SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding

Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

Time-dependent orientation coupling in equilibrium polymer melts

The motion in concentrated polymer systems is described by either the Rouse or the reptation model, which both assume that the relaxation of each polymer chain is independent of the surrounding chains. This, however, is in contradiction with several experiments. In this Letter, we propose a universal description of orientation coupling in polymer melts in terms of the time-dependent coupling parameter κ(t). We use molecular dynamics simulations to show that the coupling parameter increases with time, reaching about 50% at long times, independently of the chain length or blend composition. This leads to predictions of component dynamics in mixtures of different molecular weights from the knowledge of monodisperse dynamics for unentangled melts. Finally, we demonstrate that entanglements do not play a significant role in the observed coupling. © 2010 The American Physical Society

A novel shape feature for fast region-based pedestrian recognition

A new class of shape features for region classification and high-level recognition is introduced. The novel Randomised Region Ray (RRR) features can be used to train binary decision trees for object category classification using an abstract representation of the scene. In particular we address the problem of human detection using an over segmented input image. We therefore do not rely on pixel values for training, instead we design and train specialised classifiers on the sparse set of semantic regions which compose the image. Thanks to the abstract nature of the input, the trained classifier has the potential to be fast and applicable to extreme imagery conditions. We demonstrate and evaluate its performance in people detection using a pedestrian dataset.

Modeling camera orientation and 3D structure from a sequence of images taken by a perambulating commercial video camera

In this paper we report the degree of reliability of image sequences taken by off-the-shelf TV cameras for modeling camera rotation and reconstructing 3D structure using computer vision techniques. This is done in spite of the fact that computer vision systems usually use imaging devices that are specifically designed for the human vision. Our scenario consists of a static scene and a mobile camera moving through the scene. The scene is any long axial building dominated by features along the three principal orientations and with at least one wall containing prominent repetitive planar features such as doors, windows bricks etc. The camera is an ordinary commercial camcorder moving along the axial axis of the scene and is allowed to rotate freely within the range +/- 10 degrees in all directions. This makes it possible that the camera be held by a walking unprofessional cameraman with normal gait, or to be mounted on a mobile robot. The system has been tested successfully on sequence of images of a variety of structured, but fairly cluttered scenes taken by different walking cameramen. The potential application areas of the system include medicine, robotics and photogrammetry.

Judging size, distance and depth with an active telepresence system

A visual telepresence system has been developed at the University of Reading which utilizes eye tracing to adjust the horizontal orientation of the cameras and display system according to the convergence state of the operator's eyes. Slaving the cameras to the operator's direction of gaze enables the object of interest to be centered on the displays. The advantage of this is that the camera field of view may be decreased to maximize the achievable depth resolution. An active camera system requires an active display system if appropriate binocular cues are to be preserved. For some applications, which critically depend upon the veridical perception of the object's location and dimensions, it is imperative that the contribution of binocular cues to these judgements be ascertained because they are directly influenced by camera and display geometry. Using the active telepresence system, we investigated the contribution of ocular convergence information to judgements of size, distance and shape. Participants performed an open- loop reach and grasp of the virtual object under reduced cue conditions where the orientation of the cameras and the displays were either matched or unmatched. Inappropriate convergence information produced weak perceptual distortions and caused problems in fusing the images.

Modelling niches of arbitrary shape in genetic algorithms using Niche Linkage in the Dynamic Niche Clustering framework

We present some additions to a fuzzy variable radius niche technique called Dynamic Niche Clustering (DNC) (Gan and Warwick, 1999; 2000; 2001) that enable the identification and creation of niches of arbitrary shape through a mechanism called Niche Linkage. We show that by using this mechanism it is possible to attain better feature extraction from the underlying population.

Rheology of magmas with bimodal crystal size and shape distributions: insights from analog experiments

Magmas in volcanic conduits commonly contain microlites in association with preexisting phenocrysts, as often indicated by volcanic rock textures. In this study, we present two different experiments that inves- tigate the flow behavior of these bidisperse systems. In the first experiments, rotational rheometric methods are used to determine the rheology of monodisperse and polydisperse suspensions consisting of smaller, prolate particles (microlites) and larger, equant particles (phenocrysts) in a bubble‐free Newtonian liquid (silicate melt). Our data show that increasing the relative proportion of prolate microlites to equant pheno- crysts in a magma at constant total particle content can increase the relative viscosity by up to three orders of magnitude. Consequently, the rheological effect of particles in magmas cannot be modeled by assuming a monodisperse population of particles. We propose a new model that uses interpolated parameters based on the relative proportions of small and large particles and produces a considerably improved fit to the data than earlier models. In a second series of experiments we investigate the textures produced by shearing bimodal suspensions in gradually solidifying epoxy resin in a concentric cylinder setup. The resulting textures show the prolate particles are aligned with the flow lines and spherical particles are found in well‐organized strings, with sphere‐depleted shear bands in high‐shear regions. These observations may explain the measured variation in the shear thinning and yield stress behavior with increasing solid fraction and particle aspect ratio. The implications for magma flow are discussed, and rheological results and tex- tural observations are compared with observations on natural samples.