A conceptual approach to gene expression analysis enhanced by visual analytics

The analysis of gene expression data is a complex task for biologists wishing to understand the role of genes in the formation of diseases such as cancer. Biologists need greater support when trying to discover, and comprehend, new relationships within their data. In this paper, we describe an approach to the analysis of gene expression data where overlapping groupings are generated by Formal Concept Analysis and interactively analyzed in a tool called CUBIST. The CUBIST workflow involves querying a semantic database and converting the result into a formal context, which can be simplified to make it manageable, before it is visualized as a concept lattice and associated charts

Electronic excited states of benzene in interaction with water clusters : influence of structure and size

This work is dedicated to the theoretical investigation of the influence of water clusters' organisation and size on the electronic spectrum of an interacting benzene (Bz) molecule using both TD-DFT and CASPT2 approaches. Two series of geometries, namely $Geo_{IEI}$ and $Geo_{IED}$ were extracted from two Bz-hexagonal ice configurations leading to maximum and minimum ionization energies respectively. An appropriate basis set containing atomic diffuse and polarisation orbitals and describing the Rydberg states of Bz was determined. The TD-DFT approach was carefully benchmarked against CASPT2 results for the smallest systems.Despite some discrepancies, the trends were found to be similar at both levels of theory: the positions and intensities of the main $\pi \rightarrow \pi^{\star}$ transitions were found slightly split due to symmetry breaking. For the smallest systems, our results clearly show the dependence of the electronic transitions on the clusters' structures. Of particular interest, low energy transitions of non negligible oscillator strength from a Bz $\pi$ orbital to a virtual orbital of Rydberg character, also involving atomic diffuse functions and partially expanded on the water cluster, were found for the $Geo_{IED}$ series. The energies of such transitions were determined to be more than 2\,eV below the ionization potential of Bz. When the cluster's size increases, similar transitions were found for all structures, the virtual orbitals becoming mainly developed on the H atoms of the water molecules at the edge of the cluster. Given their nature and energy, such transitions could play a role in the photochemistry of aromatic species in interaction with water clusters or ice, such processes being of astrophysical interest.Comment: 37 pages, 15 figures, 7 table

Robust Measurement Feedback Control of an Inclined Cable

International audienceConsidering the partial differential equation model of the vibrations of an inclined cable, we are interested in applying robust control technics to stabilize the system with measurement feedback when it is submitted to external disturbances. This paper focuses indeed on the construction of a standard linear infinite dimensional state space system and an H_infinity feedback control of vibrations with partial observation of the state. The control and observation are performed using an active tendon

PAH chemistry at eV internal energies. 1. H-shifted isomers

The PAH family of organic compounds (polycyclic aromatic hydrocarbons), involved in several fields of chemistry, has received particular attention in astrochemistry, where their vibrational spectroscopy, thermodynamic, dynamic, and fragmentation properties are now abundantly documented. This survey aims at drawing trends for low spin-multiplicity surfaces of PAHs bearing internal energies in the range 1-10 eV. It addresses some typical alternatives to the ground-state regular structures of PAHs, making explicit possible intramolecular rearrangements leading to high-lying minima. These isomerisations should be taken into consideration when addressing PAH processing in astrophysical conditions. The first part of this double-entry study focuses on the hydrogen-shifted forms, which bear both a carbene center and a saturated carbon. It rests upon DFT calculations mainly performed on two emblematic PAH representatives, coronene and pyrene, in their neutral and mono and multi-cationic states. Systematically searched for in neutral species, these H-shifted minima are lying 4-5 eV above the regular all-conjugated forms, and are separated by barriers of about one eV. General hydrogen-shifting is found to be easier for cationic species as the relative energies of their H-shifted minima are 1-1.5 eV lower than those for neutral species. As much as possible, classical knowledge and concepts of organic chemistry such as aromaticity and Clar's rules are invoked for result interpretation.Comment: 35 pages, accepted by Molecular Astrophysic

PAH chemistry at eV internal energies. 2. Ring alteration and dissociation

Recognized as important interstellar constituents, polycyclic aromatic hydrocarbons (PAHs) have been intensively studied in astrochemistry and their spectroscopy, thermodynamics, dynamics, and fragmentations are now amply documented. There exists typical alternatives to the ground-state regular planar structures of PAHs, as long as they bear internal energies in the range 1-10 eV. Resulting from intramolecular rearrangements, such high-lying minima on the potential- energy surfaces should be taken into consideration in the studies of PAH processing in astrophysical conditions. Resting upon DFT calculations mainly performed on two emblematic PAH representatives, coronene and pyrene, in their neutral and mono and multi-cationic states, this second survey addresses the following alternatives: (1) opened forms containing ethynyl or 2- butynyl groups, (2) vinylidene isomers, in which phenanthrene patterns are reorganized into dibenzofulvene ones, (3) twisted forms, where external CH=CH bonds can be partly twisted, and (4) bicyclobutane forms, in which the latter are integrated in saturated bicyclic forms. A few scenarios for elimination of fragments H, H2, C2H2 and C2H4 are explored. As far as possible, familiar concepts of organic chemistry, such as aromaticity or Clar's rules, are invoked for interpretations.Comment: 65 pages, accepted by Molecular Astrophysic

Lithium conducting solid electrolyte Li1.3Al0.3Ti1.7(PO4)3 obtained via solution chemistry

NaSICON-type lithium conductor Li1.3Al0.3Ti1.7(PO4)3 (LATP) is synthesized with controlled grain size and composition using solution chemistry. After thermal treatment at 850 C, sub-micronic crystallized powders with high purity are obtained. They are converted into ceramic through Spark Plasma Sintering at 850–1000 C. By varying the processing parameters, pellet with conductivities up to 1.6 * 10−4 S/cm with density of 97% of the theoretical density have been obtained. XRD, FEG-SEM, ac-impedance and Vickers indentation were used to characterize the products. The influence of sintering parameters on pellet composition, microstructure and conductivity is discussed in addition to the analysis of the mechanical behavior of the grains interfaces

Gestion Publique ou Privée ? Un benchmarking des services d’eau en France

Nous utilisons une méthode d’Analyse par Enveloppe de Données (DEA) ainsi qu’une méthode d’Analyse par Frontière Stochastique (SFA) pour mesurer l’efficacité relative de 177 services d’eau en France, en 2009. Ces services peuvent être gérés directement par les communes (régies) ou être délégués à des opérateurs privés. L’utilisation de ces deux outils de benchmarking nous permet de distinguer la part de l’inefficience relative des services provenant de l’inefficience managériale, du contexte opérationnel et des bruits statistiques. Nos résultats indiquent tout d’abord que les opérateurs privés opèrent dans des environnements plus difficiles. Après correction de cet environnement d’exploitation, les services d’eau délégués demeurent, en moyenne, très légèrement moins efficients en comparaison des régies. Cependant, cette faible différence se dissipe lorsque les performances relatives sont mesurées économétriquement.This paper uses a Data Envelopment Analysis (DEA) and a Stochastic Frontier Analysis (SFA) to assess the relative technical efficiency of 177 decision making units in the water supply sector in France in 2009. Water utilities can be directly managed by the local authorities or contracted out and then managed by a private operator. The use of a three-stage model mixing DEA and SFA enables us to dissociate managerial inefficiencies from the structural inefficiencies and statistical noise. Our results show that private managers face more difficult environment. After having taken into account the environmental variables, private management remains on average slightly less efficient than public management. However, this small difference dissipates when relative performance is econometrically measured

Hydrogenation of C24_{24} carbon clusters : structural diversity and energetic properties

This work aims at exploring the potential energy surfaces of C$_{24}$H$_n${n=0,6,12,18,24} up to 20-25\,eV using the genetic algorithm in combination with the density functional based tight binding (DFTB) potential. The structural diversity of the non fragmented structures was analysed using order parameters which were chosen as the number of 5 or 6 carbon rings and the asphericity constant $\beta$. The most abundant and lowest energy population was found to correspond to a flakes population, constituted of isomers of variable shapes possessing a large number of 5 or 6-carbon rings. This population is characterized by a larger number of spherical isomers when $n_H/n_C$ increases. Simultaneously, the fraction of the pretzels population constituted of spherical isomers possessing fewer 5 or 6 carbon ring cycles increases. For all hydrogenation rates, the fraction of cages population remains extremely minor while the branched population is the highest energy population for all $n_H/n_C$ ratios. For all C$_{24}$H$_n${n=0,6,12,18,24} clusters, a detailed study of the evolution of the carbon ring size distribution as a function of energy clearly shows that the stability is correlated to the number of 6-carbon rings. A similar study for hybridization $sp^n$ (n=1-3) shows that the number of $sp^1$ carbon atoms increases with energy while globally the number of $sp^3$ carbon atoms increases with $n_H/n_C$. The average values of the ionization potentials of all populations were found to decrease when $n_H/n_C$ increases, ranging from 7.9\,eV down to 6.4\,eV that we correlated to carbon atoms hybridization $sp^n$ (n=1-3). These results are of astrophysical interest as they should be taken into account in astrophysical models especially regarding the role of carbonaceous species in the gas ionization.Comment: 37 pages, 13 figure