Rodents consuming the same toxic diet harbor a unique functional core microbiome.

Gut microbiota are intrinsic to an herbivorous lifestyle, but very little is known about how plant secondary compounds (PSCs), which are often toxic, influence these symbiotic partners. Here we interrogated the possibility of unique functional core microbiomes in populations of two species of woodrat (Neotoma lepida and bryanti) that have independently converged to feed on the same toxic diet (creosote bush; Larrea tridentata) and compared them to populations that do not feed on creosote bush. Leveraging this natural experiment, we collected samples across a large geographic region in the U.

A conserved sequence signature is essential for robust plant miRNA biogenesis.

Micro (mi)RNAs are 20-22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear.

Nonrigid 2D/3D registration of coronary artery models with live fluoroscopy for guidance of cardiac interventions.

A 2D/3D nonrigid registration method is proposed that brings a 3D centerline model of the coronary arteries into correspondence with bi-plane fluoroscopic angiograms. The registered model is overlaid on top of interventional angiograms to provide surgical assistance during image-guided chronic total occlusion procedures, thereby reducing the uncertainty inherent in 2D interventional images. The proposed methodology is divided into two parts: global structural alignment and local nonrigid registration.

Global error minimization in image mosaicing using graph connectivity and its applications in microscopy.

Several applications such as multiprojector displays and microscopy require the mosaicing of images (tiles) acquired by a camera as it traverses an unknown trajectory in 3D space. A homography relates the image coordinates of a point in each tile to those of a reference tile provided the 3D scene is planar. Our approach in such applications is to first perform pairwise alignment of the tiles that have imaged common regions in order to recover a homography relating the tile pair.

Image-based respiratory motion compensation for fluoroscopic coronary roadmapping.

We present a new image-based respiratory motion compensation method for coronary roadmapping in fluoroscopic images. A temporal analysis scheme is proposed to identify static structures in the image gradient domain. An extended Lucas-Kanade algorithm involving a weighted sum-of-squared-difference (WSSD) measure is proposed to estimate the soft tissue motion in the presence of static structures.

Estimating Myocardial Motion by 4D Image Warping.

A method for spatio-temporally smooth and consistent estimation of cardiac motion from MR cine sequences is proposed. Myocardial motion is estimated within a 4-dimensional (4D) registration framework, in which all 3D images obtained at different cardiac phases are simultaneously registered. This facilitates spatio-temporally consistent estimation of motion as opposed to other registration-based algorithms which estimate the motion by sequentially registering one frame to another.

Automatic image-based cardiac and respiratory cycle synchronization and gating of image sequences.

We propose a novel method to detect the current state of the quasi-periodic system from image sequences which in turn will enable us to synchronize/gate the image sequences to obtain images of the organ system at similar configurations. The method uses the cumulated phase shift in the spectral domain of successive image frames as a measure of the net motion of objects in the scene. The proposed method is applicable to 2D and 3D time varying sequences and is not specific to the imaging modality.

Biomechanically-constrained 4D estimation of myocardial motion.

We propose a method for the analysis of cardiac images with the goal of reconstructing the motion of the ventricular walls. The main feature of our method is that the inversion parameter field is the active contraction of the myocardial fibers. This is accomplished with a biophysically-constrained, four-dimensional (space plus time) formulation that aims to complement information that can be gathered from the images by a priori knowledge of cardiac mechanics.

Robust computation of mutual information using spatially adaptive meshes.

We present a new method for the fast and robust computation of information theoretic similarity measures for alignment of multi-modality medical images. The proposed method defines a non-uniform, adaptive sampling scheme for estimating the entropies of the images, which is less vulnerable to local maxima as compared to uniform and random sampling. The sampling is defined using an octree partition of the template image, and is preferable over other proposed methods of non-uniform sampling since it respects the underlying data distribution.

Consistent estimation of cardiac motions by 4D image registration.

A 4D image registration method is proposed for consistent estimation of cardiac motion from MR image sequences. Under this 4D registration framework, all 3D cardiac images taken at different time-points are registered simultaneously, and motion estimated is enforced to be spatiotemporally smooth, thereby overcoming potential limitations of some methods that typically estimate cardiac deformation sequentially from one frame to another, instead of treating the entire set of images as a 4D volume. To facilitate our image matching process, an attribute vector is designed for each point in the image to include intensity, boundary and geometric moment invariants (GMIs).

Efficient myocyte gene delivery with complete cardiac surgical isolation in situ.

Background: Previously, we used cardiopulmonary bypass with incomplete cardiac isolation and antegrade administration of vector for global cardiac gene delivery. Here we present a translatable cardiac surgical procedure that allows for complete surgical isolation of the heart in situ with retrograde (through the coronary venous circulation) administration of both vector and endothelial permeabilizing agents to increase myocyte transduction efficiency.

Methods: In 6 adult dogs the heart was completely isolated with tourniquets placed around both vena cavae and cannulas and all pulmonary veins.