Efficient parallel implementation of iterative reconstruction algorithms for electron tomography

Electron tomography (ET) combines electron microscopy and the principles of tomographic imaging in order to reconstruct the three-dimensional structure of complex biological specimens at molecular resolution. Weighted back-projection (WBP) has long been the method of choice since the reconstructions are very fast. It is well known that iterative methods produce better images, but at a very costly time penalty. In this work, it is shown that efficient parallel implementations of iterative methods, based primarily on data decomposition, can speed up such methods to an extent that they become viable alternatives to WBP. Precomputation of the coefficient matrix has also turned out to be important to substantially improve the performance regardless of the number of processors used. Matrix precomputation has made it possible to speed up the block-iterative component averaging (BICAV) algorithm, which has been studied before in the context of computerized tomography (CT) and ET, by a factor of more than 3.7. Component-averaged row projections (CARP) is a recently introduced block-parallel algorithm, which was shown to be a robust method for solving sparse systems arising from partial differential equations. It is shown that this algorithm is also suitable for single-axis ET, and is advantageous over BICAV both in terms of runtime and image quality. The experiments were carried out on several datasets of ET of various sizes, using the blob model for representing the reconstructed object.     

Problematic Instant Messaging Use

This study is an empirical investigation of problematic instant messaging (IM) use among university students in Singapore. It adapts Caplan's (2005) theoretical framework of problematic Internet use (PIU) to the context of problematic IM use by linking pre-existing human dispositions to cognitive-behavioral symptoms and negative outcomes of improper IM use. Four new factors—oral communication apprehension, polychronicity, perceived inconvenience of using offline communication means, and trait procrastination—were tested as predictors of problematic IM use. The results provided strong support for Caplan's theoretical framework of PIU and indicated that oral communication apprehension and perceived inconvenience of using offline means were significant predictors of problematic IM use, whereas polychronicity and trait procrastination were not. The implications of these findings are discussed.     

Shape deformation in continuous map generalization

Given a collection of regions on a map, we seek a method of continuously altering the regions as the scale is varied. This is formalized and brought to rigor as well-defined problems in homotopic deformation. We ask the regions to preserve topology, area-ratios, and relative position as they change over time. A solution is presented using differential methods and computational geometric techniques. Most notably, an application of this method is used to provide an algorithm to obtain cartograms.

The Geometry of the Zodiac

The zodiac is widely known as a band of twelve celestial constellations. It also contains a mathematical model for cosmographic depiction, based on observations of the sun, moon, and visible planets as they traverse the celestial ecliptic. Here wee consider the zodiac as a timepiece or calendar; how this system of planets and constellations emerges from elementary geometric patterns; and how these patterns inform the symbols of the zodiac and frame our world view.     

Outlier detection using default reasoning

Default logics are usually used to describe the regular behavior and normal properties of domain elements. In this paper we suggest, conversely, that the framework of default logics can be exploited for detecting outliers. Outliers are observations expressed by sets of literals that feature unexpected semantical characteristics. These sets of literals are selected among those explicitly embodied in the given knowledge base. Hence, essentially we perceive outlier detection as a knowledge discovery technique. This paper defines the notion of outlier in two related formalisms for specifying defaults: Reiter's default logic and extended disjunctive logic programs. For each of the two formalisms, we show that finding outliers is quite complex. Indeed, we prove that several versions of the outlier detection problem lie over the second level of the polynomial hierarchy. We believe that a thorough complexity analysis, as done here, is a useful preliminary step towards developing effective heuristics and exploring tractable subsets of outlier detection problems.     

Bacteria-Responsive Self-Assembly of Antimicrobial Peptide Nanonets for Trap-and-Kill of Antibiotic-Resistant Strains

Bacterial trapping using nanonets is a ubiquitous immune defense mechanism against infectious microbes. These nanonets can entrap microbial cells, effectively arresting their dissemination and rendering them more vulnerable to locally secreted microbicides. Inspired by this evolutionarily conserved anti-infective strategy, a series of 15 to 16 residue-long synthetic β-hairpin peptides is herein constructed with the ability to self-assemble into nanonets in response to the presence of bacteria, enabling spatiotemporal control over microbial killing. Using amyloid-specific K114 assay and confocal microscopy, the membrane components lipoteichoic acid and lipopolysaccharide are shown to play a major role in determining the amyloid-nucleating capacity as triggered by Gram-positive and Gram-negative bacteria respectively. These nanonets displayed both trapping and killing functionalities, hence offering a direct improvement from the trap-only biomimetics in literature. By substituting a single turn residue of the non-amyloidogenic BTT1 peptide, the nanonet-forming BTT1-3A analog is produced with comparable antimicrobial potency. With the same sequence manipulation approach, BTT2-4A analog modified from BTT2 peptide showed improved antimicrobial potency against colistin-resistant clinical isolates. The peptide nanonets also demonstrated robust stability against proteolytic degradation, and promising in vivo efficacy and biosafety profile. Overall, these bacteria-responsive peptide nanonets are promising clinical anti-infective alternatives for circumventing antibiotic resistance.     

An Investigation of the Relationship Between the Gaussian Process Model Parameters and Surface Area in Three Dimensions

In this paper, we study the relationship between the fitted parameters in a Gaussian process (kriging) model and the complexity of the resulting response surface. This study is done for models with one response and two input variables. An analytical calculation of surface roughness is used as a measure of the complexity of the response surface fit by the Gaussian process model. Our findings indicate that the size of the fitted model parameters as measured across different fits and data sets do not give indication as to the complexity of the surface. We do, however, show that the magnitude of each of the parameters in a single fitted model gives indication about the amount of variability in the direction of that fitted parameter. Copyright © 2015 John Wiley & Sons, Ltd.     

Thomas Jefferson��s Poplar Forest

A unique geometric construction known to Thomas Jefferson reveals a rich interplay of root-two geometric elements when applied to Jefferson’s octagonal plan of Poplar Forest, his eighteenth-century villa retreat.     

ODTLES: A multi-scale model for 3D turbulent flow based on one-dimensional turbulence modeling

A novel multi-scale approach for extending the one-dimensional turbulence (ODT) model of [A.R. Kerstein. One-dimensional turbulence: model formulation and application to homogeneous turbulence, shear flows, and buoyant stratified flows, J. Fluid Mech. 392 (1999) 277] to treat turbulent flow in three-dimensional (3D) domains is described. In this model, here called ODTLES, 3D aspects of the flow are captured by embedding three, mutually orthogonal, one-dimensional ODT domain arrays within a coarser 3D mesh. The ODTLES model is obtained by developing a consistent approach for dynamically coupling the different ODT line sets to each other and to the large scale processes that are resolved on the 3D mesh. The model is implemented computationally and its performance is tested by performing simulations of decaying isotropic turbulence at two different Reynolds numbers and comparing to the experimental data of [H. Kang, S. Chester, C. Meneveau. Decaying turbulence in an active-grid-generated flow and comparisons with large-eddy simulations, J. Fluid Mech. 480 (2003) 129; G. Comte-Bellot, S. Corrsin, Simple Eulerian correlation of full-and narrow band velocity signals in grid-generated ’isotropic’ turbulence, J. Fluid Mech. 48 (1971) 273].