Non-linear elastic deformable models for real-time surgery simulation

In this article, we describe the latest developments of the minimally invasive hepatic surgery simulator prototype developed at INRIA. A key problem with such a simulator is the physical modelling of soft tissues. We propose a new deformable model based on non-linear elasticity and the finite element method. This model is valid for large displacements, which means in particular that it is invariant with respect to rotations. This property improves the realism of the deformations and solves the problems related to the shortcomings of linear elasticity, which is only valid for small displacements. We also address the problem of volume variations by adding to our model incompressibility constraints. Finally, we demonstrate the relevance of this approach for the real-time simulation of laparoscopic surgical gestures on the liver.     

Optimal calibration marker mesh for 2D X-ray sensors in 3D reconstruction

Image intensifiers suffer from distortions due to magnetic fields. In order to use this X-ray projections images for computer-assisted medical interventions, image intensifiers need to be calibrated. Opaque markers are often used for the correction of the image distortion and the estimation of the acquisition geometry parameters. Information under the markers is then lost. In this work, we consider the calibration of image intensifiers in the framework of 3D reconstruction from several 2D X-ray projections. In this context, new schemes of marker distributions are proposed for 2D X-ray sensor calibration. They are based on efficient sampling conditions of the parallel-beam X-ray transform when the detector and source trajectory is restricted to a circle around the measured object. Efficient sampling are essentially subset of standard sampling in this situation. The idea is simply to exploit the data redundancy of standard sampling and to replace some holes of efficient schemes by markers. Optimal location of markers in the sparse efficient sampling geometry can thus be found. In this case, the markers can stay on the sensor during the measurement with--theoretically--no loss of information (when the signal-to-noise ratio is large). Even if the theory is based on the parallel-beam X-ray transform, numerical experiments on both simulated and real data are shown in the case of weakly divergent beam geometry. We show that the 3D reconstruction from simulated data with interlaced markers is essentially the same as those obtained from data with no marker. We show that efficient Fourier interpolation formulas based on optimal sparse sampling schemes can be used to recover the information hidden by the markers.     

Cloning and expression in Escherichia coli of dextranase genes from Bacteroides thetaiotaomicron

A genomic bank was constructed in Escherichia coli HB101, consisting of DNA fragments from Bacteroides thetaiotaomicron strain 489 inserted within the vector pBR322. By screening on complex medium containing blue dextran, 10 stable dextranase-positive (Dex+) clones were isolated. Seven groups of Dex+ inserts were identified on the basis of their restriction maps and hybridization responses. Dextanase activity of the recombinant clones was weak, and was revealed on the selection medium after 15 days. Subcloning of a Sau3AI partially digested 3.2-kb insert in the expression vector pDR720 greatly enhanced dextranse activity on blue dextran plates in one clone, but the delay remained unaltered. This suggested that the enzyme was released by cell lysis. Expression of this 0.7-kb subcloned insert was dependent on the promoter region of tryptophan operon carried by pDR720.     

Biome reconstruction from pollen and plant macrofossil data for Africa and the Arabian peninsula at 0 and 6000 years

Biome reconstruction from pollen and plant macrofossil data provides an objective method to reconstruct past vegetation. Biomes for Africa and the Arabian peninsula have been mapped for 6000 years bp and provide a new standard for the evaluation of simulated palaeovegetation distributions. A test using modern pollen data shows the robustness of the biomization method, which is able to predict the major vegetation types with a high confidence level. The application of the procedure to the 6000 years data set (pollen and plant macrofossil analyses) shows systematic differences from the present that are consistent with the numerous previous regional and continental interpretations, while providing a more extensive and more objective basis for such interpretations. Madagascar, eastern, southern and central Africa show only minor changes in terms of biomes, compared to present. Major changes in biome distributions occur north of 15°N, with steppe in many low-elevation sites that are now desert, and temperate xerophytic woods/scrub and warm mixed forest in the Saharan mountains. These shifts in biome distributions imply significant changes in climate, especially precipitation, between 6000 years and present, reflecting a change in monsoon extent combined with a southward expansion of Mediterranean influence.     

Solubilization of gellan gels by chelation of cations

Summary Chelation solubilization of gellan under mild conditions has been accomplished for the first time by exposure to either 10 mM sodium citrate buffer (pH 6.0) or to 1 mM sodium hexametaphosphate (pH 6.6). The citrate system was preferred for most applications since its is a ubiquitous cellular component, its solutions are autoclavable, and because viable plant tissues, fungi, and bacteria could be recovered from culture. Such recovery is not possible from more commonly used media such as agar.     

Social facilitation of long-lasting memory is mediated by CO2 in Drosophila

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Insights into Penicillium roqueforti Morphological and Genetic Diversity

Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection.     

Unveiling trade‐offs in resource selection of migratory caribou using a mechanistic movement model of availability

Habitat selection is a multi‐level, hierarchical process that should be a key component in the balance between food acquisition and predation risk avoidance (food–predation trade‐off). However, to date, studies have not fully elucidated how fine‐ and broad‐scale habitat decisions by individual prey can help balance food versus risk. We studied broad‐scale habitat selection by Newfoundland caribou Rangifer tarandus, focusing on trade‐offs between predation risk versus access to forage during the calving and post‐calving period. We improved traditional measures of habitat availability by incorporating fine‐scale movement patterns of caribou into the availability kernel, thus enabling separation of broad and fine scales of selection. Remote sensing and field surveys served to create a spatio‐temporal model of forage availability, whereas GPS telemetry locations from 66 black bears Ursus americanus and 59 coyotes Canis latrans provided models of predation risk. We then used GPS telemetry locations from 114 female caribou to assess food–predation trade‐offs through the prism of our refined model of caribou habitat availability. We noted that migratory movements of caribou were oriented mainly towards habitats with abundant forage and lower risk of bear and (to a lesser extent) coyote encounter. These findings were generally consistent across caribou herds and would not have been evident had we used traditional methods instead of our refined model when estimating habitat availability. We interpret these findings in the context of stereotypical migratory behaviour observed in Newfoundland caribou, which occurs despite the extirpation of wolves Canis lupus nearly a century ago. We submit that caribou are able to balance food acquisition against predation risk using a complex set of factors involving both finer and broader scale selection. Accordingly, our study provides a strong argument for using refined habitat availability estimates when assessing food–predation trade‐offs.