Revisitando o problema de visibilidade para visualização tridimensional

We revisit the problem of visibility, which is to determine a set of primitives potentially visible in a set of geometry data represented by a data structure, such as a mesh of polygons or triangles, we propose a solution for speeding up the three-dimensional visualization processing in applications. We introduce a lean structure , in the sense of data abstraction and reduction, which can be used for online and interactive applications. The visibility problem is especially important in 3D visualization of scenes represented by large volumes of data, when it is not worthwhile keeping all polygons of the scene in memory. This implies a greater time spent in the rendering, or is even impossible to keep them all in huge volumes of data. In these cases, given a position and a direction of view, the main objective is to determine and load a minimum ammount of primitives (polygons) in the scene, to accelerate the rendering step. For this purpose, our algorithm performs cutting primitives (culling) using a hybrid paradigm based on three known techniques. The scene is divided into a cell grid, for each cell we associate the primitives that belong to them, and finally determined the set of primitives potentially visible. The novelty is the use of triangulation Ja 1 to create the subdivision grid. We chose this structure because of its relevant characteristics of adaptivity and algebrism (ease of calculations). The results show a substantial improvement over traditional methods when applied separately. The method introduced in this work can be used in devices with low or no dedicated processing power CPU, and also can be used to view data via the Internet, such as virtual museums applications

An Adaptive and Hybrid Approach to Revisiting the Visibility Pipeline

We revisit the visibility problem, which is traditionally known in Computer Graphics and Vision fields as the process of computing a (potentially) visible set of primitives in the computational model of a scene. We propose a hybrid solution that uses a dry structure (in the sense of data reduction), a triangulation of the type , to accelerate the task of searching for visible primitives. We came up with a solution that is useful for real-time, on-line, interactive applications as 3D visualization. In such applications the main goal is to load the minimum amount of primitives from the scene during the rendering stage, as possible. For this purpose, our algorithm executes the culling by using a hybrid paradigm based on viewing-frustum, back-face culling and occlusion models. Results have shown substantial improvement over these traditional approaches if applied separately. This novel approach can be used in devices with no dedicated processors or with low processing power, as cell phones or embedded displays, or to visualize data through the Internet, as in virtual museums applications.

Direct visualization of the trimeric structure of the ASIC1a channel, using AFM imaging.

There has been confusion about the subunit stoichiometry of the degenerin family of ion channels. Recently, a crystal structure of acid-sensing ion channel (ASIC) 1a revealed that it assembles as a trimer. Here, we used atomic force microscopy (AFM) to image unprocessed ASIC1a bound to mica. We detected a mixture of subunit monomers, dimers and trimers. In some cases, triple-subunit clusters were clearly visible, confirming the trimeric structure of the channel, and indicating that the trimer sometimes disaggregated after adhesion to the mica surface. This AFM-based technique will now enable us to determine the subunit arrangement within heteromeric ASICs.

Radiolabeling of defined polymer architectures with fluorine-18 and iodine-131 for ex vivo and in vivo evaluation : visualization of structure-property relationships

Nuclear medicine imaging techniques such as PET are of increasing relevance in pharmaceutical research being valuable (pre)clinical tools to non-invasively assess drug performance in vivo. Therapeutic drugs, e.g. chemotherapeutics, often suffer from a poor balance between their efficacy and toxicity. Here, polymer based drug delivery systems can modulate the pharmacokinetics of low Mw therapeutics (prolonging blood circulation time, reducing toxic side effects, increasing target site accumulation) and therefore leading to a more efficient therapy. In this regard, poly-N-(2-hydroxypropyl)-methacrylamide (HPMA) constitutes a promising biocompatible polymer. Towards the further development of these structures, non-invasive PET imaging allows insight into structure-property relationships in vivo. This performant tool can guide design optimization towards more effective drug delivery. Hence, versatile radiolabeling strategies need to be developed and establishing 18F- as well as 131I-labeling of diverse HPMA architectures forms the basis for short- as well as long-term in vivo evaluations. By means of the prosthetic group [18F]FETos, 18F-labeling of distinct HPMA polymer architectures (homopolymers, amphiphilic copolymers as well as block copolymers) was successfully accomplished enabling their systematic evaluation in tumor bearing rats. These investigations revealed pronounced differences depending on individual polymer characteristics (molecular weight, amphiphilicity due to incorporated hydrophobic laurylmethacrylate (LMA) segments, architecture) as well as on the studied tumor model. Polymers showed higher uptake for up to 4 h p.i. into Walker 256 tumors vs. AT1 tumors (correlating to a higher cellular uptake in vitro). Highest tumor concentrations were found for amphiphilic HPMA-ran-LMA copolymers in comparison to homopolymers and block copolymers. Notably, the random LMA copolymer P4* (Mw=55 kDa, 25% LMA) exhibited most promising in vivo behavior such as highest blood retention as well as tumor uptake. Further studies concentrated on the influence of PEGylation (‘stealth effect’) in terms of improving drug delivery properties of defined polymeric micelles. Here, [18F]fluoroethylation of distinct PEGylated block copolymers (0%, 1%, 5%, 7%, 11% of incorporated PEG2kDa) enabled to systematically study the impact of PEG incorporation ratio and respective architecture on the in vivo performance. Most strikingly, higher PEG content caused prolonged blood circulation as well as a linear increase in tumor uptake (Walker 256 carcinoma). Due to the structural diversity of potential polymeric carrier systems, further versatile 18F-labeling strategies are needed. Therefore, a prosthetic 18F-labeling approach based on the Cu(I)-catalyzed click reaction was established for HPMA-based polymers, providing incorporation of fluorine-18 under mild conditions and in high yields. On this basis, a preliminary µPET study of a HPMA-based polymer – radiolabeled via the prosthetic group [18F]F-PEG3-N3 – was successfully accomplished. By revealing early pharmacokinetics, 18F-labeling enables to time-efficiently assess the potential of HPMA polymers for efficient drug delivery. Yet, investigating the long-term fate is essential, especially regarding prolonged circulation properties and passive tumor accumulation (EPR effect). Therefore, radiolabeling of diverse HPMA copolymers with the longer-lived isotope iodine-131 was accomplished enabling in vivo evaluation of copolymer P4* over several days. In this study, tumor retention of 131I-P4* could be demonstrated at least over 48h with concurrent blood clearance thereby confirming promising tumor targeting properties of amphiphilic HPMA copolymer systems based on the EPR effect.

Visualization and quantification of air embolism structure by processing postmortem MSCT data.

Venous air embolism (VAE) is an often occurring forensic finding in cases of injury to the head and neck. Whenever found, it has to be appraised in its relation to the cause of death. While visualization and quantification is difficult at traditional autopsy, Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) offer a new potential in the diagnosis of VAE. This paper reports the findings of VAE in four cases of massive head injury examined postmortem by Multislice Computed Tomography (MSCT) prior to autopsy. MSCT data of the thorax were processed using 3D air structure reconstruction software to visualize air embolism within the vascular system. Quantification of VAE was done by multiplying air containing areas on axial 2D images by their reconstruction intervals and then by summarizing the air volumes. Excellent 3D visualization of the air within the vascular system was obtained in all cases, and the intravascular gas volume was quantified.

SVis: A computational steering visualization environment for surface structure determination

The arrangement of atoms at the surface of a solid accounts for many of its properties: Hardness, chemical activity, corrosion, etc. are dictated by the precise surface structure. Hence, finding it, has a broad range of technical and industrial applications. The ability to solve this problem opens the possibility of designing by computer materials with properties tailored to specific applications. Since the search space grows exponentially with the number of atoms, its solution cannot be achieved for arbitrarily large structures. Presently, a trial and error procedure is used: an expert proposes an structure as a candidate solution and tries a local optimization procedure on it. The solution relaxes to the local minimum in the attractor basin corresponding to the initial point, that might be the one corresponding to the global minimum or not. This procedure is very time consuming and, for reasonably sized surfaces, can take many iterations and much effort from the expert. Here we report on a visualization environment designed to steer this process in an attempt to solve bigger structures and reduce the time needed. The idea is to use an immersive environment to interact with the computation. It has immediate feedback to assess the quality of the proposed structure in order to let the expert explore the space of candidate solutions. The visualization environment is also able to communicate with the de facto local solver used for this problem. The user is then able to send trial structures to the local minimizer and track its progress as they approach the minimum. This allows for simultaneous testing of candidate structures. The system has also proved very useful as an educational tool for the field.

Visualization of a peripheral stalk in V-type ATPase: Evidence for the stator structure essential to rotational catalysis

F- and V-type ATPases are central enzymes in energy metabolism that couple synthesis or hydrolysis of ATP to the translocation of H+ or Na+ across biological membranes. They consist of a soluble headpiece that contains the catalytic sites and an integral membrane-bound part that conducts the ion flow. Energy coupling is thought to occur through the physical rotation of a stalk that connects the two parts of the enzyme complex. This mechanism implies that a stator-like structure prevents the rotation of the headpiece relative to the membrane-bound part. Such a structure has not been observed to date. Here, we report the projected structure of the V-type Na+-ATPase of Clostridium fervidus as determined by electron microscopy. Besides the central stalk, a second stalk of 130 Å in length is observed that connects the headpiece and membrane-bound part in the periphery of the complex. This additional stalk is likely to be the stator.

Visualization of drip channels in meat using NMR microimaging

The progressive changes in the water distribution within rabbit muscles were studied by nuclear magnetic resonance microscopy during the first 24 h postmortem. T-2 images revealed development of interspersed lines with higher signal intensities in the muscle, reflecting formation of channels containing mobile water. The appearance of the interspersed lines progressed throughout the measuring period and became increasingly evident. After about 3 h postmortem the signal intensity also increased in areas near the surface of the samples, which reflects migration of the mobile water to the sample surface. Proton density images showed the presence of a chemical shift artifact in the interspersed lines, implying that the intrinsic development of water channels progressed in close proximity to the connective tissue. (C) 2004 Elsevier Ltd. All rights reserved.

Direct visualization of Ras proteins in spatially distinct cell surface microdomains

Localization of signaling complexes to specific micro-domains coordinates signal transduction at the plasma membrane. Using immunogold electron microscopy of plasma membrane sheets coupled with spatial point pattern analysis, we have visualized morphologically featureless microdomains including lipid rafts, in situ and at high resolution. We find that an inner-plasma membrane lipid raft marker displays cholesterol-dependent clustering in microdomains with a mean diameter of 44 nm that occupy 35% of the cell surface. Cross-linking an outer-leaflet raft protein results in the redistribution of inner leaflet rafts, but they retain their modular structure. Analysis of Ras microlocalization shows that inactive H-ras is distributed between lipid rafts and a cholesterol-independent micro-domain. Conversely, activated H-ras and K-ras reside predominantly in nonoverlapping, cholesterol-independent microdomains. Galectin-1 stabilizes the association of activated H-ras with these nonraft microdomains, whereas K-ras clustering is supported by farnesylation, but not geranylgeranylation. These results illustrate that the inner plasma membrane comprises a complex mosaic of discrete microdomains. Differential spatial localization within this framework can likely account for the distinct signal outputs from the highly homologous Ras proteins.

Long-term biosignals visualization and processing

Thesis submitted in the fulfillment of the requirements for the Degree of Master in Biomedical Engineering

Modeling and visualization of medical anesthesiology acts

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Design and characterization of novel biopolymeric structure using biocompatible ionic liquids

The main objective of this thesis was the development of polymeric structures from the dissolution of FucoPol, a bacterial exopolysaccharide (EPS), in a biocompatible ionic liquid, choline acetate. The FucoPol was produced by the bacteria Enterobacter A47 using glycerol as carbon source at controlled temperature and pH (30ºC and 7, respectively). At the end of 3 days it was produced 7 g/L of FucoPol. The net yield of Fucopol in glycerol (YP/S) was 0.22 g/g and the maximum productivity 2.37 g/L.d This polymer was characterized about its composition in sugars and acyl groups (by High-Performance Liquid Chromatography - HPLC), containing fucose (35 % mol), galactose (21 % mol), glucose (29 % mol), rhamnose (3% mol) and glucuronic acid (12% mol) as well as acetate (14.28 % mol), pyruvate (2.15 % mol) and succinate (1.80 % mol). Its content of water and ash was 15% p/p and 2% p/p, respectively, and the chemical bonds (determined by Infrared Spectroscopy - FT-IR) are consistent to the literature reports. However, due to limitations in Differential Scanning Calorimetry (DSC) equipment it was not possible to determine the glass transition temperature. In turn, the ionic liquid showed the typical behavior of a Newtonian fluid, glass transition temperature (determined by DSC) -98.03ºC and density 1.1031 g/cm3. The study of chemical bonds by FT-IR showed that amount of water (8.80%) influenced the visualization of the bands predicted to in view of their chemical structure. After the dissolution of the FucoPol in the ionic liquid at different temperatures (50, 60, 80 and 100 ° C) it was promoted the removal of this by the phase inversion method using deionized water as a solvent, followed by drying in an oven at 70 ° C. The mixtures before and after the phase inversion method were characterized through the studies mentioned above. In order to explore possible application field’s biocompatibility assays and collage on balsa wood tests were performed. It was found that the process of washing with water by the phase inversion method was not totally effective in removing the biocompatible ionic liquid, since all FucoPol – IL mixtures still contained ionic liquid in their composition as can be seen by the DSC results and FT-IR. In addition, washing the mixtures with water significantly altered the composition of FucoPol. However, these mixtures, that developed a viscous behavior typical of a non-Newtonian fluid (shear-thinning), have the potential to be applied in the biomedical field as well as biological glues.

Structure of a multisubunit complex that promotes DNA branch migration.

The RuvA and RuvB proteins of Escherichia coli, which are induced in response to DNA damage, are important in the formation of heteroduplex DNA during genetic recombination and related recombinational repair processes. In vitro studies show that RuvA binds Holiday junctions and acts as a specificity factor that targets the RuvB ATPase, a hexameric ring protein, to the junction. Together, RuvA and RuvB promote branch migration, an ATP-dependent reaction that increases the length of the heteroduplex DNA. Electron microscopic visualization of RuvAB now provides a new insight into the mechanism of this process. We observe the formation of a tripartite protein complex in which RuvA binds the crossover and is sandwiched between two hexameric rings of RuvB. The Holliday junction within this complex adopts a square-planar structure. We propose a molecular model for branch migration, a unique feature of which is the role played by the two oppositely oriented RuvB ring motors.

BIO-INSPIRED COMPUTATIONAL TECHNIQUES APPLIED TO THE CLUSTERING AND VISUALIZATION OF SPATIO-TEMPORAL GEOSPATIAL DATA

The coverage and volume of geo-referenced datasets are extensive and incessantly¦growing. The systematic capture of geo-referenced information generates large volumes¦of spatio-temporal data to be analyzed. Clustering and visualization play a key¦role in the exploratory data analysis and the extraction of knowledge embedded in¦these data. However, new challenges in visualization and clustering are posed when¦dealing with the special characteristics of this data. For instance, its complex structures,¦large quantity of samples, variables involved in a temporal context, high dimensionality¦and large variability in cluster shapes.¦The central aim of my thesis is to propose new algorithms and methodologies for¦clustering and visualization, in order to assist the knowledge extraction from spatiotemporal¦geo-referenced data, thus improving making decision processes.¦I present two original algorithms, one for clustering: the Fuzzy Growing Hierarchical¦Self-Organizing Networks (FGHSON), and the second for exploratory visual data analysis:¦the Tree-structured Self-organizing Maps Component Planes. In addition, I present¦methodologies that combined with FGHSON and the Tree-structured SOM Component¦Planes allow the integration of space and time seamlessly and simultaneously in¦order to extract knowledge embedded in a temporal context.¦The originality of the FGHSON lies in its capability to reflect the underlying structure¦of a dataset in a hierarchical fuzzy way. A hierarchical fuzzy representation of¦clusters is crucial when data include complex structures with large variability of cluster¦shapes, variances, densities and number of clusters. The most important characteristics¦of the FGHSON include: (1) It does not require an a-priori setup of the number¦of clusters. (2) The algorithm executes several self-organizing processes in parallel.¦Hence, when dealing with large datasets the processes can be distributed reducing the¦computational cost. (3) Only three parameters are necessary to set up the algorithm.¦In the case of the Tree-structured SOM Component Planes, the novelty of this algorithm¦lies in its ability to create a structure that allows the visual exploratory data analysis¦of large high-dimensional datasets. This algorithm creates a hierarchical structure¦of Self-Organizing Map Component Planes, arranging similar variables' projections in¦the same branches of the tree. Hence, similarities on variables' behavior can be easily¦detected (e.g. local correlations, maximal and minimal values and outliers).¦Both FGHSON and the Tree-structured SOM Component Planes were applied in¦several agroecological problems proving to be very efficient in the exploratory analysis¦and clustering of spatio-temporal datasets.¦In this thesis I also tested three soft competitive learning algorithms. Two of them¦well-known non supervised soft competitive algorithms, namely the Self-Organizing¦Maps (SOMs) and the Growing Hierarchical Self-Organizing Maps (GHSOMs); and the¦third was our original contribution, the FGHSON. Although the algorithms presented¦here have been used in several areas, to my knowledge there is not any work applying¦and comparing the performance of those techniques when dealing with spatiotemporal¦geospatial data, as it is presented in this thesis.¦I propose original methodologies to explore spatio-temporal geo-referenced datasets¦through time. Our approach uses time windows to capture temporal similarities and¦variations by using the FGHSON clustering algorithm. The developed methodologies¦are used in two case studies. In the first, the objective was to find similar agroecozones¦through time and in the second one it was to find similar environmental patterns¦shifted in time.¦Several results presented in this thesis have led to new contributions to agroecological¦knowledge, for instance, in sugar cane, and blackberry production.¦Finally, in the framework of this thesis we developed several software tools: (1)¦a Matlab toolbox that implements the FGHSON algorithm, and (2) a program called¦BIS (Bio-inspired Identification of Similar agroecozones) an interactive graphical user¦interface tool which integrates the FGHSON algorithm with Google Earth in order to¦show zones with similar agroecological characteristics.

Evaluating multidimensional visualization techniques in data mining tasks

Visual data mining (VDM) tools employ information visualization techniques in order to represent large amounts of high-dimensional data graphically and to involve the user in exploring data at different levels of detail. The users are looking for outliers, patterns and models – in the form of clusters, classes, trends, and relationships – in different categories of data, i.e., financial, business information, etc. The focus of this thesis is the evaluation of multidimensional visualization techniques, especially from the business user’s perspective. We address three research problems. The first problem is the evaluation of projection-based visualizations with respect to their effectiveness in preserving the original distances between data points and the clustering structure of the data. In this respect, we propose the use of existing clustering validity measures. We illustrate their usefulness in evaluating five visualization techniques: Principal Components Analysis (PCA), Sammon’s Mapping, Self-Organizing Map (SOM), Radial Coordinate Visualization and Star Coordinates. The second problem is concerned with evaluating different visualization techniques as to their effectiveness in visual data mining of business data. For this purpose, we propose an inquiry evaluation technique and conduct the evaluation of nine visualization techniques. The visualizations under evaluation are Multiple Line Graphs, Permutation Matrix, Survey Plot, Scatter Plot Matrix, Parallel Coordinates, Treemap, PCA, Sammon’s Mapping and the SOM. The third problem is the evaluation of quality of use of VDM tools. We provide a conceptual framework for evaluating the quality of use of VDM tools and apply it to the evaluation of the SOM. In the evaluation, we use an inquiry technique for which we developed a questionnaire based on the proposed framework. The contributions of the thesis consist of three new evaluation techniques and the results obtained by applying these evaluation techniques. The thesis provides a systematic approach to evaluation of various visualization techniques. In this respect, first, we performed and described the evaluations in a systematic way, highlighting the evaluation activities, and their inputs and outputs. Secondly, we integrated the evaluation studies in the broad framework of usability evaluation. The results of the evaluations are intended to help developers and researchers of visualization systems to select appropriate visualization techniques in specific situations. The results of the evaluations also contribute to the understanding of the strengths and limitations of the visualization techniques evaluated and further to the improvement of these techniques.