Probability distributed time delays: integrating spatial effects into temporal models

Background In order to provide insights into the complex biochemical processes inside a cell, modelling approaches must find a balance between achieving an adequate representation of the physical phenomena and keeping the associated computational cost within reasonable limits. This issue is particularly stressed when spatial inhomogeneities have a significant effect on system's behaviour. In such cases, a spatially-resolved stochastic method can better portray the biological reality, but the corresponding computer simulations can in turn be prohibitively expensive. Results We present a method that incorporates spatial information by means of tailored, probability distributed time-delays. These distributions can be directly obtained by single in silico or a suitable set of in vitro experiments and are subsequently fed into a delay stochastic simulation algorithm (DSSA), achieving a good compromise between computational costs and a much more accurate representation of spatial processes such as molecular diffusion and translocation between cell compartments. Additionally, we present a novel alternative approach based on delay differential equations (DDE) that can be used in scenarios of high molecular concentrations and low noise propagation. Conclusions Our proposed methodologies accurately capture and incorporate certain spatial processes into temporal stochastic and deterministic simulations, increasing their accuracy at low computational costs. This is of particular importance given that time spans of cellular processes are generally larger (possibly by several orders of magnitude) than those achievable by current spatially-resolved stochastic simulators. Hence, our methodology allows users to explore cellular scenarios under the effects of diffusion and stochasticity in time spans that were, until now, simply unfeasible. Our methodologies are supported by theoretical considerations on the different modelling regimes, i.e. spatial vs. delay-temporal, as indicated by the corresponding Master Equations and presented elsewhere.

A restrike waveform predictive model for shunt capacitor bank switching with point-on-wave recommendation

Circuit-breakers (CBs) are subject to electrical stresses with restrikes during capacitor bank operation. Stresses are caused by the overvoltages across CBs, the interrupting currents and the rate of rise of recovery voltage (RRRV). Such electrical stresses also depend on the types of system grounding and the types of dielectric strength curves. The aim of this study is to demonstrate a restrike waveform predictive model for a SF6 CB that considered the types of system grounding: grounded and non-grounded and the computation accuracy comparison on the application of the cold withstand dielectric strength and the hot recovery dielectric strength curve including the POW (point-on-wave) recommendations to make an assessment of increasing the CB remaining life. The simulation of SF6 CB stresses in a typical 400 kV system was undertaken and the results in the applications are presented. The simulated restrike waveforms produced with the identified features using wavelet transform can be used for restrike diagnostic algorithm development with wavelet transform to locate a substation with breaker restrikes. This study found that the hot withstand dielectric strength curve has less magnitude than the cold withstand dielectric strength curve for restrike simulation results. Computation accuracy improved with the hot withstand dielectric strength and POW controlled switching can increase the life for a SF6 CB.

Multiview point cloud kernels for semisupervised learning [Lecture Notes]

In semisupervised learning (SSL), a predictive model is learn from a collection of labeled data and a typically much larger collection of unlabeled data. These paper presented a framework called multi-view point cloud regularization (MVPCR), which unifies and generalizes several semisupervised kernel methods that are based on data-dependent regularization in reproducing kernel Hilbert spaces (RKHSs). Special cases of MVPCR include coregularized least squares (CoRLS), manifold regularization (MR), and graph-based SSL. An accompanying theorem shows how to reduce any MVPCR problem to standard supervised learning with a new multi-view kernel.

Turbulent velocity and suspended sediment concentration measurements in an urban environment of the Brisbane River Flood Plain at Gardens Point on 12-13 January 2011

The flood flow in urbanised areas constitutes a major hazard to the population and infrastructure as seen during the summer 2010-2011 floods in Queensland (Australia). Flood flows in urban environments have been studied relatively recently, although no study considered the impact of turbulence in the flow. During the 12-13 January 2011 flood of the Brisbane River, some turbulence measurements were conducted in an inundated urban environment in Gardens Point Road next to Brisbane's central business district (CBD) at relatively high frequency (50 Hz). The properties of the sediment flood deposits were characterised and the acoustic Doppler velocimeter unit was calibrated to obtain both instantaneous velocity components and suspended sediment concentration in the same sampling volume with the same temporal resolution. While the flow motion in Gardens Point Road was subcritical, the water elevations and velocities fluctuated with a distinctive period between 50 and 80 s. The low frequency fluctuations were linked with some local topographic effects: i.e, some local choke induced by an upstream constriction between stairwells caused some slow oscillations with a period close to the natural sloshing period of the car park. The instantaneous velocity data were analysed using a triple decomposition, and the same triple decomposition was applied to the water depth, velocity flux, suspended sediment concentration and suspended sediment flux data. The velocity fluctuation data showed a large energy component in the slow fluctuation range. For the first two tests at z = 0.35 m, the turbulence data suggested some isotropy. At z = 0.083 m, on the other hand, the findings indicated some flow anisotropy. The suspended sediment concentration (SSC) data presented a general trend with increasing SSC for decreasing water depth. During a test (T4), some long -period oscillations were observed with a period about 18 minutes. The cause of these oscillations remains unknown to the authors. The last test (T5) took place in very shallow waters and high suspended sediment concentrations. It is suggested that the flow in the car park was disconnected from the main channel. Overall the flow conditions at the sampling sites corresponded to a specific momentum between 0.2 to 0.4 m2 which would be near the upper end of the scale for safe evacuation of individuals in flooded areas. But the authors do not believe the evacuation of individuals in Gardens Point Road would have been safe because of the intense water surges and flow turbulence. More generally any criterion for safe evacuation solely based upon the flow velocity, water depth or specific momentum cannot account for the hazards caused by the flow turbulence, water depth fluctuations and water surges.

Early childhood education : the natural starting point for environmental education

Young children are most vulnerable to, and most at risk from, environmental and sustainability challenges. Early education investments aimed at addressing such issues, until recently however, have been neglected or under-rated. Fortunately, this is changing. A groundswell of practitioner interest in early childhood environmental education/ education for sustainability is emerging, in contrast to the ‘patches of green’ that have characterised previous decades. Indeed, an international coalition for early childhood education for sustainability (ECEfS) is beginning to develop, evidenced by The Gothenburg Recommendations on Education for Sustainable Development (2008) that identifies early childhood, within a framework of lifelong learning, as a ‘natural starting point’ for all ongoing education for sustainability. This document is important as it is the first international statement to explicitly identify ECEfS as contributing to education for sustainability. The next challenge for ECEfS is for practitioner mobilisation to be matched by research activity aimed at broadening and deepening practice-based responses. This is the next exciting frontier in the legitimisation of ECEfS.

Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks

This chapter focuses on the interactions and roles between delays and intrinsic noise effects within cellular pathways and regulatory networks. We address these aspects by focusing on genetic regulatory networks that share a common network motif, namely the negative feedback loop, leading to oscillatory gene expression and protein levels. In this context, we discuss computational simulation algorithms for addressing the interplay of delays and noise within the signaling pathways based on biological data. We address implementational issues associated with efficiency and robustness. In a molecular biology setting we present two case studies of temporal models for the Hes1 gene (Monk, 2003; Hirata et al., 2002), known to act as a molecular clock, and the Her1/Her7 regulatory system controlling the periodic somite segmentation in vertebrate embryos (Giudicelli and Lewis, 2004; Horikawa et al., 2006).

Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells

Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes, such as transcription and translation. In this paper, we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial τ-leap method (Bτ-DSSA). As a particular application, we apply these ideas to modeling somite segmentation in zebra fish across a number of cells in which two linked oscillatory genes (her1 and her7) are synchronized via Notch signaling between the cells.

Compensation of unmodeled aircraft dynamics in airborne inspection of linear infrastructure assets

Fixed-wing aircraft equipped with downward pointing cameras and/or LiDAR can be used for inspecting approximately piecewise linear assets such as oil-gas pipelines, roads and power-lines. Automatic control of such aircraft is important from a productivity and safety point of view (long periods of precision manual flight at low-altitude is not considered reasonable from a safety perspective). This paper investigates the effect of any unwanted coupling between guidance and autopilot loops (typically caused by unmodeled delays in the aircraft’s response), and the specific impact of any unwanted dynamics on the performance of aircraft undertaking inspection of piecewise linear corridor assets (such as powerlines). Simulation studies and experimental flight tests are used to demonstrate the benefits of a simple compensator in mitigating the unwanted lateral oscillatory behaviour (or coupling) that is caused by unmodeled time constants in the aircraft dynamics.

A node-based smoothed conforming point interpolation method (NS-CPIM) for elasticity problems

This paper formulates a node-based smoothed conforming point interpolation method (NS-CPIM) for solid mechanics. In the proposed NS-CPIM, the higher order conforming PIM shape functions (CPIM) have been constructed to produce a continuous and piecewise quadratic displacement field over the whole problem domain, whereby the smoothed strain field was obtained through smoothing operation over each smoothing domain associated with domain nodes. The smoothed Galerkin weak form was then developed to create the discretized system equations. Numerical studies have demonstrated the following good properties: NS-CPIM (1) can pass both standard and quadratic patch test; (2) provides an upper bound of strain energy; (3) avoid the volumetric locking; (4) provides the higher accuracy than those in the node-based smoothed schemes of the original PIMs.

An enriched radial point interpolation method based on weak-form and strong-form

In this article, an enriched radial point interpolation method (e-RPIM) is developed for computational mechanics. The conventional radial basis function (RBF) interpolation is novelly augmented by the suitable basis functions to reflect the natural properties of deformation. The performance of the enriched meshless RBF shape functions is first investigated using the surface fitting. The surface fitting results have proven that, compared with the conventional RBF, the enriched RBF interpolation has a much better accuracy to fit a complex surface than the conventional RBF interpolation. It has proven that the enriched RBF shape function will not only possess all advantages of the conventional RBF interpolation, but also can accurately reflect the deformation properties of problems. The system of equations for two-dimensional solids is then derived based on the enriched RBF shape function and both of the meshless strong-form and weak-form. A numerical example of a bar is presented to study the effectiveness and efficiency of e-RPIM. As an important application, the newly developed e-RPIM, which is augmented by selected trigonometric basis functions, is applied to crack problems. It has been demonstrated that the present e-RPIM is very accurate and stable for fracture mechanics problems.

Saving bitrate vs. pleasing users : where is the break-even point in mobile video quality?

This paper presents a comprehensive study to find the most efficient bitrate requirement to deliver mobile video that optimizes bandwidth, while at the same time maintains good user viewing experience. In the study, forty participants were asked to choose the lowest quality video that would still provide for a comfortable and long-term viewing experience, knowing that higher video quality is more expensive and bandwidth intensive. This paper proposes the lowest pleasing bitrates and corresponding encoding parameters for five different content types: cartoon, movie, music, news and sports. It also explores how the lowest pleasing quality is influenced by content type, image resolution, bitrate, and user gender, prior viewing experience, and preference. In addition, it analyzes the trajectory of users’ progression while selecting the lowest pleasing quality. The findings reveal that the lowest bitrate requirement for a pleasing viewing experience is much higher than that of the lowest acceptable quality. Users’ criteria for the lowest pleasing video quality are related to the video’s content features, as well as its usage purpose and the user’s personal preferences. These findings can provide video providers guidance on what quality they should offer to please mobile users.