Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts

In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.Comment: 4 pages, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014

Les Alliés occidentaux et les universités allemandes, 1945-1949

C'est une histoire passionnante, plutôt méconnue des Français, alors que les Allemands lui ont déjà consacré, pour des raisons évidentes, beaucoup de travaux, que celle des premières années d'après la Seconde Guerre mondiale dans l'Allemagne placée sous l'autorité des gouvernements militaires alliés. L'histoire, en particulier de la renaissance des universités allemandes après la capitulation, et de la politique menée en ce domaine par chacune des puissances d'occupation, a fait l'objet de no..

Forget Consensus: Science, Technology and Economic Policy in the United States, 1921-1953 et Investing in Innovation: Creating a Research and Innovation Policy that works

Pour qui veut comprendre la capacité d'innovation des États-Unis, leur aptitude à rebondir, fût-ce dans les crises d'essoufflement économique et les fonctions stratégiques que l'État fédéral peut exercer dans la stimulation des efforts de recherche-développement même du secteur privé, ces deux livres offrent des clés que les pays européens, et la France en particulier, feraient bien de méditer. Tous les observateurs s'accordent pour dire que la politique américaine de la science et de la tech..

Morte e ressurreição do capitalismo: a propósito de Schumpeter

A crise econômica e a emergência das "novas tecnologias" nos anos 70 trouxeram nova popularidade à obra de Joseph Schumpeter. Neste artigo, o autor discute como a História recente tem desmentido as previsões do economista quanto à transformação do capitalismo em socialismo. Em primeiro lugar, não ficou provado que a racionalização do progresso industrial reduz o nível de inovação, extinguindo os papéis do empresário e do inventor. Pelo contrário, o caráter aleatório da inovação é tal que uma economia não-planificada se adqua muito melhor à sua natureza. Quanto ao segundo aspecto, a presença crescente do Estado nas atividades de pesquisa-desenvolvimento, o cenário mundial de 1945 alterou-se drasticamente a partir da década de 70 quando a demanda dos mercados civis por alta tecnologia passou a superar as demandas governamentais. O terceiro ponto diz respeito ao papel dos intelectuais, pois a expansão e simultânea desvalorização do ensino superior geram uma superpopulação de indivíduos que desenvolvem uma visão critica com relação ao sistema. Mas se tal "hostilidade" nutre-se apenas de ressentimento, como Schumpeter acredita, jamais terá força para por um fim no capitalismo. Assim, se não há nada que, de um ponto de vista econômico, postule o desaparecimento do capitalimo as razões sociológicas e psicológicas apresentadas por Schumpeter têm a mesma debilidade de argumentos ideológicos.The economical crisis and the emergence of the "new technologies" in the 70's brought a new popularity to the work of Joseph Schumpeter. In this article, the author discusses how recent history has danied Schumpeter's predictions concerning the passage of capitalism to socialism. First of all, it has not been proved that rationalization of industrial progress redacts the level of inovation, extinguishing the roles of the entreprensur and the inventor. It is quite the opposite, for the aleatory character of inovation is such that a not-planned economy suits much better its nature. Concerning the second aspect, the growing role of the State in the activities of research-development, the world scene of 1945 has changed drastically from the 70 's onward when the civil markets demand for high technology outweighted the public demands. The third point relates to the function of intellectuals. The expansion and simultaneous devaluation of superior education generate an exceeding number of individual who develop a critical view towards the system. But if such "hostility" is due only to resentment, as Schumpeter believes, it will never have enought strength to put an end to capitalism. Therefore, if there is nothing, from an economical point of view, that postulates the disappearance of capitalim, the sociological and psychological reasons expouded by Schumpeter have the same weakness of ideological statements

Finding the Core-Genes of Chloroplasts

Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance

Le grand gâchis : Splendeur et misère de la science française

On peut certes toujours chipoter sur l'usage des indicateurs scientifiques, qui ne donnent jamais que des ordres de grandeur, discuter à loisir la légitimité ou la validité des évaluations fondées sur le nombre d'articles publiés (production ou productivité ?) et cités dans les meilleures revues (réalité effective ou virtuelle de l'impact ?), ou encore contester certaines comparaisons internationales liées à ces statistiques (la France, c'est quand même mieux que l'Irlande (et non que le Port..

Parareal in time 3D numerical solver for the LWR Benchmark neutron diffusion transient model

We present a parareal in time algorithm for the simulation of neutron diffusion transient model. The method is made efficient by means of a coarse solver defined with large time steps and steady control rods model. Using finite element for the space discretization, our implementation provides a good scalability of the algorithm. Numerical results show the efficiency of the parareal method on large light water reactor transient model corresponding to the Langenbuch-Maurer-Werner (LMW) benchmark [1]