Shira L. Broschat

Application of the perfectly matched layer (PML) absorbing boundary condition to elastic wave propagation

Hastings, F.D., J.B. Schneider, and S.L. Broschat, ���Application of the perfectly matched layer (PML) absorbing boundary condition to elastic wave propagation,�� J. Acoust. Soc. Am., Vol. 100, No. 5, 3061-3069, Nov. 1996. http://dx.doi.org/10.1121/1.417118.

blaCMY-2-Positive IncA/C Plasmids from Escherichia coli and Salmonella enterica Are a Distinct Component of a Larger Lineage of Plasmids

ABSTRACT Large multidrug resistance plasmids of the A/C incompatibility complex (IncA/C) have been found in a diverse group of Gram-negative commensal and pathogenic bacteria. We present three completed sequences from IncA/C plasmids that originated from Escherichia coli (cattle) and Salmonella enterica serovar Newport (human) and that carry the cephamycinase gene blaCMY-2. These large plasmids (148 to 166 kbp) share extensive sequence identity and synteny. The most divergent plasmid, peH4H, has lost several conjugation-related genes and has gained a kanamycin resistance region. Two of the plasmids (pAM04528 and peH4H) harbor two copies of blaCMY-2, while the third plasmid (pAR060302) harbors a single copy of the gene. The majority of single-nucleotide polymorphisms comprise nonsynonymous mutations in floR. A comparative analysis of these plasmids with five other published IncA/C plasmids showed that the blaCMY-2 plasmids from E. coli and S. enterica are genetically distinct from those originating from Yersinia pestis and Photobacterium damselae and distal to one originating from Yersinia ruckeri. While the overall similarity of these plasmids supports the likelihood of recent movements among E. coli and S. enterica hosts, their greater divergence from Y. pestis or Y. ruckeri suggests less recent plasmid transfer among these pathogen groups.

A Monte-Carlo FDTD technique for rough surface scattering

A Monte-Carlo finite-difference time-domain (FDTD) technique is developed for wave scattering from randomly rough, one-dimensional surfaces satisfying the Dirichlet boundary condition. Both single-scale Gaussian and multiscale Pierson-Moskowitz surface roughness spectra are considered. Bistatic radar cross sections are calculated as a function of scattering angle for incident angles of 0, 45, 70, and 80 degrees measured from the vertical. The contour path FDTD method is shown to improve accuracy for incident angles greater than 45 degrees. Results compare well with those obtained using a Monte-Carlo integral equation technique. >

Aggressive region growing for speckle reduction in ultrasound images

Abstract Speckle appears in all conventional medical B-mode ultrasonic images and can be an undesirable property since it may mask small but diagnostically significant features. In this paper, an adaptive filtering algorithm is proposed for speckle reduction. It selects a filtering region size using an appropriately estimated homogeneity value for region growth. Homogeneous regions are processed with an arithmetic mean filter. Edge pixels are filtered using a nonlinear median filter. The performance of the proposed technique is compared to two other methods––the adaptive weighted median filter and the homogeneous region growing mean filter. Results of processed images show that the method proposed reduces speckle noise and preserves edge details effectively.

An investigation of the small slope approximation for scattering from rough surfaces. Part I. Theory

Thorsos, E.I., and S.L. Broschat, An investigation of the small slope approximation for scattering from rough surfaces: Part I: Theory, J. Acoust. Soc. Am., Vol. 97, No. 4, 2082-2093, Apr. 1995. http://dx.doi.org/10.1121/1.412001.

An investigation of the small slope approximation for scattering from rough surfaces: Part II: Numerical studies

Broschat, S.L., and E.I. Thorsos, An investigation of the small slope approximation for scattering from rough surfaces: Part II: Numerical studies, J. Acoust. Soc. Am., Vol. 101, No. 5, 2615-2625, May 1997. http://dx.doi.org/10.1121/1.418502.

The Phase Perturbation Technique vs. an Exact Numerical Method for Random Rough Surface Scattering

There is a need for a solution to the problem of wave scattering from rough surfaces that is accurate when both the classical field perturbation and Kirchhoff approximations are not. In previous work it was shown numerically that the phase perturbation reflection and backscattering coefficients reduce to those of field perturbation theory and the Kirchhoff approximation in the appropriate limits; however, for cases when the classical solutions did not apply, the accuracy of the phase perturbation results could not be determined. In this paper we examine the validity of the phase perturbation technique for a region in parameter space when the two classical solutions fail. Numerical results for the bistatic scattering cross section are compared with exact numerical results for one-dimensional surfaces having a Gaussian roughness spectrum and satisfying a Dirichlet boundary condition. It is found that in the region considered the phase perturbation results agree with the exact results over all scattered angl...

ApicoAP: The First Computational Model for Identifying Apicoplast-Targeted Proteins in Multiple Species of Apicomplexa

Background Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for the survival of the parasite, but its unique properties make it an ideal drug target. The majority of apicoplast-associated proteins are nuclear encoded and targeted post-translationally to the organellar lumen via a bipartite signaling mechanism that requires an N-terminal signal and transit peptide (TP). Attempts to define a consensus motif that universally identifies apicoplast TPs have failed. Methodology/Principal Findings In this study, we propose a generalized rule-based classification model to identify apicoplast-targeted proteins (ApicoTPs) that use a bipartite signaling mechanism. Given a training set specific to an organism, this model, called ApicoAP, incorporates a procedure based on a genetic algorithm to tailor a discriminating rule that exploits the known characteristics of ApicoTPs. Performance of ApicoAP is evaluated for four labeled datasets of Plasmodium falciparum, Plasmodium yoelii, Babesia bovis, and Toxoplasma gondii proteins. ApicoAP improves the classification accuracy of the published dataset for P. falciparum to 94%, originally 90% using PlasmoAP. Conclusions/Significance We present a parametric model for ApicoTPs and a procedure to optimize the model parameters for a given training set. A major asset of this model is that it is customizable to different parasite genomes. The ApicoAP prediction software is available at http://code.google.com/p/apicoap/ and http://bcb.eecs.wsu.edu.

A finite-difference time-domain solution to scattering from a rough pressure-release surface

The finite-difference time-domain (FDTD) method is a numerical technique that makes no explicit physical approximations to the underlying problem. The quality of a FDTD-based solution typically is determined by the discretization of the computational domain—the smaller the spacing, the more accurate the solution. Unfortunately, for large computational domains, i.e., ones spanning many wavelengths, the small spatial step size needed to obtain a high-fidelity solution may lead to a prohibitively large number of unknowns. Here it is shown how the FDTD method can be used to model accurately scattering from pressure-release surfaces above a homogeneous water column. To keep the computational cost manageable, a number of enhancements to the standard FDTD algorithm are employed. These enhancements include correcting for numerical dispersion along the specular direction of the incident insonification, using locally conformal cells at the pressure-release boundary, and propagating the field through the homogeneous...

Identification of Anaplasma marginale Type IV Secretion System Effector Proteins

Background Anaplasma marginale, an obligate intracellular alphaproteobacterium in the order Rickettsiales, is a tick-borne pathogen and the leading cause of anaplasmosis in cattle worldwide. Complete genome sequencing of A. marginale revealed that it has a type IV secretion system (T4SS). The T4SS is one of seven known types of secretion systems utilized by bacteria, with the type III and IV secretion systems particularly prevalent among pathogenic Gram-negative bacteria. The T4SS is predicted to play an important role in the invasion and pathogenesis of A. marginale by translocating effector proteins across its membrane into eukaryotic target cells. However, T4SS effector proteins have not been identified and tested in the laboratory until now. Results By combining computational methods with phylogenetic analysis and sequence identity searches, we identified a subset of potential T4SS effectors in A. marginale strain St. Maries and chose six for laboratory testing. Four (AM185, AM470, AM705 [AnkA], and AM1141) of these six proteins were translocated in a T4SS-dependent manner using Legionella pneumophila as a reporter system. Conclusions The algorithm employed to find T4SS effector proteins in A. marginale identified four such proteins that were verified by laboratory testing. L. pneumophila was shown to work as a model system for A. marginale and thus can be used as a screening tool for A. marginale effector proteins. The first T4SS effector proteins for A. marginale have been identified in this work.