GreenPhylDB: A Gene Family Database for plant functional Genomics

With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by phylogenetic analysis to infer orthologs and paralogs that will be particularly helpful to study genome evolution. Previously, each cluster has to be curated (i.e. properly named and classified) using different sources of information. A web interface for plant gene families’ curation was developed for that purpose. This interface, accessible on GreenPhylDB ("http://greenphyl.cirad.fr":http://greenphyl.cirad.fr), centralizes external references (e.g. InterPro, KEGG, Swiss-Prot, PIRSF, Pubmed) related to all gene members of the clusters and shows statistics and automatic analysis. We believe that this synthetic view of data available for a gene cluster, combined with basic guidelines, is an efficient way to provide reliable method for gene family annotations

The econometric modeling of social Preferences

Experimental data on social preferences present a number of features that need to be incorporated in econometric modelling. We explore a variety of econometric modelling approaches to the analysis of such data. The approaches under consideration are: the random utility approach (in which it is assumed that each possible action yields a utility with a deterministic and a stochastic component, and that the individual selects the action yielding the highest utility); the random behavioural approach (which assumes that the individual computes the maximum of a deterministic utility function, and that computational error causes their observed behaviour to depart stochastically from this optimum); and the random preference approach (in which all variation in behaviour is attributed to stochastic variation in the parameters of the deterministic component of utility). These approaches are applied in various ways to an experiment on fairness conducted by Cappelen et al. (2007). At least two of the models that we estimate succeed in capturing the key features of the data set.Econometric modelling and estimation, model evaluation, individual behaviour, fairness

Mapping climatic risks in the EU agriculture

Replaced with revised version of paper 11/18/08.Agrometeorological models, climatic risk, European Union, Vegetation indices, Environmental Economics and Policy, Risk and Uncertainty,

Regional Yield Insurance for Arable Crops in EU-27

Replaced with revised version of paper 11/18/08.Area yield insurance, index insurance, yield risk, Agricultural Finance, Risk and Uncertainty,

The econometric modeling of social preferences

Experimental data on social preferences present a number of features that need to be incorporated in econometric modelling. We explore a variety of econometric modelling approaches to the analysis of such data. The approaches under consideration are: the random utility approach (in which it is assumed that each possible action yields a utility with a deterministic and a stochastic component, and that the individual selects the action yielding the highest utility); the random behavioural approach (which assumes that the individual computes the maximum of a deterministic utility function, and that computational error causes their observed behaviour to depart stochastically from this optimum); and the random preference approach (in which all variation in behaviour is attributed to stochastic variation in the parameters of the deterministic component of utility). These approaches are applied in various ways to an experiment on fairness conducted by Cappelen et al. (2007). At least two of the models that we estimate succeed in capturing the key features of the data set

Detection and construction of an elliptic solution to the complex cubic-quintic Ginzburg-Landau equation

In evolution equations for a complex amplitude, the phase obeys a much more intricate equation than the amplitude. Nevertheless, general methods should be applicable to both variables. On the example of the traveling wave reduction of the complex cubic-quintic Ginzburg-Landau equation (CGL5), we explain how to overcome the difficulties arising in two such methods: (i) the criterium that the sum of residues of an elliptic solution should be zero, (ii) the construction of a first order differential equation admitting the given equation as a differential consequence (subequation method).Comment: 12 pages, no figure, to appear, Theoretical and Mathematical Physic

Meromorphic traveling wave solutions of the complex cubic-quintic Ginzburg-Landau equation

We look for singlevalued solutions of the squared modulus M of the traveling wave reduction of the complex cubic-quintic Ginzburg-Landau equation. Using Clunie's lemma, we first prove that any meromorphic solution M is necessarily elliptic or degenerate elliptic. We then give the two canonical decompositions of the new elliptic solution recently obtained by the subequation method.Comment: 14 pages, no figure, to appear, Acta Applicandae Mathematica

Resonant optical control of the structural distortions that drive ultrafast demagnetization in Cr2_2O3_3

We study how the color and polarization of ultrashort pulses of visible light can be used to control the demagnetization processes of the antiferromagnetic insulator Cr$_2$O$_3$. We utilize time-resolved second harmonic generation (SHG) to probe how changes in the magnetic and structural state evolve in time. We show that, varying the pump photon-energy to excite either localized transitions within the Cr or charge transfer states, leads to markedly different dynamics. Through a full polarization analysis of the SHG signal, symmetry considerations and density functional theory calculations, we show that, in the non-equilibrium state, SHG is sensitive to {\em both} lattice displacements and changes to the magnetic order, which allows us to conclude that different excited states couple to phonon modes of different symmetries. Furthermore, the spin-scattering rate depends on the induced distortion, enabling us to control the timescale for the demagnetization process. Our results suggest that selective photoexcitation of antiferromagnetic insulators allows fast and efficient manipulation of their magnetic state.Comment: 7 pages, 5 figure