Experimental evaluation of MCDTK, the Monte Carlo DICOM Tool-Kit

The Monte Carlo DICOM Tool-Kit (MCDTK) is a software suite designed for treatment plan dose verification, using the BEAMnrc and DOSXYZnrc Monte Carlo codes. MCDTK converts DICOM-format treatment plan information into Monte Carlo input files and compares the results of Monte Carlo treatment simulations with conventional treatment planning dose calculations. In this study, a treatment is planned using a commercial treatment planning system, delivered to a pelvis phantom containing ten thermoluminescent dosimeters and simulated using BEAMnrc and DOSXYZnrc using inputs derived from MCDTK. The dosimetric accuracy of the Monte Carlo data is then evaluated via comparisons with the dose distribution obtained from the treatment planning system as well as the in-phantom point dose measurements. The simulated beam arrangement produced by MCDTK is found to be in geometric agreement with the planned treatment. An isodose display generated from the Monte Carlo data by MCDTK shows general agreement with the isodose display obtained from the treatment planning system, except for small regions around density heterogeneities in the phantom, where the pencil-beam dose calculation performed by the treatment planning systemis likely to be less accurate. All point dose measurements agree with the Monte Carlo data obtained using MCDTK, within confidence limits, and all except one of these point dose measurements show closer agreement with theMonte Carlo data than with the doses calculated by the treatment planning system. This study provides a simple demonstration of the geometric and dosimetric accuracy ofMonte Carlo simulations based on information from MCDTK.

How important is length? : mechanical testing and measurement of a cemented, polished, tapered femoral implant

Total hip arthroplasty (THA) has a proven clinical record for providing pain relief and return of function to patients with disabling arthritis. There are many successful options for femoral implant design and fixation. Cemented, polished, tapered femoral implants have been shown to have excellent results in national joint registries and long-term clinical series. These implants are usually 150mm long at their lateral aspect. Due to their length, these implants cannot always be offered to patients due to variations in femoral anatomy. Polished, tapered implants as short as 95mm exist, however their small proximal geometry (neck offset and body size) limit their use to smaller stature patients. There is a group of patients in which a shorter implant with a maintained proximal body size would be advantageous. There are also potential benefits to a shorter implant in standard patient populations such as reduced bone removal due to reduced reaming, favourable loading of the proximal femur, and the ability to revise into good proximal bone stock if required. These factors potentially make a shorter implant an option for all patient populations. The role of implant length in determining the stability of a cemented, polished, tapered femoral implant is not well defined by the literature. Before changes in implant design can be made, a better understanding of the role of each region in determining performance is required. The aim of the thesis was to describe how implant length affects the stability of a cemented, polished, tapered femoral implant. This has been determined through an extensive body of laboratory testing. The major findings are that for a given proximal body size, a reduction in implant length has no effect on the torsional stability of a polished, tapered design, while a small reduction in axial stability should be expected. These findings are important because the literature suggests that torsional stability is the major determinant of long-term clinical performance of a THA system. Furthermore, a polished, tapered design is known to be forgiving of cement-implant interface micromotion due to the favourable wear characteristics. Together these findings suggest that a shorter polished, tapered implant may be well tolerated. The effect of a change in implant length on the geometric characteristics of polished, tapered design were also determined and applied to the mechanical testing. Importantly, interface area does play a role in stability of the system; however it is the distribution of the interface and not the magnitude of the area that defines stability. Taper angle (at least in the range of angles seen in this work) was shown not to be a determinant of axial or torsional stability. A range of implants were tested, comparing variations in length, neck offset and indication (primary versus cement-in-cement revision). At their manufactured length, the 125mm implants were similar to their longer 150mm counterparts suggesting that they may be similarly well tolerated in the clinical environment. However, the slimmer cement-in-cement revision implant was shown to have a poorer mechanical performance, suggesting their use in higher demand patients may be hazardous. An implant length of 125mm has been shown to be quite stable and the results suggest that a further reduction to 100mm may be tolerated. However, further work is required. A shorter implant with maintained proximal body size would be useful for the group of patients who are unable to access the current standard length implants due to variations in femoral anatomy. Extending the findings further, the similar function with potential benefits of a shorter implant make their application to all patients appealing.

Three-dimensional medical ultrasound

A number of groups around the world are working in the field of three dimensional(3D) ultrasound (US) in order to obtain higher quality diagnostic information. 3D US, in general, involves collecting a sequence of conventional 2D US images along with information on the position and orientation of each image plane. A transformation matrix is calculated relating image space to real world space. This allows image pixels and region of interest (ROI) points drawn on the image to be displayed in 3D. The 3D data can be used for the production of volume or surface rendered images, or for the direct calculation of ROI volumes.

Quantum models of cognition and decision

Much of our understanding of human thinking is based on probabilistic models. This innovative book by Jerome R. Busemeyer and Peter D. Bruza argues that, actually, the underlying mathematical structures from quantum theory provide a much better account of human thinking than traditional models. They introduce the foundations for modelling probabilistic-dynamic systems using two aspects of quantum theory. The first, "contextuality", is a way to understand interference effects found with inferences and decisions under conditions of uncertainty. The second, "entanglement", allows cognitive phenomena to be modelled in non-reductionist ways. Employing these principles drawn from quantum theory allows us to view human cognition and decision in a totally new light...

The calculation of acoustic indices to characterise acoustic recordings of the environment

This technical report describes the methods used to obtain a list of acoustic indices that are used to characterise the structure and distribution of acoustic energy in recordings of the natural environment. In particular it describes methods for noise reduction from recordings of the environment and a fast clustering algorithm used to estimate the spectral richness of long recordings.

Are plasmons responsible for the Raman signal enhancement observed with gold nanoparticle sensors?

The electromagnetic enhancement that occurs in surface enhanced Raman scattering (SERS) substrates containing gold nanoparticles (NPs) is believed to arise through the generation of localised surface plasmons. We present results that show no SERS signals are obtained when 25 nm diameter gold NPs layered quartz substrates exposed to 2-aminopyridine are illuminated with plasmon resonant 532 nm radiation, but SERS signals are observed when the same samples are illuminated with non-resonant 785 nm radiation.

Experimental study on mechanical properties of pumpkin tissue

Purpose: The purpose of this study was to calculate mechanical properties of tough skinned vegetables as a part of Finite Element Modelling (FEM) and simulation of tissue damage during mechanical peeling of tough skinned vegetables. Design/methodology: There are some previous studies on mechanical properties of fruits and vegetables however, behaviour of tissue under different processing operations will be different. In this study indentation test was performed on Peel, Flesh and Unpeeled samples of pumpkin as a tough skinned vegetable. Additionally, the test performed in three different loading rates for peel: 1.25, 10, 20 mm/min and 20 mm/min for flesh and unpeeled samples respectively. The spherical end indenter with 8mm diameter used for the experimental tests. Samples prepare from defect free and ripped pumpkin purchased from local shops in Brisbane, Australia. Humidity and temperature were 20-55% and 20-250C respectively. Findings: Consequently, force deformation and stress and strain of samples were calculated and shown in presented figures. Relative contribution (%) of skin to different mechanical properties is computed and compared with data available from literature. According the results, peel samples had the highest value of rupture force (291N) and as well as highest value of firmness (1411Nm-1). Research limitations/implications: The proposed study focused on one type of tough skinned vegetables and one variety of pumpkin however, more tests will give better understandings of behaviours of tissue. Additionally, the behaviours of peel, unpeeled and flesh samples in different speed of loading will provide more details of tissue damages during mechanical loading. Originality/value: Mechanical properties of pumpkin tissue calculated using the results of indentation test, specifically the behaviours of peel, flesh and unpeeled samples were explored which is a new approach in Finite Element Modelling (FEM) of food processes. Keywords: Finite Element Modelling (FEM), relative contribution, firmness, toughness and rupture force.

A quantum probability perspective on borderline vagueness

The term “vagueness” describes a property of natural concepts, which normally have fuzzy boundaries, admit borderline cases, and are susceptible to Zeno’s sorites paradox. We will discuss the psychology of vagueness, especially experiments investigating the judgment of borderline cases and contradictions. In the theoretical part, we will propose a probabilistic model that describes the quantitative characteristics of the experimental finding and extends Alxatib’s and Pelletier’s (2011) theoretical analysis. The model is based on a Hopfield network for predicting truth values. Powerful as this classical perspective is, we show that it falls short of providing an adequate coverage of the relevant empirical results. In the final part, we will argue that a substan- tial modification of the analysis put forward by Alxatib and Pelletier and its probabilistic pendant is needed. The proposed modification replaces the standard notion of probabilities by quantum probabilities. The crucial phenomenon of borderline contradictions can be explained then as a quantum interference phenomenon.

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

Do thermal agents affect range of movement and mechanical properties in soft tissues? A systematic review

OBJECTIVES: To examine the effect of thermal agents on the range of movement (ROM) and mechanical properties in soft tissue and to discuss their clinical relevance. DATA SOURCES: Electronic databases (Cochrane Central Register of Controlled Trials, MEDLINE, and EMBASE) were searched from their earliest available record up to May 2011 using Medical Subjects Headings and key words. We also undertook related articles searches and read reference lists of all incoming articles. STUDY SELECTION: Studies involving human participants describing the effects of thermal interventions on ROM and/or mechanical properties in soft tissue. Two reviewers independently screened studies against eligibility criteria. DATA EXTRACTION: Data were extracted independently by 2 review authors using a customized form. Methodologic quality was also assessed by 2 authors independently, using the Cochrane risk of bias tool. DATA SYNTHESIS: Thirty-six studies, comprising a total of 1301 healthy participants, satisfied the inclusion criteria. There was a high risk of bias across all studies. Meta-analyses were not undertaken because of clinical heterogeneity; however, effect sizes were calculated. There were conflicting data on the effect of cold on joint ROM, accessory joint movement, and passive stiffness. There was limited evidence to determine whether acute cold applications enhance the effects of stretching, and further evidence is required. There was evidence that heat increases ROM, and a combination of heat and stretching is more effective than stretching alone. CONCLUSIONS: Heat is an effective adjunct to developmental and therapeutic stretching techniques and should be the treatment of choice for enhancing ROM in a clinical or sporting setting. The effects of heat or ice on other important mechanical properties (eg, passive stiffness) remain equivocal and should be the focus of future study.

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.

Mechanical properties of graphene : effects of layer number, temperature and isotope

Herein the mechanical properties of graphene, including Young’s modulus, fracture stress and fracture strain have been investigated by molecular dynamics simulations. The simulation results show that the mechanical properties of graphene are sensitive to the temperature changes but insensitive to the layer numbers in the multilayer graphene. Increasing temperature exerts adverse and significant effects on the mechanical properties of graphene. However, the adverse effect produced by the increasing layer number is marginal. On the other hand, isotope substitutions in graphene play a negligible role in modifying the mechanical properties of graphene.

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.

Porohyperelastic analysis to explore mechanical properties of chondrocytes using numerical modeling and experiments : a finite element study

There are many continuum mechanical models have been developed such as liquid drop models, solid models, and so on for single living cell biomechanics studies. However, these models do not give a fully approach to exhibit a clear understanding of the behaviour of single living cells such as swelling behaviour, drag effect, etc. Hence, the porohyperelastic (PHE) model which can capture those aspects would be a good candidature to study cells behaviour (e.g. chondrocytes in this study). In this research, an FEM model of single chondrocyte cell will be developed by using this PHE model to simulate Atomic Force Microscopy (AFM) experimental results with the variation of strain rate. This material model will be compared with viscoelastic model to demonstrate the advantages of PHE model. The results have shown that the maximum value of force applied of PHE model is lower at lower strain rates. This is because the mobile fluid does not have enough time to exude in case of very high strain rate and also due to the lower permeability of the membrane than that of the protoplasm of chondrocyte. This behavior is barely observed in viscoelastic model. Thus, PHE model is the better model for cell biomechanics studies.