3-d residual eddy current field characterisation: applied to diffusion weighted magnetic resonance imaging.

Clinical use of the Stejskal-Tanner diffusion weighted images is hampered by the geometric distortions that result from the large residual 3-D eddy current field induced. In this work, we aimed to predict, using linear response theory, the residual 3-D eddy current field required for geometric distortion correction based on phantom eddy current field measurements. The predicted 3-D eddy current field induced by the diffusion-weighting gradients was able to reduce the root mean square error of the residual eddy current field to ~1 Hz. The model's performance was tested on diffusion weighted images of four normal volunteers, following distortion correction, the quality of the Stejskal-Tanner diffusion-weighted images was found to have comparable quality to image registration based corrections (FSL) at low b-values. Unlike registration techniques the correction was not hindered by low SNR at high b-values, and results in improved image quality relative to FSL. Characterization of the 3-D eddy current field with linear response theory enables the prediction of the 3-D eddy current field required to correct eddy current induced geometric distortions for a wide range of clinical and high b-value protocols.

Gamma Knife(A (R)) 3-D Dose Distribution Mapping by Magnetic Resonance Imaging

In medical processes where ionizing radiation is used, dose planning and dose delivery are the key elements to patient safety and treatment success, particularly, when the delivered dose in a single session of treatment can be an order of magnitude higher than the regular doses of radiotherapy. Therefore, the radiation dose should be well defined and precisely delivered to the target while minimizing radiation exposure to surrounding normal tissues [1]. Several methods have been proposed to obtain three-dimensional (3-D) dose distribution [2, 3]. In this paper, we propose an alternative method, which can be easily implemented in any stereotactic radiosurgery center with a magnetic resonance imaging (MRI) facility. A phantom with or without scattering centers filled with Fricke gel solution is irradiated with Gamma Knife(A (R)) system at a chosen spot. The phantom can be a replica of a human organ such as head, breast or any other organ. It can even be constructed from a real 3-D MR image of an organ of a patient using a computer-aided construction and irradiated at a specific region corresponding to the tumor position determined by MRI. The spin-lattice relaxation time T (1) of different parts of the irradiated phantom is determined by localized spectroscopy. The T (1)-weighted phantom images are used to correlate the image pixels intensity to the absorbed dose and consequently a 3-D dose distribution with a high resolution is obtained.

Cup Implant Planning Based on 2-D/3-D Radiographic Pelvis Reconstruction-First Clinical Results.

GOAL: In the following, we will present a newly developed X-ray calibration phantom and its integration for 2-D/3-D pelvis reconstruction and subsequent automatic cup planning. Two different planning strategies were applied and evaluated with clinical data. METHODS: Two different cup planning methods were investigated: The first planning strategy is based on a combined pelvis and cup statistical atlas. Thereby, the pelvis part of the combined atlas is matched to the reconstructed pelvis model, resulting in an optimized cup planning. The second planning strategy analyzes the morphology of the reconstructed pelvis model to determine the best fitting cup implant. RESULTS: The first planning strategy was compared to 3-D CT-based planning. Digitally reconstructed radiographs of THA patients with differently severe pathologies were used to evaluate the accuracy of predicting the cup size and position. Within a discrepancy of one cup size, the size was correctly identified in 100% of the cases for Crowe type I datasets and in 77.8% of the cases for Crowe type II, III, and IV datasets. The second planning strategy was analyzed with respect to the eventually implanted cup size. In seven patients, the estimated cup diameter was correct within one cup size, while the estimation for the remaining five patients differed by two cup sizes. CONCLUSION: While both planning strategies showed the same prediction rate with a discrepancy of one cup size (87.5%), the prediction of the exact cup size was increased for the statistical atlas-based strategy (56%) in contrast to the anatomically driven approach (37.5%). SIGNIFICANCE: The proposed approach demonstrated the clinical validity of using 2-D/3-D reconstruction technique for cup planning.

The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against Gram-positive and Gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive F and. Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (F) and negative (.) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Chrysotile effects on human lung cell carcinoma in culture: 3-D reconstruction and DNA quantification by image analysis

Background: Chrysotile is considered less harmful to human health than other types of asbestos fibers. Its clearance from the lung is faster and, in comparison to amphibole forms of asbestos, chrysotile asbestos fail to accumulate in the lung tissue due to a mechanism involving fibers fragmentation in short pieces. Short exposure to chrysotile has not been associated with any histopathological alteration of lung tissue. Methods: The present work focuses on the association of small chrysotile fibers with interphasic and mitotic human lung cancer cells in culture, using for analyses confocal laser scanning microscopy and 3D reconstructions. The main goal was to perform the analysis of abnormalities in mitosis of fibers-containing cells as well as to quantify nuclear DNA content of treated cells during their recovery in fiber-free culture medium. Results: HK2 cells treated with chrysotile for 48 h and recovered in additional periods of 24, 48 and 72 h in normal medium showed increased frequency of multinucleated and apoptotic cells. DNA ploidy of the cells submitted to the same chrysotile treatment schedules showed enhanced aneuploidy values. The results were consistent with the high frequency of multipolar spindles observed and with the presence of fibers in the intercellular bridge during cytokinesis. Conclusion: The present data show that 48 h chrysotile exposure can cause centrosome amplification, apoptosis and aneuploid cell formation even when long periods of recovery were provided. Internalized fibers seem to interact with the chromatin during mitosis, and they could also interfere in cytokinesis, leading to cytokinesis failure which forms aneuploid or multinucleated cells with centrosome amplification.

A geometrical approach of 3-D FEA for educational purposes applied to electrostatic fields

A geometrical approach of the finite-element analysis applied to electrostatic fields is presented. This approach is particularly well adapted to teaching Finite Elements in Electrical Engineering courses at undergraduate level. The procedure leads to the same system of algebraic equations as that derived by classical approaches, such as variational principle or weighted residuals for nodal elements with plane symmetry. It is shown that the extension of the original procedure to three dimensions is straightforward, provided the domain be meshed in first-order tetrahedral elements. The element matrices are derived by applying Maxwell`s equations in integral form to suitably chosen surfaces in the finite-element mesh.

Multiphase flow in the vascular system of wood: From microscopic exploration to 3-D Lattice Boltzmann experiments

This paper provides insights into liquid free water dynamics in wood vessels based on Lattice Boltzmann experiments. The anatomy of real wood samples was reconstructed from systematic 3-D analyses of the vessel contours derived from successive microscopic images. This virtual vascular system was then used to supply fluid-solid boundary conditions to a two-phase Lattice Boltzmann scheme and investigate capillary invasion of this hydrophilic porous medium. Behavior of the liquid phase was strongly dependent on anatomical features, especially vessel bifurcations and reconnections. Various parameters were examined in numerical experiments with ideal vessel bifurcations, to clarify our interpretation of these features. (c) 2010 Elsevier Ltd. All rights reserved.

Convective instability of 3-D fluid-saturated geological fault zones heated from below

We conduct a theoretical analysis to investigate the convective instability of 3-D fluid-saturated geological fault zones when they are heated uniformly from below. In particular, we have derived exact analytical solutions for the critical Rayleigh numbers of different convective flow structures. Using these critical Rayleigh numbers, three interesting convective flow structures have been identified in a geological fault zone system. It has been recognized that the critical Rayleigh numbers of the system have a minimum value only for the fault zone of infinite length, in which the corresponding convective flow structure is a 2-D slender-circle flow. However, if the length of the fault zone is finite, the convective flow in the system must be 3-D. Even if the length of the fault zone is infinite, since the minimum critical Rayleigh number for the 2-D slender-circle flow structure is so close to that for the 3-D convective flow structure, the system may have almost the same chance to pick up the 3-D convective flow structures. Also, because the convection modes are so close for the 3-D convective flow structures, the convective flow may evolve into the 3-D finger-like structures, especially for the case of the fault thickness to height ratio approaching zero. This understanding demonstrates the beautiful aspects of the present analytical solution for the convective instability of 3-D geological fault zones, because the present analytical solution is valid for any value of the ratio of the fault height to thickness. Using the present analytical solution, the conditions, under which different convective flow structures may take place, can be easily determined.

High resolution 3-D imaging via multi-pass SAR

Spaceborne/airborne synthetic aperture radar (SAR) systems provide high resolution two-dimensional terrain imagery. The paper proposes a technique for combining multiple SAR images, acquired on flight paths slightly separated in the elevation direction, to generate high resolution three-dimensional imagery. The technique could be viewed as an extension to interferometric SAR (InSAR) in that it generates topographic imagery with an additional dimension of resolution. The 3-D multi-pass SAR imaging system is typically characterised by a relatively short ambiguity length in the elevation direction. To minimise the associated ambiguities we exploit the relative phase information within the set of images to track the terrain landscape. The SAR images are then coherently combined, via a nonuniform DFT, over a narrow (in elevation) volume centred on the 'dominant' terrain ground plane. The paper includes a detailed description of the technique, background theory, including achievable resolution, and the results of an experimental study.

A high throughput colorimetric assay of beta-1,3-D-glucans by Congo red dye

Mushroom strains contain complex nutritional biomolecules with a wide spectrum of therapeutic and prophylactic properties. Among these compounds, β-d-glucans play an important role in immuno-modulating and anti-tumor activities. The present work involves a novel colorimetric assay method for β-1,3-d-glucans with a triple helix tertiary structure by using Congo red. The specific interaction that occurs between Congo red and β-1,3-d-glucan was detected by bathochromic shift from 488 to 516 nm (> 20 nm) in UV–Vis spectrophotometer. A micro- and high throughput method based on a 96-well microtiter plate was devised which presents several advantages over the published methods since it requires only 1.51 μg of polysaccharides in samples, greater sensitivity, speed, assay of many samples and very cheap. β-d-Glucans of several mushrooms (i.e., Coriolus versicolor, Ganoderma lucidum, Pleurotus ostreatus, Ganoderma carnosum, Hericium erinaceus, Lentinula edodes, Inonotus obliquus, Auricularia auricular, Polyporus umbellatus, Cordyseps sinensis, Agaricus blazei, Poria cocos) were isolated by using a sequence of several extractions with cold and boiling water, acidic and alkaline conditions and quantified by this microtiter plate method. FTIR spectroscopy was used to study the structural features of β-1,3-d-glucans in these mushroom samples as well as the specific interaction of these polysaccharides with Congo red. The effect of NaOH on triple helix conformation of β-1,3-d-glucans was investigated in several mushroom species.

System zur automatischen Erstellung interindividueller 3-D Modelle biologischer Objekte aus 2-D Schnittbildern

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2011

3-D surface reconstruction using spatial frequency-based approaches under influence of perspective distortion

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2008

Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers

Recent technological advances in remote sensing have enabled investigation of the morphodynamics and hydrodynamics of large rivers. However, measuring topography and flow in these very large rivers is time consuming and thus often constrains the spatial resolution and reach-length scales that can be monitored. Similar constraints exist for computational fluid dynamics (CFD) studies of large rivers, requiring maximization of mesh-or grid-cell dimensions and implying a reduction in the representation of bedform-roughness elements that are of the order of a model grid cell or less, even if they are represented in available topographic data. These ``subgrid'' elements must be parameterized, and this paper applies and considers the impact of roughness-length treatments that include the effect of bed roughness due to ``unmeasured'' topography. CFD predictions were found to be sensitive to the roughness-length specification. Model optimization was based on acoustic Doppler current profiler measurements and estimates of the water surface slope for a variety of roughness lengths. This proved difficult as the metrics used to assess optimal model performance diverged due to the effects of large bedforms that are not well parameterized in roughness-length treatments. However, the general spatial flow patterns are effectively predicted by the model. Changes in roughness length were shown to have a major impact upon flow routing at the channel scale. The results also indicate an absence of secondary flow circulation cells in the reached studied, and suggest simpler two-dimensional models may have great utility in the investigation of flow within large rivers. Citation: Sandbach, S. D. et al. (2012), Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers, Water Resour. Res., 48, W12501, doi: 10.1029/2011WR011284.