An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.

ARGONAUTE4 (AGO4) and RNA polymerase IV (Pol IV) are required for DNA methylation guided by 24 nucleotide small interfering RNAs (siRNAs) in Arabidopsis thaliana. Here we show that AGO4 localizes to nucleolus-associated bodies along with the Pol IV subunit NRPD1b; the small nuclear RNA (snRNA) binding protein SmD3; and two markers of Cajal bodies, trimethylguanosine-capped snRNAs and the U2 snRNA binding protein U2B''. AGO4 interacts with the C-terminal domain of NRPD1b, and AGO4 protein stability depends on upstream factors that synthesize siRNAs. AGO4 is also found, along with the DNA methyltransferase DRM2, throughout the nucleus at presumed DNA methylation target sites. Cajal bodies are conserved sites for the maturation of ribonucleoprotein complexes. Our results suggest a function for Cajal bodies as a center for the assembly of an AGO4/NRPD1b/siRNA complex, facilitating its function in RNA-directed gene silencing at target loci.

Adapting data processing to compare model and experiment accurately: A discrete element model and magnetic resonance measurements of a 3d cylindrical fluidized bed

Discrete element modeling is being used increasingly to simulate flow in fluidized beds. These models require complex measurement techniques to provide validation for the approximations inherent in the model. This paper introduces the idea of modeling the experiment to ensure that the validation is accurate. Specifically, a 3D, cylindrical gas-fluidized bed was simulated using a discrete element model (DEM) for particle motion coupled with computational fluid dynamics (CFD) to describe the flow of gas. The results for time-averaged, axial velocity during bubbling fluidization were compared with those from magnetic resonance (MR) experiments made on the bed. The DEM-CFD data were postprocessed with various methods to produce time-averaged velocity maps for comparison with the MR results, including a method which closely matched the pulse sequence and data processing procedure used in the MR experiments. The DEM-CFD results processed with the MR-type time-averaging closely matched experimental MR results, validating the DEM-CFD model. Analysis of different averaging procedures confirmed that MR time-averages of dynamic systems correspond to particle-weighted averaging, rather than frame-weighted averaging, and also demonstrated that the use of Gaussian slices in MR imaging of dynamic systems is valid. © 2013 American Chemical Society.

Anisotropy preserving DTI processing

Statistical analysis of diffusion tensor imaging (DTI) data requires a computational framework that is both numerically tractable (to account for the high dimensional nature of the data) and geometric (to account for the nonlinear nature of diffusion tensors). Building upon earlier studies exploiting a Riemannian framework to address these challenges, the present paper proposes a novel metric and an accompanying computational framework for DTI data processing. The proposed approach grounds the signal processing operations in interpolating curves. Well-chosen interpolating curves are shown to provide a computational framework that is at the same time tractable and information relevant for DTI processing. In addition, and in contrast to earlier methods, it provides an interpolation method which preserves anisotropy, a central information carried by diffusion tensor data. © 2013 Springer Science+Business Media New York.

Distributed optical fiber strain sensing in a secant piled wall

An optical fiber strain sensing technique, based on Brillouin Optical Time Domain Reflectometry (BOTDR), was used to obtain the full deformation profile of a secant pile wall during construction of an adjacent basement in London. Details of the installation of sensors as well as data processing are described. By installing optical fiber down opposite sides of the pile, the distributed strain profiles obtained can be used to give both the axial and lateral movements along the pile. Measurements obtained from the BOTDR were found in good agreement with inclinometer data from the adjacent piles. The relative merits of the two different techniques are discussed. © 2007 ASCE.