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Visualization
Kinds of Visualization Terms modified by Visualization Selected AbstractsHardware architecture for a visualization classroom: VizClassCOMPUTER APPLICATIONS IN ENGINEERING EDUCATION, Issue 4 2004Tara C. Hutchinson Abstract Interactive learning, critical thinking, creative problem-solving, and problem-based learning are all critical elements for enhancing engineering education. Visualization can provide the much needed computer-assisted design and analysis environment to foster problem-based learning, while virtual reality (VR) can provide the environment for hands-on manipulation, stimulating interactive learning in the engineering classroom. To provide such a space, at the University of California, Irvine a new interactive, spatially balanced learning environment, termed VizClass, has been developed. VizClass incorporates a specially designed lecture room and laboratory integrating both 2- and 3-dimensional spatial learning by coupling a series of interactive projection display boards (touch sensitive whiteboards) and a semi-immersive 3D wall display. Control of devices integrated with VizClass is supported via a centrally located, easy to activate, touch-sensitive display. Digital material, including slides, web content, video clips, sound files, numerical simulations, or animations may be loaded and presented by instructors using either 2D or 3D modalities. This environment has already been integrated into both undergraduate and graduate level courses, providing a balanced spatial learning environment for students. This article describes the unique hardware architecture developed to support this new environment and presents the first course activities conducted within the space. © 2004 Wiley Periodicals, Inc. Comput Appl Eng Educ 12: 232,241, 2004; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20024 [source] An Exploratory Technique for Coherent Visualization of Time-varying Volume DataCOMPUTER GRAPHICS FORUM, Issue 3 2010A. Tikhonova Abstract The selection of an appropriate global transfer function is essential for visualizing time-varying simulation data. This is especially challenging when the global data range is not known in advance, as is often the case in remote and in-situ visualization settings. Since the data range may vary dramatically as the simulation progresses, volume rendering using local transfer functions may not be coherent for all time steps. We present an exploratory technique that enables coherent classification of time-varying volume data. Unlike previous approaches, which require pre-processing of all time steps, our approach lets the user explore the transfer function space without accessing the original 3D data. This is useful for interactive visualization, and absolutely essential for in-situ visualization, where the entire simulation data range is not known in advance. Our approach generates a compact representation of each time step at rendering time in the form of ray attenuation functions, which are used for subsequent operations on the opacity and color mappings. The presented approach offers interactive exploration of time-varying simulation data that alleviates the cost associated with reloading and caching large data sets. [source] Time-Adaptive Lines for the Interactive Visualization of Unsteady Flow Data SetsCOMPUTER GRAPHICS FORUM, Issue 8 2009N. Cuntz I.3.3 [Computer Graphics]: Line and Curve Generation; I.3.1 [Computer Graphics]: Parallel Processing Abstract The quest for the ideal flow visualization reveals two major challenges: interactivity and accuracy. Interactivity stands for explorative capabilities and real-time control. Accuracy is a prerequisite for every professional visualization in order to provide a reliable base for analysis of a data set. Geometric flow visualization has a long tradition and comes in very different flavors. Among these, stream, path and streak lines are known to be very useful for both 2D and 3D flows. Despite their importance in practice, appropriate algorithms suited for contemporary hardware are rare. In particular, the adaptive construction of the different line types is not sufficiently studied. This study provides a profound representation and discussion of stream, path and streak lines. Two algorithms are proposed for efficiently and accurately generating these lines using modern graphics hardware. Each includes a scheme for adaptive time-stepping. The adaptivity for stream and path lines is achieved through a new processing idea we call ,selective transform feedback'. The adaptivity for streak lines combines adaptive time-stepping and a geometric refinement of the curve itself. Our visualization is applied, among others, to a data set representing a simulated typhoon. The storage as a set of 3D textures requires special attention. Both algorithms explicitly support this storage, as well as the use of precomputed adaptivity information. [source] A Time Model for Time-Varying VisualizationCOMPUTER GRAPHICS FORUM, Issue 6 2009M. Wolter I.3.6 [Computer Graphics]: Methodology and Techniques; I.6.6 [Simulation and Modelling]: Simulation Output Analysis Abstract The analysis of unsteady phenomena is an important topic for scientific visualization. Several time-dependent visualization techniques exist, as well as solutions for dealing with the enormous size of time-varying data in interactive visualization. Many current visualization toolkits support displaying time-varying data sets. However, for the interactive exploration of time-varying data in scientific visualization, no common time model that describes the temporal properties which occur in the visualization process has been established. In this work, we propose a general time model which classifies the time frames of simulation phenomena and the connections between different time scales in the analysis process. This model is designed for intuitive interaction with time in visualization applications for the domain expert as well as for the developer of visualization tools. We demonstrate the benefits of our model by applying it to two use cases with different temporal properties. [source] 2009 Eurographics Symposium on Parallel Graphics and VisualizationCOMPUTER GRAPHICS FORUM, Issue 6 2009João Comba No abstract is available for this article. [source] Interactive Visualization of Function Fields by Range-Space SegmentationCOMPUTER GRAPHICS FORUM, Issue 3 2009John C. Anderson Abstract We present a dimension reduction and feature extraction method for the visualization and analysis of function field data. Function fields are a class of high-dimensional, multi-variate data in which data samples are one-dimensional scalar functions. Our approach focuses upon the creation of high-dimensional range-space segmentations, from which we can generate meaningful visualizations and extract separating surfaces between features. We demonstrate our approach on high-dimensional spectral imagery, and particulate pollution data from air quality simulations. [source] Direct Visualization of Deformation in VolumesCOMPUTER GRAPHICS FORUM, Issue 3 2009Stef Busking Abstract Deformation is a topic of interest in many disciplines. In particular in medical research, deformations of surfaces and even entire volumetric structures are of interest. Clear visualization of such deformations can lead to important insight into growth processes and progression of disease. We present new techniques for direct focus+context visualization of deformation fields representing transformations between pairs of volumetric datasets. Typically, such fields are computed by performing a non-rigid registration between two data volumes. Our visualization is based on direct volume rendering and uses the GPU to compute and interactively visualize features of these deformation fields in real-time. We integrate visualization of the deformation field with visualization of the scalar volume affected by the deformations. Furthermore, we present a novel use of texturing in volume rendered visualizations to show additional properties of the vector field on surfaces in the volume. [source] Particle Level Set Advection for the Interactive Visualization of Unsteady 3D FlowCOMPUTER GRAPHICS FORUM, Issue 3 2008Nicolas Cuntz Abstract Typically, flow volumes are visualized by defining their boundary as iso-surface of a level set function. Grid-based level sets offer a good global representation but suffer from numerical diffusion of surface detail, whereas particle-based methods preserve details more accurately but introduce the problem of unequal global representation. The particle level set (PLS) method combines the advantages of both approaches by interchanging the information between the grid and the particles. Our work demonstrates that the PLS technique can be adapted to volumetric dye advection via streak volumes, and to the visualization by time surfaces and path volumes. We achieve this with a modified and extended PLS, including a model for dye injection. A new algorithmic interpretation of PLS is introduced to exploit the efficiency of the GPU, leading to interactive visualization. Finally, we demonstrate the high quality and usefulness of PLS flow visualization by providing quantitative results on volume preservation and by discussing typical applications of 3D flow visualization. [source] Physically-based Dye Advection for Flow VisualizationCOMPUTER GRAPHICS FORUM, Issue 3 2008Guo-Shi Li Abstract Dye advection is widely used in experimental flow analysis but has seen less use for visualization in computational fluid dynamics. One possible reason for this disconnect is the inaccuracy of the texture-based approach, which is prone to artifacts caused by numeric diffusion and mass fluctuation. In this paper, we introduce a novel 2D dye advection scheme for flow visualization based on the concept of control volume analysis typically used in computational fluid dynamics. The evolution of dye patterns in the flow field is achieved by advecting individual control volumes, which collectively cover the entire spatial domain. The local variation of dye material, represented as a piecewise quasi-parabolic function, is integrated within each control volume resulting in mass conserving transport without excessive numerical diffusion. Due to its physically based formulation, this approach is capable of conveying intricate flow structures not shown in the traditional dye advection schemes while avoiding visual artifacts. [source] Illustrative Hybrid Visualization and Exploration of Anatomical and Functional Brain DataCOMPUTER GRAPHICS FORUM, Issue 3 2008W. M. Jainek Abstract Common practice in brain research and brain surgery involves the multi-modal acquisition of brain anatomy and brain activation data. These highly complex three-dimensional data have to be displayed simultaneously in order to convey spatial relationships. Unique challenges in information and interaction design have to be solved in order to keep the visualization sufficiently complete and uncluttered at the same time. The visualization method presented in this paper addresses these issues by using a hybrid combination of polygonal rendering of brain structures and direct volume rendering of activation data. Advanced rendering techniques including illustrative display styles and ambient occlusion calculations enhance the clarity of the visual output. The presented rendering pipeline produces real-time frame rates and offers a high degree of configurability. Newly designed interaction and measurement tools are provided, which enable the user to explore the data at large, but also to inspect specific features closely. We demonstrate the system in the context of a cognitive neurosciences dataset. An initial informal evaluation shows that our visualization method is deemed useful for clinical research. [source] Centrality Based Visualization of Small World GraphsCOMPUTER GRAPHICS FORUM, Issue 3 2008F. Van Ham Abstract Current graph drawing algorithms enable the creation of two dimensional node-link diagrams of huge graphs. However, for graphs with low diameter (of which "small world" graphs are a subset) these techniques begin to break down visually even when the graph has only a few hundred nodes. Typical algorithms produce images where nodes clump together in the center of the screen, making it hard to discern structure and follow paths. This paper describes a solution to this problem, which uses a global edge metric to determine a subset of edges that capture the graph's intrinsic clustering structure. This structure is then used to create an embedding of the graph, after which the remaining edges are added back in. We demonstrate applications of this technique to a number of real world examples. [source] Dye Advection Without the Blur: A Level-Set Approach for Texture-Based Visualization of Unsteady FlowCOMPUTER GRAPHICS FORUM, Issue 3 2004D. Weiskopf Dye advection is an intuitive and versatile technique to visualize both steady and unsteady flow. Dye can be easily combined with noise-based dense vector field representations and is an important element in user-centric visual exploration processes. However, fast texture-based implementations of dye advection rely on linear interpolation operations that lead to severe diffusion artifacts. In this paper, a novel approach for dye advection is proposed to avoid this blurring and to achieve long and clearly defined streaklines or extended streak-like patterns. The interface between dye and background is modeled as a level-set within a signed distance field. The level-set evolution is governed by the underlying flow field and is computed by a semi-Lagrangian method. A reinitialization technique is used to counteract the distortions introduced by the level-set evolution and to maintain a level-set function that represents a local distance field. This approach works for 2D and 3D flow fields alike. It is demonstrated how the texture-based level-set representation lends itself to an efficient GPU implementation and therefore facilitates interactive visualization. Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Picture/Image Generation I.3.7 [Computer Graphics]: Three-Dimensional Graphics and Realism [source] Volumetric Filtering, Modeling and Visualization for Nano-MedicineCOMPUTER GRAPHICS FORUM, Issue 3 2003Chandrajit Bajaj The 3D structures of individual proteins or small complexes, such as most of the Protein Data Bank entries, are still unable to yield the "full picture" of a functional biological complex. The study of large macromolecular complexes, such as viruses, ion channels, the ribosome and other macromolecular machines of various types, offer more complete structural and functional description of the nano-machinery of life. In addition to x-ray crystallography. NMR spectroscopy, electron cryomicroscopy (cryoEM) imaging of single particles, and in-vivo molecular tomographic imaging has become indispensable at revealing the structures of large macromolecular complexes at subnanometer resolutions. In this talk, I shall describe some of the recent computational advances in filtering, modeling, analysis and visualization, that have propelled structure determination by cryoEM and tomographic imaging, to steadily increasing accuracy. [source] Interactive Visualization with Programmable Graphics HardwareCOMPUTER GRAPHICS FORUM, Issue 3 2002Thomas Ertl One of the main scientific goals of visualization is the development of algorithms and appropriate data models which facilitate interactive visual analysis and direct manipulation of the increasingly large data sets which result from simulations running on massive parallel computer systems, from measurements employing fast high-resolution sensors, or from large databases and hierarchical information spaces. This task can only be achieved with the optimization of all stages of the visualization pipeline: filtering, compression, and feature extraction of the raw data sets, adaptive visualization mappings which allow the users to choose between speed and accuracy, and exploiting new graphics hardware features for fast and high-quality rendering. The recent introduction of advanced programmability in widely available graphics hardware has already led to impressive progress in the area of volume visualization. However, besides the acceleration of the final rendering, flexible graphics hardware is increasingly being used also for the mapping and filtering stages of the visualization pipeline, thus giving rise to new levels of interactivity in visualization applications. The talk will present recent results of applying programmable graphics hardware in various visualization algorithms covering volume data, flow data, terrains, NPR rendering, and distributed and remote applications. [source] From a Product Model to Visualization: Simulation of Indoor Flows with Lattice-Boltzmann MethodsCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 6 2004Siegfried Kühner All models are derived from a product data model based on Industry Foundation Classes. Concepts of the Lattice-Boltzmann method are described, being used as the numerical kernel of our simulation system. We take advantage of spacetrees as a central data structure for all geometry related objects. Finally, we describe some advanced postprocessing and visualization techniques allowing to efficiently analyze huge amounts of simulation data. [source] Scene Graph and Frame Update Algorithms for Smooth and Scalable 3D Visualization of Simulated Construction OperationsCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 4 2002Vineet R. Kamat One of the prime reasons inhibiting the widespread use of discrete-event simulation in construction planning is the absence of appropriate visual communication tools. Visualizing modeled operations in 3D is arguably the best form of communicating the logic and the inner working of simulation models and can be of immense help in establishing the credibility of analyses. New software development technologies emerge at incredible rates that allow engineers and scientists to create novel, domain-specific applications. The authors capitalized on a computer graphics technology based on the concept of the scene graph to design and implement a general-purpose 3D visualization system that is simulation and CAD-software independent. This system, the Dynamic Construction Visualizer, enables realistic visualization of modeled construction operations and the resulting products and can be used in conjunction with a wide variety of simulation tools. This paper describes the scene graph architecture and the frame updating algorithms used in designing the Dynamic Construction Visualizer. [source] Using GIS, Genetic Algorithms, and Visualization in Highway DevelopmentCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 6 2001Manoj K. Jha A model for highway development is presented, which uses geographic information systems (GIS), genetic algorithms (GA), and computer visualization (CV). GIS serves as a repository of geographic information and enables spatial manipulations and database management. GAs are used to optimize highway alignments in a complex search space. CV is a technique used to convey the characteristics of alternative solutions, which can be the basis of decisions. The proposed model implements GIS and GA to find an optimized alignment based on the minimization of highway costs. CV is implemented to investigate the effects of intangible parameters, such as unusual land and environmental characteristics not considered in optimization. Constrained optimization using GAs may be performed at subsequent stages if necessary using feedback received from CVs. Implementation of the model in a real highway project from Maryland indicates that integration of GIS, GAs, and CV greatly enhances the highway development process. [source] Visualization of the distant dipolar field: A numerical studyCONCEPTS IN MAGNETIC RESONANCE, Issue 6 2009Stefan Kirsch Abstract The magnetization of liquid water in an external field generates an intrinsic magnetic field in the sample called the distant dipolar field (DDF). To visualize the spatial distribution of the DDF a numerical study was performed for the case of liquid,state 1H NMR at 7 T. 2D maps of the frequency offset caused by the DDF in pure water were calculated for homogenously magnetized spherical and cylindrical samples as well as for the case of a spatially modulated magnetization distribution occurring e.g., in CRAZED (Cosy Revamped by Asymmetric Z-Gradient Echo Detection) experiments. The calculation yielded DDF induced frequency offsets in the range of 0.58 Hz to 10.24 Hz inside the homogeneously magnetized cylinders, while DDF-induced frequency offsets ,10,5 Hz were obtained inside the sphere. The calculated frequency offsets were in good agreement with analytical results available for a sphere and an infinitely long cylinder. In the case of a spatially modulated magnetization distribution, DDF-induced frequency offsets with maximum values of +0.83 Hz were obtained inside the sphere. The presented 2D maps of the DDF-induced frequency offset have tutorial character and may help to visualize this phenomenon in a direct manner. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A:357,364, 2009. [source] Cor Triatriatum Sinister with and without Left Ventricular Inflow Obstruction: Visualization of the Entire Supravalvular Membrane by Real-time Three-dimensional Echocardiography.CONGENITAL HEART DISEASE, Issue 6 2006Impact on Clinical Management of Individual Patient ABSTRACT We present 4 cases of cor triatriatum in whom the diagnosis was correctly made by 2-dimensional transthoracic echocardiography, which showed the supravalvular left atrial membrane that divides the left atrium into 2 chambers. The pulmonary veins were connected normally to the proximal left atrial chamber and the left atrial appendage was connected to the distal left atrial chamber. In 1 patient there was evidence of severe pulmonary venous obstruction to the mitral valve by Doppler examination, while in the other three, there was no venous obstruction. Patients were then examined by real-time 3-dimensional echocardiography (RT3DE, using ×4 matrix array transducer connected to Sonos 7500 echocardiographic system Phillips, Andover, Mass, USA). This showed the exact morphology of the membrane and led to cancellation of planed surgical intervention in 1 case in which the membrane was only a broad band crossing the left atrial cavity. In addition to delineating the exact morphology of the intracavitary anomaly, this novel echocardiographic imaging modality should be an additive tool to better understand the natural history of these nonobstructive left atrial membranes via longitudinal follow-up of these patients. [source] Visualization of stochastic Ca2+ signals in the formed somites during the early segmentation period in intact, normally developing zebrafish embryosDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 7 2009Christina F. Leung Localized Ca2+ signals were consistently visualized in the formed somites of intact zebrafish embryos during the early segmentation period. Unlike the regular process of somitogenesis, these signals were stochastic in nature with respect to time and location. They did, however, occur predominantly at the medial and lateral boundaries within the formed somites. Embryos were treated with modulators of [Ca2+]i to explore the signal generation mechanism and possible developmental function of the stochastic transients. Blocking elements in the phosphoinositol pathway eliminated the stochastic signals but had no obvious effect, stochastic or otherwise, on the formed somites. Such treatments did, however, result in the subsequently formed somites being longer in the mediolateral dimension. Targeted uncaging of buffer (diazo-2) or Ca2+ (NP-ethyleneglycoltetraacetic acid [EGTA]) in the presomitic mesoderm, resulted in a regular mediolateral lengthening and shortening, respectively, of subsequently formed somites. These data suggest a requirement for IP3 receptor-mediated Ca2+ release during convergence cell movements in the presomitic mesoderm, which appears to have a distinct function from that of the IP3 receptor-mediated stochastic Ca2+ signaling in the formed somites. [source] Efforts to develop methods for in vivo evaluation of the native ,-cell massDIABETES OBESITY & METABOLISM, Issue 2008S. Schneider Visualization and quantification of the native ,-cell mass in vivo in humans appear to be important in the study of the natural course of diabetes, and in ongoing trials aimed at preserving ,-cell mass in patients with diabetes. This cannot be done by biopsy sampling, and therefore there is a great need for development of a non-invasive method. This article discusses the principle theoretical requirements for reaching this goal. In addition, it provides an overview of tracer probes, which have been examined as potential ,-cell mass imaging agents in the past. Finally, some future perspectives are discussed. [source] Blood Flow Imaging,A New Angle-Independent Ultrasound Modality for the Visualization of Flow in Atrial Septal Defects in ChildrenECHOCARDIOGRAPHY, Issue 9 2007Siri Ann Nyrnes M.D. Background: Color Doppler imaging (CDI) is the most applied method for evaluation of flow in atrial septal defects (ASD). A new real time ultrasound flow imaging modality called blood flow imaging (BFI) is able to visualize the blood flow in any direction of the image and is not limited by velocity aliasing. The method thereby overcomes the two limitations most often encountered in CDI. In this study we compared BFI with CDI for the visualization of interatrial blood flow in children. Methods: We studied ASD flow in 13 children using both CDI and BFI in the same examination. CDI and BFI cineloops were prepared off-line and both optimal and suboptimal (increased color artifacts) images were presented in random order to four observers. They were asked to range from 0,100 on a visual analogue scale how certain they were of interatrial blood flow. The CDI and BFI ratings were compared using the exact Wilcoxon signed rank test for paired samples. Results: All ASDs visualized with CDI were confirmed using BFI. Two of the observers ranked BFI as being significantly better than CDI when the images were optimized. When the images were suboptimal three of the observers rated BFI as being significantly better. Conclusions: This pilot study indicates that BFI improves the visualization of interatrial blood flow in children. To include BFI in the ordinary echocardiography examination is easy and not time consuming. The method may prove to be a useful supplement to CDI in ASD imaging. [source] Three-Dimensional Transthoracic Echocardiographic Visualization of a Voluminous Left Atrial ThrombusECHOCARDIOGRAPHY, Issue 1 2006Riccardo Ieva M.D. No abstract is available for this article. [source] New Anthraquinone Derivatives as Electrochemical Redox Indicators for the Visualization of the DNA Hybridization ProcessELECTROANALYSIS, Issue 1 2010Agata Kowalczyk Abstract Interactions of dsDNA and ssDNA, at the surface of gold and silver electrodes, with three novel anthraquinone derivatives: 3-(9,,10,-dioxo-9,,10,-dihydro-anthracen-1-yl)-7,11-di(carboxymethyl)-3,7,11-triazatridecanedioic acid, (AQ-1); 1-(9,,10,-dioxo-9,,10,-dihydro-anthracen-1yl)-9-carboxymethyl-5-methyl-1,5,9-triazaundecanoicacid, (AQ-2); and N -(2-(9,10-dioxo-9,10-dihydro-anthracen-1-ylamino)ethyl)-2-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecan-7-yl)acetamide, (AQ-3) are studied. These derivatives are well soluble in water and phosphate buffer solutions. The square wave voltammetric behavior of these redox indicators is described and the parameters of interactions with DNA are reported. It is also pointed out that these compounds can be employed as the hybridization indicators. The difference in the binding ability of the particular redox indicator to single and double stranded DNA can be used for the detection of the complementary nucleic acids. [source] SECM Visualization of Spatial Variability of Enzyme-Polymer Spots.ELECTROANALYSIS, Issue 19-20 20062: Complex Interference Elimination by Means of Selection of Highest Sensitivity Sensor Substructures, Artificial Neural Networks Abstract Polymer spots with entrapped glucose oxidase were fabricated on glass surfaces and the localized enzymatic response was subsequently visualized using scanning electrochemical microscopy (SECM) in the generator,collector mode. SECM images were obtained under simultaneous variation of the concentration of glucose (0,6,mM) and ascorbic acid (0,200,,M), or, in a second set of experiments, of glucose (0,2,mM) and 2-deoxy- D(+)-glucose (0,4,mM). Aiming at the quantification of the mixture components discretization of the response surfaces of the overall enzyme/polymer spot into numerous spatially defined microsensor substructures was performed. Sensitivity of sensor substructures to measured analytes was calculated and patterns of variability in the data were analyzed before and after elimination of interferences using principal component analysis. Using artificial neural networks which were fed with the data provided by the sensor substructures showing highest sensitivity for glucose, glucose concentration could be calculated in solutions containing unknown amounts of ascorbic acid with a good accuracy (RMSE 0.17,mM). Using, as an input data set, measurements provided by sensing substructures showing highest sensitivity for ascorbic acid in combination with the response of the sensors showing highest dependence on the glucose concentration, the error of the ascorbic acid concentration calculation in solution containing the unknown amount of glucose was 10,,M. Similarly, prediction of the glucose concentration in the presence of 2-deoxy- D(+)-glucose was possible with a RMSE of 0.1,mM while the error of the calculation of 2-deoxy- D(+)-glucose concentrations in the presence of unknown concentrations of glucose was 0.36,mM. [source] Visualization of Differential Gene Expression , Using Fluorescence-Based cDNA-AFLPENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 1 2004S. Gigliotti Abstract cDNA-AFLP is one of the techniques developed to study differentially expressed genes. This recent technique is advantageous because it does not need prior sequence knowledge and is reliable due to highly stringent PCR conditions. The traditional cDNA-AFLP method uses radioactively labelled products and is characterised by high sensitivity and resolution. Here, the use of Cy5-labelled primers to detect products on polyacrylamide gels is reported. This non-radioactive method, based on fluorescence, is shown to be faster and the recovery of interesting bands is easier. The study of the differential gene expression of the interaction between potato and Phytophthora infestans was used for the valuation of this method. Different gene expression profiles , such as up-regulation, down-regulation or point expression , were obtained. Moreover, this technique was shown to be highly reproducible. [source] Visualization of corticofugal projections during early cortical development in a ,-GFP-transgenic mouseEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 1 2007Erin C. Jacobs Abstract The first postmitotic neurons in the developing neocortex establish the preplate layer. These early-born neurons have a significant influence on the circuitry of the developing cortex. However, the exact timing and trajectory of their projections, between cortical hemispheres and intra- and extra-cortical regions, remain unresolved. Here, we describe the creation of a transgenic mouse using a 1.3 kb golli promoter element of the myelin basic protein gene to target expression of a ,,green fluorescent protein (GFP) fusion protein in the cell bodies and processes of pioneer cortical neurons. During embryonic and early neonatal development, the timing and patterning of process extension from these neurons was examined. Analysis of ,-GFP fluorescent fibers revealed that progression of early labeled projections was interrupted unexpectedly by transient pauses at the corticostriatal and telencephalic,diencephalic boundaries before invading the thalamus just prior to birth. After birth the pioneering projections differentially invaded the thalamus, excluding some nuclei, e.g. medial and lateral geniculate, until postnatal days 10,14. Early labeled projections were also found to cross to the contralateral hemisphere as well as to the superior colliculus. These results indicate that early corticothalamic projections appear to pause before invading specific subcortical regions during development, that there is developmental regulation of innervation of individual thalamic nuclei, and that these early-generated neurons also establish early projections to commissural and subcortical targets. [source] Visualization of local Ca2+ dynamics with genetically encoded bioluminescent reportersEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 3 2005Kelly L. Rogers Abstract Measurements of local Ca2+ signalling at different developmental stages and/or in specific cell types is important for understanding aspects of brain functioning. The use of light excitation in fluorescence imaging can cause phototoxicity, photobleaching and auto-fluorescence. In contrast, bioluminescence does not require the input of radiative energy and can therefore be measured over long periods, with very high temporal resolution. Aequorin is a genetically encoded Ca2+ -sensitive bioluminescent protein, however, its low quantum yield prevents dynamic measurements of Ca2+ responses in single cells. To overcome this limitation, we recently reported the bi-functional Ca2+ reporter gene, GFP-aequorin (GA), which was developed specifically to improve the light output and stability of aequorin chimeras [V. Baubet, et al., (2000) PNAS, 97, 7260,7265]. In the current study, we have genetically targeted GA to different microdomains important in synaptic transmission, including to the mitochondrial matrix, endoplasmic reticulum, synaptic vesicles and to the postsynaptic density. We demonstrate that these reporters enable ,real-time' measurements of subcellular Ca2+ changes in single mammalian neurons using bioluminescence. The high signal-to-noise ratio of these reporters is also important in that it affords the visualization of Ca2+ dynamics in cell,cell communication in neuronal cultures and tissue slices. Further, we demonstrate the utility of this approach in ex-vivo preparations of mammalian retina, a paradigm in which external light input should be controlled. This represents a novel molecular imaging approach for non-invasive monitoring of local Ca2+ dynamics and cellular communication in tissue or whole animal studies. [source] Visualization of the interaction between archaeal DNA polymerase and uracil-containing DNA by atomic force microscopyGENES TO CELLS, Issue 1 2006Yasuo Asami Deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. Interestingly, B-family DNA polymerases from hyperthermophilic Archaea recognize the presence of uracil in DNA and stall DNA synthesis. To better understand the recognition mechanism, the binding modes of DNA polymerase B1 of Sulfolobus solfataricus (Pol B1) to uracil-containing DNA were examined by gel mobility shift assays and atomic force microscopy. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency was substantially enhanced by the initiation of DNA synthesis. Analysis by the atomic force microscopy showed a number of double-stranded DNA (dsDNA) in the products of DNA synthesis. The generation of ds DNA was significantly inhibited, however, by the presence of template uracil, and intermediates where monomeric forms of Pol B1 appeared to bind to uracil-containing DNA were observed. These results suggest that Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution, and that single molecules of Pol B1 bind to template uracil and stall DNA synthesis. [source] Visualization of anterior skull base defects with intraoperative cone-beam CTHEAD & NECK: JOURNAL FOR THE SCIENCES & SPECIALTIES OF THE HEAD AND NECK, Issue 4 2010Gideon Bachar MD Abstract Background The role of cone-beam CT (CBCT) in demonstrating anterior skull base defects (ASBDs), differing in size and location, was investigated. The study was designed to describe the potential advantage of CBCT in the setting of an intraoperative cerebrospinal fluid (CSF) leak. Methods In all, 120 ASBD were evaluated in 5 cadaver heads. Orthogonal and oblique slices were reconstructed. Observer studies assessed the visibility of ASBD in each location as a function of defect size. Results For 1-, 2-, and 4-mm defects, the percentage that were undetectable ranged from 20% to 33%, 0% to 14%, and 0% to 5%, respectively. Confident breach detection increased with defect size and was most challenging in the lateral lamella and cribriform. CBCT permitted confident detection of ASBD as small as about 2 mm in the fovea ethmoidalis and planum. Oblique views were found to be superior to orthogonal planes. Conclusions The ability to identify ASBD depended on the size and location of defect. Oblique viewing planes were optimal for ASBD visualization. © 2009 Wiley Periodicals, Inc. Head Neck, 2010 [source] | |||||||||||||||||||||||||||||||||||||||||||||||||