Post-processing and visualization techniques in 2D boundary element analysis

Most post-processors for boundary element (BE) analysis use an auxiliary domain mesh to display domain results, working against the profitable modelling process of a pure boundary discretization. This paper introduces a novel visualization technique which preserves the basic properties of the boundary element methods. The proposed algorithm does not require any domain discretization and is based on the direct and automatic identification of isolines. Another critical aspect of the visualization of domain results in BE analysis is the effort required to evaluate results in interior points. In order to tackle this issue, the present article also provides a comparison between the performance of two different BE formulations (conventional and hybrid). In addition, this paper presents an overview of the most common post-processing and visualization techniques in BE analysis, such as the classical algorithms of scan line and the interpolation over a domain discretization. The results presented herein show that the proposed algorithm offers a very high performance compared with other visualization procedures.

3D CFD Simulation of Vortex-induced Vibration of Cylinder

The 3D flow around a circular cylinder free to oscillate transversely to the free stream was simulated using Computational Fluid Dynamics (CFD) and the Spalart-Allmaras Detached Eddy Simulation (DES) turbulence model for a Reynolds number Re = 10(4). Simulations were carried out for a small mass-damping parameter m*zeta = 0.00858, where m* = 3.3 and zeta = 0.0026. We found good agreement between the numerical results and experimental data. The simulations predicted the high observed amplitudes of the upper branch of vortex-induced vibrations for low mass-damping parameters.

Flow Visualization in Arteriovenous Fistula and Aneurysm Using Computational Fluid Dynamics

The arteriovenous fistula (AVF) is characterized by enhanced blood flow and is the most widely used vascular access for chronic haemodialysis (Sivanesan et al., 1998). A large proportion of the AVF late failures are related to local haemodynamics (Sivanesan et al., 1999a). As in AVF, blood flow dynamics plays an important role in growth, rupture, and surgical treatment of aneurysm. Several techniques have been used to study the flow patterns in simplified models of vascular anastomose and aneurysm. In the present investigation, Computational Fluid Dynamics (CFD) is used to analyze the flow patterns in AVF and aneurysm through the velocity waveform obtained from experimental surgeries in dogs (Galego et al., 2000), as well as intra-operative blood flow recordings of patients with radiocephalic AVF ( Sivanesan et al., 1999b) and physiological pulses (Aires, 1991), respectively. The flow patterns in AVF for dog and patient surgeries data are qualitatively similar. Perturbation, recirculation and separation zones appeared during cardiac cycle, and these were intensified in the diastole phase for the AVF and aneurysm models. The values of wall shear stress presented in this investigation of AVF and aneurysm models oscillated in the range that can both cause damage to endothelial cells and develop atherosclerosis.

Animated solid model of the lung constructed from unsynchronized MR sequential images

This work discusses a 4D lung reconstruction method from unsynchronized MR sequential images. The lung, differently from the heart, does not have its own muscles, turning impossible to see its real movements. The visualization of the lung in motion is an actual topic of research in medicine. CT (Computerized Tomography) can obtain spatio-temporal images of the heart by synchronizing with electrocardiographic waves. The FOV of the heart is small when compared to the lung`s FOV. The lung`s movement is not periodic and is susceptible to variations in the degree of respiration. Compared to CT, MR (Magnetic Resonance) imaging involves longer acquisition times and it is not possible to obtain instantaneous 3D images of the lung. For each slice, only one temporal sequence of 2D images can be obtained. However, methods using MR are preferable because they do not involve radiation. In this paper, based on unsynchronized MR images of the lung an animated B-Repsolid model of the lung is created. The 3D animation represents the lung`s motion associated to one selected sequence of MR images. The proposed method can be divided in two parts. First, the lung`s silhouettes moving in time are extracted by detecting the presence of a respiratory pattern on 2D spatio-temporal MR images. This approach enables us to determine the lung`s silhouette for every frame, even on frames with obscure edges. The sequence of extracted lung`s silhouettes are unsynchronized sagittal and coronal silhouettes. Using our algorithm it is possible to reconstruct a 3D lung starting from a silhouette of any type (coronal or sagittal) selected from any instant in time. A wire-frame model of the lung is created by composing coronal and sagittal planar silhouettes representing cross-sections. The silhouette composition is severely underconstrained. Many wire-frame models can be created from the observed sequences of silhouettes in time. Finally, a B-Rep solid model is created using a meshing algorithm. Using the B-Rep solid model the volume in time for the right and left lungs were calculated. It was possible to recognize several characteristics of the 3D real right and left lungs in the shaded model. (C) 2007 Elsevier Ltd. All rights reserved.

3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.

Inhibition of immune complex-mediated neutrophil oxidative metabolism: A pharmacophore model for 3-phenylcoumarin derivatives using GRIND-based 3D-QSAR and 2D-QSAR procedures

In this study, twenty hydroxylated and acetoxylated 3-phenylcoumarin derivatives were evaluated as inhibitors of immune complex-stimulated neutrophil oxidative metabolism and possible modulators of the inflammatory tissue damage found in type III hypersensitivity reactions. By using lucigenin- and luminol-enhanced chemiluminescence assays (CL-luc and CL-lum, respectively), we found that the 6,7-dihydroxylated and 6,7-diacetoxylated 3-phenylcoumarin derivatives were the most effective inhibitors. Different structural features of the other compounds determined CL-luc and/or CL-lum inhibition. The 2D-QSAR analysis suggested the importance of hydrophobic contributions to explain these effects. In addition, a statistically significant 3D-QSAR model built applying GRIND descriptors allowed us to propose a virtual receptor site considering pharmacophoric regions and mutual distances. Furthermore, the 3-phenylcoumarins studied were not toxic to neutrophils under the assessed conditions. (C) 2007 Elsevier Masson SAS. All rights reserved.

Scalable Visualization of Galaxies, Oceans, and Brains

One of the challenges in scientific visualization is to generate software libraries suitable for the large-scale data emerging from tera-scale simulations and instruments. We describe the efforts currently under way at SDSC and NPACI to address these challenges. The scope of the SDSC project spans data handling, graphics, visualization, and scientific application domains. Components of the research focus on the following areas: intelligent data storage, layout and handling, using an associated “Floor-Plan” (meta data); performance optimization on parallel architectures; extension of SDSC’s scalable, parallel, direct volume renderer to allow perspective viewing; and interactive rendering of fractional images (“imagelets”), which facilitates the examination of large datasets. These concepts are coordinated within a data-visualization pipeline, which operates on component data blocks sized to fit within the available computing resources. A key feature of the scheme is that the meta data, which tag the data blocks, can be propagated and applied consistently. This is possible at the disk level, in distributing the computations across parallel processors; in “imagelet” composition; and in feature tagging. The work reflects the emerging challenges and opportunities presented by the ongoing progress in high-performance computing (HPC) and the deployment of the data, computational, and visualization Grids.

A reproducible method for automated extraction of brain volumes from 3D human head MR images

An automated method for extracting brain volumes from three commonly acquired three-dimensional (3D) MR images (proton density, T1 weighted, and T2-weighted) of the human head is described. The procedure is divided into four levels: preprocessing, segmentation, scalp removal, and postprocessing. A user-provided reference point is the sole operator-dependent input required, The method's parameters were first optimized and then fixed and applied to 30 repeat data sets from 15 normal older adult subjects to investigate its reproducibility. Percent differences between total brain volumes (TBVs) for the subjects' repeated data sets ranged from .5% to 2.2%. We conclude that the method is both robust and reproducible and has the potential for wide application.

3D reconstruction and quantification of macropores using X-ray computed tomography and image analysis

Axial X-ray Computed tomography (CT) scanning provides a convenient means of recording the three-dimensional form of soil structure. The technique has been used for nearly two decades, but initial development has concentrated on qualitative description of images. More recently, increasing effort has been put into quantifying the geometry and topology of macropores likely to contribute to preferential now in soils. Here we describe a novel technique for tracing connected macropores in the CT scans. After object extraction, three-dimensional mathematical morphological filters are applied to quantify the reconstructed structure. These filters consist of sequences of so-called erosions and/or dilations of a 32-face structuring element to describe object distances and volumes of influence. The tracing and quantification methodologies were tested on a set of undisturbed soil cores collected in a Swiss pre-alpine meadow, where a new earthworm species (Aporrectodea nocturna) was accidentally introduced. Given the reduced number of samples analysed in this study, the results presented only illustrate the potential of the method to reconstruct and quantify macropores. Our results suggest that the introduction of the new species induced very limited chance to the soil structured for example, no difference in total macropore length or mean diameter was observed. However. in the zone colonised by, the new species. individual macropores tended to have a longer average length. be more vertical and be further apart at some depth. Overall, the approach proved well suited to the analysis of the three-dimensional architecture of macropores. It provides a framework for the analysis of complex structures, which are less satisfactorily observed and described using 2D imaging. (C) 2002 Elsevier Science B.V. All rights reserved.

Visualization of learning in multilayer perceptron networks using principal component analysis

This paper is concerned with the use of scientific visualization methods for the analysis of feedforward neural networks (NNs). Inevitably, the kinds of data associated with the design and implementation of neural networks are of very high dimensionality, presenting a major challenge for visualization. A method is described using the well-known statistical technique of principal component analysis (PCA). This is found to be an effective and useful method of visualizing the learning trajectories of many learning algorithms such as back-propagation and can also be used to provide insight into the learning process and the nature of the error surface.

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.

The usefulness of acetic acid wash and chemiluminescent illumination (Vizilite) in the visualization of oral mucosal white lesions

A diligent and careful examination of the mouth and oral structures has been historically deficient in revealing premalignant and malignant oral lesions. Conventional screening practice for oral neoplastic lesions involves visual scrutiny of the oral tissues with the naked eye under projected incandescent or halogen illumination. Visualization is the principal strategy used to find patients with lesions at risk for malignant transformation; hence, any procedure which highlights neoplastic lesions should aid the clinician. This pilot study examined the usefulness of acetic acid wash and chemiluminescent light (Vizilite) in enhancing visualization of oral mucosal white lesions, and its ability to highlight malignant and potentially malignant lesions. Fifty five patients referred for assessment of a white lesion, were prospectively screened with Vizilite, and an incisional biopsy performed for a definitive diagnosis. The age, sex, and smoking status of all patients were recorded, and all lesions were photographed. The visibility, location, size, border, and presence of satellite lesions, were also recorded. The Vizilite tool enhanced intraoral visualization of 26 white lesions, but it could not distinguish between epithelial hyperplasia, dysplasia, or carcinoma. Indeed, all lesions appeared ‘‘aceto-white’’, regardless of the definitive diagnosis. On one occasion, Vizilite aided in the identification of a satellite lesion that was not observed by routine visual inspection. Vizilite appears to be a useful visualization tool, but it does not aid in the identification of malignant and potentially malignant lesions of the oral mucosa.

Results of high dose-rate brachytherapy boost before 2D or 3D external beam irradiation for prostate cancer

Background and purpose: To evaluate biochemical control and treatment related toxicity of patients with localized adenocarcinoma of the prostate treated with high dose-rate brachytherapy (HDRB) combined with conventional 2D or 3D-conformal external beam irradiation (EBI). Material and methods: Four-hundred and three patients treated between December 2000 and March 2004. HDRB was delivered with three fractions of 5.5-7 Gy with a single implant, followed by 45 Gy delivered with 2D or 3D conformal EBI. Results: The median follow-up was 48.4 months. Biochemical failure (BF) occurred in 9.6% according to both ASTRO and Phoenix consensus criteria. Mean time to relapse was 13 and 26 months, respectively. The 5-year BF free survival using the ASTRO criteria was 94.3%, 86.9% and 86.6% for the low, intermediate and high risk groups, respectively; using Phoenix criteria, 92.4%, 88.0% and 85.3%, respectively. The only predictive factor of BF in the multivariate analysis by both ASTRO and Phoenix criteria was the presence of prostate nodules detected by digital palpation, and patients younger than 60 years presented a higher chance of failure using Phoenix criteria only. Conclusions: Treatment scheme is feasible and safe with good efficacy. (C) 2011 Elsevier Ireland Ltd All rights reserved. Radiotherapy and Oncology 98 (2011) 169-174

INTENSITY-MODULATED AND 3D-CONFORMAL RADIOTHERAPY FOR WHOLE-VENTRICULAR IRRADIATION AS COMPARED WITH CONVENTIONAL WHOLE-BRAIN IRRADIATION IN THE MANAGEMENT OF LOCALIZED CENTRAL NERVOUS SYSTEM GERM CELL TUMORS

Purpose: To compare the sparing potential of cerebral hemispheres with intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT) for whole-ventricular irradiation (WVI) and conventional whole-brain irradiation (WBI) in the management of localized central nervous system germ cell tumors (CNSGCTs). Methods and Materials: Ten cases of patients with localized CNSGCTs and submitted to WVI by use of IMRT with or without a ""boost"" to the primary lesion were selected. For comparison purposes, similar treatment plans were produced by use of 3D-CRT (WVI with or without boost) and WBI (opposed lateral fields with or without boost), and cerebral hemisphere sparing was evaluated at dose levels ranging from 2 Gy to 40 Gy. Results: The median prescription dose for WVI was 30.6 Gy (range, 25.2-37.5 Gy), and that for the boost was 16.5 Gy (range, 0-23.4 Gy). Mean irradiated cerebral hemisphere volumes were lower for WVI with IMRT than for 3D-CRT and were lower for WVI with 3D-CRT than for WBI. Intensity-modulated radiotherapy was associated with the lowest irradiated volumes, with reductions of 7.5%, 12.2%, and 9.0% at dose levels., compared with 3D-CRT. Intensity-modulated radiotherapy provided of 20, 30, and 40 Gy, respectively statistically significant reductions of median irradiated volumes at all dose levels (p = 0.002 or less). However, estimated radiation doses to peripheral areas of the body were 1.9 times higher with IMRT than with 3D-CRT. Conclusions: Although IMRT is associated with increased radiation doses to peripheral areas of the body, its use can spare a significant amount of normal central nervous system tissue compared with 3D-CRT or WBI in the setting of CNSGCT treatment. (C) 2010 Elsevier Inc.