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The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized. [ABSTRACT FROM AUTHOR]

A fast method is described for computing the acoustic field of ultrasound transducers with application to rectangular elements that are cylindrically focused. The efficiency is gained by using a separable approximation to the Green's function and the tradeoff between accuracy and spatial sampling rate is analyzed for determining appropriate parameters for a specific transducer.

In this paper, we report new progress in developing the instrument and software platform of a combined X-ray mammography/diffuse optical breast imaging system. Particularly, we focus on system validation using a series of balloon phantom experiments and the optical image analysis of 49 healthy patients. Using the finite-element method for forward modeling and a regularized Gauss-Newton method for parameter reconstruction, we recovered the inclusions inside the phantom and the hemoglobin images of the human breasts. An enhanced coupling coefficient estimation scheme was also incorporated to improve the accuracy and robustness of the reconstructions. The recovered average total hemoglobin concentration (HbT) and oxygen saturation (S[O.sub.2]) from 68 breast measurements are 16.2 [micro]m and 71%, respectively, where the HbT presents a linear trend with breast density. The low HbT value compared to literature is likely due to the associated mammographic compression. From the spatially co-registered optical/X-ray images, we can identify the chest-wall muscle, fatty tissue, and fibroglandular regions with an average HbT of 20.1 [+ or -] 6.1 [micro]m for fibroglandular tissue, 15.4 [+ or -] 5.0 [micro]m for adipose, and 22.2 [+ or -] 7.3 [micro]m for muscle tissue. The differences between fibroglandular tissue and the corresponding adipose tissue are significant (p < 0.0001). At the same time, we recognize that the optical images are influenced, to a certain extent, by mammographicai compression. The optical images from a subset of patients show composite features from both tissue structure and pressure distribution. We present mechanical simulations which further confirm this hypothesis. Index Terms--Breast imaging, multimodality imaging, tomograhy.

Voxel-based reconstructions in diffuse optical tomography (DOT) using a quadratic regularization functional tend to produce very smooth images due to the attenuation of high spatial frequencies. This then causes difficulty in estimating the spatial extent and contrast of anomalous regions such as tumors. Given an assumption that the target image is piecewise constant, we can employ a parametric model to estimate the boundaries and contrast of an inhomogeneity directly. In this paper, we describe a method to directly reconstruct such a shape boundary from diffuse optical measurements. We parameterized the object boundary using a spherical harmonic basis, and derived a method to compute sensitivities of measurements with respect to shape parameters. We introduced a centroid constraint to ensure uniqueness of the combined shape/center parameter estimate, and a projected Newton method was utilized to optimize the object center position and shape parameters simultaneously. Using the shape Jacobian, we also computed the Cramer-Rao lower bound on the theoretical estimator accuracy given a particular measurement configuration, object shape, and level of measurement noise. Knowledge of the shape sensitivity matrix and of the measurement noise variance allows us to visualize the shape uncertainty region in three dimensions, giving a confidence region for our shape estimate. We have implemented our shape reconstruction method, using a finite-difference-based forward model to compute the forward and ad-joint fields. Reconstruction results are shown for a number of simulated target shapes, and we investigate the problem of model order selection using realistic levels of measurement noise. Assuming a signal-to-noise ratio in the amplitude measurements of 40 dB and a standard deviation in the phase measurements of 0.1[degrees], we are able to estimate an object represented with an eighth-order spherical harmonic model having an absorption contrast of 0.15 [cm.sup.-1] and a volume of 4.82 [cm.sup.3] with errors of less than 10% in object volume and absorption contrast. We also investigate the robustness of our shape-based reconstruction approach to a violation of the assumption that the medium is purely piecewise constant. Index Terms--optical tomography, image reconstruction, inverse problems, shape-based imaging.

A new parameter-free graph-morphology-based segmentation algorithm is proposed to address the problem of partitioning a 3D triangular mesh into disjoint submeshes that correspond to the physical parts of the underlying object. Curvedness, which is a rotation and translation invariant shape descriptor, is computed at every vertex in the input triangulation. Iterative graph dilation and morphological filtering of the outlier curvedness values result in multiple disjoint maximally connected submeshes such that each submesh contains a set of vertices with similar curvedness values, and vertices in disjoint submeshes have significantly different cu rvedness values. Experimental evaluations using the triangulations of a number of complex objects demonstrate the robustness and the efficiency of the proposed algorithm and the results prove that it compares well with a number of state-of-the-art mesh segmentation algorithms. Index Terms--Mesh segmentation, shape descriptor, curvedness, graph morphology.

We consider the problem of classifying buried objects using electromagnetic induction data collected in a setting where there are errors in sensor positioning. Using a series of decay constants (or equivalently, Laplace plane poles) as features for classification, our algorithm seeks to estimate these poles and, subsequently, to determine the type of object in the sensor field of view. In many practical scenarios, a set of data is often accompanied by domain knowledge that the location of the transmitters and/or receivers is only known to within some degree of accuracy (e.g., 10 cm in the along-track direction and 5-cm cross-track). Here, we develop an approach to the extraction of information from such data sets in which the quantitative positional bound information is used in the context of a min--max optimization strategy. Specifically, we look for the parameters of interest that minimize the maximum data residual, where the maximum error is computed over ellipsoids or polyhedra of possible sensor locations defined by the bound information. Our formulation admits data collection with independent or dependent positional uncertainty values at successive nominal collection locations. Our algorithms for solving this optimization problem are validated using simulated and measured data. Index Terms--Bounded-data uncertainty, dynamic programming, electromagnetic induction (EMI), min--max optimization, object classification, parameter estimation, positional uncertainty, subsurface sensing.

This paper proposes a new inverse method for microwave-based subsurface sensing of lossy dielectric objects embedded in a dispersive lossy ground with an unknown rough surface. An iterative inversion algorithm is employed to reconstruct the geometry and dielectric properties of the half-space ground as well as that of the buried object. B-splines are used to model the shape of the object as well as the height of the rough surface. In both cases, the control points for the spline function represent the unknowns to be recovered. A single-pole rational transfer function is used to capture the dispersive nature of the background. Here, the coefficients in the numerator and denominator are the unknowns. The approach presented in this paper is based on the state-of-the-art semianalytic mode matching forward model, which is a fast and efficient algorithm to determine the scattered electromagnetic fields. Numerical experiments involving two-dimensional geometries and TM incident plane waves demonstrate the accuracy and reliability of this inverse method. Index Terms--B-splines, dispersive media, ground-penetrating radar (GPR), inversion methods, nonlinear optimization, rough surface, subsurface sensing.

A reconstruction algorithm to simultaneously estimate the shape and location of three-dimensional breast cancer tumor is presented and its utility is analyzed. The approach is based on a spherical harmonic decomposition to capture the shape of the tumor. We combine a gradient descent optimization method with a direct electromagnetic solver to determine the coefficients in the harmonic expansion as well as the coordinates of the center of the tumor. The results demonstrate the potential advantage of collecting data using a multiple-view/tomographic-type strategy. We show how the order of the harmonic expansion must be increased to capture increasingly 'irregularly' shaped tumors and explore the resulting increase in the central processing unit (CPU) time required by the algorithm. Our approach shows accurate reconstruction of the tumor image regardless of the source polarization. This work demonstrates the promise of the algorithm when used on data corrupted with Gaussian noise and when perfect knowledge of the tumor electrical properties is not available. Index Terms--Breast cancer imaging, electromagnetic scattering, shape reconstruction problems, steepest descent gradient method.

A general framework for incorporating single and multiple priors in diffuse optical tomography is described. We explore the use of this framework for simultaneously utilizing spatial and spectral priors in the context of imaging breast cancer. The utilization of magnetic resonance images of water and lipid content as a statistical spatial prior for the diffuse optical image reconstructions is also discussed. Simulations are performed to demonstrate the significant improvement in image quality afforded by combining spatial and spectral priors. OCIS codes: 170.3010, 170.3880, 170.5280, 170.66960,

A fast algorithm for reconstructing the profile of random rough surfaces using electromagnetic scattering data is presented. The algorithm is based on merging a fast forward solver and an efficient optimization technique. The steepest descent fast multipole method is used as the three-dimensional fast forward solver. A rapidly convergent descent method employing a 'marching-on' strategy for processing multifrequency and multi-incidence angle data is introduced to minimize an underlying cost function. The cost function represents the error between true (synthetic) and simulated scattered field data. Several key issues that impact the accuracy in reconstructing the rough profile are examined in this work, e.g., the location and number of receivers, the incident and scattered directions, the surface roughness, and details regarding the manner in which sensitivity information is computed in the inversion scheme. The results show that using the multiple-incidence (one angle at a time) and the multifrequency (one frequency at a time) strategies lead to improve the profile reconstruction. Index Terms--Fast algorithms, inverse scattering, optimization techniques, profile reconstruction, rough surface scattering.

We introduce a modified Tikhonov regularization method to include three-dimensional x-ray mammography as a prior in the diffuse optical tomography reconstruction. With simulations we show that the optical image reconstruction resolution and contrast are improved by implementing this x-ray-guided spatial constraint. We suggest an approach to find the optimal regularization parameters. The presented preliminary clinical result indicates the utility of the method. OCIS codes: 170.6960, 170.5280, 170.3830, 170.3010, 170.3880, 170.0110.

Optimized versions of frequency-wavenumber (F-K) migration methods are introduced to better focus ground-penetrating radar {{;PR} data in applications of shallow subsurface object localization, e.g., landmine remediation. Migration methods are based on the wave equation and operate by backpropagating the received data into the earth so as to localize buried objects. Traditional F-K migration is based on an underlying assumption that the wavefields propagate in a homogeneous medium. The presence of a rough air-ground interface in the GPR case degrades the localization ability. To overcome this problem in the context of the F-K algorithm, we introduce lateral variations in the velocity of waves in the medium. An optimization approach is employed to choose that velocity function that results in a well-focused image where an entropy-like criterion is used to quantify the notion of focus. Extension of the basic method to lossy medium is also described. The utility of these techniques is demonstrated using field data from a number of GPR systems. Index Terms--Complex-velocity frequency-wavenumber (F-K) migration, dispersive medium, frequency-wavenumber (F-K) migration, minimum entropy optimization, Tikhonov regularization, varimax norm.

We present a shape-based approach to three-dimensional image reconstruction from diffuse optical data. Our approach differs from others in the literature in that we jointly reconstruct object and background characterization and localization simultaneously, rather than sequentially process for optical properties and postprocess for edges. The key to the efficiency and robustness of our algorithm is in the model we propose for the optical properties of the background and anomaly: We use a low-order parameterization of the background and another for the interior of the anomaly, and we use an ellipsoid to describe the boundary of the anomaly. This model has the effect of regularizing the inversion problem and provides a natural means of including additional physical properties if they are known a priori. A Gauss--Newton-type algorithm with line search is implemented to solve the underlying nonlinear least-squares problem and thereby determine the coefficients of the parameterizations and the descriptors of the ellipsoid. Numerical results show the effectiveness of this method. OCIS codes: 100.3190, 100.3010, 100.6890.

The problem of how to locate an object in an image when size and rotation are not known is investigated and discussed.