Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

A Finite Element Numerical Algorithm for Modelling and Data Fitting in Complex Systems

Numerical modelling methodologies are important by their application to engineering and scientific problems, because there are processes where analytical mathematical expressions cannot be obtained to model them. When the only available information is a set of experimental values for the variables that determine the state of the system, the modelling problem is equivalent to determining the hyper-surface that best fits the data. This paper presents a methodology based on the Galerkin formulation of the finite elements method to obtain representations of relationships that are defined a priori, between a set of variables: y = z(x1, x2,...., xd). These representations are generated from the values of the variables in the experimental data. The approximation, piecewise, is an element of a Sobolev space and has derivatives defined in a general sense into this space. The using of this approach results in the need of inverting a linear system with a structure that allows a fast solver algorithm. The algorithm can be used in a variety of fields, being a multidisciplinary tool. The validity of the methodology is studied considering two real applications: a problem in hydrodynamics and a problem of engineering related to fluids, heat and transport in an energy generation plant. Also a test of the predictive capacity of the methodology is performed using a cross-validation method.

New insights into plant salt acclimation: the roles of vesicle trafficking and reactive oxygen species signalling in mitochondria and the endomembrane system

In this study, we investigated the cellular and molecular mechanisms that regulate salt acclimation. The main objective was to obtain new insights into the molecular mechanisms that control salt acclimation. Therefore, we carried out a multidisciplinary study using proteomic, transcriptomic, subcellular and physiological techniques. We obtained a Nicotiana tabacum BY-2 cell line acclimated to be grown at 258 mM NaCl as a model for this study. The proteomic and transcriptomic data indicate that the molecular response to stress (chaperones, defence proteins, etc.) is highly induced in these salt-acclimated cells. The subcellular results show that salt induces sodium compartmentalization in the cell vacuoles and seems to be mediated by vesicle trafficking in tobacco salt-acclimated cells. Our results demonstrate that abscisic acid (ABA) and proline metabolism are crucial in the cellular signalling of salt acclimation, probably regulating reactive oxygen species (ROS) production in the mitochondria. ROS may act as a retrograde signal, regulating the cell response. The network of endoplasmic reticulum and Golgi apparatus is highly altered in salt-acclimated cells. The molecular and subcellular analysis suggests that the unfolded protein response is induced in salt-acclimated cells. Finally, we propose that this mechanism may mediate cell death in salt-acclimated cells.