Patient motion during an MRI exam can result in major degradation of image quality, and is of increasing concern due to the aging population and its associated diseases. This work presents a general strategy for real-time, intraimage compensation of rigidbody motion that is compatible with multiple imaging sequences. Image quality improvements are established for structural brain MRI acquired during volunteer motion. A headband integrated with three active markers is secured to the forehead. Prospective correction is achieved by interleaving a rapid track-and-update module into the imaging sequence. For every repetition of this module, a short tracking pulse-sequence remeasures the marker positions; during head motion, the rigid-body transformation that realigns the markers to their initial positions is fed back to adaptively update the image-plane-maintaining it at a fixed orientation relative to the head-before the next imaging segment of k-space is acquired. In cases of extreme motion, corrupted lines of kspace are rejected and reacquired with the updated geometry. Patient movement is a fundamental problem in virtually all in vivo MR applications. Motion induces local field variations, causes erroneous positional encoding of k-space data, and corrupts the spin-excitation history between slices; these phenomena manifest in image-space as misregistrations, blurring, and ghosting. Even a few millimeters of movement during scanning can produce severe artifacts in reconstructed data, thus rendering images unusable. Often, it is subject populations with the highest potential diagnostic benefit in which the utility of MRI is curtailed by motion artifacts. In a study of 17 patients with frontoparietal tumors, data from five had to be rejected due to gross motion artifacts (1). Even among a healthy elderly population, our experience suggests that significant artifacts may appear in 10% to 20% of high-resolution structural brain scans; typically used for diagnostic and morphological analysis, such scans are especially prone to motion artifact due to their longer duration. To address these concerns, a motion-correction strategy for brain MRI is presented.The fact that the head is a rigid-body (to a very close approximation) allows an arbitrary motion to be described by six degrees-of-freedom (6-DOF)-three rotations about a three-dimensional (3D) orthogonal coordinate-system, and three translations. Retrospective motion-compensation methods, such as those used to coregister multiple image volumes in functional MRI (fMRI) studies, are well established. The most popular algorithms (2) determine the 6-DOF via minimization of a least-squares cost function and only correct for interimage motion. Retrospective correction involves interpolation, which can cause image blurring, and is further limited by its inability to fully correct for the influences of through-plane motion on local spin-history.In contrast, prospective strategies compensate for motion in the acquisition stage by keeping the image-plane at a fixed orientation ...

Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1 SUMMARYMany Gram-negative bacteria use a type III secretion system (T3SS) to establish associations with their hosts. The T3SS is a conduit for direct injection of type-III effector proteins into host cells, where they manipulate the host for the benefit of the infecting bacterium. For plant-associated pathogens, the variations in number and amino acid sequences of type-III effectors, as well as their functional redundancy, make studying type-III effectors challenging. To mitigate this challenge, we developed a stable delivery system for individual or defined sets of type-III effectors into plant cells. We used recombineering and Tn5-mediated transposition to clone and stably integrate, respectively, the complete hrp/hrc region from Pseudomonas syringae pv. syringae 61 into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. We describe our development of Effector-to-Host Analyzer (EtHAn), and demonstrate its utility for studying effectors for their in planta functions.

Planning, problem solving, and inhibitory abilities are significantly affected by alcohol abuse, with decisional and cognitive forms of impulsivity most impacted. Cognitive remediation targeting these deficits might increase the related functions that mediate the ability to moderate or abstain from alcohol, and so lead to improved treatment results.

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

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