Tree species diversity and ecosystem function: Can tropical multi-species plantations generate greater productivity?

Results from the humid tropics of Australia demonstrate that diverse plantations can achieve greater productivity than monocultures. We found that increases in both the observed species number and the effective species richness were significantly related to increased levels of productivity as measured by stand basal area or mean individual tree basal area. Four of five plantation species were more productive in mixtures with other species than in monocultures, offering on average, a 55% increase in mean tree basal area. A general linear model suggests that species richness had a significant effect on mean individual tree basal area when environmental variables were included in the model. As monoculture plantations are currently the preferred reforestation method throughout the tropics these results suggest that significant productivity and ecological gains could be made if multi-species plantations are more broadly pursued. (c) 2006 Elsevier B.V. All rights reserved.

A simple method to localise pleiotropic susceptibility loci using univariate linkage analyses of correlated traits

Univariate linkage analysis is used routinely to localise genes for human complex traits. Often, many traits are analysed but the significance of linkage for each trait is not corrected for multiple trait testing, which increases the experiment-wise type-I error rate. In addition, univariate analyses do not realise the full power provided by multivariate data sets. Multivariate linkage is the ideal solution but it is computationally intensive, so genome-wide analysis and evaluation of empirical significance are often prohibitive. We describe two simple methods that efficiently alleviate these caveats by combining P-values from multiple univariate linkage analyses. The first method estimates empirical pointwise and genome-wide significance between one trait and one marker when multiple traits have been tested. It is as robust as an appropriate Bonferroni adjustment, with the advantage that no assumptions are required about the number of independent tests performed. The second method estimates the significance of linkage between multiple traits and one marker and, therefore, it can be used to localise regions that harbour pleiotropic quantitative trait loci (QTL). We show that this method has greater power than individual univariate analyses to detect a pleiotropic QTL across different situations. In addition, when traits are moderately correlated and the QTL influences all traits, it can outperform formal multivariate VC analysis. This approach is computationally feasible for any number of traits and was not affected by the residual correlation between traits. We illustrate the utility of our approach with a genome scan of three asthma traits measured in families with a twin proband.

Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.

An equivalent distributed magnetic current based FDTD method for the calculation of e-fields induced by gradient coils in MRI

This paper evaluates a low-frequency FDTD method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current (DEMC) is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretizing of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modeling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multilayered spherical phantom model and a complete body model.

Boosting the tree augmented naive bayes classifier

The Tree Augmented Naïve Bayes (TAN) classifier relaxes the sweeping independence assumptions of the Naïve Bayes approach by taking account of conditional probabilities. It does this in a limited sense, by incorporating the conditional probability of each attribute given the class and (at most) one other attribute. The method of boosting has previously proven very effective in improving the performance of Naïve Bayes classifiers and in this paper, we investigate its effectiveness on application to the TAN classifier.

A new indexing method for high dimensional dataset

Indexing high dimensional datasets has attracted extensive attention from many researchers in the last decade. Since R-tree type of index structures are known as suffering curse of dimensionality problems, Pyramid-tree type of index structures, which are based on the B-tree, have been proposed to break the curse of dimensionality. However, for high dimensional data, the number of pyramids is often insufficient to discriminate data points when the number of dimensions is high. Its effectiveness degrades dramatically with the increase of dimensionality. In this paper, we focus on one particular issue of curse of dimensionality; that is, the surface of a hypercube in a high dimensional space approaches 100% of the total hypercube volume when the number of dimensions approaches infinite. We propose a new indexing method based on the surface of dimensionality. We prove that the Pyramid tree technology is a special case of our method. The results of our experiments demonstrate clear priority of our novel method.

Efficient spatial clustering algorithm using binary tree

In this paper we present an efficient k-Means clustering algorithm for two dimensional data. The proposed algorithm re-organizes dataset into a form of nested binary tree*. Data items are compared at each node with only two nearest means with respect to each dimension and assigned to the one that has the closer mean. The main intuition of our research is as follows: We build the nested binary tree. Then we scan the data in raster order by in-order traversal of the tree. Lastly we compare data item at each node to the only two nearest means to assign the value to the intendant cluster. In this way we are able to save the computational cost significantly by reducing the number of comparisons with means and also by the least use to Euclidian distance formula. Our results showed that our method can perform clustering operation much faster than the classical ones. © Springer-Verlag Berlin Heidelberg 2005

Towards more personalized web: Extraction and integration of dynamic content from the Web

Information and content integration are believed to be a possible solution to the problem of information overload in the Internet. The article is an overview of a simple solution for integration of information and content on the Web. Previous approaches to content extraction and integration are discussed, followed by introduction of a novel technology to deal with the problems, based on XML processing. The article includes lessons learned from solving issues of changing webpage layout, incompatibility with HTML standards and multiplicity of the results returned. The method adopting relative XPath queries over DOM tree proves to be more robust than previous approaches to Web information integration. Furthermore, the prototype implementation demonstrates the simplicity that enables non-professional users to easily adopt this approach in their day-to-day information management routines.

A D-optimal designed population pharmacokinetic study of itraconazole capsules and solution in adults with cystic fibrosis

Background: Oral itraconazole (ITRA) is used for the treatment of allergic bronchopulmonary aspergillosis in patients with cystic fibrosis (CF) because of its antifungal activity against Aspergillus species. ITRA has an active hydroxy-metabolite (OH-ITRA) which has similar antifungal activity. ITRA is a highly lipophilic drug which is available in two different oral formulations, a capsule and an oral solution. It is reported that the oral solution has a 60% higher relative bioavailability. The influence of altered gastric physiology associated with CF on the pharmacokinetics (PK) of ITRA and its metabolite has not been previously evaluated. Objectives: 1) To estimate the population (pop) PK parameters for ITRA and its active metabolite OH-ITRA including relative bioavailability of the parent after administration of the parent by both capsule and solution and 2) to assess the performance of the optimal design. Methods: The study was a cross-over design in which 30 patients received the capsule on the first occasion and 3 days later the solution formulation. The design was constrained to have a maximum of 4 blood samples per occasion for estimation of the popPK of both ITRA and OH-ITRA. The sampling times for the population model were optimized previously using POPT v.2.0.[1] POPT is a series of applications that run under MATLAB and provide an evaluation of the information matrix for a nonlinear mixed effects model given a particular design. In addition it can be used to optimize the design based on evaluation of the determinant of the information matrix. The model details for the design were based on prior information obtained from the literature, which suggested that ITRA may have either linear or non-linear elimination. The optimal sampling times were evaluated to provide information for both competing models for the parent and metabolite and for both capsule and solution simultaneously. Blood samples were assayed by validated HPLC.[2] PopPK modelling was performed using FOCE with interaction under NONMEM, version 5 (level 1.1; GloboMax LLC, Hanover, MD, USA). The PK of ITRA and OH‑ITRA was modelled simultaneously using ADVAN 5. Subsequently three methods were assessed for modelling concentrations less than the LOD (limit of detection). These methods (corresponding to methods 5, 6 & 4 from Beal[3], respectively) were (a) where all values less than LOD were assigned to half of LOD, (b) where the closest missing value that is less than LOD was assigned to half the LOD and all previous (if during absorption) or subsequent (if during elimination) missing samples were deleted, and (c) where the contribution of the expectation of each missing concentration to the likelihood is estimated. The LOD was 0.04 mg/L. The final model evaluation was performed via bootstrap with re-sampling and a visual predictive check. The optimal design and the sampling windows of the study were evaluated for execution errors and for agreement between the observed and predicted standard errors. Dosing regimens were simulated for the capsules and the oral solution to assess their ability to achieve ITRA target trough concentration (Cmin,ss of 0.5-2 mg/L) or a combined Cmin,ss for ITRA and OH-ITRA above 1.5mg/L. Results and Discussion: A total of 241 blood samples were collected and analysed, 94% of them were taken within the defined optimal sampling windows, of which 31% where taken within 5 min of the exact optimal times. Forty six per cent of the ITRA values and 28% of the OH-ITRA values were below LOD. The entire profile after administration of the capsule for five patients was below LOD and therefore the data from this occasion was omitted from estimation. A 2-compartment model with 1st order absorption and elimination best described ITRA PK, with 1st order metabolism of the parent to OH-ITRA. For ITRA the clearance (ClItra/F) was 31.5 L/h; apparent volumes of central and peripheral compartments were 56.7 L and 2090 L, respectively. Absorption rate constants for capsule (kacap) and solution (kasol) were 0.0315 h-1 and 0.125 h-1, respectively. Comparative bioavailability of the capsule was 0.82. There was no evidence of nonlinearity in the popPK of ITRA. No screened covariate significantly improved the fit to the data. The results of the parameter estimates from the final model were comparable between the different methods for accounting for missing data, (M4,5,6)[3] and provided similar parameter estimates. The prospective application of an optimal design was found to be successful. Due to the sampling windows, most of the samples could be collected within the daily hospital routine, but still at times that were near optimal for estimating the popPK parameters. The final model was one of the potential competing models considered in the original design. The asymptotic standard errors provided by NONMEM for the final model and empirical values from bootstrap were similar in magnitude to those predicted from the Fisher Information matrix associated with the D-optimal design. Simulations from the final model showed that the current dosing regimen of 200 mg twice daily (bd) would provide a target Cmin,ss (0.5-2 mg/L) for only 35% of patients when administered as the solution and 31% when administered as capsules. The optimal dosing schedule was 500mg bd for both formulations. The target success for this dosing regimen was 87% for the solution with an NNT=4 compared to capsules. This means, for every 4 patients treated with the solution one additional patient will achieve a target success compared to capsule but at an additional cost of AUD $220 per day. The therapeutic target however is still doubtful and potential risks of these dosing schedules need to be assessed on an individual basis. Conclusion: A model was developed which described the popPK of ITRA and its main active metabolite OH-ITRA in adult CF after administration of both capsule and solution. The relative bioavailability of ITRA from the capsule was 82% that of the solution, but considerably more variable. To incorporate missing data, using the simple Beal method 5 (using half LOD for all samples below LOD) provided comparable results to the more complex but theoretically better Beal method 4 (integration method). The optimal sparse design performed well for estimation of model parameters and provided a good fit to the data.

A new relaxation method for roll forming problems

Finite element analysis (FEA) of nonlinear problems in solid mechanics is a time consuming process, but it can deal rigorously with the problems of both geometric, contact and material nonlinearity that occur in roll forming. The simulation time limits the application of nonlinear FEA to these problems in industrial practice, so that most applications of nonlinear FEA are in theoretical studies and engineering consulting or troubleshooting. Instead, quick methods based on a global assumption of the deformed shape have been used by the roll-forming industry. These approaches are of limited accuracy. This paper proposes a new form-finding method - a relaxation method to solve the nonlinear problem of predicting the deformed shape due to plastic deformation in roll forming. This method involves applying a small perturbation to each discrete node in order to update the local displacement field, while minimizing plastic work. This is iteratively applied to update the positions of all nodes. As the method assumes a local displacement field, the strain and stress components at each node are calculated explicitly. Continued perturbation of nodes leads to optimisation of the displacement field. Another important feature of this paper is a new approach to consideration of strain history. For a stable and continuous process such as rolling and roll forming, the strain history of a point is represented spatially by the states at a row of nodes leading in the direction of rolling to the current one. Therefore the increment of the strain components and the work-increment of a point can be found without moving the object forward. Using this method we can find the solution for rolling or roll forming in just one step. This method is expected to be faster than commercial finite element packages by eliminating repeated solution of large sets of simultaneous equations and the need to update boundary conditions that represent the rolls.

Monitoring the condition of savanna riparian zones in Northern Australia using high spatial resolution imagery and a field based rapid assessment method

Government agencies responsible for riparian environments are assessing the combined utility of field survey and remote sensing for mapping and monitoring indicators of riparian zone condition. The objective of this work was to compare the Tropical Rapid Appraisal of Riparian Condition (TRARC) method to a satellite image based approach. TRARC was developed for rapid assessment of the environmental condition of savanna riparian zones. The comparison assessed mapping accuracy, representativeness of TRARC assessment, cost-effectiveness, and suitability for multi-temporal analysis. Two multi-spectral QuickBird images captured in 2004 and 2005 and coincident field data covering sections of the Daly River in the Northern Territory, Australia were used in this work. Both field and image data were processed to map riparian health indicators (RHIs) including percentage canopy cover, organic litter, canopy continuity, stream bank stability, and extent of tree clearing. Spectral vegetation indices, image segmentation and supervised classification were used to produce RHI maps. QuickBird image data were used to examine if the spatial distribution of TRARC transects provided a representative sample of ground based RHI measurements. Results showed that TRARC transects were required to cover at least 3% of the study area to obtain a representative sample. The mapping accuracy and costs of the image based approach were compared to those of the ground based TRARC approach. Results proved that TRARC was more cost-effective at smaller scales (1-100km), while image based assessment becomes more feasible at regional scales (100-1000km). Finally, the ability to use both the image and field based approaches for multi-temporal analysis of RHIs was assessed. Change detection analysis demonstrated that image data can provide detailed information on gradual change, while the TRARC method was only able to identify more gross scale changes. In conclusion, results from both methods were considered to complement each other if used at appropriate spatial scales.

Canonical solution groups of a homomorphism : manipulator kinematics, nonparametric regression and distributed object systems

The kinematic mapping of a rigid open-link manipulator is a homomorphism between Lie groups. The homomorphisrn has solution groups that act on an inverse kinematic solution element. A canonical representation of solution group operators that act on a solution element of three and seven degree-of-freedom (do!) dextrous manipulators is determined by geometric analysis. Seven canonical solution groups are determined for the seven do! Robotics Research K-1207 and Hollerbach arms. The solution element of a dextrous manipulator is a collection of trivial fibre bundles with solution fibres homotopic to the Torus. If fibre solutions are parameterised by a scalar, a direct inverse funct.ion that maps the scalar and Cartesian base space coordinates to solution element fibre coordinates may be defined. A direct inverse pararneterisation of a solution element may be approximated by a local linear map generated by an inverse augmented Jacobian correction of a linear interpolation. The action of canonical solution group operators on a local linear approximation of the solution element of inverse kinematics of dextrous manipulators generates cyclical solutions. The solution representation is proposed as a model of inverse kinematic transformations in primate nervous systems. Simultaneous calibration of a composition of stereo-camera and manipulator kinematic models is under-determined by equi-output parameter groups in the composition of stereo-camera and Denavit Hartenberg (DH) rnodels. An error measure for simultaneous calibration of a composition of models is derived and parameter subsets with no equi-output groups are determined by numerical experiments to simultaneously calibrate the composition of homogeneous or pan-tilt stereo-camera with DH models. For acceleration of exact Newton second-order re-calibration of DH parameters after a sequential calibration of stereo-camera and DH parameters, an optimal numerical evaluation of DH matrix first order and second order error derivatives with respect to a re-calibration error function is derived, implemented and tested. A distributed object environment for point and click image-based tele-command of manipulators and stereo-cameras is specified and implemented that supports rapid prototyping of numerical experiments in distributed system control. The environment is validated by a hierarchical k-fold cross validated calibration to Cartesian space of a radial basis function regression correction of an affine stereo model. Basic design and performance requirements are defined for scalable virtual micro-kernels that broker inter-Java-virtual-machine remote method invocations between components of secure manageable fault-tolerant open distributed agile Total Quality Managed ISO 9000+ conformant Just in Time manufacturing systems.

Antimicrobial efficacy of chlorhexidine digluconate alone and in combination with eucalyptus oil, tea tree oil and thymol against planktonic and biofilm cultures of Staphylococcus epidermidis

Objectives Effective skin antisepsis and disinfection of medical devices are key factors in preventing many healthcare-acquired infections associated with skin microorganisms, particularly Staphylococcus epidermidis. The aim of this study was to investigate the antimicrobial efficacy of chlorhexidine digluconate (CHG), a widely used antiseptic in clinical practice, alone and in combination with tea tree oil (TTO), eucalyptus oil (EO) and thymol against planktonic and biofilm cultures of S. epidermidis. Methods Antimicrobial susceptibility assays against S. epidermidis in a suspension and in a biofilm mode of growth were performed with broth microdilution and ATP bioluminescence methods, respectively. Synergy of antimicrobial agents was evaluated with the chequerboard method. Results CHG exhibited antimicrobial activity against S. epidermidis in both suspension and biofilm (MIC 2–8 mg/L). Of the essential oils thymol exhibited the greatest antimicrobial efficacy (0.5–4 g/L) against S. epidermidis in suspension and biofilm followed by TTO (2–16 g/L) and EO (4–64 g/L). MICs of CHG and EO were reduced against S. epidermidis biofilm when in combination (MIC of 8 reduced to 0.25–1 mg/L and MIC of 32–64 reduced to 4 g/L for CHG and EO, respectively). Furthermore, the combination of EO with CHG demonstrated synergistic activity against S. epidermidis biofilm with a fractional inhibitory concentration index of <0.5. Conclusions The results from this study suggest that there may be a role for essential oils, in particular EO, for improved skin antisepsis when combined with CHG.

Hairpin vortex solution in planar Couette flow: a tapestry of knotted vortices

A numerical continuation method has been carried out seeking solutions for two distinct flow configurations, planar Couette flow (PCF) and laterally heated flow in a vertical slot (LHF). We found that the spanwise vortex solution in LHF identifies a new solution in PCF. The vortical structure of our new solution has the shape of a hairpin observed ubiquitously in high-Reynolds-number turbulent flow, and we believe this discovery may provide the paradigm for a hierarchical organization of coherent structures in turbulent shear layers.

Expert systems for fault tree synthesis

Hazard and operability (HAZOP) studies on chemical process plants are very time consuming, and often tedious, tasks. The requirement for HAZOP studies is that a team of experts systematically analyse every conceivable process deviation, identifying possible causes and any hazards that may result. The systematic nature of the task, and the fact that some team members may be unoccupied for much of the time, can lead to tedium, which in turn may lead to serious errors or omissions. An aid to HAZOP are fault trees, which present the system failure logic graphically such that the study team can readily assimilate their findings. Fault trees are also useful to the identification of design weaknesses, and may additionally be used to estimate the likelihood of hazardous events occurring. The one drawback of fault trees is that they are difficult to generate by hand. This is because of the sheer size and complexity of modern process plants. The work in this thesis proposed a computer-based method to aid the development of fault trees for chemical process plants. The aim is to produce concise, structured fault trees that are easy for analysts to understand. Standard plant input-output equation models for major process units are modified such that they include ancillary units and pipework. This results in a reduction in the nodes required to represent a plant. Control loops and protective systems are modelled as operators which act on process variables. This modelling maintains the functionality of loops, making fault tree generation easier and improving the structure of the fault trees produced. A method, called event ordering, is proposed which allows the magnitude of deviations of controlled or measured variables to be defined in terms of the control loops and protective systems with which they are associated.