequately describe the chaotic part of the experimental difference moment, which implies that anomalous diffusion manifests itself in these natural signals. The results of this study make it possible to broaden the range of complex natural processes in which anomalous diffusion can be identified. The relation between the interpolation expression and a diffusion model, which is derived in the paper, allows one to simulate the chaotic processes in the open complex systems with anomalous diffusion.Comment: 47 pages, 15 figures; Submitted to Physical Review

Blue mussel shell shape plasticity and natural environments: a quantitative approach

Shape variability represents an important direct response of organisms to selective environments. Here, we use a combination of geometric morphometrics and generalised additive mixed models (GAMMs) to identify spatial patterns of natural shell shape variation in the North Atlantic and Arctic blue mussels, Mytilus edulis and M. trossulus, with environmental gradients of temperature, salinity and food availability across 3980 km of coastlines. New statistical methods and multiple study systems at various geographical scales allowed the uncoupling of the developmental and genetic contributions to shell shape and made it possible to identify general relationships between blue mussel shape variation and environment that are independent of age and species influences. We find salinity had the strongest effect on the latitudinal patterns of Mytilus shape, producing shells that were more elongated, narrower and with more parallel dorsoventral margins at lower salinities. Temperature and food supply, however, were the main drivers of mussel shape heterogeneity. Our findings revealed similar shell shape responses in Mytilus to less favourable environmental conditions across the different geographical scales analysed. Our results show how shell shape plasticity represents a powerful indicator to understand the alterations of blue mussel communities in rapidly changing environments.The work was funded by the European Union Seventh Framework Programme, Marie Curie ITN under grant agreement n° 605051

Sudden drop of fractal dimension of electromagnetic emissions recorded prior to significant earthquake

The variation of fractal dimension and entropy during a damage evolution process, especially approaching critical failure, has been recently investigated. A sudden drop of fractal dimension has been proposed as a quantitative indicator of damage localization or a likely precursor of an impending catastrophic failure. In this contribution, electromagnetic emissions recorded prior to significant earthquake are analysed to investigate whether they also present such sudden fractal dimension and entropy drops as the main catastrophic event is approaching. The pre-earthquake electromagnetic time series analysis results reveal a good agreement to the theoretically expected ones indicating that the critical fracture is approaching

Blue mussel shell shape plasticity and natural environments: a quantitative approach

Shape variability represents an important direct response of organisms to selective environments. Here, we use a combination of geometric morphometrics and generalised additive mixed models (GAMMs) to identify spatial patterns of natural shell shape variation in the North Atlantic and Arctic blue mussels, Mytilus edulis and M. trossulus, with environmental gradients of temperature, salinity and food availability across 3980 km of coastlines. New statistical methods and multiple study systems at various geographical scales allowed the uncoupling of the developmental and genetic contributions to shell shape and made it possible to identify general relationships between blue mussel shape variation and environment that are independent of age and species influences. We find salinity had the strongest effect on the latitudinal patterns of Mytilus shape, producing shells that were more elongated, narrower and with more parallel dorsoventral margins at lower salinities. Temperature and food supply, however, were the main drivers of mussel shape heterogeneity. Our findings revealed similar shell shape responses in Mytilus to less favourable environmental conditions across the different geographical scales analysed. Our results show how shell shape plasticity represents a powerful indicator to understand the alterations of blue mussel communities in rapidly changing environments

Density-functional study of the evolution of the electronic structure of oligomers of thiophene:Towards a model Hamiltonian

We present density-functional and time-dependent density-functional studies of the ground, ionic, and excited states of a series of oligomers of thiophene. We show that, for the physical properties, the most relevant highest occupied and lowest unoccupied molecular orbitals develop gradually from monomer molecular orbitals into occupied and unoccupied broad bands in the large length limit. We show that band gap and ionization potentials decrease with size, as found experimentally and from empirical calculations. This gives credence to a simple tight-binding model Hamiltonian approach to these systems. We demonstrate that the length dependence of the experimental excitation spectra for both singlet and triplet excitations can be very well explained with an extended Hubbard-like Hamiltonian, with a monomer on-site Coulomb and exchange interaction and a nearest-neighbor Coulomb interaction. We also study the ground and excited-state electronic structures as functions of the torsion angle between the units in a dimer, and find almost equal stabilities for the transoid and cisoid isomers, with a transition energy barrier for isomerization of only 4.3 kcal/mol. Fluctuations in the torsion angle turn out to be very low in energy, and therefore of great importance in describing even the room-temperature properties. At a torsion angle of 90° the hopping integral is switched off for the highest occupied molecular orbital levels because of symmetry, allowing a first-principles estimate of the on-site interaction minus the next-neighbor Coulomb interaction as it enters in a Hubbard-like model Hamiltonian