Vibrational spectroscopic study of the minerals nekoite Ca3Si6O15•7H2O and okenite Ca10Si18O46•18H2O : implications for the molecular structure

Nekoite Ca3Si6O15•7H2O and okenite Ca10Si18O46•18H2O are both hydrated calcium silicates found respectively in contact metamorphosed limestone and in association with zeolites from the alteration of basalts. The minerals form two-Dimensional infinite sheets with other than six-membered rings with 3-, 4-, or 5-membered rings and 8-membered rings. The two minerals have been characterised by Raman, near-infrared and infrared spectroscopy. The Raman spectrum of nekoite is characterised by two sharp peaks at 1061 and 1092 cm-1 with bands of lesser intensity at 974, 994, 1023 and 1132 cm-1. The Raman spectrum of okenite shows an intense single Raman band at 1090 cm-1 with a shoulder band at 1075 cm-1.These bands are assigned to the SiO stretching vibrations of Si2O5 units. Raman water stretching bands of nekoite are observed at 3071, 3380, 3502 and 3567 cm-1. Raman spectrum of okenite shows water stretching bands at 3029, 3284, 3417, 3531 and 3607 cm-1. NIR spectra of the two minerals are subtly different inferring water with different hydrogen bond strengths. By using a Libowitzky empirical formula, hydrogen bond distances based upon these OH stretching vibrations. Two types of hydrogen bonds are distinguished: strong hydrogen bonds associated with structural water and weaker hydrogen bonds assigned to space filling water molecules.

A new tip area function for instrumented nanoindentation at extremely small contact depths

The accuracy of measurement of mechanical properties of a material using instrumented nanoindentation at extremely small penetration depths heavily relies on the determination of the contact area of the indenter. Our experiments have demonstrated that the conventional area function could lead to a significant error when the contact depth was below 40. nm, due to the singularity in the first derivation of the function in this region and thus, the resultant unreasonable sharp peak on the function curve. In this paper, we proposed a new area function that was used to calculate the contact area for the indentations where the contact depths varied from 10 to 40. nm. The experimental results have shown that the new area function has produced better results than the conventional function. © 2011 Elsevier B.V.

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the “reduced-bias” mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of nonhistorical signal, such as from compositional nonstationarity.

Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed “WoodKing” (woodpeckers/rollers/kingfishers), “SCA” (owls/potoos/owlet-nightjars/hummingbirds/swifts), and “Conglomerati.” In general, the support is highly significant with just two exceptions, the owls move from the “SCA” group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the “Conglomerati”. Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.

Vibrational spectroscopic study of multianion mineral clinotyrolite Ca2Cu9[(As,S)O4]4(OH)10•10(H2O)

The molecular structure of the mixed anion mineral Clinotyrolite Ca2Cu9[(As,S)O4]4(OH)10•10(H2O) has been determined by the combination of Raman and infrared spectroscopy. Characteristic bands associated with arsenate, sulphate and hydroxyl units are identified. Broad bands in the OH stretching region are observed and are resolved into component bands. Estimates of hydrogen bond distances were made using a Libowitzky function and both short and long hydrogen bonds are identified. Two intense Raman bands at 842 and ~796 cm-1 are assigned to the ν1 (AsO4)3- symmetric stretching and ν3 (AsO4)3- antisymmetric stretching modes. The comparatively sharp Raman band at 980 cm-1 is assigned to the ν1 (SO4)2- symmetric stretching mode and a broad Raman spectral profile centred upon 1100 cm-1 is attributed to the ν3 (SO4)2- antisymmetric stretching mode.

Children physical activity correlates and parent physical activity do not have a strong association with physical activity amongst adolescents

Background: Physical activity is a key modifiable behavior impacting a number of important health outcomes. The path to developing chronic diseases commonly commences with lifestyle patterns developed during childhood and adolescence. This study examined whether parent physical activity and other factors correlated with physical activity amongst children are associated with self-reported physical activity in adolescents. Methods: A total of 115 adolescents (aged 12-14) and their parents completed questionnaire assessments. Self-reported physical activity was measured amongst adolescents and their parents using the International Physical Activity Questionnaire for Adolescents (IPAQ-A), and the International Physical Activity Questionnaire (IPAQ) respectively. Adolescents also completed the Children’s Physical Activity Correlates (CPAC), which measured factors that have previously demonstrated association with physical activity amongst children. To examine whether parent physical activity or items from the CPAC were associated with self-reported adolescent physical activity, backward step-wise regression was undertaken. One item was removed at each step in descending order of significance (until two tailed item alpha=0.05 was achieved). Results: A total of 93 (80.9%) adolescents and their parents had complete data sets and were included in the analysis. Independent variables were removed in the order: perceptions of parental role modeling; importance of exercise; perceptions of parental encouragement; peer acceptance; fun of physical exertion; perceived competence; parent physical activity; self-esteem; liking of exercise; and parental influence. The only variable remaining in the model was ‘liking of games and sport’ (p=0.003, adjusted r-squared=0.085). Discussion: These findings indicate that factors associated with self-reported physical activity in adolescents are not necessarily the same as younger children (aged 8-11). While ‘liking of games and sport’ was included in the final model, the r-squared value did not indicate a strong association. Interestingly, parent self-reported physical activity was not included in the final model. It is likely that adolescent physical activity may be influenced by a variety of direct and indirect forms of socialization. These findings do support the view that intrinsically motivated themes such as the liking of games and sport take precedence over outside influences, like those presented by parents, in determining youth physical activity behaviors. These findings do not suggest that parents have no influence on adolescent physical activity patterns, but rather, the influence is likely to be more complex than physical activity behavior modeling perceived by the adolescent. Further research in this field is warranted in order to better understand potential contributors to successful physical activity promotion interventions amongst young adolescents.

PLDA based speaker recognition on short utterances

This paper investigates the effects of limited speech data in the context of speaker verification using a probabilistic linear discriminant analysis (PLDA) approach. Being able to reduce the length of required speech data is important to the development of automatic speaker verification system in real world applications. When sufficient speech is available, previous research has shown that heavy-tailed PLDA (HTPLDA) modeling of speakers in the i-vector space provides state-of-the-art performance, however, the robustness of HTPLDA to the limited speech resources in development, enrolment and verification is an important issue that has not yet been investigated. In this paper, we analyze the speaker verification performance with regards to the duration of utterances used for both speaker evaluation (enrolment and verification) and score normalization and PLDA modeling during development. Two different approaches to total-variability representation are analyzed within the PLDA approach to show improved performance in short-utterance mismatched evaluation conditions and conditions for which insufficient speech resources are available for adequate system development. The results presented within this paper using the NIST 2008 Speaker Recognition Evaluation dataset suggest that the HTPLDA system can continue to achieve better performance than Gaussian PLDA (GPLDA) as evaluation utterance lengths are decreased. We also highlight the importance of matching durations for score normalization and PLDA modeling to the expected evaluation conditions. Finally, we found that a pooled total-variability approach to PLDA modeling can achieve better performance than the traditional concatenated total-variability approach for short utterances in mismatched evaluation conditions and conditions for which insufficient speech resources are available for adequate system development.

PLDA based speaker verification with weighted LDA techniques

This paper investigates the use of the dimensionality-reduction techniques weighted linear discriminant analysis (WLDA), and weighted median fisher discriminant analysis (WMFD), before probabilistic linear discriminant analysis (PLDA) modeling for the purpose of improving speaker verification performance in the presence of high inter-session variability. Recently it was shown that WLDA techniques can provide improvement over traditional linear discriminant analysis (LDA) for channel compensation in i-vector based speaker verification systems. We show in this paper that the speaker discriminative information that is available in the distance between pair of speakers clustered in the development i-vector space can also be exploited in heavy-tailed PLDA modeling by using the weighted discriminant approaches prior to PLDA modeling. Based upon the results presented within this paper using the NIST 2008 Speaker Recognition Evaluation dataset, we believe that WLDA and WMFD projections before PLDA modeling can provide an improved approach when compared to uncompensated PLDA modeling for i-vector based speaker verification systems.

An implicit RBF meshless method for a fractal mobile/immobile transport model

Fractional differential equation is used to describe a fractal model of mobile/immobile transport with a power law memory function. This equation is the limiting equation that governs continuous time random walks with heavy tailed random waiting times. In this paper, we firstly propose a finite difference method to discretize the time variable and obtain a semi-discrete scheme. Then we discuss its stability and convergence. Secondly we consider a meshless method based on radial basis functions (RBF) to discretize the space variable. By contrast to conventional FDM and FEM, the meshless method is demonstrated to have distinct advantages: calculations can be performed independent of a mesh, it is more accurate and it can be used to solve complex problems. Finally the convergence order is verified from a numerical example is presented to describe the fractal model of mobile/immobile transport process with different problem domains. The numerical results indicate that the present meshless approach is very effective for modeling and simulating of fractional differential equations, and it has good potential in development of a robust simulation tool for problems in engineering and science that are governed by various types of fractional differential equations.

Heating effects in nanofocusing metal wedges

This paper investigates theoretically and numerically local heating effects in plasmon nanofocusing structures with a particular focus on the sharp free-standing metal wedges. The developed model separates plasmon propagation in the wedge from the resultant heating effects. Therefore, this model is only applicable where the temperature increments in a nanofocusing structure are sufficiently small not to result in significant variations of the metal permittivity in the wedge. The problem is reduced to a one-dimensional heating model with a distributed heat source resulting from plasmon dissipation in the metal wedge. A simple heat conduction equation governing the local heating effects in a nanofocusing structure is derived and solved numerically for plasmonic pulses of different lengths and reasonable energies. Both the possibility of achieving substantial local temperature increments in the wedge (with a significant self-influence of the heating plasmonic pulses), and the possibility of relatively weak heating (to ensure the validity of the previously developed nanofocusing theory) are demonstrated and discussed, including the future applications of the obtained results. Applicability conditions for the developed model are also derived and discussed.

Linear and nonlinear propagation of localised plasmon in metallic nanostructures

A major challenge in modern photonics and nano-optics is the diffraction limit of light which does not allow field localisation into regions with dimensions smaller than half the wavelength. Localisation of light into nanoscale regions (beyond its diffraction limit) has applications ranging from the design of optical sensors and measurement techniques with resolutions as high as a few nanometres, to the effective delivery of optical energy into targeted nanoscale regions such as quantum dots, nano-electronic and nano-optical devices. This field has become a major research direction over the last decade. The use of strongly localised surface plasmons in metallic nanostructures is one of the most promising approaches to overcome this problem. Therefore, the aim of this thesis is to investigate the linear and non-linear propagation of surface plasmons in metallic nanostructures. This thesis will focus on two main areas of plasmonic research –– plasmon nanofocusing and plasmon nanoguiding. Plasmon nanofocusing – The main aim of plasmon nanofocusing research is to focus plasmon energy into nanoscale regions using metallic nanostructures and at the same time achieve strong local field enhancement. Various structures for nanofocusing purposes have been proposed and analysed such as sharp metal wedges, tapered metal films on dielectric substrates, tapered metal rods, and dielectric V-grooves in metals. However, a number of important practical issues related to nanofocusing in these structures still remain unclear. Therefore, one of the main aims of this thesis is to address two of the most important of issues which are the coupling efficiency and heating effects of surface plasmons in metallic nanostructures. The method of analysis developed throughout this thesis is a general treatment that can be applied to a diversity of nanofocusing structures, with results shown here for the specific case of sharp metal wedges. Based on the geometrical optics approximation, it is demonstrated that the coupling efficiency from plasmons generated with a metal grating into the nanofocused symmetric or quasi-symmetric modes may vary between ~50% to ~100% depending on the structural parameters. Optimal conditions for nanofocusing with the view to minimise coupling and dissipative losses are also determined and discussed. It is shown that the temperature near the tip of a metal wedge heated by nanosecond plasmonic pulses can increase by several hundred degrees Celsius. This temperature increase is expected to lead to nonlinear effects, self-influence of the focused plasmon, and ultimately self-destruction of the metal tip. This thesis also investigates a different type of nanofocusing structure which consists of a tapered high-index dielectric layer resting on a metal surface. It is shown that the nanofocusing mechanism that occurs in this structure is somewhat different from other structures that have been considered thus far. For example, the surface plasmon experiences significant backreflection and mode transformation at a cut-off thickness. In addition, the reflected plasmon shows negative refraction properties that have not been observed in other nanofocusing structures considered to date. Plasmon nanoguiding – Guiding surface plasmons using metallic nanostructures is important for the development of highly integrated optical components and circuits which are expected to have a superior performance compared to their electronicbased counterparts. A number of different plasmonic waveguides have been considered over the last decade including the recently considered gap and trench plasmon waveguides. The gap and trench plasmon waveguides have proven to be difficult to fabricate. Therefore, this thesis will propose and analyse four different modified gap and trench plasmon waveguides that are expected to be easier to fabricate, and at the same time acquire improved propagation characteristics of the guided mode. In particular, it is demonstrated that the guided modes are significantly screened by the extended metal at the bottom of the structure. This is important for the design of highly integrated optics as it provides the opportunity to place two waveguides close together without significant cross-talk. This thesis also investigates the use of plasmonic nanowires to construct a Fabry-Pérot resonator/interferometer. It is shown that the resonance effect can be achieved with the appropriate resonator length and gap width. Typical quality factors of the Fabry- Pérot cavity are determined and explained in terms of radiative and dissipative losses. The possibility of using a nanowire resonator for the design of plasmonic filters with close to ~100% transmission is also demonstrated. It is expected that the results obtained in this thesis will play a vital role in the development of high resolution near field microscopy and spectroscopy, new measurement techniques and devices for single molecule detection, highly integrated optical devices, and nanobiotechnology devices for diagnostics of living cells.

Raman spectroscopic study of the minerals apophyllite-(KF) KCa4Si8O20F.8H2O and apophyllite-(KOH) KCa4Si8O20(F,OH).8H2O

Raman spectroscopy complimented with infrared spectroscopy has been used to study the variation in molecular structure of two minerals of the apophyllite mineral group, namely apophyllite-(KF)KCa4Si8O20F.8H2O and apophyllite-(KOH) KCa4Si8O20(F,OH).8H2O. apophyllite-(KF) and apophyllite-(KOH) are different minerals only because of the difference in the percentage of fluorine to hydroxyl ions. The Raman spectra are dominated by a very intense sharp peak at 1059 cm -1. A band at around 846 cm -1 is assigned to the water librational mode. It is proposed that the difference between apophyllite-(KF) and apophyllite-(KOH) is the observation of two Raman bands in the OH stretching region at around 3563 and 3625 cm -1. Multiple water stretching and bending modes are observed showing that there is much variation in hydrogen bonding between water and the silicate surfaces.

Prognostic significance of IGF and ECM induced signalling proteins in breast cancer patients

Breast cancer is a leading contributor to the burden of disease in Australia. Fortunately, the recent introduction of diverse therapeutic strategies have improved the survival outcome for many women. Despite this, the clinical management of breast cancer remains problematic as not all approaches are sufficiently sophisticated to take into account the heterogeneity of this disease and are unable to predict disease progression, in particular, metastasis. As such, women with good prognostic outcomes are exposed to the side effects of therapies without added benefit. Furthermore, women with aggressive disease for whom these advanced treatments would deliver benefit cannot be distinguished and opportunities for more intensive or novel treatment are lost. This study is designed to identify novel factors associated with disease progression, and the potential to inform disease prognosis. Frequently overlooked, yet common mediators of disease are the interactions that take place between the insulin-like growth factor (IGF) system and the extracellular matrix (ECM). Our laboratory has previously demonstrated that multiprotein insulin-like growth factor-I (IGF-I): insulin-like growth factor binding protein (IGFBP): vitronectin (VN) complexes stimulate migration of breast cancer cells in vitro, via the cooperative involvement of the insulin-like growth factor type I receptor (IGF-IR) and VN-binding integrins. However, the effects of IGF and ECM protein interactions on the dissemination and progression of breast cancer in vivo are unknown. It was hypothesised that interactions between proteins required for IGF induced signalling events and those within the ECM contribute to breast cancer metastasis and are prognostic and predictive indicators of patient outcome. To address this hypothesis, semiquantitative immunohistochemistry (IHC) analyses were performed to compare the extracellular and subcellular distribution of IGF and ECM induced signalling proteins between matched normal, primary cancer, and metastatic cancer among archival formalin-fixed paraffin-embedded (FFPE) breast tissue samples collected from women attending the Princess Alexandra Hospital, Brisbane. Multivariate Cox proportional hazards (PH) regression survival models in conjunction with a modified „purposeful selection of covariates. method were applied to determine the prognostic potential of these proteins. This study provides the first in-depth, compartmentalised analysis of the distribution of IGF and ECM induced signalling proteins. As protein function and protein localisation are closely correlated, these findings provide novel insights into IGF signalling and ECM protein function during breast cancer development and progression. Distinct IGF signalling and ECM protein immunoreactivity was observed in the stroma and/or in subcellular locations in normal breast, primary cancer and metastatic cancer tissues. Analysis of the presence and location of stratifin (SFN) suggested a causal relationship in ECM remodelling events during breast cancer development and progression. The results of this study have also suggested that fibronectin (FN) and ¥â1 integrin are important for the formation of invadopodia and epithelial-to-mesenchymal transition (EMT) events. Our data also highlighted the importance of the temporal and spatial distribution of IGF induced signalling proteins in breast cancer metastasis; in particular, SFN, enhancer-of-split and hairy-related protein 2 (SHARP-2), total-akt/protein kinase B 1 (Total-AKT1), phosphorylated-akt/protein kinase B (P-AKT), extracellular signal-related kinase-1 and extracellular signal-related kinase-2 (ERK1/2) and phosphorylated-extracellular signal-related kinase-1 and extracellular signal-related kinase-2 (P-ERK1/2). Multivariate survival models were created from the immunohistochemical data. These models were found to fit well with these data with very high statistical confidence. Numerous prognostic confounding effects and effect modifications were identified among elements of the ECM and IGF signalling cascade and corroborate the survival models. This finding provides further evidence for the prognostic potential of IGF and ECM induced signalling proteins. In addition, the adjusted measures of associations obtained in this study have strengthened the validity and utility of the resulting models. The findings from this study provide insights into the biological interactions that occur during the development of breast tissue and contribute to disease progression. Importantly, these multivariate survival models could provide important prognostic and predictive indicators that assist the clinical management of breast disease, namely in the early identification of cancers with a propensity to metastasise, and/or recur following adjuvant therapy. The outcomes of this study further inform the development of new therapeutics to aid patient recovery. The findings from this study have widespread clinical application in the diagnosis of disease and prognosis of disease progression, and inform the most appropriate clinical management of individuals with breast cancer.

The benefits of tree-based models for stock selection

The identification of the primary drivers of stock returns has been of great interest to both financial practitioners and academics alike for many decades. Influenced by classical financial theories such as the CAPM (Sharp, 1964; Lintner, 1965) and APT (Ross, 1976), a linear relationship is conventionally assumed between company characteristics as derived from their financial accounts and forward returns. Whilst this assumption may be a fair approximation to the underlying structural relationship, it is often adopted for the purpose of convenience. It is actually quite rare that the assumptions of distributional normality and a linear relationship are explicitly assessed in advance even though this information would help to inform the appropriate choice of modelling technique. Non-linear models have nevertheless been applied successfully to the task of stock selection in the past (Sorensen et al, 2000). However, their take-up by the investment community has been limited despite the fact that researchers in other fields have found them to be a useful way to express knowledge and aid decision-making...

Integrated sustainable urban infrastructure management : the Brisbane urban growth model

Sustainable urban development and the liveability of a city are increasingly important issues in the context of land use planning and infrastructure management. In recent years, the promotion of sustainable urban development in Australia and overseas is facing various physical, socioeconomic and environmental challenges. These challenges and problems arise from the lack of capability of local governments to accommodate the needs of the population and economy in a relatively short timeframe. The planning of economic growth and development is often dealt with separately and not included in the conventional land use planning process. There is also a sharp rise in the responsibilities and roles of local government for infrastructure planning and management. This increase in responsibilities means that local elected officials and urban planners have less time to prepare background information and make decisions. The Brisbane Urban Growth Model has proven initially successful in providing a dynamic platform to ensure timely and coordinated delivery of urban infrastructure. Most importantly, this model is the first step for local governments in moving toward a systematic approach to pursuing sustainable and effective urban infrastructure management.