Sensitivity of the NMR density matrix to pulse sequence parameters : a simplified analytic approach

We present a formalism for the analysis of sensitivity of nuclear magnetic resonance pulse sequences to variations of pulse sequence parameters, such as radiofrequency pulses, gradient pulses or evolution delays. The formalism enables the calculation of compact, analytic expressions for the derivatives of the density matrix and the observed signal with respect to the parameters varied. The analysis is based on two constructs computed in the course of modified density-matrix simulations: the error interrogation operators and error commutators. The approach presented is consequently named the Error Commutator Formalism (ECF). It is used to evaluate the sensitivity of the density matrix to parameter variation based on the simulations carried out for the ideal parameters, obviating the need for finite-difference calculations of signal errors. The ECF analysis therefore carries a computational cost comparable to a single density-matrix or product-operator simulation. Its application is illustrated using a number of examples from basic NMR spectroscopy. We show that the strength of the ECF is its ability to provide analytic insights into the propagation of errors through pulse sequences and the behaviour of signal errors under phase cycling. Furthermore, the approach is algorithmic and easily amenable to implementation in the form of a programming code. It is envisaged that it could be incorporated into standard NMR product-operator simulation packages.

Deprivation is an independent predictor of 1-year mortality in outpatients with chronic obstructive pulmonary disease

Deprivation is linked to increased incidence in a number of chronic diseases but its relationship to chronic obstructive pulmonary disease (COPD) is uncertain despite suggestions that the socioeconomic gradient seen in COPD is as great, if not greater, than any other disease (Prescott and Vestbo).1 There is also a need to take into account the confounding effects of malnutrition which have been shown to be independently linked to increased mortality (Collins et al).2 The current study investigated the influence of social deprivation on 1-year survival rates in COPD outpatients, independently of malnutrition. 424 outpatients with COPD were routinely screened for malnutrition risk using the ‘Malnutrition Universal Screening Tool’; ‘MUST’ (Elia),3 between July and May 2009; 222 males and 202 females; mean age 73 (SD 9.9) years; body mass index 25.8 (SD 6.3) kg/m2. Each individual's deprivation was calculated using the index of multiple deprivation (IMD) which was established according to the geographical location of each patient's address (postcode). IMD includes a number of indicators covering economic, housing and social issues (eg, health, education and employment) into a single deprivation score (Nobel et al).4 The lower the IMD score, the lower an individual's deprivation. The IMD was assigned to each outpatient at the time of screening and related to1-year mortality from the date screened. Outpatients who died within 1-year of screening were significantly more likely to reside within a deprived postcode (IMD 19.7±SD 13.1 vs 15.4±SD 10.7; p=0.023, OR 1.03, 95% CI 1.00 to 1.06) than those that did not die. Deprivation remained a significant independent risk factor for 1-year mortality even when adjusted for malnutrition as well as age, gender and disease severity (binary logistic regression; p=0.008, OR 1.04, 95% CI 1.04 to 1.07). Deprivation was not associated with disease-severity (p=0.906) or body mass index, kg/m2 (p=0.921) using ANOVA. This is the first study to show that deprivation, assessed using IMD, is associated with increased 1-year mortality in outpatients with COPD independently of malnutrition, age and disease severity. Deprivation should be considered in the targeted management of these patients.

Concentration and oxidative potential of on-road particle emissions and their relationship with traffic composition : Relevance to exposure assessment

Particles emitted by vehicles are known to cause detrimental health effects, with their size and oxidative potential among the main factors responsible. Therefore, understanding the relationship between traffic composition and both the physical characteristics and oxidative potential of particles is critical. To contribute to the limited knowledge base in this area, we investigated this relationship in a 4.5 km road tunnel in Brisbane, Australia. On-road concentrations of ultrafine particles (<100 nm, UFPs), fine particles (PM2.5), CO, CO2 and particle associated reactive oxygen species (ROS) were measured using vehicle-based mobile sampling. UFPs were measured using a condensation particle counter and PM2.5 with a DustTrak aerosol photometer. A new profluorescent nitroxide probe, BPEAnit, was used to determine ROS levels. Comparative measurements were also performed on an above-ground road to assess the role of emission dilution on the parameters measured. The profile of UFP and PM2.5 concentration with distance through the tunnel was determined, and demonstrated relationships with both road gradient and tunnel ventilation. ROS levels in the tunnel were found to be high compared to an open road with similar traffic characteristics, which was attributed to the substantial difference in estimated emission dilution ratios on the two roadways. Principal component analysis (PCA) revealed that the levels of pollutants and ROS were generally better correlated with total traffic count, rather than the traffic composition (i.e. diesel and gasoline-powered vehicles). A possible reason for the lack of correlation with HDV, which has previously been shown to be strongly associated with UFPs especially, was the low absolute numbers encountered during the sampling. This may have made their contribution to in-tunnel pollution largely indistinguishable from the total vehicle volume. For ROS, the stronger association observed with HDV and gasoline vehicles when combined (total traffic count) compared to when considered individually may signal a role for the interaction of their emissions as a determinant of on-road ROS in this pilot study. If further validated, this should not be overlooked in studies of on- or near-road particle exposure and its potential health effects.

Assessing of circuit breaker restrike risks using computer simulation and wavelet analysis

A breaker restrike is an abnormal arcing phenomenon, leading to a possible breaker failure. Eventually, this failure leads to interruption of the transmission and distribution of the electricity supply system until the breaker is replaced. Before 2008, there was little evidence in the literature of monitoring techniques based on restrike measurement and interpretation produced during switching of capacitor banks and shunt reactor banks in power systems. In 2008 a non-intrusive radiometric restrike measurement method and a restrike hardware detection algorithm were developed by M.S. Ramli and B. Kasztenny. However, the limitations of the radiometric measurement method are a band limited frequency response as well as limitations in amplitude determination. Current restrike detection methods and algorithms require the use of wide bandwidth current transformers and high voltage dividers. A restrike switch model using Alternative Transient Program (ATP) and Wavelet Transforms which support diagnostics are proposed. Restrike phenomena become a new diagnostic process using measurements, ATP and Wavelet Transforms for online interrupter monitoring. This research project investigates the restrike switch model Parameter „A. dielectric voltage gradient related to a normal and slowed case of the contact opening velocity and the escalation voltages, which can be used as a diagnostic tool for a vacuum circuit-breaker (CB) at service voltages between 11 kV and 63 kV. During current interruption of an inductive load at current quenching or chopping, a transient voltage is developed across the contact gap. The dielectric strength of the gap should rise to a point to withstand this transient voltage. If it does not, the gap will flash over, resulting in a restrike. A straight line is fitted through the voltage points at flashover of the contact gap. This is the point at which the gap voltage has reached a value that exceeds the dielectric strength of the gap. This research shows that a change in opening contact velocity of the vacuum CB produces a corresponding change in the slope of the gap escalation voltage envelope. To investigate the diagnostic process, an ATP restrike switch model was modified with contact opening velocity computation for restrike waveform signature analyses along with experimental investigations. This also enhanced a mathematical CB model with the empirical dielectric model for SF6 (sulphur hexa-fluoride) CBs at service voltages above 63 kV and a generalised dielectric curve model for 12 kV CBs. A CB restrike can be predicted if there is a similar type of restrike waveform signatures for measured and simulated waveforms. The restrike switch model applications are used for: computer simulations as virtual experiments, including predicting breaker restrikes; estimating the interrupter remaining life of SF6 puffer CBs; checking system stresses; assessing point-on-wave (POW) operations; and for a restrike detection algorithm development using Wavelet Transforms. A simulated high frequency nozzle current magnitude was applied to an Equation (derived from the literature) which can calculate the life extension of the interrupter of a SF6 high voltage CB. The restrike waveform signatures for a medium and high voltage CB identify its possible failure mechanism such as delayed opening, degraded dielectric strength and improper contact travel. The simulated and measured restrike waveform signatures are analysed using Matlab software for automatic detection. Experimental investigation of a 12 kV vacuum CB diagnostic was carried out for the parameter determination and a passive antenna calibration was also successfully developed with applications for field implementation. The degradation features were also evaluated with a predictive interpretation technique from the experiments, and the subsequent simulation indicates that the drop in voltage related to the slow opening velocity mechanism measurement to give a degree of contact degradation. A predictive interpretation technique is a computer modeling for assessing switching device performance, which allows one to vary a single parameter at a time; this is often difficult to do experimentally because of the variable contact opening velocity. The significance of this thesis outcome is that it is a non-intrusive method developed using measurements, ATP and Wavelet Transforms to predict and interpret a breaker restrike risk. The measurements on high voltage circuit-breakers can identify degradation that can interrupt the distribution and transmission of an electricity supply system. It is hoped that the techniques for the monitoring of restrike phenomena developed by this research will form part of a diagnostic process that will be valuable for detecting breaker stresses relating to the interrupter lifetime. Suggestions for future research, including a field implementation proposal to validate the restrike switch model for ATP system studies and the hot dielectric strength curve model for SF6 CBs, are given in Appendix A.

A least squares based finite volume method for the Cahn-Hilliard and Cahn-Hilliard-reaction equations

A vertex-centred finite volume method (FVM) for the Cahn-Hilliard (CH) and recently proposed Cahn-Hilliard-reaction (CHR) equations is presented. Information at control volume faces is computed using a high-order least-squares approach based on Taylor series approximations. This least-squares problem explicitly includes the variational boundary condition (VBC) that ensures that the discrete equations satisfy all of the boundary conditions. We use this approach to solve the CH and CHR equations in one and two dimensions and show that our scheme satisfies the VBC to at least second order. For the CH equation we show evidence of conservative, gradient stable solutions, however for the CHR equation, strict gradient-stability is more challenging to achieve.

The persistence of phase-separation in LiFePO4 with two-dimensional Li+ transport : the Cahn-Hilliard-reaction equation and the role of defects

We examine the solution of the two-dimensional Cahn-Hilliard-reaction (CHR) equation in the xy plane as a model of Li+ intercalation into LiFePO4 material. We validate our numerical solution against the solution of the depth-averaged equation, which has been used to model intercalation in the limit of highly orthotropic diffusivity and gradient penalty tensors. We then examine the phase-change behaviour in the full CHR system as these parameters become more isotropic, and find that as the Li+ diffusivity is increased in the x direction, phase separation persists at high currents, even in small crystals with averaged coherency strain included. The resulting voltage curves decrease monotonically, which has previously been considered a hallmark of crystals that fill homogeneously.

Tactically-driven nonmonotone travelling waves

Models of cell invasion incorporating directed cell movement up a gradient of an external substance and carrying capacity-limited proliferation give rise to travelling wave solutions. Travelling wave profiles with various shapes, including smooth monotonically decreasing, shock-fronted monotonically decreasing and shock-fronted nonmonotone shapes, have been reported previously in the literature. The existence of tacticallydriven shock-fronted nonmonotone travelling wave solutions is analysed for the first time. We develop a necessary condition for nonmonotone shock-fronted solutions. This condition shows that some of the previously reported shock-fronted nonmonotone solutions are genuine while others are a consequence of numerical error. Our results demonstrate that, for certain conditions, travelling wave solutions can be either smooth and monotone, smooth and nonmonotone or discontinuous and nonmonotone. These different shapes correspond to different invasion speeds. A necessary and sufficient condition for the travelling wave with minimum wave speed to be nonmonotone is presented. Several common forms of the tactic sensitivity function have the potential to satisfy the newly developed condition for nonmonotone shock-fronted solutions developed in this work.

Clines in cuticular hydrocarbons in two Drosophila species with independent population histories

We took a comparative approach utilizing clines to investigate the extent to which natural selection may have shaped population divergence in cuticular hydrocarbons (CHCs) that are also under sexual selection in Drosophila. We detected the presence of CHC clines along a latitudinal gradient on the east coast of Australia in two fly species with independent phylogenetic and population histories, suggesting adaptation to shared abiotic factors. For both species, significant associations were detected between clinal variation in CHCs and temperature variation along the gradient, suggesting temperature maxima as a candidate abiotic factor shaping CHC variation among populations. However, rainfall and humidity correlated with CHC variation to differing extents in the two species, suggesting that response to these abiotic factors may vary in a species-specific manner. Our results suggest that natural selection, in addition to sexual selection, plays a significant role in structuring among-population variation in sexually selected traits in Drosophila.

A dual-scale modelling approach for drying hygroscopic porous media

A new dualscale modelling approach is presented for simulating the drying of a wet hygroscopic porous material that couples the porous medium (macroscale) with the underlying pore structure (microscale). The proposed model is applied to the convective drying of wood at low temperatures and is valid in the so-called hygroscopic range, where hygroscopically held liquid water is present in the solid phase and water exits only as vapour in the pores. Coupling between scales is achieved by imposing the macroscopic gradients of moisture content and temperature on the microscopic field using suitably-defined periodic boundary conditions, which allows the macroscopic mass and thermal fluxes to be defined as averages of the microscopic fluxes over the unit cell. This novel formulation accounts for the intricate coupling of heat and mass transfer at the microscopic scale but reduces to a classical homogenisation approach if a linear relationship is assumed between the microscopic gradient and flux. Simulation results for a sample of spruce wood highlight the potential and flexibility of the new dual-scale approach. In particular, for a given unit cell configuration it is not necessary to propose the form of the macroscopic fluxes prior to the simulations because these are determined as a direct result of the dual-scale formulation.

Chimaeric HIV-1 subtype C Gag molecules with large in-frame C-terminal polypeptide fusions form virus-like particles

HIV-1 Pr55 Gag virus-like particles (VLPs) are strong immunogens with potential as candidate HIV vaccines. VLP immunogenicity can be broadened by making chimaeric Gag molecules: however, VLPs incorporating polypeptides longer than 200 aa fused in frame with Gag have not yet been reported. We constructed a range of gag-derived genes encoding in-frame C-terminal fusions of myristoylation-competent native Pr55Gag and p6-truncated Gag (Pr50Gag) to test the effects of polypeptide length and sequence on VLP formation and morphology, in an insect cell expression system. Fused sequences included a modified reverse transcriptase-Tat-Nef fusion polypeptide (RTTN, 778 aa), and truncated versions of RTTN ranging from 113 aa to 450 aa. Baculovirus-expressed chimaeric proteins were examined by western blot and electron microscopy. All chimaeras formed VLPs which could be purified by sucrose gradient centrifugation. VLP diameter increased with protein MW, from ∼100 nm for Pr55Gag to ∼250 nm for GagRTTN. The presence or absence of the Gag p6 region did not obviously affect VLP formation or appearance. GagRT chimaeric particles were successfully used in mice to boost T-cell responses to Gag and RT that were elicited by a DNA vaccine encoding a GagRTTN polypeptide, indicating the potential of such chimaeras to be used as candidate HIV vaccines. © 2008 Elsevier B.V. All rights reserved.

The causes of sinuous crustal-scale deformation patterns in hot orogens: Evidence from scaled analogue experiments and the southern Central Andes

The cause of upper-crustal segmentation into rhomb-shaped, shear zone-bound domains associated with contractional sedimentary basins in hot, wide orogens is not well understood. Here we use scaled multilayered analogue experiments to investigate the role of an orogen-parallel crustal-strength gradient on the formation of such structures. We show that the aspect ratio and size of domains, the sinuous character and abundance of transpressional shear zones vary with the integrated mechanical strength of crust. Upper-crustal deformation patterns and the degree of strain localization in the experiments are controlled by the ratio between the brittle and ductile strength in the model crust as well as gradients in tectonic and buoyancy forces. The experimental results match the first-order kinematic and structural characteristics of the southern Central Andes and provide insight on the dynamics of underlying deformation patterns in hot, wide orogens.

Community wide interventions for increasing physical activity (protocol)

This is the protocol for a review and there is no abstract. The objectives are as follows: Primary research objective To determine the effects of community wide, multi-strategic interventions upon community levels of physical activity. Secondary research objectives 1. To explore whether any effects of the intervention are different within and between populations, and whether these differences form an equity gradient. 2. To describe other health (e.g. cardiovascular disease morbidity) and behavioural effects (e.g. diet) where appropriate outcomes are available. 3. To explore the influence of context in the design, delivery, and outcomes of the interventions. 4. To explore the relationship between the number of components, duration, and effects of the interventions. 5. To highlight implications for further research and research methods to improve knowledge of the interventions in relation to the primary research objective.

Critical timescales and time intervals for coupled linear processes

In 1991, McNabb introduced the concept of mean action time (MAT) as a finite measure of the time required for a diffusive process to effectively reach steady state. Although this concept was initially adopted by others within the Australian and New Zealand applied mathematics community, it appears to have had little use outside this region until very recently, when in 2010 Berezhkovskii and coworkers rediscovered the concept of MAT in their study of morphogen gradient formation. All previous work in this area has been limited to studying single–species differential equations, such as the linear advection–diffusion–reaction equation. Here we generalise the concept of MAT by showing how the theory can be applied to coupled linear processes. We begin by studying coupled ordinary differential equations and extend our approach to coupled partial differential equations. Our new results have broad applications including the analysis of models describing coupled chemical decay and cell differentiation processes, amongst others.

Referral patterns and proximity to palliative care inpatient services by level of socio-economic disadvantage : a national study using spatial analysis

Background: A range of health outcomes at a population level are related to differences in levels of social disadvantage. Understanding the impact of any such differences in palliative care is important. The aim of this study was to assess, by level of socio-economic disadvantage, referral patterns to specialist palliative care and proximity to inpatient services. Methods: All inpatient and community palliative care services nationally were geocoded (using postcode) to one nationally standardised measure of socio-economic deprivation – Socio-Economic Index for Areas (SEIFA; 2006 census data). Referral to palliative care services and characteristics of referrals were described through data collected routinely at clinical encounters. Inpatient location was measured from each person’s home postcode, and stratified by socio-economic disadvantage. Results: This study covered July – December 2009 with data from 10,064 patients. People from the highest SEIFA group (least disadvantaged) were significantly less likely to be referred to a specialist palliative care service, likely to be referred closer to death and to have more episodes of inpatient care for longer time. Physical proximity of a person’s home to inpatient care showed a gradient with increasing distance by decreasing levels of socio-economic advantage. Conclusion: These data suggest that a simple relationship of low socioeconomic status and poor access to a referral-based specialty such as palliative care does not exist. Different patterns of referral and hence different patterns of care emerge.