Radiotherapy Monte Carlo simulation using cloud computing technology

Cloud computing allows for vast computational resources to be leveraged quickly and easily in bursts as and when required. Here we describe a technique that allows for Monte Carlo radiotherapy dose calculations to be performed using GEANT4 and executed in the cloud, with relative simulation cost and completion time evaluated as a function of machine count. As expected, simulation completion time decreases as 1=n for n parallel machines, and relative simulation cost is found to be optimal where n is a factor of the total simulation time in hours. Using the technique, we demonstrate the potential usefulness of cloud computing as a solution for rapid Monte Carlo simulation for radiotherapy dose calculation without the need for dedicated local computer hardware as a proof of principal. Funding source Cancer Australia (Department of Health and Ageing) Research Grant 614217

GWCarb v1.0: carbonate speciation tool

This spreadsheet calculates carbonate speciation using carbonate equilibrium equations at standard conditions (T=25°C) with ionic strength corrections. The user will typically be able to calculate the different carbonate species by entering total alkalinity and pH. This spreadsheet contains additional tools to calculate the Langelier Index for calcium and the SAR of the water. Note that in this last calculation the potential for calcium precipitation is not taken into account. The last tool presented here is a carbonate speciation tool in open systems (e.g. open to the atmosphere) which takes into account atmospheric pressure.

Nagelschmidtite bioceramics with osteostimulation properties : material chemistry activating osteogenic genes and WNT signalling pathway of human bone marrow stromal cells

Bioactive materials with osteostimulation properties are of great importance to promote osteogenic differentiation of human bone marrow stromal cells (hBMSCs) for potential bone regeneration. We have recently synthesized nagelschmidtite (NAGEL, Ca7Si2P2O16) ceramic powders which showed excellent apatite-mineralization ability. The aim of this study was to investigate the interaction of hBMSCs with NAGEL bioceramic bulks and their ionic extracts, and to explore the osteostimulation properties of NAGEL bioceramics and the possible molecular mechanism. The cell attachment, proliferation, bone-related gene expression (ALP, OPN and OCN) and WNT signalling pathways (WNT3a, FZD6, AXIN2 and CTNNB) of hBMSCs cultured on NAGEL bioceramic disks were systematically studied. We further investigated the biological effects of ionic products from NAGEL powders on cell proliferation and osteogenic differentiation of hBMSCs by culturing cells with NAGEL extracts. Furthermore, the effect of NAGEL bioceramics on the osteogenic differentiation in hBMSCs was also investigated with the addition of cardamonin, a WNT inhibitor. The results showed that NAGEL bioceramic disks supported the attachment and proliferation of hBMSCs, and significantly enhanced the bone-related gene expression and WNT signalling pathway of hBMSCs, compared to conventional beta-tricalcium phosphate (β-TCP) bioceramic disks and blank controls. The ionic products from NAGEL powders also significantly promoted the proliferation, bone and WNT-related gene expression of hBMSCs. It was also identified that NAGEL bioceramics could bypass the action of the WNT inhibitor (10 μM) to stimulate the selected osteogenic genes in hBMSCs. Our results suggest that NAGEL bioceramics possess excellent in vitro osteostimulation properties. The possible mechanism for the osteostimulation may be directly related to the released Si, Ca and P-containing ionic products from NAGEL bioceramics which activate bone-related gene expression and WNT signalling pathway of hBMSCs. The present study suggests that NAGEL bioceramics are a potential bone regeneration material with significant osteostimulation capacity.

The Chemistry Discipline Network: One Year On

The Chemistry Discipline Network was funded in mid-2011, with the aim of improving communication between chemistry academics in Australia. In our first year of operation, we have grown to over 100 members, established a web presence, and produced substantial mapping reports on chemistry teaching in Australia. We are now working on the definition of standards for a chemistry degree based on the Threshold Learning Outcomes published by the Learning and Teaching Academic Standards Project.

Does teaching sequence matter when teaching high school chemistry with scientific visualisations?

Five Canadian high school Chemistry classes in one school, taught by three different teachers, studied the concepts of dynamic chemical equilibria and Le Chatelier’s Principle. Some students received traditional teacher-led explanations of the concept first and used an interactive scientific visualisation second, while others worked with the visualisation first and received the teacher-led explanation second. Students completed a test of their conceptual understanding of the relevant concepts prior to instruction, after the first instructional session and at the end of instruction. Data on students’ academic achievement (highest, middle or lowest third of the class on the mid-term exam) and gender were also collected to explore the relationship between these factors, conceptual development and instructional sequencing. Results show, within this context at least, that teaching sequence is not important in terms of students’ conceptual learning gains.

Linking three-dimensional geological modelling and multivariate statistical analysis to define groundwater chemistry baseline and identify inter-aquifer connectivity within the Clarence-Moreton Basin, Southeast Queensland, Australia

The Clarence-Moreton Basin (CMB) covers approximately 26000 km2 and is the only sub-basin of the Great Artesian Basin (GAB) in which there is flow to both the south-west and the east, although flow to the south-west is predominant. In many parts of the basin, including catchments of the Bremer, Logan and upper Condamine Rivers in southeast Queensland, the Walloon Coal Measures are under exploration for Coal Seam Gas (CSG). In order to assess spatial variations in groundwater flow and hydrochemistry at a basin-wide scale, a 3D hydrogeological model of the Queensland section of the CMB has been developed using GoCAD modelling software. Prior to any large-scale CSG extraction, it is essential to understand the existing hydrochemical character of the different aquifers and to establish any potential linkage. To effectively use the large amount of water chemistry data existing for assessment of hydrochemical evolution within the different lithostratigraphic units, multivariate statistical techniques were employed.

The development of a Monte Carlo system to verify radiotherapy treatment dose calculations

Recent advances in the planning and delivery of radiotherapy treatments have resulted in improvements in the accuracy and precision with which therapeutic radiation can be administered. As the complexity of the treatments increases it becomes more difficult to predict the dose distribution in the patient accurately. Monte Carlo methods have the potential to improve the accuracy of the dose calculations and are increasingly being recognised as the “gold standard” for predicting dose deposition in the patient. In this study, software has been developed that enables the transfer of treatment plan information from the treatment planning system to a Monte Carlo dose calculation engine. A database of commissioned linear accelerator models (Elekta Precise and Varian 2100CD at various energies) has been developed using the EGSnrc/BEAMnrc Monte Carlo suite. Planned beam descriptions and CT images can be exported from the treatment planning system using the DICOM framework. The information in these files is combined with an appropriate linear accelerator model to allow the accurate calculation of the radiation field incident on a modelled patient geometry. The Monte Carlo dose calculation results are combined according to the monitor units specified in the exported plan. The result is a 3D dose distribution that could be used to verify treatment planning system calculations. The software, MCDTK (Monte Carlo Dicom ToolKit), has been developed in the Java programming language and produces BEAMnrc and DOSXYZnrc input files, ready for submission on a high-performance computing cluster. The code has been tested with the Eclipse (Varian Medical Systems), Oncentra MasterPlan (Nucletron B.V.) and Pinnacle3 (Philips Medical Systems) planning systems. In this study the software was validated against measurements in homogenous and heterogeneous phantoms. Monte Carlo models are commissioned through comparison with quality assurance measurements made using a large square field incident on a homogenous volume of water. This study aims to provide a valuable confirmation that Monte Carlo calculations match experimental measurements for complex fields and heterogeneous media.

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010 : a systematic analysis for the Global Burden of Disease Study 2010

Background Non-fatal health outcomes from diseases and injuries are a crucial consideration in the promotion and monitoring of individual and population health. The Global Burden of Disease (GBD) studies done in 1990 and 2000 have been the only studies to quantify non-fatal health outcomes across an exhaustive set of disorders at the global and regional level. Neither effort quantified uncertainty in prevalence or years lived with disability (YLDs). Methods Of the 291 diseases and injuries in the GBD cause list, 289 cause disability. For 1160 sequelae of the 289 diseases and injuries, we undertook a systematic analysis of prevalence, incidence, remission, duration, and excess mortality. Sources included published studies, case notification, population-based cancer registries, other disease registries, antenatal clinic serosurveillance, hospital discharge data, ambulatory care data, household surveys, other surveys, and cohort studies. For most sequelae, we used a Bayesian meta-regression method, DisMod-MR, designed to address key limitations in descriptive epidemiological data, including missing data, inconsistency, and large methodological variation between data sources. For some disorders, we used natural history models, geospatial models, back-calculation models (models calculating incidence from population mortality rates and case fatality), or registration completeness models (models adjusting for incomplete registration with health-system access and other covariates). Disability weights for 220 unique health states were used to capture the severity of health loss. YLDs by cause at age, sex, country, and year levels were adjusted for comorbidity with simulation methods. We included uncertainty estimates at all stages of the analysis. Findings Global prevalence for all ages combined in 2010 across the 1160 sequelae ranged from fewer than one case per 1 million people to 350 000 cases per 1 million people. Prevalence and severity of health loss were weakly correlated (correlation coefficient −0·37). In 2010, there were 777 million YLDs from all causes, up from 583 million in 1990. The main contributors to global YLDs were mental and behavioural disorders, musculoskeletal disorders, and diabetes or endocrine diseases. The leading specific causes of YLDs were much the same in 2010 as they were in 1990: low back pain, major depressive disorder, iron-deficiency anaemia, neck pain, chronic obstructive pulmonary disease, anxiety disorders, migraine, diabetes, and falls. Age-specific prevalence of YLDs increased with age in all regions and has decreased slightly from 1990 to 2010. Regional patterns of the leading causes of YLDs were more similar compared with years of life lost due to premature mortality. Neglected tropical diseases, HIV/AIDS, tuberculosis, malaria, and anaemia were important causes of YLDs in sub-Saharan Africa. Interpretation Rates of YLDs per 100 000 people have remained largely constant over time but rise steadily with age. Population growth and ageing have increased YLD numbers and crude rates over the past two decades. Prevalences of the most common causes of YLDs, such as mental and behavioural disorders and musculoskeletal disorders, have not decreased. Health systems will need to address the needs of the rising numbers of individuals with a range of disorders that largely cause disability but not mortality. Quantification of the burden of non-fatal health outcomes will be crucial to understand how well health systems are responding to these challenges. Effective and affordable strategies to deal with this rising burden are an urgent priority for health systems in most parts of the world. Funding Bill & Melinda Gates Foundation.

Chemistry, Raman and infrared spectroscopic characterization of the phosphate mineral reddingite: (MnFe)3(PO4)2(H2O,OH)3, a mineral found in lithium-bearing pegmatite

Detailed investigation of an intermediate member of the reddingite–phosphoferrite series, using infrared and Raman spectroscopy, scanning electron microcopy and electron microprobe analysis, has been carried out on a homogeneous sample from a lithium-bearing pegmatite named Cigana mine, near Conselheiro Pena, Minas Gerais, Brazil. The determined formula is (Mn1.60Fe1.21Ca0.01Mg0.01)∑2.83(PO4)2.12⋅(H2O2.85F0.01)∑2.86 indicating predominance in the reddingite member. Raman spectroscopy coupled with infrared spectroscopy supports the concept of phosphate, hydrogen phosphate and dihydrogen phosphate units in the structure of reddingite-phosphoferrite. Infrared and Raman bands attributed to water and hydroxyl stretching modes are identified. Vibrational spectroscopy adds useful information to the molecular structure of reddingite–phosphoferrite.

Embedding environmental sustainability in the undergraduate chemistry curriculum : a case study

In spite of increasing attention devoted to the importance of embedding sustainability in university curricula, few Australian universities include specific green chemistry units, and there is no mention of green or sustainable chemistry concepts in the majority of units. In this paper, an argument is posited that all universities should embed sustainable chemistry within all Chemistry courses because it is the morally correct stance to minimise the harm of climate change. Attitudes of chemistry lecturers towards integrating sustainability into their teaching have been probed and it was found, using an established model, that personal environmental perspectives are critical to their attitude. Importantly, academic staff whose research has an environmental component were more likely to incorporate sustainability into their teaching while others struggled to find ways to do so even when they believed it to be important. This paper will recommend that resources are required to assist academic staff without a green chemistry research program to incorporate sustainability into their teaching and several suggestions are provided.

Graphene nanocomposites

Graphene, one of the allotropes (diamond, carbon nanotube, and fullerene) of carbon, is a monolayer of honeycomb lattice of carbon atoms discovered in 2004. The Nobel Prize in Physics 2010 was awarded to Andre Geim and Konstantin Novoselov for their ground breaking experiments on the twodimensional graphene [1]. Since its discovery, the research communities have shown a lot of interest in this novel material owing to its unique properties. As shown in Figure 1, the number of publications on graphene has dramatically increased in recent years. It has been confirmed that graphene possesses very peculiar electrical properties such as anomalous quantum hall effect, and high electron mobility at room temperature (250000 cm2/Vs). Graphene is also one of the stiffest (modulus ~1 TPa) and strongest (strength ~100 GPa) materials. In addition, it has exceptional thermal conductivity (5000 Wm-1K-1). Based on these exceptional properties, graphene has found its applications in various fields such as field effect devices, sensors, electrodes, solar cells, energy storage devices and nanocomposites. Only adding 1 volume per cent graphene into polymer (e.g. polystyrene), the nanocomposite has a conductivity of ~0.1 Sm-1 [2], sufficient for many electrical applications. Significant improvement in strength, fracture toughness and fatigue strength has also been achieved in these nanocomposites [3-5]. Therefore, graphene-polymer nanocomposites have demonstrated a great potential to serve as next generation functional or structural materials.

Numerical Modelling of Mechanical Behaviour of Graphene

Graphene, one of the allotropes (diamond, carbon nanotube, and fullerene) of element carbon, is a monolayer of honeycomb lattice of carbon atoms, which was discovered in 2004. The Nobel Prize in Physics 2010 was awarded to Andre Geim and Konstantin Novoselov for their ground breaking work on the two-dimensional (2D) graphene [1]. Since its discovery, the research communities have shown a lot of interest in this novel material owing to its intriguing electrical, mechanical and thermal properties. It has been confirmed that grapheme possesses very peculiar electrical properties such as anomalous quantum hall effect, and high electron mobility at room temperature (250000 cm2/Vs). Graphene also has exceptional mechanical properties. It is one of the stiffest (modulus ~1 TPa) and strongest (strength ~100 GPa) materials. In addition, it has exceptional thermal conductivity (5000 Wm-1K-1). Due to these exceptional properties, graphene has demonstrated its potential for broad applications in micro and nano devices, various sensors, electrodes, solar cells and energy storage devices and nanocomposites. In particular, the excellent mechanical properties of graphene make it more attractive for development next generation nanocomposites and hybrid materials...

Inter-cycle variability of in-cylinder pressure parameters in an ethanol fumigated common rail diesel engine

The effects of ethanol fumigation on the inter-cycle variability of key in-cylinder pressure parameters in a modern common rail diesel engine have been investigated. Specifically, maximum rate of pressure rise, peak pressure, peak pressure timing and ignition delay were investigated. A new methodology for investigating the start of combustion was also proposed and demonstrated—which is particularly useful with noisy in-cylinder pressure data as it can have a significant effect on the calculation of an accurate net rate of heat release indicator diagram. Inter-cycle variability has been traditionally investigated using the coefficient of variation. However, deeper insight into engine operation is given by presenting the results as kernel density estimates; hence, allowing investigation of otherwise unnoticed phenomena, including: multi-modal and skewed behaviour. This study has found that operation of a common rail diesel engine with high ethanol substitutions (>20% at full load, >30% at three quarter load) results in a significant reduction in ignition delay. Further, this study also concluded that if the engine is operated with absolute air to fuel ratios (mole basis) less than 80, the inter-cycle variability is substantially increased compared to normal operation.