Extended free-form deformation : a sculpturing tool for 3D geometric modeling

Projet SYNTIMCurrent research efforts focus on providing more efficient and effective design methods for 3D modeling systems. In this paper a new deformation technique is presented. Among other things, arbitrarily shaped bump can be designed and surfaces can be bent along arbitrarily shaped curves. The purpose of this research is to define a highly interactive and intuitive modeling technique for designers and stylists. A natural way of thinking is to mimic traditional trades, such as sculpturing and moulding. Furthermore, with this deformation technique, the modeling tool paradigm is introduced. The object is deformed with a user-defined deformation tool. This method is an extension of the Free-Form Deformation (FFD) technique proposed by Sederberg and Parry

Identification of cellulolytic bacteria in soil by stable isotope probing

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Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation

Limitations on the availability of Fe(III) as an electron acceptor are thought to play an important role in restricting the growth and activity of Geobacter species during bioremediation of contaminated subsurface environments, but the possibility that these organisms might also be limited in the subsurface by the availability of iron for assimilatory purposes was not previously considered because copious quantities of Fe(II) are produced as the result of Fe(III) reduction. Analysis of multiple Geobacteraceae genomes revealed the presence of a three-gene cluster consisting of homologues of two irondependent regulators, fur and dtxR (ideR), separated by a homologue of feoB, which encodes an Fe(II) uptake protein. This cluster appears to be conserved among members of the Geobacteraceae and was detected in several environments. Expression of the fur-feoB-ideR cluster decreased as Fe(II) concentrations increased in chemostat cultures. The number of Geobacteraceae feoB transcripts in groundwater samples from a site undergoing in situ uranium bioremediation was relatively high until the concentration of dissolved Fe(II) increased near the end of the field experiment. These results suggest that, because much of the Fe(II) is sequestered in solid phases, Geobacter species, which have a high requirement for iron for iron-sulfur proteins, may be limited by the amount of iron available for assimilatory purposes. These results demonstrate the ability of transcript analysis to reveal previously unsuspected aspects of the in situ physiology of microorganisms in subsurface environments

Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information

Hierarchical clustering is a popular method for grouping together similar elements based on a distance measure between them. In many cases, annotations for some elements are known beforehand, which can aid the clustering process. We present a novel approach for decomposing a hierarchical clustering into the clusters that optimally match a set of known annotations, as measured by the variation of information metric. Our approach is general and does not require the user to enter the number of clusters desired. We apply it to two biological domains: finding protein complexes within protein interaction networks and identifying species within metagenomic DNA samples. For these two applications, we test the quality of our clusters by using them to predict complex and species membership, respectively. We find that our approach generally outperforms the commonly used heuristic methods. © Springer-Verlag Berlin Heidelberg 2009