Superpatterns and Universal Point Sets

An old open problem in graph drawing asks for the size of a universal point set, a set of points that can be used as vertices for straight-line drawings of all n-vertex planar graphs. We connect this problem to the theory of permutation patterns, where another open problem concerns the size of superpatterns, permutations that contain all patterns of a given size. We generalize superpatterns to classes of permutations determined by forbidden patterns, and we construct superpatterns of size n^2/4 + Theta(n) for the 213-avoiding permutations, half the size of known superpatterns for unconstrained permutations. We use our superpatterns to construct universal point sets of size n^2/4 - Theta(n), smaller than the previous bound by a 9/16 factor. We prove that every proper subclass of the 213-avoiding permutations has superpatterns of size O(n log^O(1) n), which we use to prove that the planar graphs of bounded pathwidth have near-linear universal point sets.Comment: GD 2013 special issue of JGA

Efficient Processing of Spatial Joins Using R-Trees

Abstract: In this paper, we show that spatial joins are very suitable to be processed on a parallel hardware platform. The parallel system is equipped with a so-called shared virtual memory which is well-suited for the design and implementation of parallel spatial join algorithms. We start with an algorithm that consists of three phases: task creation, task assignment and parallel task execu-tion. In order to reduce CPU- and I/O-cost, the three phases are processed in a fashion that pre-serves spatial locality. Dynamic load balancing is achieved by splitting tasks into smaller ones and reassigning some of the smaller tasks to idle processors. In an experimental performance compar-ison, we identify the advantages and disadvantages of several variants of our algorithm. The most efficient one shows an almost optimal speed-up under the assumption that the number of disks is sufficiently large. Topics: spatial database systems, parallel database systems

Some relations of subsequences in permutations to graph theory with algorithmic applications

A thesis submitted to the Faculty d£ Science of the University of the Witwatersfand in fulfillment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 1977.The representation of some types of graphs as permutations, is utilized in devising efficient algorithms on those graphs. Maximum 'cliques in permutation graphs and circle graphs are found, by searching for a longest ascending or descending subsequence in their representing permutation. The correspondence between n-noded binary trees and the set SSn of stack-sortable permutations, forms the basis of an algorithm for generating and indexing such trees. The-relations between a graph and its representing p ermutation, are also employed in the proof of theorems concerning properties of subsequences in this permutation. In particular, expressions for the average lengths of the longest ascending and descending subsequence a in a random member of SSn , and the average number of inversions in such a permutation, are derived using properties of binary trees. Finally, a correspondence between the set SSn , and the set of permutations of order n With no descending subsequence of length 3, is demonstrated

Towards energy aware cloud computing application construction

The energy consumption of cloud computing continues to be an area of significant concern as data center growth continues to increase. This paper reports on an energy efficient interoperable cloud architecture realised as a cloud toolbox that focuses on reducing the energy consumption of cloud applications holistically across all deployment models. The architecture supports energy efficiency at service construction, deployment and operation. We discuss our practical experience during implementation of an architectural component, the Virtual Machine Image Constructor (VMIC), required to facilitate construction of energy aware cloud applications. We carry out a performance evaluation of the component on a cloud testbed. The results show the performance of Virtual Machine construction, primarily limited by available I/O, to be adequate for agile, energy aware software development. We conclude that the implementation of the VMIC is feasible, incurs minimal performance overhead comparatively to the time taken by other aspects of the cloud application construction life-cycle, and make recommendations on enhancing its performance

Do Neuro-Muscular Adaptations Occur in Endurance-Trained Boys and Men?

Most research on the effects of endurance training has focused on endurance training's health-related benefits and metabolic effects in both children and adults. The purpose of this study was to examine the neuromuscular effects of endurance training and to investigate whether they differ in children (9.0-12.9 years) and adults (18.4-35.6 years). Maximal isometric torque, rate of torque development (RTD), rate of muscle activation (Q30), electromechanical delay (EMD), and time to peak torque and peak RTD were determined by isokinetic dynamometry and surface electromyography (EMG) in elbow and knee flexion and extension. The subjects were 12 endurance-trained and 16 untrained boys, and 15 endurance-trained and 20 untrained men. The adults displayed consistently higher peak torque, RTD, and Q30, in both absolute and normalized values, whereas the boys had longer EMD (64.7+/-17.1 vs. 56.6+/-15.4 ms) and time to peak RTD (98.5+/-32.1 vs. 80.4+/-15.0 ms for boys and men, respectively). Q30, normalized for peak EMG amplitude, was the only observed training effect (1.95+/-1.16 vs. 1.10+/-0.67 ms for trained and untrained men, respectively). This effect could not be shown in the boys. The findings show normalized muscle strength and rate of activation to be lower in children compared with adults, regardless of training status. Because the observed higher Q30 values were not matched by corresponding higher performance measures in the trained men, the functional and discriminatory significance of Q30 remains unclear. Endurance training does not appear to affect muscle strength or rate of force development in either men or boys

Permafrost saline water and Early to mid-Holocene permafrost aggradation in Svalbard

Deglaciation in Svalbard was followed by seawater ingression and deposition of marine (deltaic) sediments in fjord valleys, while elastic rebound resulted in fast land uplift and the exposure of these sediments to the atmosphere, whereby the formation of epigenetic permafrost was initiated. This was then followed by the accumulation of aeolian sediments, with syngenetic permafrost formation. Permafrost was studied in the eastern Adventdalen valley, Svalbard, 3–4 km from the maximum up-valley reach of post-deglaciation seawater ingression, and its ground ice was analysed for its chemistry. While ground ice in the syngenetic part is basically fresh, the epigenetic part has a frozen freshwater–saline water interface (FSI), with chloride concentrations increasing from the top of the epigenetic part (at 5.5 m depth) to about 15 % that of seawater at 11 m depth. We applied a one-dimensional freezing model to examine the rate of top-down permafrost formation, which could be accommodated by the observed frozen FSI. The model examined permafrost development under different scenarios of mean average air temperature, water freezing temperature and degree of pore-water freezing. We found that even at the relatively high air temperatures of the Early to mid-Holocene, permafrost could aggrade quite fast down to 20 to 37 m (the whole sediment fill of 25 m at this location) within 200 years. This, in turn, allowed freezing and preservation of the freshwater–saline water interface despite the relatively fast rebound rate, which apparently resulted in an increase in topographic gradients toward the sea. The permafrost aggradation rate could also be enhanced due to non-complete pore-water freezing. We conclude that freezing must have started immediately after the exposure of the marine sediment to atmospheric conditions.</p

Investigating the Responses of Human Epithelial Cells to Predatory Bacteria

One beguiling alternative to antibiotics for treating multi-drug resistant infections are Bdellovibrio-and-like-organisms (BALOs), predatory bacteria known to attack human pathogens. Consequently, in this study, the responses from four cell lines (three human and one mouse) were characterized during an exposure to different predatory bacteria, Bdellovibrio bacteriovorus HD100, Bacteriovorus BY1 and Bacteriovorax stolpii EB1. TNF-alpha levels were induced in Raw 264.7 mouse macrophage cultures with each predator, but paled in comparison to those obtained with E. coli. This was true even though the latter strain was added at an 11.1-fold lower concentration (p &lt; 0.01). Likewise, E. coli led to a significant (54%) loss in the Raw 264.7 murine macrophage viability while the predatory strains had no impact. Tests with various epithelial cells, including NuLi-1 airway, Caco2, HT29 and T84 colorectal cells, gave similar results, with E. coli inducing IL-8 production. The viabilities of the NuLi-1 and Caco-2 cells were slightly reduced (8%) when exposed to the predators, while T84 viability remained steady. In no cases did the predatory bacteria induce actin rearrangement. These results clearly demonstrate the gentle natures of predatory bacteria and their impacts on human cells.ope

Bilayer-spanning DNA nanopores with voltage-switching between open and closed state.

Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.The SH lab is supported by the Leverhulme Trust (RPG-170), UCL Chemistry, EPSRC (Institutional Sponsorship Award), the National Physical Laboratory, and Oxford Nanopore Technologies. KG acknowledges funding from the Winton Program of Physics for Sustainability, Gates Cambridge and the Oppenheimer Trust. UFK was supported by an ERC starting grant #261101.This is the final version of the article. It was first published by ACS under the ACS AuthorChoice license at http://dx.doi.org/10.1021/nn5039433 This permits copying and redistribution of the article or any adaptations for non-commercial purposes