Fast tessellated solid navigation in GEANT4

Navigation through tessellated solids in GEANT4 can degrade computational performance, especially if the tessellated solid is large and is comprised of many facets. Redefining a tessellated solid as a mesh of tetrahedra is common in other computational techniques such as finite element analysis as computations need only consider local tetrahedrons rather than the tessellated solid as a whole. Here within we describe a technique that allows for automatic tetrahedral meshing of tessellated solids in GEANT4 and the subsequent loading of these meshes as assembly volumes; loading nested tessellated solids and tetrahedral meshes is also examined. As the technique makes the geometry suitable for automatic optimisation using smartvoxels, navigation through a simple tessellated volume has been found to be more than two orders of magnitude faster than that through the equivalent tessellated solid. Speed increases of more than two orders of magnitude were also observed for a more complex tessellated solid with voids and concavities. The technique was benchmarked for geometry load time, simulation run time and memory usage. Source code enabling the described functionality in GEANT4 has been made freely available on the Internet.

Evidence for carbonate platform failure during rapid sea-level rise; ca 14 000 year old bioclastic flow deposits in the Lesser Antilles

Bioclastic flow deposits offshore from the Soufrie`re Hills volcano on Montserrat in the Lesser Antilles were deposited by the largest volume sediment flows near this active volcano in the last 26 kyr. The volume of these deposits exceeds that of the largest historic volcanic dome collapse in the world, which occurred on Montserrat in 2003. These flows were most probably generated by a large submarine slope failure of the carbonate shelf comprising the south west flank of Antigua or the east flank of Redonda; adjacent islands that are not volcanically active. The bioclastic flow deposits are relatively coarse-grained and either ungraded or poorly graded, and were deposited by non cohesive debris flow and high density turbidity currents. The bioclastic deposit often comprises multiple sub-units that cannot be correlated between core sites; some located just 2 km apart. Multiple sub-units in the bioclastic deposit result from either flow reflection, stacking of multiple debris flow lobes, and/or multi-stage collapse of the initial landslide. This study provides unusually precise constraints on the age of this mass flow event that occurred at ca 14 ka. Few large submarine landslides have been well dated, but the slope failures that have been dated are commonly associated with periods of rapid sea-level change.

Prevalence and trends of the diabetes epidemic in South Asia : a systematic review and meta-analysis

Background Diabetes mellitus has reached epidemic proportions worldwide. South Asians are known to have an increased predisposition for diabetes which has become an important health concern in the region. We discuss the prevalence of pre-diabetes and diabetes in South Asia and explore the differential risk factors reported. Methods Prevalence data were obtained by searching the Medline® database with; ‘prediabetes’ and ‘diabetes mellitus’ (MeSH major topic) and ‘Epidemology/EP’ (MeSH subheading). Search limits were articles in English, between 01/01/1980–31/12/2011, on human adults (≥19 years). The conjunction of the above results was narrowed down with country names. Results The most recent reported prevalence of pre-diabetes:diabetes in regional countries were; Bangladesh–4.7%:8.5% (2004–2005;Rural), India–4.6%:12.5% (2007;Rural); Maldives–3.0%:3.7% (2004;National), Nepal–19.5%:9.5% (2007;Urban), Pakistan–3.0%:7.2% (2002;Rural), Sri Lanka–11.5%:10.3% (2005–2006;National). Urban populations demonstrated a higher prevalence of diabetes. An increasing trend in prevalence of diabetes was observed in urban/rural India and rural Sri Lanka. The diabetes epidemicity index decreased with the increasing prevalence of diabetes in respective countries. A high epidemicity index was seen in Sri Lanka (2005/2006–52.8%), while for other countries, the epidemicity index was comparatively low (rural India 2007–26.9%; urban India 2002/2005–31.3%, and urban Bangladesh–33.1%). Family history, urban residency, age, higher BMI, sedentary lifestyle, hypertension and waist-hip ratio were associated with an increased risks of diabetes. Conclusion A significant epidemic of diabetes is present in the South Asian region with a rapid increase in prevalence over the last two decades. Hence there is a need for urgent preventive and curative strategies .

Improved surgical safety after laparoscopic compared to open surgery for apparent early stage endometrial cancer : results from a randomised controlled trial

AIM: To compare Total Laparoscopic Hysterectomy (TLH) and Total Abdominal Hysterectomy (TAH) with regard to surgical safety. METHODS: Between October 2005 and June 2010, 760 patients with apparent early stage endometrial cancer were enroled in a multicentre, randomised clinical trial (LACE) comparing outcomes following TLH or TAH. The main study end points for this analysis were surgical adverse events (AE), hospital length of stay, conversion from laparoscopy to laparotomy, including 753 patients who completed at least 6 weeks of follow-up. Postoperative AEs were graded according to Common Toxicity Criteria (V3), and those immediately life-threatening, requiring inpatient hospitalisation or prolonged hospitalisation, or resulting in persistent or significant disability/incapacity were regarded as serious AEs. RESULTS: The incidence of intra-operative AEs was comparable in either group. The incidence of post-operative AE CTC grade 3+ (18.6% in TAH, 12.9% in TLH, p 0.03) and serious AE (14.3% in TAH, 8.2% in TLH, p 0.007) was significantly higher in the TAH group compared to the TLH group. Mean operating time was 132 and 107 min, and median length of hospital stay was 2 and 5 days in the TLH and TAH group, respectively (p<0.0001). The decline of haemoglobin from baseline to day 1 postoperatively was 2g/L less in the TLH group (p 0.006). CONCLUSIONS: Compared to TAH, TLH is associated with a significantly decreased risk of major surgical AEs. A laparoscopic surgical approach to early stage endometrial cancer is safe.

Spatial and temporal analysis of Barmah Forest virus disease in Queensland, Australia

Barmah Forest virus (BFV) disease is one of the most widespread mosquito-borne diseases in Australia. The number of outbreaks and the incidence rate of BFV in Australia have attracted growing concerns about the spatio-temporal complexity and underlying risk factors of BFV disease. A large number of notifications has been recorded continuously in Queensland since 1992. Yet, little is known about the spatial and temporal characteristics of the disease. I aim to use notification data to better understand the effects of climatic, demographic, socio-economic and ecological risk factors on the spatial epidemiology of BFV disease transmission, develop predictive risk models and forecast future disease risks under climate change scenarios. Computerised data files of daily notifications of BFV disease and climatic variables in Queensland during 1992-2008 were obtained from Queensland Health and Australian Bureau of Meteorology, respectively. Projections on climate data for years 2025, 2050 and 2100 were obtained from Council of Scientific Industrial Research Organisation. Data on socio-economic, demographic and ecological factors were also obtained from relevant government departments as follows: 1) socio-economic and demographic data from Australian Bureau of Statistics; 2) wetlands data from Department of Environment and Resource Management and 3) tidal readings from Queensland Department of Transport and Main roads. Disease notifications were geocoded and spatial and temporal patterns of disease were investigated using geostatistics. Visualisation of BFV disease incidence rates through mapping reveals the presence of substantial spatio-temporal variation at statistical local areas (SLA) over time. Results reveal high incidence rates of BFV disease along coastal areas compared to the whole area of Queensland. A Mantel-Haenszel Chi-square analysis for trend reveals a statistically significant relationship between BFV disease incidence rates and age groups (ƒÓ2 = 7587, p<0.01). Semi-variogram analysis and smoothed maps created from interpolation techniques indicate that the pattern of spatial autocorrelation was not homogeneous across the state. A cluster analysis was used to detect the hot spots/clusters of BFV disease at a SLA level. Most likely spatial and space-time clusters are detected at the same locations across coastal Queensland (p<0.05). The study demonstrates heterogeneity of disease risk at a SLA level and reveals the spatial and temporal clustering of BFV disease in Queensland. Discriminant analysis was employed to establish a link between wetland classes, climate zones and BFV disease. This is because the importance of wetlands in the transmission of BFV disease remains unclear. The multivariable discriminant modelling analyses demonstrate that wetland types of saline 1, riverine and saline tidal influence were the most significant risk factors for BFV disease in all climate and buffer zones, while lacustrine, palustrine, estuarine and saline 2 and saline 3 wetlands were less important. The model accuracies were 76%, 98% and 100% for BFV risk in subtropical, tropical and temperate climate zones, respectively. This study demonstrates that BFV disease risk varied with wetland class and climate zone. The study suggests that wetlands may act as potential breeding habitats for BFV vectors. Multivariable spatial regression models were applied to assess the impact of spatial climatic, socio-economic and tidal factors on the BFV disease in Queensland. Spatial regression models were developed to account for spatial effects. Spatial regression models generated superior estimates over a traditional regression model. In the spatial regression models, BFV disease incidence shows an inverse relationship with minimum temperature, low tide and distance to coast, and positive relationship with rainfall in coastal areas whereas in whole Queensland the disease shows an inverse relationship with minimum temperature and high tide and positive relationship with rainfall. This study determines the most significant spatial risk factors for BFV disease across Queensland. Empirical models were developed to forecast the future risk of BFV disease outbreaks in coastal Queensland using existing climatic, socio-economic and tidal conditions under climate change scenarios. Logistic regression models were developed using BFV disease outbreak data for the existing period (2000-2008). The most parsimonious model had high sensitivity, specificity and accuracy and this model was used to estimate and forecast BFV disease outbreaks for years 2025, 2050 and 2100 under climate change scenarios for Australia. Important contributions arising from this research are that: (i) it is innovative to identify high-risk coastal areas by creating buffers based on grid-centroid and the use of fine-grained spatial units, i.e., mesh blocks; (ii) a spatial regression method was used to account for spatial dependence and heterogeneity of data in the study area; (iii) it determined a range of potential spatial risk factors for BFV disease; and (iv) it predicted the future risk of BFV disease outbreaks under climate change scenarios in Queensland, Australia. In conclusion, the thesis demonstrates that the distribution of BFV disease exhibits a distinct spatial and temporal variation. Such variation is influenced by a range of spatial risk factors including climatic, demographic, socio-economic, ecological and tidal variables. The thesis demonstrates that spatial regression method can be applied to better understand the transmission dynamics of BFV disease and its risk factors. The research findings show that disease notification data can be integrated with multi-factorial risk factor data to develop build-up models and forecast future potential disease risks under climate change scenarios. This thesis may have implications in BFV disease control and prevention programs in Queensland.

Using staffing ratios for workforce planning : evidence on nine allied health professions - a narrative review

Background: Modern healthcare managers are faced with pressure to deliver effective, efficient services within the context of fixed budget constraints. This requires decisions regarding the skill mix of the workforce particularly when staffing new services. One measure used to identify numbers and mix of staff in healthcare settings is workforce ratio. The aim of this study was to identify workforce ratios in nine allied health professions and to identify whether these measures are useful for planning allied health workforce requirements. Method: A systematic literature search using relevant MeSH headings of business, medical and allied health databases and relevant grey literature for the period 2000-2008 was undertaken. Results: Twelve articles were identified which described the use of workforce ratios in allied health services. Only one of these was a staffing ratio linked to clinical outcomes. The most comprehensive measures were identified in rehabilitation medicine. Conclusions: The evidence for use of staffing ratios for allied health practitioners is scarce and lags behind the fields of nursing and medicine.

A coupled SPH-DEM model for fluid and solid mechanics of apple parenchyma cells during drying

A coupled SPH-DEM based two-dimensional (2-D) micro-scale single cell model is developed to predict basic cell-level shrinkage effects of apple parenchyma cells during air drying. In this newly developed drying model, Smoothed Particle Hydrodynamics (SPH) is used to model the low Reynolds Number fluid motions of the cell protoplasm, and a Discrete Element Method (DEM) is employed to simulate the polymer-like cell wall. Simulations results reasonably agree with published experimental drying results on cellular shrinkage properties such as cellular area, diameter and perimeter. These preliminary results indicate that the model is effective for the modelling and simulation of apple parenchyma cells during air drying.

A particle-based micromechanics approach to simulate structural changes of plant cells during drying

This paper is concerned with applying a particle-based approach to simulate the micro-level cellular structural changes of plant cells during drying. The objective of the investigation was to relate the micro-level structural properties such as cell area, diameter and perimeter to the change of moisture content of the cell. Model assumes a simplified cell which consists of two basic components, cell wall and cell fluid. The cell fluid is assumed to be a Newtonian fluid with higher viscosity compared to water and cell wall is assumed to be a visco-elastic solid boundary located around the cell fluid. Cell fluid is modelled with Smoothed Particle Hydrodynamics (SPH) technique and for the cell wall; a Discrete Element Method (DEM) is used. The developed model is two-dimensional, but accounts for three-dimensional physical properties of real plant cells. Drying phenomena is simulated as fluid mass reductions and the model is used to predict the above mentioned structural properties as a function of cell fluid mass. Model predictions are found to be in fairly good agreement with experimental data in literature and the particle-based approach is demonstrated to be suitable for numerical studies of drying related structural deformations. Also a sensitivity analysis is included to demonstrate the influence of key model parameters to model predictions.

A simulation-based training system for surgical wound debridement

A simulation-based training system for surgical wound debridement was developed and comprises a multimedia introduction, a surgical simulator (tutorial component), and an assessment component. The simulator includes two PCs, a haptic device, and mirrored display. Debridement is performed on a virtual leg model with a shallow laceration wound superimposed. Trainees are instructed to remove debris with forceps, scrub with a brush, and rinse with saline solution to maintain sterility. Research and development issues currently under investigation include tissue deformation models using mass-spring system and finite element methods; tissue cutting using a high-resolution volumetric mesh and dynamic topology; and accurate collision detection, cutting, and soft-body haptic rendering for two devices within the same haptic space.

Prevalence of papillary changes and folliculosis of the palpebral conjunctiva in asymptomatic Chinese children

Purpose To determine the prevalence of papillary changes of the upper palpebral conjunctiva and folliculosis of the lower palpebral conjunctiva in Chinese children with no history of contact lens wear. Method Ninety-nine subjects (aged 6–15 years old) who were interested in a myopia control study were screened for papillary changes and folliculosis of the palpebral conjunctiva. Photodocumentation was performed under white and blue light (after the application of fluorescein) with a yellow filter and the photographs were graded by a group of practitioners according to a pre-set grading scale. Analysis was performed with the subjects divided into groups according to gender and age. Results More than 48% of the subjects had clinically significant (≥Grade 3) papillary changes in the upper palpebral conjunctiva. The prevalence of significant folliculosis in the lower lid was about 33%. The prevalence of significant papillary changes and folliculosis were similar between genders. No differences were observed between younger (age ≤ 10 years old) and older (age > 10 years old) in papillary changes but younger subjects showed a higher prevalence of folliculosis. Conclusions The prevalences of clinically significant papillary changes and folliculosis of unknown aetiology are high in Chinese children.

Mixed convection over a horizontal plate with streamwise non-uniform surface temperature distribution

Numerical investigation on mixed convection of a two-dimensional incompressible laminar flow over a horizontal flat plate with streamwise sinusoidal distribution of surface temperature has been performed for different values of Rayleigh number, Reynolds number and frequency of periodic temperature for constant Prandtl number and amplitude of periodic temperature. Finite element method adapted to rectangular non-uniform mesh elements by a non-linear parametric solution algorithm basis numerical scheme has been employed. The investigating parameters are the Rayleigh number, the Reynolds number and frequency of periodic temperature. The effect of variation of individual investigating parameters on mixed convection flow characteristics has been studied to observe the hydrodynamic and thermal behavior for while keeping the other parameters constant. The fluid considered in this study is air with Prandtl number 0.72. The results are obtained for the Rayleigh number range of 102 to 104, Reynolds number ranging from 1 to 100 and the frequency of periodic temperature from 1 to 5. Isotherms, streamlines, average and local Nusselt numbers are presented to show the effect of the different values of aforementioned investigating parameters on fluid flow and heat transfer.

A hybrid smoothed finite element method (H-SFEM) to solid mechanics problems

In this paper, a hybrid smoothed finite element method (H-SFEM) is developed for solid mechanics problems by combining techniques of finite element method (FEM) and Node-based smoothed finite element method (NS-FEM) using a triangular mesh. A parameter is equipped into H-SFEM, and the strain field is further assumed to be the weighted average between compatible stains from FEM and smoothed strains from NS-FEM. We prove theoretically that the strain energy obtained from the H-SFEM solution lies in between those from the compatible FEM solution and the NS-FEM solution, which guarantees the convergence of H-SFEM. Intensive numerical studies are conducted to verify these theoretical results and show that (1) the upper and lower bound solutions can always be obtained by adjusting ; (2) there exists a preferable at which the H-SFEM can produce the ultrasonic accurate solution.

A coupled SPH/FEM analysis of portable water filled barriers

Portable water filled barriers (PWFB) are semi-rigid roadside barriers which have the potential to display good crash attenuation characteristics at low and moderate impact speeds. The traditional mesh based numerical methods alone fail to simulate this type of impact with precision, stability and efficiency. This paper proposes to develop an advanced simulation model based on the combination of Smoothed Particles Hydrodynamics (SPH), a meshless method, and finite element method (FEM) for fluid-structure analysis using the commercially available software package LS-Dyna. The interaction between SPH particles and FEA elements is studied in this paper. Two methods of element setup at the element boundary were investigated. The response of the impacted barrier and fluid inside were analysed and compared. The system response and lagging were observed and reported in this paper. It was demonstrated that coupled SPH/FEM can be used in full scale PWFB modelling application. This will aid the research in determining the best initial setup to couple FEA and SPH in road safety barrier for impact response and safety analysis in the future.

Faster Monte Carlo simulation of radiotherapy geometries

Using Monte Carlo simulation for radiotherapy dose calculation can provide more accurate results when compared to the analytical methods usually found in modern treatment planning systems, especially in regions with a high degree of inhomogeneity. These more accurate results acquired using Monte Carlo simulation however, often require orders of magnitude more calculation time so as to attain high precision, thereby reducing its utility within the clinical environment. This work aims to improve the utility of Monte Carlo simulation within the clinical environment by developing techniques which enable faster Monte Carlo simulation of radiotherapy geometries. This is achieved principally through the use new high performance computing environments and simpler alternative, yet equivalent representations of complex geometries. Firstly the use of cloud computing technology and it application to radiotherapy dose calculation is demonstrated. As with other super-computer like environments, the time to complete a simulation decreases as 1=n with increasing n cloud based computers performing the calculation in parallel. Unlike traditional super computer infrastructure however, there is no initial outlay of cost, only modest ongoing usage fees; the simulations described in the following are performed using this cloud computing technology. The definition of geometry within the chosen Monte Carlo simulation environment - Geometry & Tracking 4 (GEANT4) in this case - is also addressed in this work. At the simulation implementation level, a new computer aided design interface is presented for use with GEANT4 enabling direct coupling between manufactured parts and their equivalent in the simulation environment, which is of particular importance when defining linear accelerator treatment head geometry. Further, a new technique for navigating tessellated or meshed geometries is described, allowing for up to 3 orders of magnitude performance improvement with the use of tetrahedral meshes in place of complex triangular surface meshes. The technique has application in the definition of both mechanical parts in a geometry as well as patient geometry. Static patient CT datasets like those found in typical radiotherapy treatment plans are often very large and present a significant performance penalty on a Monte Carlo simulation. By extracting the regions of interest in a radiotherapy treatment plan, and representing them in a mesh based form similar to those used in computer aided design, the above mentioned optimisation techniques can be used so as to reduce the time required to navigation the patient geometry in the simulation environment. Results presented in this work show that these equivalent yet much simplified patient geometry representations enable significant performance improvements over simulations that consider raw CT datasets alone. Furthermore, this mesh based representation allows for direct manipulation of the geometry enabling motion augmentation for time dependant dose calculation for example. Finally, an experimental dosimetry technique is described which allows the validation of time dependant Monte Carlo simulation, like the ones made possible by the afore mentioned patient geometry definition. A bespoke organic plastic scintillator dose rate meter is embedded in a gel dosimeter thereby enabling simultaneous 3D dose distribution and dose rate measurement. This work demonstrates the effectiveness of applying alternative and equivalent geometry definitions to complex geometries for the purposes of Monte Carlo simulation performance improvement. Additionally, these alternative geometry definitions allow for manipulations to be performed on otherwise static and rigid geometry.