Anna Puig

Phages of enteric bacteria in fresh water with different levels of faecal pollution.

Levels of somatic and F‐specific coliphages, and phages infecting Bacteroides fragilis were measured in 257 samples collected in different freshwater environments with different levels and characteristics of faecal pollution. In samples with recent pollution of domestic origin, the numbers of the three groups of phages were highly correlated, thus showing that their excretion is fairly constant. In this set of samples somatic coliphages, which were the most abundant, and F‐specific coliphages outnumbered significantly Bact. fragilis phages. Normalized lines of the numbers of the three groups of phages in water samples and their sediments show that they settle similarly. The correlation between the values of the three groups of phages was not observed in waters with intermediate levels of pollution. An increase in the relative numbers of coliphages with respect to numbers of phages infecting Bact. fragilis was observed. In waters with persistent faecal pollution a dramatic change was recorded in the relative numbers of the different groups of phages. Phages infecting Bact. fragilis suffered the lowest reduction in numbers.

Optimisation and standardisation of a method for detecting and enumerating bacteriophages infecting Bacteroides fragilis

A method for the detection and enumeration of bacteriophages infecting Bacteroides fragilis has been standardised. The recommended host strain is RYC2056 (ATCC 700786) because of the relatively high counts (10(4)-10(5) PFU/100ml) that it recovers in sewage from very different geographical areas. The addition of 0.25% bile to the culture and assay media and the manipulation of the host strain under strict anaerobic conditions resulted in a significant increase (more than 100%) in the number of phages detected. No other changes in the media and culture conditions resulted in changes in the phage counts detected. However, these increases do not justify changing the culture conditions and media described, taking into consideration that bile renders the media cloudy making it difficult to follow the host growth and that most laboratories do not have the facilities to work under strict anaerobic conditions. Nalidixic acid (100 microg/ml) and kanamycin (100 microg/ml) in the assay medium significantly reduce the background flora from polluted samples without affecting the phage counts. Freezing cultures just before the end of the log-phage growth at (-70+/-10) degrees C with BSA-sucrose as cryoprotector, storing of 1-2 ml in glass vials at (-70+/-10) degrees C and using them directly to inoculate fresh broth allows the obtention of cultures ready for phage enumeration in about 2.5 h. All these developments have been incorporated into a procedure that makes the method for detecting phages infecting B. fragilis as workable as the standardised methods available for the detection of coliphages.

A framework for fusion methods and rendering techniques of multimodal volume data

Many different direct volume rendering methods have been developed to visualize 3D scalar fields on uniform rectilinear grids. However, little work has been done on rendering simultaneously various properties of the same 3D region measured with different registration devices or at different instants of time. The demand for this type of visualization is rapidly increasing in scientific applications such as medicine in which the visual integration of multiple modalities allows a better comprehension of the anatomy and a perception of its relationships with activity. This paper presents different strategies of direct multimodal volume rendering (DMVR). It is restricted to voxel models with a known 3D rigid alignment transformation. The paper evaluates at which steps of the rendering pipeline the data fusion must be realized in order to accomplish the desired visual integration and to provide fast re‐renders when some fusion parameters are modified. In addition, it analyses how existing monomodal visualization algorithms can be extended to multiple datasets and it compares their efficiency and their computational cost. Copyright

3D simulation of tool machining

Abstract This paper describes a 3D tool machining simulation system. The initial tool and the grinding wheels are integrated with the machine tool. The application reads and interprets the CNC program code that controls the machine, it computes the positions and the motion of components and it translates the sequence of machining operations into Boolean operations. The machining is computed for 2D sections and, later, a 3D model of the tool is reconstructed. The application is ready to yield tool visualization, it gives measurements on sections and it can show an interactive animation of the whole process. A novel aspect of the simulation is that it is able to deal with 6-axes machines, whereas most of previous work is limited to 3- and 4-axes machines. In addition, it allows to interrupt the machining process and to show partially machined tools. A major contribution is the fact that the Boolean operations are performed in 2D and the 3D model is reconstructed from the cross sections, which provides user control on the resolution of the operations at a low cost.

Simple concentration method for bacteriophages of Bacteroides fragilis in drinking water.

A membrane of inorganic material with a honeycomb pore structure was used to concentrate phages infecting Bacteroides fragilis from drinking water. Phages were removed from the membrane with 0.25 M glycine buffer pH 9.5. Phages were not inactivated by storage in this buffer neutralized to pH 7.0 for at least 9 days at 4 degrees C. The method allows recovery of around 50% in drinking water. When the turbidity of the water increased, the efficiency of the concentration decreased markedly. The efficiency of concentration was evaluated versus a presence/absence test in 317 water samples with turbidity level below the threshold of drinking water. Results obtained by concentration of 11 provided data which were significantly more informative than the presence/absence tests carried out on 100 ml. A number of additional tests carried out with both somatic and F-specific coliphages indicated that these conclusions can be extended to these groups of bacteriophages.

Decision trees for accelerating unimodal, hybrid and multimodal rendering models

This paper deals with the rendering of segmented unimodal, hybrid and aligned multimodal voxel models. We propose a data structure that classifies the segmented voxels into categories, so that whenever the model has to be traversed, only the selected categories are visited and the empty and non-selected voxels are skipped. This strategy is based on: (i) a decision tree, called the rendering decision tree (RDT), which represents the hierarchy of the classification process and (ii) an intermediate run-length encoding (RLE) of the classified voxel model. The traversal of the voxel model given a user query consists of two steps: first, the RDT is traversed and the set of selected categories computed; next, the RLE is visited, but the non-selected runs are skipped and only the voxels of the original model that are codified are accessed in selected runs of the RLE. This strategy has been used to render a voxel model by back-to-front traversal and splatting as well as to construct 3D textures for hardware-driven 3D texture mapping. The results show that the voxel model traversal is significantly accelerated.

Identification of cell wall proteins of Bacteroides fragilis to which bacteriophage B40-8 binds specifically.

Bacteriophage infecting Bacteroides fragilis, one of the most abundant bacteria in the human colon, have been proposed as indicators of virological faecal pollution. The first identification of a receptor for a bacteriophage in B. fragilis is reported here. First, resistant mutants were characterized following phage inactivation, and it was shown that cell wall proteins are involved in phage binding. Then the proteins involved were identified by various approaches: (i) comparison of the protein profiles of wild-type B. fragilis HSP40 and phage-resistant mutants; (ii) application of a modification of the virus overlay protein blot assay (VOPBA). At least two proteins of B. fragilis, with apparent molecular masses of 35 +/- 5 kDa and 65 +/- 5 kDa, bind to B40-8. This result was later confirmed by running a complex consisting of this phage bound to radiolabelled proteins of B. fragilis on an immunoaffinity column loaded with a specific antibody against the phage. Cell proteins retained in the column also coincided with the proteins that differed in the profiles of resistant mutants. Finally, to identify the potential function of these two proteins, their N-terminal sequences were determined and compared to published sequences, but no homologies were found.

Boolean operations for 3D simulation of CNC machining of drilling tools

Abstract This paper addresses the simulation of drilling tools CNC machining. It describes a novel approach for the computation of the boundary representation of the machined tools. Machining consists of a sequence of boolean operations of difference between the tool and the grinding wheels through time. The proposed method performs the dynamic boolean operations on cross sections of the tool and it reconstructs the 3Dmodel by tiling between the cross sections. The method is based on classical computational geometry algorithms such as intersection tests, hull computations, 2D boolean operations and surface tiling. This approach is efficient and it provides user control on the resolution of the operations.

Hybrid Model for Vascular Tree Structures

This paper proposes a new representation scheme of the cerebral blood vessels. This model provides information on the semantics of the vascular structure: the topological relationships between vessels and the labeling of vascular accidents such as aneurysms and stenoses. In addition, the model keeps information of the inner surface geometry as well as of the vascular map volume properties, i.e. the tissue density, the blood flow velocity and the vessel wall elasticity.

Intelligent Objects to Facilitate Human Participation in Virtual Institutions

Our research combines electronic institutions and 3D virtual worlds for the construction of virtual institutions which are virtual worlds with normative regulation of interactions. That is, a virtual world where participants actions have to comply with predefined institutional rules. In this context, the actions a participant may perform depend on the institutional rules and the current execution state. We propose to include iObjects, intelligent objects, as entities having both visualization properties and decision mechanisms in the virtual institution. They are a new key element to improve users participation in virtual institutions. We situate them in a middleware infrastructure in order to be independent of 3D virtual world platform and to provide a general solution in which participants could be connected from different immersive environment platforms.