Modelling within-host spatiotemporal dynamics of invasive bacterial disease

Mechanistic determinants of bacterial growth, death, and spread within mammalian hosts cannot be fully resolved studying a single bacterial population. They are also currently poorly understood. Here, we report on the application of sophisticated experimental approaches to map spatiotemporal population dynamics of bacteria during an infection. We analyzed heterogeneous traits of simultaneous infections with tagged Salmonella enterica populations (wild-type isogenic tagged strains [WITS]) in wild-type and gene-targeted mice. WITS are phenotypically identical but can be distinguished and enumerated by quantitative PCR, making it possible, using probabilistic models, to estimate bacterial death rate based on the disappearance of strains through time. This multidisciplinary approach allowed us to establish the timing, relative occurrence, and immune control of key infection parameters in a true host-pathogen combination. Our analyses support a model in which shortly after infection, concomitant death and rapid bacterial replication lead to the establishment of independent bacterial subpopulations in different organs, a process controlled by host antimicrobial mechanisms. Later, decreased microbial mortality leads to an exponential increase in the number of bacteria that spread locally, with subsequent mixing of bacteria between organs via bacteraemia and further stochastic selection. This approach provides us with an unprecedented outlook on the pathogenesis of S. enterica infections, illustrating the complex spatial and stochastic effects that drive an infectious disease. The application of the novel method that we present in appropriate and diverse host-pathogen combinations, together with modelling of the data that result, will facilitate a comprehensive view of the spatial and stochastic nature of within-host dynamics. © 2008 Grant et al.

Probabilistic graphical models for semi-supervised traffic classification

Traffic classification using machine learning continues to be an active research area. The majority of work in this area uses off-the-shelf machine learning tools and treats them as black-box classifiers. This approach turns all the modelling complexity into a feature selection problem. In this paper, we build a problem-specific solution to the traffic classification problem by designing a custom probabilistic graphical model. Graphical models are a modular framework to design classifiers which incorporate domain-specific knowledge. More specifically, our solution introduces semi-supervised learning which means we learn from both labelled and unlabelled traffic flows. We show that our solution performs competitively compared to previous approaches while using less data and simpler features. Copyright © 2010 ACM.

Assessment of the contribution of surface roughness to airframe noise

The generation of sound by turbulent boundary-layer flow at low Mach number over a rough wall is investigated by applying a theoretical model that describes the scattering of the turbulence near field into sound by roughness elements. Attention is focused on the numerical method to approximately quantify the absolute level of far-field radiated roughness noise. Models for the source statistics are obtained by scaling smooth-wall data by the increased skin friction velocity and boundary-layer thickness for a rough surface. Numerical integration is performed to determine the roughness noise, and it reproduces the spectral characteristics of the available empirical formula and experimental data. Experiments are conducted to measure the radiated sound from two rough plates in an open jet The measured noise spectra of the rough plates are above that of a smooth plate in 1-2.5 kHz frequency and exhibit reasonable agreement with the predicted level. Estimates of the roughness noise for a Boeing 757 sized aircraft wing with idealized levels of surface roughness show that hi the high-frequency region the sound radiated from surface roughness may exceed that from the trailing edge, and higher overall sound pressure levels are observed for the roughness noise. The trailing edge noise is also enhanced by surface roughness somewhat A parametric study indicates that roughness height and roughness density significantly affect the roughness noise with roughness height having the dominant effect The roughness noise directivity varies with different levels of surface roughness. Copyright © 2007 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Effects of surface roughness on airframe noise

The generation of sound by turbulent boundary layer flow at low Mach number over a rough wall is investigated by applying the theoretical model which describes the scattering of the turbulence near field into sound by roughness elements. Attention is focused on the numerical method to approximately quantify the absolute level of the roughness noise radiated to far field. Empirical models for the source statistics are obtained by scaling smooth-wall data through increased skin friction velocity and boundary layer thickness for the rough surface. Numerical integration is performed to determine the roughness noise, and it reproduces the spectral characteristics of the available empirical formula and experimental data. Experiments are conducted to measure the radiated sound from two rough plates in an open jet by four 1/2'' free-field condenser microphones. The measured noise spectra of the rough plates are above that of a smooth plate in 1-2.5 kHz frequency and exhibits encouraging agreement with the predicted spectra. Also, a phased microphone array is utilized to localize the sound source, and it confirms that the rough plates generate higher source strengthes in this frequency range. A parametric study illustrates that the roughness height and roughness density significantly affect the far-field radiated roughness noise with the roughness height having the dominant effect. The estimates of the roughness noise for a Boeing 757 sized aircraft wing show that in high frequency region the sound radiated from surface roughness may exceed that from the trailing edge, and higher overall sound pressure levels for the roughness noise are also observed.

Numerical simulations of unsteady wet steam flows with non-equilibrium condensation in the nozzle and the steam turbine

Numerical techniques for non-equilibrium condensing flows are presented. Conservation equations for homogeneous gas-liquid two-phase compressible flows are solved by using a finite volume method based on an approximate Riemann solver. The phase change consists of the homogeneous nucleation and growth of existing droplets. Nucleation is computed with the classical Volmer-Frenkel model, corrected for the influence of the droplet temperature being higher than the steam temperature due to latent heat release. For droplet growth, two types of heat transfer model between droplets and the surrounding steam are used: a free molecular flow model and a semi-empirical two-layer model which is deemed to be valid over a wide range of Knudsen number. The computed pressure distribution and Sauter mean droplet diameters in a convergent-divergent (Laval) nozzle are compared with experimental data. Both droplet growth models capture qualitatively the pressure increases due to sudden heat release by the non-equilibrium condensation. However the agreement between computed and experimental pressure distributions is better for the two-layer model. The droplet diameter calculated by this model also agrees well with the experimental value, whereas that predicted by the free molecular model is too small. Condensing flows in a steam turbine cascade are calculated at different Mach numbers and inlet superheat conditions and are compared with experiments. Static pressure traverses downstream from the blade and pressure distributions on the blade surface agree well with experimental results in all cases. Once again, droplet diameters computed with the two-layer model give best agreement with the experiments. Droplet sizes are found to vary across the blade pitch due to the significant variation in expansion rate. Flow patterns including oblique shock waves and condensation-induced pressure increases are also presented and are similar to those shown in the experimental Schlieren photographs. Finally, calculations are presented for periodically unsteady condensing flows in a low expansion rate, convergent-divergent (Laval) nozzle. Depending on the inlet stagnation subcooling, two types of self-excited oscillations appear: a symmetric mode at lower inlet subcooling and an asymmetric mode at higher subcooling. Plots of oscillation frequency versus inlet sub-cooling exhibit a hysteresis loop, in accord with observations made by other researchers for moist air flow. Copyright © 2006 by ASME.

Machine Vision-Based Infrastructure As-Built Documentation Using Edge Points

The existing machine vision-based 3D reconstruction software programs provide a promising low-cost and in some cases automatic solution for infrastructure as-built documentation. However in several steps of the reconstruction process, they only rely on detecting and matching corner-like features in multiple views of a scene. Therefore, in infrastructure scenes which include uniform materials and poorly textured surfaces, these programs fail with high probabilities due to lack of feature points. Moreover, except few programs that generate dense 3D models through significantly time-consuming algorithms, most of them only provide a sparse reconstruction which does not necessarily include required points such as corners or edges; hence these points have to be manually matched across different views that could make the process considerably laborious. To address these limitations, this paper presents a video-based as-built documentation method that automatically builds detailed 3D maps of a scene by aligning edge points between video frames. Compared to corner-like features, edge points are far more plentiful even in untextured scenes and often carry important semantic associations. The method has been tested for poorly textured infrastructure scenes and the results indicate that a combination of edge and corner-like features would allow dealing with a broader range of scenes.

Shape vs. volume: Invariant shape descriptors for 3D region of interest characterization in MRI

We propose a new approach for quantifying regions of interest (ROIs) in medical image data. Rotationally invariant shape descriptors (ISDs) were applied to 3D brain regions extracted from MRI scans of 5 Parkinson's patients and 10 control subjects. We concentrated on the thalamus and the caudate nucleus since prior studies have suggested they are affected in Parkinson's disease (PD). In the caudate, both the ISD and volumetric analyses found significant differences between control and PD subjects. The ISD analysis however revealed additional differences between the left and right caudate nuclei in both control and PD subjects. In the thalamus, the volumetric analysis showed significant differences between PD and control subjects, while ISD analysis found significant differences between the left and right thalami in control subjects but not in PD patients, implying disease-induced shape changes. These results suggest that employing ISDs for ROI characterization both complements and extends traditional volumetric analyses. © 2006 IEEE.