Robotics toolbox for MATLAB, release 9 [Software]

The ninth release of the Toolbox, represents over fifteen years of development and a substantial level of maturity. This version captures a large number of changes and extensions generated over the last two years which support my new book “Robotics, Vision & Control”. The Toolbox has always provided many functions that are useful for the study and simulation of classical arm-type robotics, for example such things as kinematics, dynamics, and trajectory generation. The Toolbox is based on a very general method of representing the kinematics and dynamics of serial-link manipulators. These parameters are encapsulated in MATLAB ® objects - robot objects can be created by the user for any serial-link manipulator and a number of examples are provided for well know robots such as the Puma 560 and the Stanford arm amongst others. The Toolbox also provides functions for manipulating and converting between datatypes such as vectors, homogeneous transformations and unit-quaternions which are necessary to represent 3-dimensional position and orientation. This ninth release of the Toolbox has been significantly extended to support mobile robots. For ground robots the Toolbox includes standard path planning algorithms (bug, distance transform, D*, PRM), kinodynamic planning (RRT), localization (EKF, particle filter), map building (EKF) and simultaneous localization and mapping (EKF), and a Simulink model a of non-holonomic vehicle. The Toolbox also including a detailed Simulink model for a quadcopter flying robot.

Spatio-temporal patterns of Barmah Forest virus disease in Queensland, Australia

Background Barmah Forest virus (BFV) disease is a common and wide-spread mosquito-borne disease in Australia. This study investigated the spatio-temporal patterns of BFV disease in Queensland, Australia using geographical information system (GIS) tools and geostatistical analysis. Methods/Principal Findings We calculated the incidence rates and standardised incidence rates of BFV disease. Moran's I statistic was used to assess the spatial autocorrelation of BFV incidences. Spatial dynamics of BFV disease was examined using semi-variogram analysis. Interpolation techniques were applied to visualise and display the spatial distribution of BFV disease in statistical local areas (SLAs) throughout Queensland. Mapping of BFV disease by SLAs reveals the presence of substantial spatio-temporal variation over time. Statistically significant differences in BFV incidence rates were identified among age groups (χ2 = 7587, df = 7327,p<0.01). There was a significant positive spatial autocorrelation of BFV incidence for all four periods, with the Moran's I statistic ranging from 0.1506 to 0.2901 (p<0.01). Semi-variogram analysis and smoothed maps created from interpolation techniques indicate that the pattern of spatial autocorrelation was not homogeneous across the state. Conclusions/Significance This is the first study to examine spatial and temporal variation in the incidence rates of BFV disease across Queensland using GIS and geostatistics. The BFV transmission varied with age and gender, which may be due to exposure rates or behavioural risk factors. There are differences in the spatio-temporal patterns of BFV disease which may be related to local socio-ecological and environmental factors. These research findings may have implications in the BFV disease control and prevention programs in Queensland.

A tissue engineering solution for segmental defect regeneration in load-bearing long bones

The reconstruction of large defects (>10 mm) in humans usually relies on bone graft transplantation. Limiting factors include availability of graft material, comorbidity, and insufficient integration into the damaged bone. We compare the gold standard autograft with biodegradable composite scaffolds consisting of medical-grade polycaprolactone and tricalcium phosphate combined with autologous bone marrow-derived mesenchymal stem cells (MSCs) or recombinant human bone morphogenetic protein 7 (rhBMP-7). Critical-sized defects in sheep - a model closely resembling human bone formation and structure - were treated with autograft, rhBMP-7, or MSCs. Bridging was observed within 3 months for both the autograft and the rhBMP-7 treatment. After 12 months, biomechanical analysis and microcomputed tomography imaging showed significantly greater bone formation and superior strength for the biomaterial scaffolds loaded with rhBMP-7 compared to the autograft. Axial bone distribution was greater at the interfaces. With rhBMP-7, at 3 months, the radial bone distribution within the scaffolds was homogeneous. At 12 months, however, significantly more bone was found in the scaffold architecture, indicating bone remodeling. Scaffolds alone or with MSC inclusion did not induce levels of bone formation comparable to those of the autograft and rhBMP-7 groups. Applied clinically, this approach using rhBMP-7 could overcome autograft-associated limitations.

Characteristics of foot structure and footwear associated with hallux valgus : a systematic review

Objective Factors associated with the development of hallux valgus (HV) are multifactorial and remain unclear. The objective of this systematic review and meta-analysis was to investigate characteristics of foot structure and footwear associated with HV. Design Electronic databases (Medline, Embase, and CINAHL) were searched to December 2010. Cross-sectional studies with a valid definition of HV and a non-HV comparison group were included. Two independent investigators quality rated all included papers. Effect sizes and 95% confidence intervals (CIs) were calculated (standardized mean differences (SMDs) for continuous data and risk ratios (RRs) for dichotomous data). Where studies were homogeneous, pooling of SMDs was conducted using random effects models. Results A total of 37 papers (34 unique studies) were quality rated. After exclusion of studies without reported measurement reliability for associated factors, data were extracted and analysed from 16 studies reporting results for 45 different factors. Significant factors included: greater first intermetatarsal angle (pooled SMD = 1.5, CI: 0.88–2.1), longer first metatarsal (pooled SMD = 1.0, CI: 0.48–1.6), round first metatarsal head (RR: 3.1–5.4), and lateral sesamoid displacement (RR: 5.1–5.5). Results for clinical factors (e.g., first ray mobility, pes planus, footwear) were less conclusive regarding their association with HV. Conclusions Although conclusions regarding causality cannot be made from cross-sectional studies, this systematic review highlights important factors to monitor in HV assessment and management. Further studies with rigorous methodology are warranted to investigate clinical factors associated with HV.

Dirichlet process mixture models for unsupervised clustering of symptoms in Parkinson's disease

In this paper, the goal of identifying disease subgroups based on differences in observed symptom profile is considered. Commonly referred to as phenotype identification, solutions to this task often involve the application of unsupervised clustering techniques. In this paper, we investigate the application of a Dirichlet Process mixture (DPM) model for this task. This model is defined by the placement of the Dirichlet Process (DP) on the unknown components of a mixture model, allowing for the expression of uncertainty about the partitioning of observed data into homogeneous subgroups. To exemplify this approach, an application to phenotype identification in Parkinson’s disease (PD) is considered, with symptom profiles collected using the Unified Parkinson’s Disease Rating Scale (UPDRS). Clustering, Dirichlet Process mixture, Parkinson’s disease, UPDRS.

Analysis of a negatively buoyant jet

The behavior of plane fountains, resulting from the injection of dense fluid (water) upwards into a large container of homogeneous fluid of lower density (air),was investigated. In this study the behavior of fountains was examined numerically and experimentally for different Froude and Reynolds numbers. The flow rate and nozzle diameter of the inlet of the fountain was varied to cover a wide range of Reynolds and Froude numbers. The effect of inclination angle of the inlet for different nozzle diameter and flow rate on fountain behavior was observed. It was found that the height of the fountain greatly depends on Froude number. An empirical correlation was developed for non-dimensional fountain height with Froude number. However the non-dimensional fountain height can more accurately be represented when regressed with both Reynolds and Froude number by the following relationship H/r=exp(5.94)*Re^-0.72*Fr^2.26. The result are compared with previous numerical and experimental results and found to be consistent.

Poly(2-oxazoline) hydrogel monoliths via thiol-ene coupling

Copoly(2-oxazoline)s, prepared by cationic ring-opening polymerization of 2-(dec-9-enyl)-2-oxazoline with either 2-methyl-2-oxazoline or 2-ethyl-2-oxazoline, have been crosslinked with small dithiol molecules under UV-irradiation to form homogeneous networks. In-situ monitoring of the crosslinking reaction by photo-rheology revealed network formation within minutes. The degree of swelling in water was found to be tunable by the hydrophilicity of the starting macromers and the proportion of alkene side arms. Furthermore, degradable hydrogels have been prepared based on a hydrolytically cleavable dithiol crosslinker.

Spatial and temporal analysis of Barmah Forest virus disease in Queensland, Australia

Barmah Forest virus (BFV) disease is one of the most widespread mosquito-borne diseases in Australia. The number of outbreaks and the incidence rate of BFV in Australia have attracted growing concerns about the spatio-temporal complexity and underlying risk factors of BFV disease. A large number of notifications has been recorded continuously in Queensland since 1992. Yet, little is known about the spatial and temporal characteristics of the disease. I aim to use notification data to better understand the effects of climatic, demographic, socio-economic and ecological risk factors on the spatial epidemiology of BFV disease transmission, develop predictive risk models and forecast future disease risks under climate change scenarios. Computerised data files of daily notifications of BFV disease and climatic variables in Queensland during 1992-2008 were obtained from Queensland Health and Australian Bureau of Meteorology, respectively. Projections on climate data for years 2025, 2050 and 2100 were obtained from Council of Scientific Industrial Research Organisation. Data on socio-economic, demographic and ecological factors were also obtained from relevant government departments as follows: 1) socio-economic and demographic data from Australian Bureau of Statistics; 2) wetlands data from Department of Environment and Resource Management and 3) tidal readings from Queensland Department of Transport and Main roads. Disease notifications were geocoded and spatial and temporal patterns of disease were investigated using geostatistics. Visualisation of BFV disease incidence rates through mapping reveals the presence of substantial spatio-temporal variation at statistical local areas (SLA) over time. Results reveal high incidence rates of BFV disease along coastal areas compared to the whole area of Queensland. A Mantel-Haenszel Chi-square analysis for trend reveals a statistically significant relationship between BFV disease incidence rates and age groups (ƒÓ2 = 7587, p<0.01). Semi-variogram analysis and smoothed maps created from interpolation techniques indicate that the pattern of spatial autocorrelation was not homogeneous across the state. A cluster analysis was used to detect the hot spots/clusters of BFV disease at a SLA level. Most likely spatial and space-time clusters are detected at the same locations across coastal Queensland (p<0.05). The study demonstrates heterogeneity of disease risk at a SLA level and reveals the spatial and temporal clustering of BFV disease in Queensland. Discriminant analysis was employed to establish a link between wetland classes, climate zones and BFV disease. This is because the importance of wetlands in the transmission of BFV disease remains unclear. The multivariable discriminant modelling analyses demonstrate that wetland types of saline 1, riverine and saline tidal influence were the most significant risk factors for BFV disease in all climate and buffer zones, while lacustrine, palustrine, estuarine and saline 2 and saline 3 wetlands were less important. The model accuracies were 76%, 98% and 100% for BFV risk in subtropical, tropical and temperate climate zones, respectively. This study demonstrates that BFV disease risk varied with wetland class and climate zone. The study suggests that wetlands may act as potential breeding habitats for BFV vectors. Multivariable spatial regression models were applied to assess the impact of spatial climatic, socio-economic and tidal factors on the BFV disease in Queensland. Spatial regression models were developed to account for spatial effects. Spatial regression models generated superior estimates over a traditional regression model. In the spatial regression models, BFV disease incidence shows an inverse relationship with minimum temperature, low tide and distance to coast, and positive relationship with rainfall in coastal areas whereas in whole Queensland the disease shows an inverse relationship with minimum temperature and high tide and positive relationship with rainfall. This study determines the most significant spatial risk factors for BFV disease across Queensland. Empirical models were developed to forecast the future risk of BFV disease outbreaks in coastal Queensland using existing climatic, socio-economic and tidal conditions under climate change scenarios. Logistic regression models were developed using BFV disease outbreak data for the existing period (2000-2008). The most parsimonious model had high sensitivity, specificity and accuracy and this model was used to estimate and forecast BFV disease outbreaks for years 2025, 2050 and 2100 under climate change scenarios for Australia. Important contributions arising from this research are that: (i) it is innovative to identify high-risk coastal areas by creating buffers based on grid-centroid and the use of fine-grained spatial units, i.e., mesh blocks; (ii) a spatial regression method was used to account for spatial dependence and heterogeneity of data in the study area; (iii) it determined a range of potential spatial risk factors for BFV disease; and (iv) it predicted the future risk of BFV disease outbreaks under climate change scenarios in Queensland, Australia. In conclusion, the thesis demonstrates that the distribution of BFV disease exhibits a distinct spatial and temporal variation. Such variation is influenced by a range of spatial risk factors including climatic, demographic, socio-economic, ecological and tidal variables. The thesis demonstrates that spatial regression method can be applied to better understand the transmission dynamics of BFV disease and its risk factors. The research findings show that disease notification data can be integrated with multi-factorial risk factor data to develop build-up models and forecast future potential disease risks under climate change scenarios. This thesis may have implications in BFV disease control and prevention programs in Queensland.

Networking of shear zones at the brittle-to-viscous transition (Cap de Creus, NE Spain)

A crustal-scale shear zone network at the fossil brittle-to-viscous transition exposed at Cap de Creus, NE Spain evolved by coeval fracturing and viscous, mylonitic overprinting of an existing foliation. Initial fracturing led to mylonitic shearing as rock softened in ductilely deformed zones surrounding the fractures. Mylonitic shear zones widened by lateral branching of fractures from these shear zones and by synthetic rotation of the existing foliation between the fractures and shear zones. Shear zones lengthened by a combination of fracturing and mylonitic shearing in front of the shear zone tips. Shear zones interconnected along and across their shearing planes, separating rhomb-shaped lozenges of less deformed rock. Lozenges were subsequently incorporated into the mylonitic shear zones by widening in the manner described above. In this way, deformation became homogeneous on the scale of initial fracturing (metre- to decametre-scale). In contrast, the shear zone network represents localisation of strain on a decametre-length scale. The strength of the continental crust at the time of coeval fracturing and viscous shearing is inferred to have decreased with time and strain, as fracturing evolved to mylonitic shearing, and as the shear zones coalesced to form a through-going network subparallel to the shearing plane. Crustal strength must therefore be considered as strain- and scale-dependent.

Review of refugee mental health interventions following resettlement : best practice and recommendations

There are increasing numbers of refugees worldwide, with approximately 16 million refugees in 2007 and over 2.5 million refugees resettled in the United States since the start of its humanitarian program. Psychologists and other health professionals who deliver mental health services for individuals from refugee backgrounds need to have confidence that the therapeutic interventions they employ are appropriate and effective for the clients with whom they work. The current review briefly surveys refugee research, examines empirical evaluations of therapeutic interventions in resettlement contexts, and provides recommendations for best practices and future directions in resettlement countries. The resettlement interventions found to be most effective typically target culturally homogeneous client samples and demonstrate moderate to large outcome effects on aspects of traumatic stress and anxiety reduction. Further evaluations of the array of psychotherapeutic, psychosocial, pharmacological, and other therapeutic approaches, including psychoeducational and community-based interventions that facilitate personal and community growth and change, are encouraged. There is a need for increased awareness, training and funding to implement longitudinal interventions that work collaboratively with clients from refugee backgrounds through the stages of resettlement.

Micas in experimentally shocked gneiss

Biotites and muscovites from a gneiss have been experimentally shocked between 18 and 70 GPa using powder-propellant guns at NASA Johnson Space Center and at the California Institute of Technology. This study shows that shock in biotite and muscovite can produce homogeneous and devolatilized glasses within microseconds. Shock-deformed micas display fracturing, kinking, and complex extinction patterns over the entire pressure range investigated. However, these deformation features are not a sensitive pressure indicator. Localized melting of micas begins at 33 GPa and goes to completion at 70 GPa. Melted biotite and muscovite are optically opaque, but show extensive microvesiculation and flow when observed with the SEM. Electron diffraction confirms that biotite and muscovite have transformed to a glass. The distribution of vesicles in shock-vitrified mica shows escape of volatiles within the short duration of the shock experiment. Experimentally shocked biotite and muscovite undergo congruent melting. Compositions of the glasses are similar to the unshocked micas except for volatiles (H2O loss and K loss). These unusual glasses derived from mica may be quenched by rapid cooling conditions during the shock experiment. Based on these results, the extremely low H2O content of tektites may be reconciled with a terrestrial origin by impact. Release of volatiles in shock-melted micas affects the melting behavior of coexisting dry silicates during the short duration of the shock experiment. Transportation and escape of volatiles released from shock-melted micas may provide plausible mechanisms for the origin of protoatmospheres on terrestrial planets, hydrothermal activity on phyllosilicate-rich meteorite parent bodies, and fluid entrapment in meteorites.

Pinned fronts in heterogeneous media of jump type

In this paper, we analyse the impact of a (small) heterogeneity of jump type on the most simple localized solutions of a 3-component FitzHugh–Nagumo-type system. We show that the heterogeneity can pin a 1-front solution, which travels with constant (non-zero) speed in the homogeneous setting, to a fixed, explicitly determined, distance from the heterogeneity. Moreover, we establish the stability of this heterogeneous pinned 1-front solution. In addition, we analyse the pinning of 1-pulse, or 2-front, solutions. The paper is concluded with simulations in which we consider the dynamics and interactions of N-front patterns in domains with M heterogeneities of jump type (N = 3, 4, M ≥ 1).

Automatic Audio Segmentation Using the Generalized Likelihood Ratio

This paper presents a novel technique for segmenting an audio stream into homogeneous regions according to speaker identities, background noise, music, environmental and channel conditions. Audio segmentation is useful in audio diarization systems, which aim to annotate an input audio stream with information that attributes temporal regions of the audio into their specific sources. The segmentation method introduced in this paper is performed using the Generalized Likelihood Ratio (GLR), computed between two adjacent sliding windows over preprocessed speech. This approach is inspired by the popular segmentation method proposed by the pioneering work of Chen and Gopalakrishnan, using the Bayesian Information Criterion (BIC) with an expanding search window. This paper will aim to identify and address the shortcomings associated with such an approach. The result obtained by the proposed segmentation strategy is evaluated on the 2002 Rich Transcription (RT-02) Evaluation dataset, and a miss rate of 19.47% and a false alarm rate of 16.94% is achieved at the optimal threshold.

Comparison of antigen detection and quantitative PCR in the detection of chlamydial infection in koalas (Phascolarctos cinereus)

The gold standard method for detecting chlamydial infection in domestic and wild animals is PCR, but the technique is not suited to testing animals in the field when a rapid diagnosis is frequently required. The objective of this study was to compare the results of a commercially available enzyme immunoassay test for Chlamydia against a quantitative Chlamydia pecorum-specific PCR performed on swabs collected from the conjunctival sac, nasal cavity and urogenital sinuses of naturally infected koalas (Phascolarctos cinereus). The level of agreement for positive results between the two assays was low (43.2%). The immunoassay detection cut-off was determined as approximately 400 C. pecorum copies, indicating that the test was sufficiently sensitive to be used for the rapid diagnosis of active chlamydial infections.