MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.

The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-Dependent RNA Polymerase 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. Nearly all known miRNAs were enriched in this mutant and we identified 13 new miRNAs, all of which were relatively low abundance and constitute new families. Trans-acting siRNAs (ta-siRNAs) were even more highly enriched. Computational and gel blot analyses suggested that the minimal number of miRNAs in Arabidopsis is approximately 155. The size profile of small RNAs in rdr2 reflected enrichment of 21-nt miRNAs and other classes of siRNAs like ta-siRNAs, and a significant reduction in 24-nt heterochromatic siRNAs. Other classes of small RNAs were found to be RDR2-independent, particularly those derived from long inverted repeats and a subset of tandem repeats. The small RNA populations in other Arabidopsis small RNA biogenesis mutants were also examined; a dcl2/3/4 triple mutant showed a similar pattern to rdr2, whereas dcl1-7 and rdr6 showed reductions in miRNAs and ta-siRNAs consistent with their activities in the biogenesis of these types of small RNAs. Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs.

Exploring the impacts of the interactions between lifecycles and other dynamics that influence the development of technology-based industries

To address future uncertainty within strategy and innovation, managers extrapolate past patterns and trends into the future. Several disciplines make use of lifecycles, often with a linear sequence of identified phases, to make predictions and address likely uncertainties. Often the aggregation of several cycles is then interpreted as a new cycle - such as product lifecycles into an industry lifecycle. However, frequently different lifecycle terms - technology, product, industry - are used interchangeably and without clear definition. Within the interdisciplinary context of technology management, this juxtaposition of dynamics can create confusion, rather than clarification. This paper explores some typical dynamics associated with technology-based industries, using illustrative examples from the automotive industry. A wide range of dimensions are seen to influence the path of a technology-based industry, and stakeholders need to consider the likely causality and synchronicity of these. Some curves can simply present the aggregation of components; other dynamics incur time lags, rather than being superimposed, but still have a significant impact. To optimise alignment of the important dimensions within any development, and for future strategy decisions, understanding these interactions will be critical. © 2011 IEEE.

Synchronization in climate dynamics and other extended systems

Synchronization is now well established as representing coherent behaviour between two or more otherwise autonomous nonlinear systems subject to some degree of coupling. Such behaviour has mainly been studied to date, however, in relatively low-dimensional discrete systems or networks. But the possibility of similar kinds of behaviour in continuous or extended spatiotemporal systems has many potential practical implications, especially in various areas of geophysics. We review here a range of cyclically varying phenomena within the Earth's climate system for which there may be some evidence or indication of the possibility of synchronized behaviour, albeit perhaps imperfect or highly intermittent. The exploitation of this approach is still at a relatively early stage within climate science and dynamics, in which the climate system is regarded as a hierarchy of many coupled sub-systems with complex nonlinear feedbacks and forcings. The possibility of synchronization between climate oscillations (global or local) and a predictable external forcing raises important questions of how models of such phenomena can be validated and verified, since the resulting response may be relatively insensitive to the details of the model being synchronized. The use of laboratory analogues may therefore have an important role to play in the study of natural systems that can only be observed and for which controlled experiments are impossible. We go on to demonstrate that synchronization can be observed in the laboratory, even in weakly coupled fluid dynamical systems that may serve as direct analogues of the behaviour of major components of the Earth's climate system. The potential implications and observability of these effects in the long-term climate variability of the Earth is further discussed. © 2010 Springer-Verlag Berlin Heidelberg.

Wrapping the cube and other polyhedra

An infinite series of twofold, two-way weavings of the cube, corresponding to 'wrappings', or double covers of the cube, is described with the aid of the two-parameter Goldberg- Coxeter construction. The strands of all such wrappings correspond to the central circuits (CCs) of octahedrites (four-regular polyhedral graphs with square and triangular faces), which for the cube necessarily have octahedral symmetry. Removing the symmetry constraint leads to wrappings of other eight-vertex convex polyhedra. Moreover, wrappings of convex polyhedra with fewer vertices can be generated by generalizing from octahedrites to i-hedrites, which additionally include digonal faces. When the strands of a wrapping correspond to the CCs of a four-regular graph that includes faces of size greater than 4, non-convex 'crinkled' wrappings are generated. The various generalizations have implications for activities as diverse as the construction of woven-closed baskets and the manufacture of advanced composite components of complex geometry. © 2012 The Royal Society.

PH-dependent leaching behaviour and other performance properties of cement-treated mixed contaminated soil

Portland cement has been widely used for stabilisation/solidification (S/S) treatment of contaminated soils. However, there is a dearth of literature on pH-dependent leaching of contaminants from cement-treated soils. This study investigates the leachability of Cu, Pb, Ni, Zn and total petroleum hydrocarbons (TPH) from a mixed contaminated soil. A sandy soil was spiked with 3000 mg/kg each of Cd, Cu, Pb, Ni and Zn, and 10,000 mg/kg of diesel, and treated with ordinary Portland cement (CEM I). Four different binder dosages, 5%, 10%, 15% and 20% (m/m) and different water contents ranging from 13%-19% dry weight were used in order to find a safe operating envelope for the treatment process. The pH-dependent leaching behaviour of the treated soil was monitored over an 84-day period using a 3-point acid neutralisation capacity (ANC) test. The monolithic leaching test was also conducted. Geotechnical properties such as unconfined compressive strength (UCS), hydraulic conductivity and porosity were assessed over time. The treated soils recorded lower leachate concentrations of Ni and Zn compared to the untreated soil at the same pH depending on binder dosage. The binder had problems with Pb stabilisation and TPH leachability was independent of pH and binder dosage. The hydraulic conductivity of the mixes was generally of the order, 10-8 m/sec, while the porosity ranged from 26%-44%. The results of selected performance properties are compared with regulatory limits and the range of operating variables that lead to acceptable performance described. © 2012 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences.

Simultaneous colour search renders other object properties less salient

A common approach to visualise multidimensional data sets is to map every data dimension to a separate visual feature. It is generally assumed that such visual features can be judged independently from each other. However, we have recently shown that interactions between features do exist [Hannus et al. 2004; van den Berg et al. 2005]. In those studies, we first determined individual colour and size contrast or colour and orientation contrast necessary to achieve a fixed level of discrimination performance in single feature search tasks. These contrasts were then used in a conjunction search task in which the target was defined by a combination of a colour and a size or a colour and an orientation. We found that in conjunction search, despite the matched feature discriminability, subjects significantly more often chose an item with the correct colour than one with correct size or orientation. This finding may have consequences for visualisation: the saliency of information coded by objects' size or orientation may change when there is a need to simultaneously search for colour that codes another aspect of the information. In the present experiment, we studied whether a colour bias can also be found in a more complex and continuous task, Subjects had to search for a target in a node-link diagram consisting of SO nodes, while their eye movements were being tracked, Each node was assigned a random colour and size (from a range of 10 possible values with fixed perceptual distances). We found that when we base the distances on the mean threshold contrasts that were determined in our previous experiments, the fixated nodes tend to resemble the target colour more than the target size (Figure 1a). This indicates that despite the perceptual matching, colour is judged with greater precision than size during conjunction search. We also found that when we double the size contrast (i.e. the distances between the 10 possible node sizes), this effect disappears (Figure 1b). Our findings confirm that the previously found decrease in salience of other features during colour conjunction search is also present in more complex (more 'visualisation- realistic') visual search tasks. The asymmetry in visual search behaviour can be compensated for by manipulating step sizes (perceptual distances) within feature dimensions. Our results therefore also imply that feature hierarchies are not completely fixed and may be adapted to the requirements of a particular visualisation. Copyright © 2005 by the Association for Computing Machinery, Inc.

The Random Forest Kernel and other kernels for big data from random partitions

We present Random Partition Kernels, a new class of kernels derived by demonstrating a natural connection between random partitions of objects and kernels between those objects. We show how the construction can be used to create kernels from methods that would not normally be viewed as random partitions, such as Random Forest. To demonstrate the potential of this method, we propose two new kernels, the Random Forest Kernel and the Fast Cluster Kernel, and show that these kernels consistently outperform standard kernels on problems involving real-world datasets. Finally, we show how the form of these kernels lend themselves to a natural approximation that is appropriate for certain big data problems, allowing $O(N)$ inference in methods such as Gaussian Processes, Support Vector Machines and Kernel PCA.