GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data

Background: Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. Results: We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. Conclusions: GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.Department of Agriculture, Food and the MarineEuropean Commission - Seventh Framework Programme (FP7)Science Foundation IrelandUniversity College Dubli

Multidetachment analogue models of fold reactivation in transpression : the NW Persian Gulf

Two deformation events have been documented in the NW Persian Gulf during the Late Cretaceous and the Late Cenozoic. The most distinctive feature in this part of the Persian Gulf is the reactivation of the Late Cretaceous NNE-SSW Arabian trending folds by NE-SW shortening during the Late Cenozoic Zagros orogeny. In general, if a set of folds with horizontal axes is shortened roughly parallel to its fold axis, a dome-basin fold interference pattern is produced. In the NW Persian Gulf, reactivation of some old folds occurred instead of a fold interference pattern. Reactivation may be influenced by the following factors: i) the presence of incompetent layers (i.e. evaporites), ii) a variable overburden, iii) basement faults, and iv) obliquity between the younger deformation shortening axis and fold axis. It is this last factor that we investigated by means of analogue modelling. The experimental apparatus is similar to that commonly used for experiments with brittle-ductile systems at the Laboratory of Experimental Tectonics of Géosciences Rennes. The model consisted of an alternation of ductile and brittle horizontal layers with a stratigraphy similar to the one found in the NW Persian Gulf. The model was deformed by two deformation events with an angle a between the two directions of shortening. After deformation, the resulting structure resembled a fold facing the static wall with internal thrust faults and detachment faults arranged into a geometry similar to a fish tail. In the second shortening event, the fold was reactivated without formation of an interference pattern. Moreover, the displacement on both the reactivated and newly formed faults varied between almost pure thrust faults for low a and oblique thrust faults with a strike-slip component for high a. The models suggest that the presence of incompetent layers plays an important role in fold reactivation and confirm that basement faults are not necessary

Effects of margin-parallel shortening and density contrasts on back-arc extension during subduction: Experimental insights and possible application to Anatolia

International audienceSo as to investigate the parameters influencing subduction and back-arc extension, we have done three series of laboratory experiments (32 in all) on physical models. Each model consisted of adjacent oceanic and continental plates, floating on an asthenosphere. In experiments of Series A, a wide rigid piston, moving horizontally, controlled the rate of convergence of the oceanic and continental plates, whereas, in Series B or C, a wide or narrow piston produced lateral compression, parallel to the continent-ocean boundary (COB) and perpendicular to the subduction direction. The parameters that we tested were (1) the velocity of plate convergence (Series A), (2) the width of the compressing piston (Series B and C), and (3) the density ratio between oceanic and continental plates (Series B and C). This density ratio was a key factor. For a ratio of 1.4, the amount of extension in the continental plate increased regularly throughout time; for a ratio of 1.3, the extension remained small, until the piston stopped moving laterally; and for a ratio of 1.1, there was little or no extension. The width of the compressing piston had a smaller effect, although a narrow piston provided more space, into which the continental plate could extend. One possible application of our models is to Anatolia. Despite similar geological settings, the areas north of the Hellenic and Cyprus subduction zones differ, in that extension is large in the former and much smaller in the latter. We suggest that one of the main driving forces for Aegean extension may have been a high density ratio between subducting oceanic lithosphere and a Hellenic-Balkanic upper plate

Pion radii in nonlocal chiral quark model

The electromagnetic radius of the charged pion and the transition radius of the neutral pion are calculated in the framework of the nonlocal chiral quark model. It is shown in this model that the contributions of vector mesons to the pion radii are noticeably suppressed in comparison with a similar contribution in the local Nambu--Jona-Lasinio model. The form-factor for the process gamma*pi+pi- is calculated for the -1 GeV^2<q^2<1.6 GeV^2. Our results are in satisfactory agreement with experimental data.Comment: 7 pages, 7 figure

Collapse of the N=28 shell closure in 42^{42}Si

The energies of the excited states in very neutron-rich $^{42}$Si and $^{41,43}$P have been measured using in-beam $\gamma$-ray spectroscopy from the fragmentation of secondary beams of $^{42,44}$S at 39 A.MeV. The low 2$^+$ energy of $^{42}$Si, 770(19) keV, together with the level schemes of $^{41,43}$P provide evidence for the disappearance of the Z=14 and N=28 spherical shell closures, which is ascribed mainly to the action of proton-neutron tensor forces. New shell model calculations indicate that $^{42}$Si is best described as a well deformed oblate rotor.Comment: 4 pages, 3 figures, accepted for publication in Phys. Rev. let

Multifragmentation process for different mass asymmetry in the entrance channel around the Fermi energy

The influence of the entrance channel asymmetry upon the fragmentation process is addressed by studying heavy-ion induced reactions around the Fermi energy. The data have been recorded with the INDRA 4pi array. An event selection method called the Principal Component Analysis is presented and discussed. It is applied for the selection of central events and furthermore to multifragmentation of single source events. The selected subsets of data are compared to the Statistical Multifragmentation Model (SMM) to check the equilibrium hypothesis and get the source characteristics. Experimental comparisons show the evidence of a decoupling between thermal and compresional (radial flow) degrees of freedom in such nuclear systems.Comment: 28 pages, 15 figures, article sumitted to Nuclear Physics

Response of CsI(Tl) scintillators over a large range in energy and atomic number of ions (Part I): recombination and delta -- electrons

A simple formalism describing the light response of CsI(Tl) to heavy ions, which quantifies the luminescence and the quenching in terms of the competition between radiative transitions following the carrier trapping at the Tl activator sites and the electron-hole recombination, is proposed. The effect of the delta rays on the scintillation efficiency is for the first time quantitatively included in a fully consistent way. The light output expression depends on four parameters determined by a procedure of global fit to experimental data.Comment: 28 pages, 6 figures, submitted to Nucl. Inst. Meth.

Statistical Multifragmentation of Non-Spherical Expanding Sources in Central Heavy-Ion Collisions

We study the anisotropy effects measured with INDRA at GSI in central collisions of Xe+Sn at 50 A.MeV and Au+Au at 60, 80, 100 A.MeV incident energy. The microcanonical multifragmentation model with non-spherical sources is used to simulate an incomplete shape relaxation of the multifragmenting system. This model is employed to interpret observed anisotropic distributions in the fragment size and mean kinetic energy. The data can be well reproduced if an expanding prolate source aligned along the beam direction is assumed. An either non-Hubblean or non-isotropic radial expansion is required to describe the fragment kinetic energies and their anisotropy. The qualitative similarity of the results for the studied reactions suggests that the concept of a longitudinally elongated freeze-out configuration is generally applicable for central collisions of heavy systems. The deformation decreases slightly with increasing beam energy.Comment: 35 pages, 19 figures, submitted to Nuclear Physics

Structure of unbound neutron-rich 9^{9}He studied using single-neutron transfer

The 8He(d,p) reaction was studied in inverse kinematics at 15.4A MeV using the MUST2 Si-CsI array in order to shed light on the level structure of 9He. The well known 16O(d,p)17O reaction, performed here in reverse kinematics, was used as a test to validate the experimental methods. The 9He missing mass spectrum was deduced from the kinetic energies and emission angles of the recoiling protons. Several structures were observed above the neutron-emission threshold and the angular distributions were used to deduce the multipolarity of the transitions. This work confirms that the ground state of 9He is located very close to the neutron threshold of 8He and supports the occurrence of parity inversion in 9He.Comment: Exp\'erience GANIL/SPIRAL1/MUST