Publications

Pathogenesis-related (PR) proteins of class 10 are abundant in higher plants. Some of these proteins are induced under stress conditions as part of the plant defence mechanism. Other homologues are developmentally regulated and their expression varies in different plant organs. The PR-10 proteins are encoded by multigene families, have a weight of about 17 kDa and are found in the cytosol. In yellow lupin, nine different homologues have been identified and divided into two subclasses, LlPR-10.1 and LlPR-10.2. Within each subclass the sequence identity is about 75-91%, while across the subclasses it is only 59-60%. Here, the crystal structure of a yellow lupin PR-10 protein from the second subclass, LlPR-10.2A, is presented. The structure was solved by molecular replacement and refined to R = 0.205 using 1.9 A resolution data. The general fold of LlPR-10.2A resembles that of the other PR-10 proteins and consists of a long C-terminal alpha-helix surrounded by a seven-stranded antiparallel beta-sheet, with two shorter alpha-helices located between strands beta1 and beta2. The most variable part of the structure, the C-terminal helix, is strongly kinked towards the beta-sheet core in both LlPR-10.2A molecules present in the asymmetric unit. This unexpected feature reduces the size of the hydrophobic cavity observed in other PR-10 proteins that is reported to be the ligand-binding site. As in other PR-10 structures, a surface loop located near the entrance to the cavity shows very high structural conservation and stability despite the high glycine content in its sequence.

In this paper, a novel method for the boundary detection of human kidneys from three dimensional (3D) ultrasound (US) is proposed. The inherent difficulty of interpretation of such images, even by a trained expert, makes the problem unsuitable for classical methods. The method here proposed finds the kidney contours in each slice. It is a probabilistic Bayesian method. The prior defines a Markov field of deformations and imposes the restriction of contour smoothness. The likelihood function imposes a probabilistic behavior to the data, conditioned to the contour position. This second function, which is also Markov, uses an empirical model of distribution of the echographical data and a function of the gradient of the data. The model finally includes, as a volumetric extension of the prior, a term that forces smoothness along the depth coordinate. The experiments that have been carried out on echographies from real patients validate the model here proposed. A sensitivity analysis of the model parameters has also been carried out.

The goal of this functional magnetic resonance imaging (fMRI) study was to compare the central effects of electroacupuncture at different frequencies with traditional Chinese manual acupuncture. Although not as time-tested as manual acupuncture, electroacupuncture does have the advantage of setting stimulation frequency and intensity objectively and quantifiably. Manual acupuncture, electroacupuncture at 2 Hz and 100 Hz, and tactile control stimulation were carried out at acupoint ST-36. Overall, electroacupuncture (particularly at low frequency) produced more widespread fMRI signal increase than manual acupuncture did, and all acupuncture stimulations produced more widespread responses than did our placebo-like tactile control stimulation. Acupuncture produced hemodynamic signal increase in the anterior insula, and decrease in limbic and paralimbic structures including the amygdala, anterior hippocampus, and the cortices of the subgenual and retrosplenial cingulate, ventromedial prefrontal cortex, frontal, and temporal poles, results not seen for tactile control stimulation. Only electroacupuncture produced significant signal increase in the anterior middle cingulate cortex, whereas 2-Hz electroacupuncture produced signal increase in the pontine raphe area. All forms of stimulation (acupuncture and control) produced signal increase in SII. These findings support a hypothesis that the limbic system is central to acupuncture effect regardless of specific acupuncture modality, although some differences do exist in the underlying neurobiologic mechanisms for these modalities, and may aid in optimizing their future usage in clinical applications.

In this work (1)H NMR self-diffusion experiments have been performed to determine the self-diffusion coefficients of n-octyl beta-d-glucoside and n-nonyl beta-d-glucoside in alpha-cyclodextrin and beta-cyclodextrin solutions at 25 degrees C. Two questions are addressed. The first concerns the general influence on nonionic surfactant transport properties when cyclodextrins are present in solution. The second question concerns the influence of surfactant-chain length and cyclodextrin cavity volume on the association constant. The self-diffusion coefficients of the alkyl glucosides, in cyclodextrin-containing solutions, depend on the cyclodextrin concentration on account of the formation of complexes. The cyclodextrin diffusion is only mildly influenced, since the complex has similar diffusion coefficients as the free cyclodextrin. There are some obstruction effects at the highest surfactant concentrations which decrease the cyclodextrin diffusion. A set of equations to model the self-diffusion coefficients of the surfactant and cyclodextrin was developed and is presented. On the basis of such equations, properties such as association constants, and micelle and complex diffusion coefficients can be estimated.

Fractional low order moments have been reported as beneficial for sampling computations using the K distribution. However, it has been recently pointed out that this it not the case for the homodyned-K distribution for a tissue discrimination problem. In this paper we show that such an statement is not fully justified. To that end, we follow a standard pattern recognition procedure both to determine class separability measures and to classify data with several classifiers. We conclude that the optimum order of the moments is intimately linked to the specific statistical properties of the tissues to be discriminated. Some ideas on how to choose the optimum order are discussed.

This work presents a novel approach to analyze the shape of anatomical structures. Our methodology is rooted in classical physics and in particular Poisson’s equation, a fundamental partial differential equation, The solution to this equation and more specifically its equipotential surfaces display properties that are useful for shape analysis. We present a numerical algorithm to calculate the length of streamlines formed by the gradient field of the solution to this equation for 2D and 3D objects. The length of the streamlines along the equipotential surfaces was used to build a new function which can characterize the shape of objects. We illustrate our method on 2D synthetic and natural shapes as well as 3D medical data.

Improving the resolution of magnetic resonance imaging (MRI), or, alternatively, reducing the acquisition time, can be quite beneficial for many applications. The main motivation of this work is the assumption that any information that is a priori available on the target image could be used to achieve this goal. In order to demonstrate this approach, we present a novel partial acquisition strategy and reconstruction algorithm, suitable for the special case of detection of pseudoperiodic patterns. Pseudoperiodic patterns are frequently encountered in the cerebral cortex due to its columnar functional organization (best exemplified by orientation columns and ocular dominance columns of the visual cortex). We present a new MRI research methodology, in which we seek an activity pattern, and a pattern-specific experiment is devised to detect it. Such specialized experiments extend the limits of conventional MRI experiments by substantially reducing the scan time. Using the fact that pseudoperiodic patterns are localized in the Fourier domain, we present an optimality criterion for partial acquisition of the MR signal and a strategy for obtaining the optimal discrete Fourier transform (DFT) coefficients. A by-product of this strategy is an optimal linear extrapolation estimate. We also present a nonlinear spectral extrapolation algorithm, based on projections onto convex sets (POCSs), used to perform the actual reconstruction. The proposed strategy was tested and analyzed on simulated signals and in MRI phantom experiments.

This paper describes a general theoretical framework that combines non-Fourier (NF) spatially-encoded MRI with multichannel acquisition parallel MRI. The two spatial-encoding mechanisms are physically and analytically separable, which allows NF encoding to be expressed as complementary to the inherent encoding imposed by RF receiver coil sensitivities. Consequently, the number of NF spatial-encoding steps necessary to fully encode an FOV is reduced. Furthermore, by casting the FOV reduction of parallel imaging techniques as a dimensionality reduction of the k-space that is NF-encoded, one can obtain a speed-up of each digital NF spatial excitation in addition to accelerated imaging. Images acquired at speed-up factors of 2x to 8x with a four-element RF receiver coil array demonstrate the utility of this framework and the efficiency afforded by it.

Hemisphere asymmetry was explored in normal healthy subjects and in patients with schizophrenia using a novel voxel-based tensor analysis applied to fractional anisotropy (FA) of the diffusion tensor. Our voxel-based approach, which requires precise spatial normalization to remove the misalignment of fiber tracts, includes generating a symmetrical group average template of the diffusion tensor by applying nonlinear elastic warping of the demons algorithm. We then normalized all 32 diffusion tensor MRIs from healthy subjects and 23 from schizophrenic subjects to the symmetrical average template. For each brain, six channels of tensor component images and one T2-weighted image were used for registration to match tensor orientation and shape between images. A statistical evaluation of white matter asymmetry was then conducted on the normalized FA images and their flipped images. In controls, we found left-higher-than-right anisotropic asymmetry in the anterior part of the corpus callosum, cingulum bundle, the optic radiation, and the superior cerebellar peduncle, and right-higher-than-left anisotropic asymmetry in the anterior limb of the internal capsule and the anterior limb’s prefrontal regions, in the uncinate fasciculus, and in the superior longitudinal fasciculus. In patients, the asymmetry was lower, although still present, in the cingulum bundle and the anterior corpus callosum, and not found in the anterior limb of the internal capsule, the uncinate fasciculus, and the superior cerebellar peduncle compared to healthy subjects. These findings of anisotropic asymmetry pattern differences between healthy controls and patients with schizophrenia are likely related to neurodevelopmental abnormalities in schizophrenia.

Endovascular surgery provides a minimally invasive solution for the treatment of aortic aneurysms. Fluoroscopic guidance involves X-rays exposure and loss of space information. We have developed a navigation system allowing real-time visualisation of the endovascular tools in a 3D model of the vessels without any radiation exposure. A modified endoprosthesis is equipped with a magnetic sensor tracked by the Aurora magnetic localizer. The registration step uses 2.5D ultrasonography to replace pre-operative CT data in the Operating Room referential. The Virtual Reality based navigation system shows the location of the endoprosthesis inside a 3D CT model of the aorta. Endovascular procedure benefits from a reduced radiation exposure.