Calculation of dose kernels for radiotherapy applications using the GEANT 4 Monte Carlo toolkit

Dose kernels may be used to calculate dose distributions in radiotherapy (as described by Ahnesjo et al., 1999). Their calculation requires use of Monte Carlo methods, usually by forcing interactions to occur at a point. The Geant4 Monte Carlo toolkit provides a capability to force interactions to occur in a particular volume. We have modified this capability and created a Geant4 application to calculate dose kernels in cartesian, cylindrical, and spherical scoring systems. The simulation considers monoenergetic photons incident at the origin of a 3 m x 3 x 9 3 m water volume. Photons interact via compton, photo-electric, pair production, and rayleigh scattering. By default, Geant4 models photon interactions by sampling a physical interaction length (PIL) for each process. The process returning the smallest PIL is then considered to occur. In order to force the interaction to occur within a given length, L_FIL, we scale each PIL according to the formula: PIL_forced = L_FIL 9 (1 - exp(-PIL/PILo)) where PILo is a constant. This ensures that the process occurs within L_FIL, whilst correctly modelling the relative probability of each process. Dose kernels were produced for an incident photon energy of 0.1, 1.0, and 10.0 MeV. In order to benchmark the code, dose kernels were also calculated using the EGSnrc Edknrc user code. Identical scoring systems were used; namely, the collapsed cone approach of the Edknrc code. Relative dose difference images were then produced. Preliminary results demonstrate the ability of the Geant4 application to reproduce the shape of the dose kernels; median relative dose differences of 12.6, 5.75, and 12.6 % were found for an incident photon energy of 0.1, 1.0, and 10.0 MeV respectively.

Carbonate cementation in sandstones of the Plover Formation, North West Shelf, W.A

Ancient sandstones include important reservoirs for hydrocarbons (oil and gas), but, in many cases, their ability to serve as reservoirs is heavily constrained by the effects of carbonate cements on porosity and permeability. This study investigated the controls on distribution and abundance of carbonate cements within the Jurassic Plover Formation, Browse Basin, North West Shelf, Australia. Samples were analysed petrographically with point counting of 59 thin sections and mineralogically with x-ray diffraction from two wells within the Torosa Gas Field. Selected samples were also analysed for stable isotopes of O and C. Sandstones are classified into eleven groups. Most abundant are quartzarenites and then calcareous quartzarenites. Lithology ranged between sandstones consisting of mostly quartz with scant or no carbonate in the form of cement or allochems, to sandstones with as much as 40% carbonate. The major sources of carbonate cement in Torosa 1 and Torosa 4 sandstones were found to be early, shallow marine diagenetic processes (including cementation), followed by calcite cementation and recrystallisation of cements and allochems during redistribution by meteoric waters. Blocky and sparry calcite cements, indicative of meteoric environments on the basis of stable isotope values and palaeotemperature assessment, overprinted the initial shallow marine cement phase in all cases and meteoric cements are dominant. Torosa 4 was influenced more by marine settings than Torosa 1, and thus has the greater potential for calcite cement. The relatively low compaction of calcite-cemented sandstones and the stable isotope data suggest deep burial cementation was not a major factor. Insufficient volcanic rock fragments or authigenic clay content infers alteration of feldspars was not a major source of calcite. Very little feldspar is present, altered or otherwise. Hence, increased alkalinity from feldspar dissolution is not a contributing factor in cement formation. Increased alkalinity from bacterial sulphate reduction in organic–rich fine sediments may have driven limited cementation in some samples. The main definable and significant source of diagenetic marine calcite cement originated from original marine cements and the nearby dissolution of biogenic sources (allochems) at relatively shallow depths. Later diagenetic fluids emplaced minor dolomite, but this cement did not greatly affect the reservoir quality in the samples studied.

A multi-layered approach for site detection in UAS emergency landing scenarios using geometry-based image segmentation

This paper presents an alternative approach to image segmentation by using the spatial distribution of edge pixels as opposed to pixel intensities. The segmentation is achieved by a multi-layered approach and is intended to find suitable landing areas for an aircraft emergency landing. We combine standard techniques (edge detectors) with novel developed algorithms (line expansion and geometry test) to design an original segmentation algorithm. Our approach removes the dependency on environmental factors that traditionally influence lighting conditions, which in turn have negative impact on pixel-based segmentation techniques. We present test outcomes on realistic visual data collected from an aircraft, reporting on preliminary feedback about the performance of the detection. We demonstrate consistent performances over 97% detection rate.

Point of no return : exploring katabatic narrative and deterritorialisation in the Australian outback novel

This thesis consists of the novel Brolga and an exegesis examining in what ways the ideas of katabasis and deterritorialisation inform an understanding of descent narratives in contemporary Australian outback fiction. When writing the creative piece, it was observed that Joseph Campbell’s Hero’s Journey was an imprecise model for my manuscript and indeed for many of the contemporary novels I had read written in similar outback settings. On analysis a better fit lies in the idea of a heroic journey from which there is no clear return from the underworld. This narrative form is defined in this thesis as a katabatic narrative. To unpack this narrative trope, the inverse of territoriality, deterritorialisation, is used as a lens to examine the complex thematic and symbolic resonances of the outback in both Brolga and analogous works of contemporary outback fiction.

Reconstructing 3D x-ray CT images of polymer gel dosimeters using the zero-scan method

In this study x-ray CT has been used to produce a 3D image of an irradiated PAGAT gel sample, with noise-reduction achieved using the ‘zero-scan’ method. The gel was repeatedly CT scanned and a linear fit to the varying Hounsfield unit of each pixel in the 3D volume was evaluated across the repeated scans, allowing a zero-scan extrapolation of the image to be obtained. To minimise heating of the CT scanner’s x-ray tube, this study used a large slice thickness (1 cm), to provide image slices across the irradiated region of the gel, and a relatively small number of CT scans (63), to extrapolate the zero-scan image. The resulting set of transverse images shows reduced noise compared to images from the initial CT scan of the gel, without being degraded by the additional radiation dose delivered to the gel during the repeated scanning. The full, 3D image of the gel has a low spatial resolution in the longitudinal direction, due to the selected scan parameters. Nonetheless, important features of the dose distribution are apparent in the 3D x-ray CT scan of the gel. The results of this study demonstrate that the zero-scan extrapolation method can be applied to the reconstruction of multiple x-ray CT slices, to provide useful 2D and 3D images of irradiated dosimetry gels.

Multiple scattering in deep inelastic neutron scattering : Monte Carlo simulations and experiments at the ISIS eVS inverse geometry spectrometer

A procedure for the evaluation of multiple scattering contributions is described, for deep inelastic neutron scattering (DINS) studies using an inverse geometry time-of-flight spectrometer. The accuracy of a Monte Carlo code DINSMS, used to calculate the multiple scattering, is tested by comparison with analytic expressions and with experimental data collected from polythene, polycrystalline graphite and tin samples. It is shown that the Monte Carlo code gives an accurate representation of the measured data and can therefore be used to reliably correct DINS data.

The influence of temperature and introduction point on the detection of Rhyzopertha dominica in stored grain

The presence of insect pests in grain storages throughout the supply chain is a significant problem for farmers, grain handlers, and distributors world-wide. Insect monitoring and sampling programmes are used in the stored grains industry for the detection and estimation of pest populations. At the low pest densities dictated by economic and commercial requirements, the accuracy of both detection and abundance estimates can be influenced by variations in the spatial structure of pest populations over short distances. Geostatistical analysis of Rhyzopertha dominica populations in 2 and 3 dimensions showed that insect numbers were positively correlated over short (0.5 cm) distances, and negatively correlated over longer (.10 cm) distances. At 35 C, insects were located significantly further from the grain surface than at 25 and 30 C. Dispersion metrics showed statistically significant aggregation in all cases. The observed heterogeneous spatial distribution of R. dominica may also be influenced by factors such as the site of initial infestation and disturbance during handling. To account for these additional factors, I significantly extended a simulation model that incorporates both pest growth and movement through a typical stored-grain supply chain. By incorporating the effects of abundance, initial infestation site, grain handling, and treatment on pest spatial distribution, I developed a supply chain model incorporating estimates of pest spatial distribution. This was used to examine several scenarios representative of grain movement through a supply chain, and determine the influence of infestation location and grain disturbance on the sampling intensity required to detect pest infestations at various infestation rates. This study has investigated the effects of temperature, infestation point, and grain handling on the spatial distribution and detection of R. dominica. The proportion of grain infested was found to be dependent upon abundance, initial pest location, and grain handling. Simulation modelling indicated that accounting for these factors when developing sampling strategies for stored grain has the potential to significantly reduce sampling costs while simultaneously improving detection rate, resulting in reduced storage and pest management cost while improving grain quality.

Energy dependence of methyl-radical adsorption on diamond (001)-(2×1) surface

The deposition of hyperthermal CH3 on diamond (001)-(2×1) surface at room temperature has been studied by means of molecular dynamics simulation using the many-body hydrocarbon potential. The energy threshold effect has been observed. That is, with fixed collision geometry, chemisorption can occur only when the incident energy of CH3 is above a critical value (Eth). Increasing the incident energy, dissociation of hydrogen atoms from the incident molecule was observed. The chemisorption probability of CH3 as a function of its incident energy was calculated and compared with that of C2H2. We found that below 10 eV, the chemisorption probability of C2H2 is much lower than that of CH3 on the same surface. The interesting thing is that it is even lower than that of CH3 on a hydrogen covered surface at the same impact energy. It indicates that the reactive CH3 molecule is the more important species than C2H2 in diamond synthesis at low energy, which is in good agreement with the experimental observation.

Electrical property and characterization of nano-SnO2/wollastonite composite materials

Nano-tin oxide was deposited on the surface of wollastonite using the mixed solution including stannic chloride pentahydrate precursor and wollastonite by a hydrolysis precipitation process. The antistatic properties of the wollastonite materials under different calcined conditions and composite materials (nano-SnO2/wollastonite, SW) were measured by rubber sheeter and four-point probe (FPP) sheet resistance measurement. Effects of hydrolysis temperature and time, calcination temperature and time, pH value and nano-SnO2 coating amount on the resistivity of SW powders were studied, and the optimum experimental conditions were obtained. The microstructure and surface properties of wollastonite, precipitate and SW were characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectrometry (EDS), specific surface area analyzer (BET), thermogravimetry (TG), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and Fourier translation infrared spectroscopy (FTIR) respectively. The results showed that the nano-SnO2/wollastonite composite materials under optimum preparation conditions showed better antistatic properties, the resistivity of which was reduced from 1.068 × 104 Ω cm to 2.533 × 103 Ω cm. From TG and XRD analysis, the possible mechanism for coating of SnO2 nanoparticles on the surface of wollastonite was proposed. The infrared spectrum indicated that there were a large number of the hydroxyl groups on the surface of wollastonite. This is beneficial to the heterogeneous nucleation reaction. Through morphology, EDS and XPS analysis, the surface of wollastonite fiber was coated with a layer of 10–15 nm thickness of tin oxide grains the distribution of which was uniform.

Aircraft collision avoidance using spherical visual predictive control and single point features

This paper presents practical vision-based collision avoidance for objects approximating a single point feature. Using a spherical camera model, a visual predictive control scheme guides the aircraft around the object along a conical spiral trajectory. Visibility, state and control constraints are considered explicitly in the controller design by combining image and vehicle dynamics in the process model, and solving the nonlinear optimization problem over the resulting state space. Importantly, range is not required. Instead, the principles of conical spiral motion are used to design an objective function that simultaneously guides the aircraft along the avoidance trajectory, whilst providing an indication of the appropriate point to stop the spiral behaviour. Our approach is aimed at providing a potential solution to the See and Avoid problem for unmanned aircraft and is demonstrated through a series.

How long does it take for aquifer recharge or aquifer discharge processes to reach steady state?

Groundwater flow models are usually characterized as being either transient flow models or steady state flow models. Given that steady state groundwater flow conditions arise as a long time asymptotic limit of a particular transient response, it is natural for us to seek a finite estimate of the amount of time required for a particular transient flow problem to effectively reach steady state. Here, we introduce the concept of mean action time (MAT) to address a fundamental question: How long does it take for a groundwater recharge process or discharge processes to effectively reach steady state? This concept relies on identifying a cumulative distribution function, $F(t;x)$, which varies from $F(0;x)=0$ to $F(t;x) \to \infty$ as $t\to \infty$, thereby providing us with a measurement of the progress of the system towards steady state. The MAT corresponds to the mean of the associated probability density function $f(t;x) = \dfrac{dF}{dt}$, and we demonstrate that this framework provides useful analytical insight by explicitly showing how the MAT depends on the parameters in the model and the geometry of the problem. Additional theoretical results relating to the variance of $f(t;x)$, known as the variance of action time (VAT), are also presented. To test our theoretical predictions we include measurements from a laboratory–scale experiment describing flow through a homogeneous porous medium. The laboratory data confirms that the theoretical MAT predictions are in good agreement with measurements from the physical model.

A case study of interactions between flood flow and buildings in an urban environment : Gardens Point during the 12-13 January 2011 flood of the Brisbane River (Australia)

Flood flows in inundated urban environment constitute a natural hazard. During the 12- 13 January 2011 flood of the Brisbane River, detailed water elevation, velocity and suspended sediment data were recorded in an inundated street at the peak of the flood. The field observations highlighted a number of unusual flow interactions with the urban surroundings. These included some slow fluctuations in water elevations and velocity with distinctive periods between 50 and 100 s caused by some local topographic effect (choking), superposed with some fast turbulent fluctuations. The suspended sediment data highlighted some significant suspended sediment loads in the inundated zone.

Unique X-linked familial FSGS with co-segregating heart block disorder is associated with a mutation in the NXF5 gene

Focal segmental glomerulosclerosis (FSGS) is the consequence of a disease process that attacks the kidney's filtering system, causing serious scarring. More than half of FSGS patients develop chronic kidney failure within 10 years, ultimately requiring dialysis or renal transplantation. There are currently several genes known to cause the hereditary forms of FSGS (ACTN4, TRPC6, CD2AP, INF2, MYO1E and NPHS2). This study involves a large, unique, multigenerational Australian pedigree in which FSGS co-segregates with progressive heart block with apparent X-linked recessive inheritance. Through a classical combined approach of linkage and haplotype analysis, we identified a 21.19 cM interval implicated on the X chromosome. We then used a whole exome sequencing approach to identify two mutated genes, NXF5 and ALG13, which are located within this linkage interval. The two mutations NXF5-R113W and ALG13-T141L segregated perfectly with the disease phenotype in the pedigree and were not found in a large healthy control cohort. Analysis using bioinformatics tools predicted the R113W mutation in the NXF5 gene to be deleterious and cellular studies support a role in the stability and localization of the protein suggesting a causative role of this mutation in these co-morbid disorders. Further studies are now required to determine the functional consequence of these novel mutations to development of FSGS and heart block in this pedigree and to determine whether these mutations have implications for more common forms of these diseases in the general population.

An X chromosome association scan of the Norfolk Island genetic isolate provides evidence for a novel migraine susceptibility locus at Xq12

Migraine is a common and debilitating neurovascular disorder with a complex envirogenomic aetiology. Numerous studies have demonstrated a preponderance of women affected with migraine and previous pedigree linkage studies in our laboratory have identified susceptibility loci on chromosome Xq24-Xq28. In this study we have used the genetic isolate of Norfolk Island to further analyse the X chromosome for migraine susceptibility loci. An association approach was employed to analyse 14,124 SNPs spanning the entire X chromosome. Genotype data from 288 individuals comprising a large core-pedigree, of which 76 were affected with migraine, were analysed. Although no SNP reached chromosome-wide significance (empirical α = 1×10−5) ranking by P-value revealed two primary clusters of SNPs in the top 25. A 10 SNP cluster represents a novel migraine susceptibility locus at Xq12 whilst a 11 SNP cluster represents a previously identified migraine susceptibility locus at Xq27. The strongest association at Xq12 was seen for rs599958 (OR = 1.75, P = 8.92×10−4), whilst at Xq27 the strongest association was for rs6525667 (OR = 1.53, P = 1.65×10−4). Further analysis of SNPs at these loci was performed in 5,122 migraineurs from the Women’s Genome Health Study and provided additional evidence for association at the novel Xq12 locus (P<0.05). Overall, this study provides evidence for a novel migraine susceptibility locus on Xq12. The strongest effect SNP (rs102834, joint P = 1.63×10−5) is located within the 5′UTR of the HEPH gene, which is involved in iron homeostasis in the brain and may represent a novel pathway for involvement in migraine pathogenesis.

Confirmation that Xq27 and Xq28 are susceptibility loci for migraine in independent pedigrees and a case-control cohort

Investigations into migraine genetics have suggested that susceptibility loci exist on the X chromosome. These reports are supported by evidence that demonstrates male probands as having a higher proportion of affected first-degree relatives as well as the female preponderance of 3:1 that the disorder displays. We have previously implicated the Xq24-28 locus in migraine using two independent multigenerational Australian pedigrees that demonstrated excess allele sharing at the Xq24, Xq27 and Xq28 loci. Here, we expand this work to investigate a further six independent migraine pedigrees using 11 microsatellite markers spanning the Xq27–28 region. Furthermore, 11 candidate genes are investigated in an Australian case-control cohort consisting of 500 cases and 500 controls. Microsatellite analysis showed evidence of excess allele sharing to the Xq27 marker DXS8043 (LOD* 1.38 P = 0.005) in MF879 whilst a second independent pedigree showed excess allele sharing to DXS8061 at Xq28 (LOD* 1.5 P = 0.004). Furthermore, analysis of these key markers in a case control cohort showed significant association to migraine in females at the DXS8043 marker (T1 P = 0.009) and association with MO at DXS8061 (T1 P = 0.05). Further analysis of 11 key genes across these regions showed significant association of a three-marker risk haplotype in the NSDHL gene at Xq28 (P = 0.0082). The results of this study add further support to the presence of migraine susceptibility loci on chromosome Xq27 and Xq28 as well as point to potential candidate genes in the regions that warrant further investigation.