ASSET : a dataset for tuning and evaluation of sentence simplification models with multiple rewriting transformations

In order to simplify a sentence, human editors perform multiple rewriting transformations: they split it into several shorter sentences, paraphrase words (i.e. replacing complex words or phrases by simpler synonyms), reorder components, and/or delete information deemed unnecessary. Despite these varied range of possible text alterations, current models for automatic sentence simplification are evaluated using datasets that are focused on a single transformation, such as lexical paraphrasing or splitting. This makes it impossible to understand the ability of simplification models in more realistic settings. To alleviate this limitation, this paper introduces ASSET, a new dataset for assessing sentence simplification in English. ASSET is a crowdsourced multi-reference corpus where each simplification was produced by executing several rewriting transformations. Through quantitative and qualitative experiments, we show that simplifications in ASSET are better at capturing characteristics of simplicity when compared to other standard evaluation datasets for the task. Furthermore, we motivate the need for developing better methods for automatic evaluation using ASSET, since we show that current popular metrics may not be suitable when multiple simplification transformations are performed

MOMO - multi-objective metabolic mixed integer optimization : application to yeast strain engineering

BACKGROUND: In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering. RESULTS: Production of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. CONCLUSIONS: The multi-objective programming framework we developed, called MOMO, is open-source and uses POLYSCIP (Available at http://polyscip.zib.de/). as underlying multi-objective solver. MOMO is available at http://momo-sysbio.gforge.inria.fr

Tri-thermal device sizing for thermophoresis deposition measurements of nanoparticle soot aggregates

Paper presented to the 10th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, Florida, 14-16 July 2014.Thermophoresis is the motion of particles from the hot to the cold region of a gas subjected to a thermal gradient. This phenomenon contributes to the fouling of EGR (Exhaust Gas Recycling) systems in automotive applications. The aim of this work is to develop a tri thermal device to study the collect of soot particles by thermophoresis. In this device soot particles flow in the annular space between two concentric tubes with imposed temperatures. We will use the so called penetration method which is based on the measurement of particle deposition in the test section. The precision of this method is often limited by the low deposition rates; the main objective of this study is then to size an efficient and compact device for thermophoretic deposition, while respecting mechanical and thermal constraints. We used CFD (Computational Fluid Dynamic) numerical simulations and model results to choose an optimal design of the device, which is composed of hot and cold tubes with diameter respectively equal to 87 and 85mm and with 0.5 meter long tubes.cf201

A combinatorial algorithm for microbial consortia synthetic design

International audienceSynthetic biology has boomed since the early 2000s when it started being shown that it was possible to efficiently synthetize compounds of interest in a much more rapid and effective way by using other organisms than those naturally producing them. However, to thus engineer a single organism, often a microbe, to optimise one or a collection of metabolic tasks may lead to difficulties when attempting to obtain a production system that is efficient, or to avoid toxic effects for the recruited microorganism. The idea of using instead a microbial consortium has thus started being developed in the last decade. This was motivated by the fact that such consortia may perform more complicated functions than could single populations and be more robust to environmental fluctuations. Success is however not always guaranteed. In particular, establishing which consortium is best for the production of a given compound or set thereof remains a great challenge. This is the problem we address in this paper. We thus introduce an initial model and a method that enable to propose a consortium to synthetically produce compounds that are either exogenous to it, or are endogenous but where interaction among the species in the consortium could improve the production line. Synthetic biology has been defined by the European Commission as " the application of science, technology, and engineering to facilitate and accelerate the design, manufacture, and/or modification of genetic materials in living organisms to alter living or nonliving materials ". It is a field that has boomed since the early 2000s when in particular Jay Keasling showed that it was possible to efficiently synthetise a compound–artemisinic acid–which after a few more tricks then leads to an effective anti-malaria drug, artemisini

Enumeration of minimal stoichiometric precursor sets in metabolic networks

Background: What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. Results: Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. Conclusions: The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr

Effets d’une finition des agneaux à l’herbe sur les qualités nutritionnelles et gustatives de la viande

This study was carried out within the framework of the ECOLAGNO project which focuses on lambmeat production according to agro ecological practices. Two experiments were conducted for two successive yearsby the interregional center of information and research on ovine production (CIIRPO) in order to measure the effectof the type of lamb fattening on sensory and nutritional qualities of their meat, and on breeding performances. In2016 and 2017, three groups of 30 suckled lambs on pasture, weaned at 125 days of age, were compared. Thecontrol group was fattened with concentrated feed indoors and the other two groups were grass-fed in order tofinish lambs only on grass, either within a continuous grazing system on plots with multispecies crops such asgrass, legumes and tannin-rich plants or with cellular grazing. There were little differences between the threegroups for lamb breeding performances and carcass qualities. On average 50 kg RM of concentrated feed weresaved per lamb fattened on pasture. Grazing did not alter odor or flavor of lamb chops. However, the fatty acidprofile of meat was improved for grass-fed animals.Cette étude a été menée dans le cadre du projet ECOLAGNO s’intéressant à la production de vianded’agneau selon des pratiques agro-écologiques. Deux essais conduits sur deux années consécutives par le CentreInterrégional d’Information et de Recherche en Production Ovine (CIIRPO) avaient pour objectif de mesurerl’impact du mode de finition des agneaux, à l’herbe ou en bergerie, sur les qualités gustatives et nutritionnelles dela viande, ainsi que sur les aspects zootechniques. En 2016 et 2017, trois lots de 30 agneaux à l’herbe, allaitéspuis sevrés à 125 jours, ont été comparés. Le témoin était fini en bergerie avec un aliment concentré, les deuxautres au pâturage dans l’objectif de finir les agneaux exclusivement avec de l’herbe : l’un en pâturage continu surdes parcelles multi-espèces composées de graminées, légumineuses et plantes riches en tanins ; l’autre enpâturage cellulaire. Les performances zootechniques et les qualités de la carcasse des agneaux sont peudifférentes entre les trois lots. L’économie de concentré s’est située en moyenne à 50 kg brut par agneau avec unefinition à l’herbe. Il n’y a pas eu de dégradation de l’odeur ou de la flaveur des côtelettes lors des finitions aupâturage ; en revanche, le profil en acides gras des viandes a été amélioré

MOMO - multi-objective metabolic mixed integer optimization : application to yeast strain engineering

In this paper, we explore the concept of multi-objective optimization in the field of metabolic engineering when both continuous and integer decision variables are involved in the model. In particular, we propose a multi-objective model that may be used to suggest reaction deletions that maximize and/or minimize several functions simultaneously. The applications may include, among others, the concurrent maximization of a bioproduct and of biomass, or maximization of a bioproduct while minimizing the formation of a given by-product, two common requirements in microbial metabolic engineering. Production of ethanol by the widely used cell factory Saccharomyces cerevisiae was adopted as a case study to demonstrate the usefulness of the proposed approach in identifying genetic manipulations that improve productivity and yield of this economically highly relevant bioproduct. We did an in vivo validation and we could show that some of the predicted deletions exhibit increased ethanol levels in comparison with the wild-type strain. The multi-objective programming framework we developed, called Momo, is open-source and uses PolySCIP‡ as underlying multi-objective solver. Momo is available at http://momo-sysbio.gforge.inria.f