Effect of CT electron density identification on Monte Carlo simulations of radiotherapeutic treatments

Introduction: The accurate identification of tissue electron densities is of great importance for Monte Carlo (MC) dose calculations. When converting patient CT data into a voxelised format suitable for MC simulations, however, it is common to simplify the assignment of electron densities so that the complex tissues existing in the human body are categorized into a few basic types. This study examines the effects that the assignment of tissue types and the calculation of densities can have on the results of MC simulations, for the particular case of a Siemen’s Sensation 4 CT scanner located in a radiotherapy centre where QA measurements are routinely made using 11 tissue types (plus air). Methods: DOSXYZnrc phantoms are generated from CT data, using the CTCREATE user code, with the relationship between Hounsfield units (HU) and density determined via linear interpolation between a series of specified points on the ‘CT-density ramp’ (see Figure 1(a)). Tissue types are assigned according to HU ranges. Each voxel in the DOSXYZnrc phantom therefore has an electron density (electrons/cm3) defined by the product of the mass density (from the HU conversion) and the intrinsic electron density (electrons /gram) (from the material assignment), in that voxel. In this study, we consider the problems of density conversion and material identification separately: the CT-density ramp is simplified by decreasing the number of points which define it from 12 down to 8, 3 and 2; and the material-type-assignment is varied by defining the materials which comprise our test phantom (a Supertech head) as two tissues and bone, two plastics and bone, water only and (as an extreme case) lead only. The effect of these parameters on radiological thickness maps derived from simulated portal images is investigated. Results & Discussion: Increasing the degree of simplification of the CT-density ramp results in an increasing effect on the resulting radiological thickness calculated for the Supertech head phantom. For instance, defining the CT-density ramp using 8 points, instead of 12, results in a maximum radiological thickness change of 0.2 cm, whereas defining the CT-density ramp using only 2 points results in a maximum radiological thickness change of 11.2 cm. Changing the definition of the materials comprising the phantom between water and plastic and tissue results in millimetre-scale changes to the resulting radiological thickness. When the entire phantom is defined as lead, this alteration changes the calculated radiological thickness by a maximum of 9.7 cm. Evidently, the simplification of the CT-density ramp has a greater effect on the resulting radiological thickness map than does the alteration of the assignment of tissue types. Conclusions: It is possible to alter the definitions of the tissue types comprising the phantom (or patient) without substantially altering the results of simulated portal images. However, these images are very sensitive to the accurate identification of the HU-density relationship. When converting data from a patient’s CT into a MC simulation phantom, therefore, all possible care should be taken to accurately reproduce the conversion between HU and mass density, for the specific CT scanner used. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital (RBWH), Brisbane, Australia. The authors are grateful to the staff of the RBWH, especially Darren Cassidy, for assistance in obtaining the phantom CT data used in this study. The authors also wish to thank Cathy Hargrave, of QUT, for assistance in formatting the CT data, using the Pinnacle TPS. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

Infrared and Raman spectroscopic characterization of the borate mineral colemanite – CaB3O4(OH)3·H2O – implications for the molecular structure

Colemanite CaB3O4(OH)3 H2O is a secondary borate mineral formed from borax and ulexite in evaporate deposits of alkaline lacustrine sediments. The basic structure of colemanite contains endless chains of interlocking BO2(OH) triangles and BO3(OH) tetrahedrons with the calcium, water and extra hydroxide units interspersed between these chains. The Raman spectra of colemanite is characterized by an intense band at 3605 cm-1 assigned to the stretching vibration of OH units and a series of bands at 3182, 3300, 3389 and 3534 cm-1 assigned to water stretching vibrations. Infrared bands are observed in similar positions. The BO stretching vibrations of the trigonal and tetrahedral boron are characterized by Raman bands at 876, 1065 and 1084 cm-1. The OBO bending mode is defined by the Raman band at 611 cm-1. It is important to characterize the very wide range of borate minerals including colemanite because of the very wide range of applications of boron containing minerals.

Deformation and failure of graphene sheet and graphene-polymer interface

With a monolayer honeycomb-lattice of sp2-hybridized carbon atoms, graphene has demonstrated exceptional electrical, mechanical and thermal properties. One of its promising applications is to create graphene-polymer nanocomposites with tailored mechanical and physical properties. In general, the mechanical properties of graphene nanofiller as well as graphene-polymer interface govern the overall mechanical performance of graphene-polymer nanocomposites. However, the strengthening and toughening mechanisms in these novel nanocomposites have not been well understood. In this work, the deformation and failure of graphene sheet and graphene-polymer interface were investigated using molecular dynamics (MD) simulations. The effect of structural defects on the mechanical properties of graphene and graphene-polymer interface was investigated as well. The results showed that structural defects in graphene (e.g. Stone-Wales defect and multi-vacancy defect) can significantly deteriorate the fracture strength of graphene but may still make full utilization of corresponding strength of graphene and keep the interfacial strength and the overall mechanical performance of graphene-polymer nanocomposites.

Thermal transport in graphene-polymer nanocomposites

Graphene-polymer nanocomposites have attracted considerable attention due to their unique properties, such as high thermal conductivity (~3000 W mK-1), mechanical stiffness (~ 1 TPa) and electronic transport properties. Relatively, the thermal performance of graphene-polymer composites has not been well investigated. The major technical challenge is to understand the interfacial thermal transport between graphene nanofiller and polymer matrix at small material length scale. To this end, we conducted molecular dynamics simulations to investigate the thermal transport in graphene-polyethylene nanocomposite. The influence of functionalization with hydrocarbon chains on the interfacial thermal conductivity was studied, taking into account of the effects of model size and thermal conductivity of graphene. The results are considered to contribute to development of new graphene-polymer nanocomposites with tailored thermal properties.

Computer modeling of diffusion in biological tissues

Molecular-level computer simulations of restricted water diffusion can be used to develop models for relating diffusion tensor imaging measurements of anisotropic tissue to microstructural tissue characteristics. The diffusion tensors resulting from these simulations can then be analyzed in terms of their relationship to the structural anisotropy of the model used. As the translational motion of water molecules is essentially random, their dynamics can be effectively simulated using computers. In addition to modeling water dynamics and water-tissue interactions, the simulation software of the present study was developed to automatically generate collagen fiber networks from user-defined parameters. This flexibility provides the opportunity for further investigations of the relationship between the diffusion tensor of water and morphologically different models representing different anisotropic tissues.

Lattice-free models of cell invasion : discrete simulations and travelling waves

Invasion waves of cells play an important role in development, disease and repair. Standard discrete models of such processes typically involve simulating cell motility, cell proliferation and cell-to-cell crowding effects in a lattice-based framework. The continuum-limit description is often given by a reaction–diffusion equation that is related to the Fisher–Kolmogorov equation. One of the limitations of a standard lattice-based approach is that real cells move and proliferate in continuous space and are not restricted to a predefined lattice structure. We present a lattice-free model of cell motility and proliferation, with cell-to-cell crowding effects, and we use the model to replicate invasion wave-type behaviour. The continuum-limit description of the discrete model is a reaction–diffusion equation with a proliferation term that is different from lattice-based models. Comparing lattice based and lattice-free simulations indicates that both models lead to invasion fronts that are similar at the leading edge, where the cell density is low. Conversely, the two models make different predictions in the high density region of the domain, well behind the leading edge. We analyse the continuum-limit description of the lattice based and lattice-free models to show that both give rise to invasion wave type solutions that move with the same speed but have very different shapes. We explore the significance of these differences by calibrating the parameters in the standard Fisher–Kolmogorov equation using data from the lattice-free model. We conclude that estimating parameters using this kind of standard procedure can produce misleading results.

Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions

We define a pair-correlation function that can be used to characterize spatiotemporal patterning in experimental images and snapshots from discrete simulations. Unlike previous pair-correlation functions, the pair-correlation functions developed here depend on the location and size of objects. The pair-correlation function can be used to indicate complete spatial randomness, aggregation or segregation over a range of length scales, and quantifies spatial structures such as the shape, size and distribution of clusters. Comparing pair-correlation data for various experimental and simulation images illustrates their potential use as a summary statistic for calibrating discrete models of various physical processes.

Advances in mesoporous molecular sieve MCM-41

The discovery of mesoporous molecular sieves, MCM-41, which possesses a regular hexagonal array of uniform pore openings, aroused a worldwide resurgence in this field. This is not only because it has brought about a series of novel mesoporous materials with various compositions which may find applications in catalysis, adsorption, and guest-host chemistry, but also it has opened a new avenue for creating zeotype materials. This paper presents a comprehensive overview of recent advances in the field of MCM-41. Beginning with the chemistry of surfactant/silicate solutions, progresses made in design and synthesis, characterization, and physicochemical property evaluation of MCM-41 are enumerated. Proposed formation mechanisms are presented, discussed, and identified. Potential applications are reviewed and projected. More than 100 references are cited.

Encapsulation of transition metal species into zeolites and molecular sieves as redox catalysts: Part I-preparation and characterisation of nanosized TiO2, CdO and ZnO semiconductor particles anchored in NaY zeolite

In this paper, we report the preparation and characterisation of nanometer-sized TiO2, CdO, and ZnO semiconductor particles trapped in zeolite NaY. Preparation of these particles was carried out via the traditional ion exchange method and subsequent calcination procedure. It was found that the smaller cations, i.e., Cd2+ and Zn2+ could be readily introduced into the SI′ and SII′ sites located in the sodalite cages, through ion exchange; while this is not the case for the larger Ti species, i.e., Ti monomer [TiO]2+ or dimer [Ti2O3]2+ which were predominantly dispersed on the external surface of zeolite NaY. The subsequent calcination procedure promoted these Ti species to migrate into the internal surface of the supercages. These semiconductor particles confined in NaY zeolite host exhibited a significant blue shift in the UV-VIS absorption spectra, in contrast to the respective bulk semiconductor materials, due to the quantum size effect (QSE). The particle sizes calculated from the UV-VIS optical absorption spectra using the effective mass approximation model are in good agreement with the atomic absorption data.

Molecular characterisation and expression analysis of interferon gamma in response to natural chlamydia infection in the koala, phascolarctos cinereus

Interferon gamma (IFNγ) is a key Th1 cytokine, with a principal role in the immune response against intracellular organisms such as Chlamydia. Along with being responsible for significant morbidity in human populations, Chlamydia is also responsible for wide spread infection and disease in many animal hosts, with reports that many Australian koala subpopulations are endemically infected. An understanding of the role played by IFNγ in koala chlamydial diseases is important for the establishment of better prophylactic and therapeutic approaches against chlamydial infection in this host. A limited number of IFNγ sequences have been published from marsupials and no immune reagents to measure expression have been developed. Through preliminary analysis of the koala transcriptome, we have identified the full coding sequence of the koala IFNγ gene. Transcripts were identified in spleen and lymph node tissue samples. Phylogenetic analysis demonstrated that koala IFNγ is closely related to other marsupial IFNγ sequences and more distantly related to eutherian mammals. To begin to characterise the role of this important cytokine in the koala's response to chlamydial infection, we developed a quantitative real time PCR assay and applied it to a small cohort of koalas with and without active chlamydial disease, revealing significant differences in expression patterns between the groups. Description of the IFNγ sequence from the koala will not only assist in understanding this species' response to its most important pathogen but will also provide further insight into the evolution of the marsupial immune system

Molecular cocrystals of 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine: hydrogen bonding in the structures of the 1:1 adduct with 2-(naphthalen-2-yloxy)acetic acid and the salt with 3,5-dinitrobenzoic acid

The structures of the anhydrous products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with (2-naphthoxy)acetic acid, the 1:1 adduct C8H6BrN3S . C12H10O3 (I) and 3,5-dinitrobenzoic acid, the salt C8H7BrN3S+ C7H3N2O6- (II) have been determined. In the adduct (I), a heterodimer is formed through a cyclic hydrogen-bonding motif [graph set R2/2(8)], involving carboxylic acid O-H...N(hetero)and amine N-H...O(carboxyl) interactions. The heterodimers are essentially planar with a thiadiazole to naphthyl ring dihedral angle of 15.9(2)deg. and the intramolecular thiadiazole to phenyl ring angle of 4.7(2)deg. An amine N-H...N(hetero) hydrogen bond between the heterodimers generates a one-dimensional chain structure extending down [001]. Also present are weak benzene-benzene and naphthalene-naphthalene pi-pi stacking interactions down the b axis [minimum ring centroid separation, 3.936(3) Ang.]. With the salt (II), the cation-anion association is also through a cyclic R2/2(8) motif but involving duplex N-H...O(carboxyl) hydrogen bonds, giving a heterodimer which is close to planar [dihedral angles between the thiadiazole ring and the two benzene rings, 5.00(16)deg. (intra) and 7.23(15)deg. (inter)]. A secondary centrosymmetric cyclic N-H...O(carboxyl) hydrogen-bonding association involving the second amino H-atom generates a heterotetramer. Also present in the crystal are weak pi-pi i-\p interactions between thiadiazolium rings [minimum ring centroid separation, 3.936(3)Ang.], as well as a short Br...O(nitro) interaction [3.314(4)Ang.]. The two structures reported here now provide a total of three crystallographically characterized examples of co-crystalline products from the interaction of 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazole with carboxylic acids, of which only one involves proton-transfer.

Assessment of the molecular structure of natrodufrénite – NaFe2+Fe3+5(PO4)4(OH)6•2(H2O), a secondary pegmatite phosphate mineral from Minas Gerais, Brazil

The mineral natrodufrénite a secondary pegmatite phosphate mineral from Minas Gerais, Brazil, has been studied by a combination of scanning electron microscopy and vibrational spectroscopic techniques. Electron probe analysis shows the formula of the studied mineral as (Na0.88Ca0.12)∑1.00(Mn0.11Mg0.08Ca0.04Zr0.01Cu0.01)∑0.97(Al0.02)∑4.91(PO4)3.96(OH6.15F0.07)6.22⋅2.05(H2O). Raman spectroscopy identifies an intense peak at 1003 cm−1 assigned to the ν1 symmetric stretching mode. Raman bands are observed at 1059 and 1118 cm−1 and are attributed to the ν3 antisymmetric stretching vibrations. A comparison is made with the spectral data of other hydrate hydroxy phosphate minerals including cyrilovite and wardite. Raman bands at 560, 582, 619 and 668 cm−1 are assigned to the ν4 bending modes and Raman bands at 425, 444, 477 and 507 cm−1 are due to the ν2 bending modes. Raman bands in the 2600–3800 cm−1 spectral range are attributed to water and OH stretching vibrations. Vibrational spectroscopy enables aspects of the molecular structure of natrodufrénite to be assessed.

Molecular genetics of migraine

Migraine is a common neurological disorder with a significantly heritable component. It is a complex disease and despite numerous molecular genetic studies, the exact pathogenesis causing the neurological disturbance remains poorly understood. Although several known molecular mechanisms have been associated with an increased risk for developing migraine, there remains significant scope for future studies. The majority of studies have investigated the most plausible candidate genes involved in common migraine pathogenesis utilising criteria that takes into account a combination of physiological functionality in conjunction with regions of genomic association. Thus, far genes involved in neurological, vascular or hormonal pathways have been identified and investigated on this basis. Genome-wide association studies (GWAS) studies have helped to identify novel regions that may be associated with migraine and have aided in providing the basis for further molecular investigations. However, further studies utilising sequencing technologies are required to characterise the genetic basis for migraine.

Identification of molecular genetic factors that influence migraine

Migraine is a common neurological disorder with a strong genetic basis. However, the complex nature of the disorder has meant that few genes or susceptibility loci have been identified and replicated consistently to confirm their involvement in migraine. Approaches to genetic studies of the disorder have included analysis of the rare migraine subtype, familial hemiplegic migraine with several causal genes identified for this severe subtype. However, the exact genetic contributors to the more common migraine subtypes are still to be deciphered. Genome-wide studies such as genome-wide association studies and linkage analysis as well as candidate genes studies have been employed to investigate genes involved in common migraine. Neurological, hormonal and vascular genes are all considered key factors in the pathophysiology of migraine and are a focus of many of these studies. It is clear that the influence of individual genes on the expression of this disorder will vary. Furthermore, the disorder may be dependent on gene–gene and gene–environment interactions that have not yet been considered. In addition, identifying susceptibility genes may require phenotyping methods outside of the International Classification of Headache Disorders II criteria, such as trait component analysis and latent class analysis to better define the ambit of migraine expression.