An efficient and generic extension to ITK to process arbitrary shaped regions of interest

The paper describes a software method to extend ITK (Insight ToolKit, supported by the National Library of Medicine), leading to ITK++. This method, which is based on the extension of the iterator design pattern, allows the processing of regions of interest with arbitrary shapes, without modifying the existing ITK code. We experimentally evaluate this work by considering the practical case of the liver vessel segmentation from CT-scan images, where it is pertinent to constrain processings to the liver area. Experimental results clearly prove the interest of this work: for instance, the anisotropic filtering of this area is performed in only 16 s with our proposed solution, while it takes 52 s using the native ITK framework. A major advantage of this method is that only add-ons are performed: this facilitates the further evaluation of ITK++ while preserving the native ITK framework.     

Three-dimensional analysis of contrast-filled microvessel diameters

Organ blood flow is controlled, in part, by changes in diameter of resistance vessels. In thick tissue, vessels can be imaged with a microscope using contrast-enhancing methods (e.g., fluorescence) and image analysis techniques can be used for quantitative diameter estimations. However, a change in the position of a vessel with respect to the plane of focus can be misinterpreted as a diameter change. In order to address this problem, a 3D image in a light microscope is obtained by serial optical sectioning, and a 3D deconvolution procedure (Avinash et al., 1991, "Fourteenth Association for Research in Otolaryngology Midwinter Meeting, St. Petersberg, FL," Abstract 156) is used to deblur 3D image data. Deblurred sections are computationally projected onto a 2D plane to give an extended-focus image, from which diameter estimates of microvessels are made using a quantitative, 2D diameter-tracking algorithm (Miles, 1987, "Semiautomatic Quantitative Image Analysis of Dynamic in Vivo Cochlear Microvessel Diameters." Ph.D. dissertation, Univ. Michigan; Miles and Nuttall, 1992, IEEE Trans. Biomed. Eng.). Justification for 3D preprocessing before diameter analysis is provided by absolute and relative error analyses using computer-generated synthetic vessels. The 3D diameter analysis technique is validated using a capillary tube of known diameter, filled with fluorescent solution. Demonstration of its applicability is shown in diameter measurements from the vessels of guinea pig cochlea. Our approach, using extended-focus images, minimizes overestimation of microvascular diameters and underestimation of relative diameter changes. Therefore, unambiguous diameter measurements are possible with extended-focus images.     

Natural Borna disease in domestic animals others than horses and sheep

In 24 cats (Uppsala, Sweden) with neurological signs of "staggering disease" and typical neuropathology, 44% had Borna disease virus (BDV)-specific antibodies. In 173 cat sera (Berlin, Germany) of animals with unknown record, 7% were BDV positive. Out of 24 cats with undefined neurological disorders, 13% were BDV positive. Similarities in staggering disease of cats and Borna disease of horses and sheep suggest related etiological agents.     

Generalized Lévy-walk model for DNA nucleotide sequences

We propose a generalized Lévy walk to model fractal landscapes observed in noncoding DNA sequences. We find that this model provides a very close approximation to the empirical data and explains a number of statistical properties of genomic DNA sequences such as the distribution of strand-biased regions (those with an excess of one type of nucleotide) as well as local changes in the slope of the correlation exponent alpha. The generalized Lévy-walk model simultaneously accounts for the long-range correlations in noncoding DNA sequences and for the apparently paradoxical finding of long subregions of biased random walks (length lj) within these correlated sequences. In the generalized Lévy-walk model, the lj are chosen from a power-law distribution P(lj) varies as lj(-mu). The correlation exponent alpha is related to mu through alpha = 2-mu/2 if 2 < mu < 3. The model is consistent with the finding of "repetitive elements" of variable length interspersed within noncoding DNA.     

Steroid-responsive encephalomyelitis in childhood

The syndrome of parainfectious encephalomyelitis evolves from an antecedent infection. Several etiologic agents have been associated with this complication, although the pathogenesis in each instance may prove to be more uniform. Considerable evidence suggests that the syndrome is mediated immunologically. The seven cases reported here were clinically similar, although the infectious etiologies were diverse. Leptospirosis antedated the neurologic syndrome in two cases, and a "viral" illness preceded the other five cases. The evolution of the syndrome was slowly progressive in each case, and six patients had prominent involvement of rhombencephalic structures. The progressive course was reversed rapidly with eventual full recovery in each instance after initiation of corticosteroid therapy. Our experience with these cases coupled with a review of the literature suggests that corticosteroid therapy should be considered in the subacute or chronic cases of parainfectious encephalomyelitis.     

为．NET应用程序实现一个类似Word的对象模型

所有的Microsoft Office应用程序都构建在支持自动化的对象模型之上。任何开发人员都能够使用对象模型来驱动应用程序UI以及添加、编辑和删除内容，就像一个真正的用户在与应用程序交互。丰富对象模型结合自动化支持使Office应用程序真正成为可扩展和可插接的。为了扩展Microsoft Word的行为而满足每个人自身的需要，任何人都能够在很短的时间里编写出一个强大的外接程序。作为优秀的面向对象开发人员，我们使用丰富的结构和优秀合理的对象模型（遵循模型一视图一控制器设计模式（MVC）来开发自己的应用程序。     

Purification and characterization of maize starch synthase I and its truncated forms

A number of imidazole-based compounds were tested for their utility as (1)H NMR molecular probes of intracellular pH. Imidazole, previously found useful as a probe of erythrocyte pH, reported a pH in perfused canine glioma cells that was more than 1 pH unit lower than that reported by inorganic phosphate, consistent with the known lysosomal compartmentation of the molecule. Imidazole acetate, also proposed as an NMR probe of cellular pH, was found not to enter the cells of this study. Histidine was found to be readily taken up by cells and reported a pH consistent with that reported by inorganic phosphate. Using the chemical shift of the histidine H2 proton in cells incubated with 10 mM histidine, cellular pH measurements could be obtained in less than 1 s. This compares quite favorably with the measurement time, typically several minutes, needed to assess in vivo pH by (31)P NMR. The use of histidine as a probe of pH is demonstrated in perfused canine and rat glioma cells subjected to ischemia or to low extracellular pH.     

Multi-scale mechanistic modelling of the host defence in invasive aspergillosis reveals leucocyte activation and iron acquisition as drivers of infection outcome

Aspergillus species are ubiquitous environmental moulds, with spores inhaled daily by most humans. Immunocompromised hosts can develop an invasive infection resulting in high mortality. There is, therefore, a pressing need for host-centric therapeutics for this infection. To address it, we created a multi-scale computational model of the infection, focused on its interaction with the innate immune system and iron, a critical nutrient for the pathogen. The model, parameterized using published data, was found to recapitulate a wide range of biological features and was experimentally validated in vivo. Conidial swelling was identified as critical in fungal strains with high growth, whereas the siderophore secretion rate seems to be an essential prerequisite for the establishment of the infection in low-growth strains. In immunocompetent hosts, high growth, high swelling probability and impaired leucocyte activation lead to a high conidial germination rate. Similarly, in neutropenic hosts, high fungal growth was achieved through synergy between high growth rate, high swelling probability, slow leucocyte activation and high siderophore secretion. In summary, the model reveals a small set of parameters related to fungal growth, iron acquisition and leucocyte activation as critical determinants of the fate of the infection.     

Modelling of sprays in containment applications with A CMFD code

During the course of a hypothetical severe accident in a Pressurized Water Reactor (PWR), spray systems are used in the containment in order to prevent overpressure in case of a steam line break, and to enhance the gas mixing in case of the presence of hydrogen.In the frame of the Severe Accident Research Network (SARNET) of the 6th EC Framework Programme, two tests was produced in the TOSQAN facility in order to study the spray behaviour under severe accident conditions: TOSQAN 101 and TOSQAN 113.The TOSQAN facility is a closed cylindrical vessel. The inner spray system is located on the top of the enclosure on the vertical axis. For the TOSQAN 101 case, an initial pressurization in the vessel is performed with superheated steam up to 2.5 bar. Then, steam injection is stopped and spraying starts simultaneously at a given water temperature (around 25 °C) and water mass flow-rate (around 30 g/s). The depressurization transient starts and continues until the equilibrium phase, which corresponds to the stabilization of the average temperature and pressure of the gaseous mixture inside the vessel.The purpose of the TOSQAN 113 cold spray test is to study helium mixing due to spray activation without heat and mass transfers between gas and droplets.We present in this paper the spray modelling implemented in NEPTUNE_CFD, a three-dimensional multi-fluid code developed especially for nuclear reactor applications. A new model dedicated to the droplet evaporation at the wall is also detailed. Keeping in mind the Best Practice Guidelines,¹ closure laws have been selected to ensure a grid-dependence as weak as possible.For the TOSQAN 113 case, the time evolution of the helium volume fraction calculated shows that the physical approach described in the paper is able to reproduce the mixing of helium by the spray. The prediction of the transient behaviour should be improved by including in the model corrections based on better understanding of the influence of the dispersed phase on the turbulence of the continuous phase.For the TOSQAN 101 case, droplet velocity, steam volume fraction and gas temperature profiles compare favourably with the experimental results. In the frame of the SARNET network, the results obtained with the physical modelling implemented in the NEPTUNE_CFD code reproduce correctly the entrainment phenomena and the condensation zone (Malet and Métier, 2007).