Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on http://www.tcoffee.or

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on

Numerical Characterisation of a HP Compressor Stage Equipped with a Closed Shrouded Stator Cavity

International audienceAbstract In axial compressors, shrouded stator cavity flows are responsible for performance degradation due to their interaction with the power stream. The present paper aims at exploring the possibility of employing a single stage high pressure axial compressor as a test vehicle for cavity flows investigations. In a first step, the robustness of the adopted RANS approach is tested against experimental data on the closed-cavity baseline configuration (i.e. no downstream-to-upstream recirculation). In a second phase, the effect of different hub cavities layouts of different levels of realism is numerically investigated. The focus is set on the representativeness of a closed cavity configuration with injection. The cavity flow topology and impact on the overall performance are considered in the analysis. At its final extent, this paper provides numerical and experimental guidelines for the robust assessment of cavity flows topology and performance effects

Outside observer, an enhanced training methodology: bringing back the expert's eye whilst training alone

Traditional surgical teaching requires an expert trainer to be present during training. This training model allows an expert to observe a novice's performance and provide corrective feedback as errors are made. Virtual simulations offer a much needed alternative to learning through error and allow the trainee to hone skills without the presence of a skilled surgical trainer. However, current simulations limit the scope of training to tool directed learning, focusing training around instrumented simulated tool tips. This paper identifies a need for trainee centered virtual training to complement current approaches. The Outside Observer training methodology provides training feedback based on the observation of surgical tool tip manipulations in conjunction with the external movements a trainee performs during a procedure. It is thought that integrating movement and posture training with current tool tracking methods will provide more effective and accelerated learning

COMPOSITE MATERIAL COMBINING MOF NANOPARTICLES AND METAL NANOPARTICLES

La présente invention se rapporte à un matériau composite utilisable comme indicateur optique, associant (a) au moins un MOF cristallin poreux, de préférence sous forme de nanoparticules, adapté à l’adsorption de composés organiques volatils , et (b) des nanoparticules de forme anisotrope d’au moins un métal ou alliage de métaux ayant une bande plasmon dans le visible, le métal étant choisi parmi Au, Ag, Cu et Pd ou mélange homogène ou non ou alliage de ceux-ci. L’invention se rapporte également à un procédé de préparation du matériau composite, à un dispositif pour la détection optique de la saturation d’un adsorbant MOF en composés organiques volatils, ainsi qu’à l’utilisation du matériau composite comme indicateur optique pour la saturation d’un adsorbant MOF en composés organiques volatils

Automated visibility map of the internal colon surface from colonoscopy video

International audiencePurposeOptical colonoscopy is a prominent procedure by which clinicians examine the surface of the colon for cancerous polyps using a flexible colonoscope. One of the main concerns regarding the quality of the colonoscopy is to ensure that the whole colonic surface has been inspected for abnormalities. In this paper, we aim at estimating areas that have not been covered thoroughly by providing a map from the internal colon surface.MethodsCamera parameters were estimated using optical flow between consecutive colonoscopy frames. A cylinder model was fitted to the colon structure using 3D pseudo stereo vision and projected into each frame. A circumferential band from the cylinder was extracted to unroll the internal colon surface (band image). By registering these band images, drift in estimating camera motion could be reduced, and a visibility map of the colon surface could be generated, revealing uncovered areas by the colonoscope. Hidden areas behind haustral folds were ignored in this study. The method was validated on simulated and actual colonoscopy videos. The realistic simulated videos were generated using a colonoscopy simulator with known ground truth, and the actual colonoscopy videos were manually assessed by a clinical expert.ResultsThe proposed method obtained a sensitivity and precision of 98 and 96 % for detecting the number of uncovered areas on simulated data, whereas validation on real videos showed a sensitivity and precision of 96 and 78 %, respectively. Error in camera motion drift could be reduced by almost 50 % using results from band image registration.ConclusionUsing a simple cylindrical model for the colon and reducing drift by registering band images allows for the generation of visibility maps. The current results also suggest that the provided feedback through the visibility map could enhance clinicians’ awareness of uncovered areas, which in return could reduce the probability of missing polyps