Hierarchical Bayesian models for estimating the extent of plant pest invasions

Plant biosecurity requires statistical tools to interpret field surveillance data in order to manage pest incursions that threaten crop production and trade. Ultimately, management decisions need to be based on the probability that an area is infested or free of a pest. Current informal approaches to delimiting pest extent rely upon expert ecological interpretation of presence / absence data over space and time. Hierarchical Bayesian models provide a cohesive statistical framework that can formally integrate the available information on both pest ecology and data. The overarching method involves constructing an observation model for the surveillance data, conditional on the hidden extent of the pest and uncertain detection sensitivity. The extent of the pest is then modelled as a dynamic invasion process that includes uncertainty in ecological parameters. Modelling approaches to assimilate this information are explored through case studies on spiralling whitefly, Aleurodicus dispersus and red banded mango caterpillar, Deanolis sublimbalis. Markov chain Monte Carlo simulation is used to estimate the probable extent of pests, given the observation and process model conditioned by surveillance data. Statistical methods, based on time-to-event models, are developed to apply hierarchical Bayesian models to early detection programs and to demonstrate area freedom from pests. The value of early detection surveillance programs is demonstrated through an application to interpret surveillance data for exotic plant pests with uncertain spread rates. The model suggests that typical early detection programs provide a moderate reduction in the probability of an area being infested but a dramatic reduction in the expected area of incursions at a given time. Estimates of spiralling whitefly extent are examined at local, district and state-wide scales. The local model estimates the rate of natural spread and the influence of host architecture, host suitability and inspector efficiency. These parameter estimates can support the development of robust surveillance programs. Hierarchical Bayesian models for the human-mediated spread of spiralling whitefly are developed for the colonisation of discrete cells connected by a modified gravity model. By estimating dispersal parameters, the model can be used to predict the extent of the pest over time. An extended model predicts the climate restricted distribution of the pest in Queensland. These novel human-mediated movement models are well suited to demonstrating area freedom at coarse spatio-temporal scales. At finer scales, and in the presence of ecological complexity, exploratory models are developed to investigate the capacity for surveillance information to estimate the extent of red banded mango caterpillar. It is apparent that excessive uncertainty about observation and ecological parameters can impose limits on inference at the scales required for effective management of response programs. The thesis contributes novel statistical approaches to estimating the extent of pests and develops applications to assist decision-making across a range of plant biosecurity surveillance activities. Hierarchical Bayesian modelling is demonstrated as both a useful analytical tool for estimating pest extent and a natural investigative paradigm for developing and focussing biosecurity programs.

Cluster analysis of movement patterns in multiarticular actions: A tutorial

The present paper proposes a technical analysis method for extracting information about movement patterning in studies of motor control, based on a cluster analysis of movement kinematics. In a tutorial fashion, data from three different experiments are presented to exemplify and validate the technical method. When applied to three different basketball-shooting techniques, the method clearly distinguished between the different patterns. When applied to a cyclical wrist supination-pronation task, the cluster analysis provided the same results as an analysis using the conventional discrete relative phase measure. Finally, when analyzing throwing performance constrained by distance to target, the method grouped movement patterns together according to throwing distance. In conclusion, the proposed technical method provides a valuable tool to improve understanding of coordination and control in different movement models, including multiarticular actions.

Expected values for pedometer-determined physical activity in youth

This review assembles pedometry literature focused on youth, with particular attention to expected values for habitual, school day, physical education class, recess, lunch break, out-of-school, weekend, and vacation activity. From 31 studies published since 1999, we constructed a youth habitual activity step-curve that indicates: (a) from ages 6 to 18 years, boys typically take more steps per day than girls; (b) for both sexes the youngest age groups appear to take fewer steps per day than those immediately older; and (c) from a young age, boys decline more in steps per day to become move consistent with girls at older ages. Additional studies revealed that boys take approximately 42-49% of daily steps during the school day; girls take 41-47%. Steps taken during physical education class contribute to total steps per day by 8.7-23.7% in boys and 11.4-17.2% in girls. Recess represents 8-11% and lunch break represents 15-16% of total steps per day. After-school activity contributes approximately 47-56% of total steps per day for boys and 47-59% for girls. Weekdays range from approximately 12,000 to 16,000 steps per day in boys and 10,000 to 14,000 steps per day in girls. The corresponding values for weekend days are 12,000-13,000 steps per day in boys and 10,000-12,000 steps per day in girls.

Pedometry methods for assessing free-living youth

The purpose of this review is to integrate and summarize specific measurement topics (instrument and metric choice, validity, reliability, how many and what types of days, reactivity, and data treatment) appropriate to the study of youth physical activity. Research quality pedometers are necessary to aid interpretation of steps per day collected in a range of young populations under a variety of circumstances. Steps per day is the most appropriate metric choice, but steps per minute can be used to interpret time-in-intensity in specifically delimited time periods (e.g., physical education class). Reported intraclass correlations (ICC) have ranged from .65 over 2 days (although higher values also have been reported for 2 days) to .87 over 8 days (although higher values have been reported for fewer days). Reported ICCs are lower on weekend days (.59) versus weekdays (.75) and lower over vacation days (.69) versus school days (.74). There is no objective evidence of reactivity at this time. Data treatment includes (a) identifying and addressing missing values, (b) identifying outliers and reducing data appropriately if necessary, and (c) transforming the data as required in preparation for inferential analysis. As more pedometry studies in young populations are published, these preliminary methodological recommendations should be modified and refined.

Response to "a step in the right direction : commentary on expected values for pedometer-determined physical activity in youth"

The figure Beets took exception to displays sex‐ and age‐specific median values of aggregated published expected values for pedometer determined physical activity.

Assigning metabolic equivalent (MET) values to the 2002 Census Occupational Classification System

Background: The Current Population Survey (CPS) and the American Time Use Survey (ATUS) use the 2002 census occupation system to classify workers into 509 separate occupations arranged into 22 major occupational categories. Methods: We describe the methods and rationale for assigning detailed MET estimates to occupations and present population estimates (comparing outputs generated by analysis of previously published summary MET estimates to the detailed MET estimates) of intensities of occupational activity using the 2003 ATUS data comprised of 20,720 respondents, 5,323 (2,917 males and 2,406 females) of whom reported working 6+ hours at their primary occupation on their assigned reporting day. Results: Analysis using the summary MET estimates resulted in 4% more workers in sedentary occupations, 6% more in light, 7% less in moderate, and 3% less in vigorous compared to using the detailed MET estimates. The detailed estimates are more sensitive to identifying individuals who do any occupational activity that is moderate or vigorous in intensity resulting in fewer workers in sedentary and light intensity occupations. Conclusions: Since CPS/ATUS regularly captures occupation data it will be possible to track prevalence of the different intensity levels of occupations. Updates will be required with inevitable adjustments to future occupational classification systems.

Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae)

Restrictions to effective dispersal and gene flow caused by the fragmentation of ancient supercontinents are considered to have driven diversification and speciation on disjunct landmasses globally. Investigating the role that these processes have played in the development of diversity within and among taxa is crucial to understanding the origins and evolution of regional biotas. Within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae), a group of genera that are distributed across the austral continents (Australia, New Zealand, South America) have been proposed to represent a relict Gondwanan clade. We used a molecular approach to resolve relationships among taxa with the aim to determine the relative roles that vicariance and dispersal may have played in the evolution of this group. Continental biotas did not form monophyletic groups, in accordance with expectations given existing morphological evidence. Patterns of phylogenetic relationships among taxa did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent. Likewise, divergence time estimates, particularly for New Zealand taxa, largely post-dated continental fragmentation and implied instead that several transoceanic dispersal events may have occurred post-vicariance. Passive dispersal of gravid female chironomid adults is the most likely mechanism for transoceanic movement, potentially facilitated by West Wind Drift or anti-cyclone fronts. Estimated timings of divergence among Australian and South American Botryocladius, on the other hand, were congruent with the proposed ages of separation of the two continents from Antarctica. Taken together, these data suggest that a complex relationship between both vicariance and dispersal may explain the evolution of this group. The sampling regime we implemented here was the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly revealed several novel taxa that will require formal description.

A mathematical model of chlamydial infection incorporating movement of chlamydial particles

We present a spatiotemporal mathematical model of chlamydial infection, host immune response and spatial movement of infectious particles. The re- sulting partial differential equations model both the dynamics of the infection and changes in infection profile observed spatially along the length of the host genital tract. This model advances previous chlamydia modelling by incorporating spatial change, which we also demonstrate to be essential when the timescale for movement of infectious particles is equal to, or shorter than, the developmental cycle timescale. Numerical solutions and model analysis are carried out, and we present a hypothesis regarding the potential for treatment and prevention of infection by increasing chlamydial particle motility.

From Deep North to international governance exemplar : Fitzgerald's impact on the international anti-corruption movement

In pre-Fitzgerald Queensland, the existence of corruption was widely known but its extent and modes of operation were not fully evident. The Fitzgerald Report identified the need for reform of the structure, procedures and efficiency in public administration in Queensland. What was most striking in the Queensland reform process was that a new model for combatting corruption had been developed. Rather than rely upon a single law and a single institution, existing institutions were strengthened and new institutions were introduced to create a set of mutually supporting and mutually checking institutions, agencies and laws that jointly sought to improve governmental standards and combat corruption. Some of the reforms were either unique to Queensland or very rare. One of the strengths of this approach was that it avoided creating a single over-arching institution to fight corruption. There are many powerful opponents of reform. Influential institutions and individuals resist any interference with their privileges. In order to cause a mass exodus from an entrenched corruption system, a seminal event or defining process is needed to alter expectations and incentives that are sufficient to encourage significant numbers of individuals to desert the corruption system and assist the integrity system in exposing and destroying it. The Fitzgerald Inquiry was such an event. This article also briefly addresses methods for destroying national corruption systems where they emerge and exist.

The spermostatic and microbicidal actions of quinones and malemides : towards a dual-purpose contraceptive agent

There is an urgent need to develop safe, effective, dual-purpose contraceptive agents that combine the prevention of pregnancy with protection against sexually transmitted diseases. Here we report the identification of a group of compounds that on contact with human spermatozoa induce a state of “spermostasis,” characterized by the extremely rapid inhibition of sperm movement without compromising cell viability. These spermostatic agents were more active and significantly less toxic than the reagent in current clinical use, nonoxynol 9, giving therapeutic indices (ratio of spermostatic to cytotoxic activity) that were orders of magnitude greater than this traditional spermicide. Although certain compounds could trigger reactive oxygen species generation by spermatozoa, this activity was not correlated with spermostasis. Rather, the latter was associated with alkylation of two major sperm tail proteins that were identified as A Kinase-Anchoring Proteins (AKAP3 and AKAP4) by mass spectrometry. As a consequence of disrupted AKAP function, the abilities of cAMP to drive protein kinase A-dependent activities in the sperm tail, such as the activation of SRC and the consequent stimulation of tyrosine phosphorylation, were suppressed. Furthermore, analysis of microbicidal activity using Chlamydia muridarum revealed powerful inhibitory effects at the same low micromolar doses that suppressed sperm movement. In this case, the microbicidal action was associated with alkylation of Major Outer Membrane Protein (MOMP), a major chlamydial membrane protein. Taken together, these results have identified for the first time a novel set of cellular targets and chemical principles capable of providing simultaneous defense against both fertility and the spread of sexually transmitted disease.

From deep North to global governance exemplar : Fitzgerald's impact on the International Anti-corruption Movement

In pre-Fitzgerald Queensland, the existence of corruption was widely known but its extent and modes of operation were not fully evident. The Fitzgerald Report identified the need for reform of the structure, procedures and efficiency in public administration in Queensland. What was most striking in the Queensland reform process was that a new model for combating corruption had been developed. Rather than rely upon a single law and a single institution, existing institutions were strengthened and new institutions were instituted to create a set of mutually supporting and mutually checking institutions, agencies and laws that jointly sought to improve governmental standards and combat corruption. Some of the reforms were either unique to Queensland or very rare. One of the strengths of this approach was that it avoided creating a single overarching institution to fight corruption. There are many powerful opponents of reform. Influential institutions and individuals resist any interference with their privileges. In order to cause a mass exodus from an entrenched corruption system, a seminal event or defining process is needed to alter expectations and incentives that are sufficient to encourage significant numbers of individuals to desert the corruption system and assist the integrity system in exposing and destroying it. The Fitzgerald Inquiry was such an event. The article also briefly addresses methods for destroying national corruption system where they emerge and exist.

Identifying constraints on children with movement difficulties : implications for pedagogues and clinicians

A constraints- based framework for understanding processes of movement coordination and control is predicated on a range of theoretical ideas including the work of Bernstein (1967), Gibson (1979), Newell (1986) and Kugler, Kelso & Turvey (1982). Contrary to a normative perspective that focuses on the production of idealized movement patterns to be acquired by children during development and learning (see Alain & Brisson, 1986), this approach formulates the emergence of movement co- ordination as a function of the constraints imposed upon each individual. In this framework, cognitive, perceptual and movement difficulties and disorders are considered to be constraints on the perceptual- motor system, and children’s movements are viewed as emergent functional adaptations to these constraints (Davids et al., 2008; Rosengren, Savelsbergh & van der Kamp, 2003). From this perspective, variability of movement behaviour is not viewed as noise or error to be eradicated during development, but rather, as essentially functional in facilitating the child to satisfy the unique constraints which impinge on his/her developing perceptual- motor and cognitive systems in everyday life (Davids et al., 2008). Recently, it has been reported that functional neurobiological variability is predicated on system degeneracy, an inherent feature of neurobiological systems which facilitates the achievement of task performance goals in a variety of different ways (Glazier & Davids, 2009). Degeneracy refers to the capacity of structurally different components of complex movement systems to achieve different performance outcomes in varying contexts (Tononi et al., 1999; Edelman & Gally, 2001). System degeneracy allows individuals with and without movement disorders to achieve their movement goals by harnessing movement variability during performance. Based on this idea, perceptual- motor disorders can be simply viewed as unique structural and functional system constraints which individuals have to satisfy in interactions with their environments. The aim of this chapter is to elucidate how the interaction of structural and functional organismic, and environmental constraints can be harnessed in a nonlinear pedagogy by individuals with movement disorders.

Facial expression recognition using facial movement features

Facial expression is an important channel for human communication and can be applied in many real applications. One critical step for facial expression recognition (FER) is to accurately extract emotional features. Current approaches on FER in static images have not fully considered and utilized the features of facial element and muscle movements, which represent static and dynamic, as well as geometric and appearance characteristics of facial expressions. This paper proposes an approach to solve this limitation using ‘salient’ distance features, which are obtained by extracting patch-based 3D Gabor features, selecting the ‘salient’ patches, and performing patch matching operations. The experimental results demonstrate high correct recognition rate (CRR), significant performance improvements due to the consideration of facial element and muscle movements, promising results under face registration errors, and fast processing time. The comparison with the state-of-the-art performance confirms that the proposed approach achieves the highest CRR on the JAFFE database and is among the top performers on the Cohn-Kanade (CK) database.

Community-based protest against construction projects : a case study of movement continuity

Community-based activism against proposed construction projects is growing. Many protests are poorly managed and escalate into long-term and sometimes acrimonious disputes which damage communities, firms and the construction industry as a whole. Using a thematic storytelling approach which draws on ethnographic method, within a single case study framework, new insights into the social forces that shape and sustain community-based protest against construction projects are provided. A conceptual model of protest movement continuity is presented which highlights the factors that sustain protest continuity over time. The model illustrates how social contagion leads to common community perceptions of development risk and opportunity, to a positive internalization of collective values and identity, to a strategic utilization of social capital and an awareness of the need to manage the emotional dynamics of protest through mechanisms such as symbolic artefacts.