Inter-and Intra-Site Genetic Diversity of Natural Field Populations of Rice Tungro Bacilliform Virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations within and between growing sites was analyzed in a collection of natural field isolates from different rice varieties grown in eight tungro-endemic sites of the Philippines. Total DNA extracts from 345 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV, a procedure shown in preliminary experiments capable of revealing high levels of polymorphism in RTBV field isolates. In the total population, 17 distinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isabela and North Cotabato provinces suggesting a geographic isolation of virus populations. However, among the sites in each province, there were few significant differences in the genotype compositions of virus populations. The number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from season to season indicating a genetic stability for the local virus population. Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no apparent selection pressures. Insect transmission experiments on selected RTBV field isolates showed that dramatic shifts in genotype and phenotype distributions can occur in response to host /environmental shifts.

Genetic Composition and Complexity of Virus Populations at Tungro-Endemic and Outbreak Rice Sites

We have recently demonstrated the geographic isolation of rice tungro bacilliform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of Lanao del Norte, a province adjacent to North Cotabato. We also analyzed the virus populations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV. In the total population, 22 EcoRV-restricted genome profiles (genotypes) were identified. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier from North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combined with restriction analysis, the results suggest a fragmented spatial distribution of RTBV local populations in the three countries. Because RTBV depends on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbreak sites within the Philippines. The RTBV genotypes and the coat protein RTSV genotypes were used as indicators for virus diversity. A shift in population structure of both viruses was observed at the outbreak sites with a reduced RTBV but increased RTSV gene diversity

Eschewing the fat: strong production but Neil LaBute below his best : a review

AWARD-WINNING American play and screen writer Neil LaBute is known for producing character-driven dramas that concentrate on the darker side of human nature and desire. In Fat Pig, LaBute picks up on a familiar theme: the way a perverse social preference for physical perfection affects human relationships. It is a topic LaBute has tackled before in The Shape of Things, a compelling play in which a beautiful young woman's efforts to help her new boyfriend pursue a program of self-improvement are eventually revealed to be part of a bizarre human experiment for her master-of-fine-arts degree.

Contemporary take on deconstructed Medea : a review

THEATRE: The New Dead: Medea Material. By Heiner Muller. Stella Electrika in association with La Boite Theatre Company, Brisbane, November 19. THERE has been a lot of intensity in independent theatre in Brisbane during the past year, as companies, production houses and producers have begun building new programs and platforms to support an expansion of pathways within the local theatre ecology. Audiences have been exposed to works signalling the diversity of what Brisbane theatre makers want to see on stage, from productions of new local and international pieces to new devised works, and the results of residencies and development programs. La Boite Theatre Company closes its inaugural indie season with a work that places it at the contemporary, experimental end of the spectrum. The New Dead: Medea Material is emerging director Kat Henry's interpretation of Heiner Muller's 1981 text Despoiled Shore Medea Material Landscape with Argonauts. Start of sidebar. Skip to end of sidebar. End of sidebar. Return to start of sidebar. Muller is known for his radical adaptations of historical dramas, from the Greeks to Shakespeare, and for deconstructed texts in which the characters - in this case, Medea - violently reject the familial, cultural and political roles society has laid out for them. Muller's combination of deconstructed characters, disconnected poetic language and constant references to aspects of popular culture and the Cold War politics he sought to abjure make his texts challenging to realise. The poetry entices but the density, together with the increasing distance of the Cold War politics in the texts, leaves contemporary directors with clear decisions to make about how to adapt these open texts. In The New Dead: Medea Material, Henry works with some interesting imagery and conceptual territory. Lucinda Shaw as Medea, Guy Webster as Jason and Kimie Tsukakoshi as King Creon's daughter Glauce, the woman for whom Jason forsakes his wife Medea, each reference different aspects of contemporary culture. Medea is a bitter, drunken, satin-gowned diva with bite; Jason - first seen lounging in front of the television with a beer in an image reminiscent of Sarah Kane's in-yer-face characterisation of Hippolytus in Phaedra's Love - has something of the rock star about him; and Glauce is a roller-skating, karaoke-singing, pole-dancing young temptress. The production is given a contemporary tone, dominated by Medea's twisted love and loss, rather than by any commentary on her circumstances. Its strength is the aesthetic Henry creates, supported by live electro-pop music, a band stage that stands as a metaphor for Jason's sea voyage, and multimedia that inserts images of the story unfolding beyond these characters' speeches as sorts of subconscious flashes. While Tsukakoshi is engaging throughout, there are moments when Shaw and Webster's performances - particularly in the songs - are diminished by a lack of clarity. The result is a piece that, while slightly lacking in its realisation at times, undoubtedly flags Henry's facility as an emerging director and what she wants to bring to the Brisbane theatre scene.

Informational city

Many cities worldwide face the prospect of major transformation as the world moves towards a global information order. In this new era, urban economies are being radically altered by dynamic processes of economic and spatial restructuring. The result is the creation of ‘informational cities’ or its new and more popular name, ‘knowledge cities’. For the last two centuries, social production had been primarily understood and shaped by neo-classical economic thought that recognized only three factors of production: land, labor and capital. Knowledge, education, and intellectual capacity were secondary, if not incidental, factors. Human capital was assumed to be either embedded in labor or just one of numerous categories of capital. In the last decades, it has become apparent that knowledge is sufficiently important to deserve recognition as a fourth factor of production. Knowledge and information and the social and technological settings for their production and communication are now seen as keys to development and economic prosperity. The rise of knowledge-based opportunity has, in many cases, been accompanied by a concomitant decline in traditional industrial activity. The replacement of physical commodity production by more abstract forms of production (e.g. information, ideas, and knowledge) has, however paradoxically, reinforced the importance of central places and led to the formation of knowledge cities. Knowledge is produced, marketed and exchanged mainly in cities. Therefore, knowledge cities aim to assist decision-makers in making their cities compatible with the knowledge economy and thus able to compete with other cities. Knowledge cities enable their citizens to foster knowledge creation, knowledge exchange and innovation. They also encourage the continuous creation, sharing, evaluation, renewal and update of knowledge. To compete nationally and internationally, cities need knowledge infrastructures (e.g. universities, research and development institutes); a concentration of well-educated people; technological, mainly electronic, infrastructure; and connections to the global economy (e.g. international companies and finance institutions for trade and investment). Moreover, they must possess the people and things necessary for the production of knowledge and, as importantly, function as breeding grounds for talent and innovation. The economy of a knowledge city creates high value-added products using research, technology, and brainpower. Private and the public sectors value knowledge, spend money on its discovery and dissemination and, ultimately, harness it to create goods and services. Although many cities call themselves knowledge cities, currently, only a few cities around the world (e.g., Barcelona, Delft, Dublin, Montreal, Munich, and Stockholm) have earned that label. Many other cities aspire to the status of knowledge city through urban development programs that target knowledge-based urban development. Examples include Copenhagen, Dubai, Manchester, Melbourne, Monterrey, Singapore, and Shanghai. Knowledge-Based Urban Development To date, the development of most knowledge cities has proceeded organically as a dependent and derivative effect of global market forces. Urban and regional planning has responded slowly, and sometimes not at all, to the challenges and the opportunities of the knowledge city. That is changing, however. Knowledge-based urban development potentially brings both economic prosperity and a sustainable socio-spatial order. Its goal is to produce and circulate abstract work. The globalization of the world in the last decades of the twentieth century was a dialectical process. On one hand, as the tyranny of distance was eroded, economic networks of production and consumption were constituted at a global scale. At the same time, spatial proximity remained as important as ever, if not more so, for knowledge-based urban development. Mediated by information and communication technology, personal contact, and the medium of tacit knowledge, organizational and institutional interactions are still closely associated with spatial proximity. The clustering of knowledge production is essential for fostering innovation and wealth creation. The social benefits of knowledge-based urban development extend beyond aggregate economic growth. On the one hand is the possibility of a particularly resilient form of urban development secured in a network of connections anchored at local, national, and global coordinates. On the other hand, quality of place and life, defined by the level of public service (e.g. health and education) and by the conservation and development of the cultural, aesthetic and ecological values give cities their character and attract or repel the creative class of knowledge workers, is a prerequisite for successful knowledge-based urban development. The goal is a secure economy in a human setting: in short, smart growth or sustainable urban development.

Can hybridization cause local extinction : the case for demographic swamping of the Australian native, Senecio pinnatifolius, by the invasive, S. madagascariensis?

The outcome of interspecific hybridization between native and invasive species depends on the relative frequencies of parental taxa and viability of hybrid progeny. We investigated individual and population level consequences of hybridization between the Australian native, Senecio pinnatifolius, and the exotic S. madagascariensis, with AFLP markers and used this information to simulate the expected outcome of hybridization.A high frequency (range 8.3-75.6 %) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations indicating that sympatric populations represent tension zones. A hybridization advantage was observed for S. madagascariensis,where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Simulations indicated S. pinnatifolius could be replaced in sympatric populations if hybridization was density dependent.For this native-exotic pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. Due to asymmetric hybridization, S. pinnatifolius appears under threat from demographic swamping, and local extinction is possible where it occurs in sympatry with S. madagascariensis.

Person-independent facial expression detection using constrained local models

In automatic facial expression detection, very accurate registration is desired which can be achieved via a deformable model approach where a dense mesh of 60-70 points on the face is used, such as an active appearance model (AAM). However, for applications where manually labeling frames is prohibitive, AAMs do not work well as they do not generalize well to unseen subjects. As such, a more coarse approach is taken for person-independent facial expression detection, where just a couple of key features (such as face and eyes) are tracked using a Viola-Jones type approach. The tracked image is normally post-processed to encode for shift and illumination invariance using a linear bank of filters. Recently, it was shown that this preprocessing step is of no benefit when close to ideal registration has been obtained. In this paper, we present a system based on the Constrained Local Model (CLM) which is a generic or person-independent face alignment algorithm which gains high accuracy. We show these results against the LBP feature extraction on the CK+ and GEMEP datasets.

Biceps brachii muscle oxygenation in electrical muscle stimulation

The purpose of this study was to compare between electrical muscle stimulation (EMS) and maximal voluntary (VOL) isometric contractions of the elbow flexors for changes in biceps brachii muscle oxygenation (tissue oxygenation index, TOI) and haemodynamics (total haemoglobin volume, tHb = oxygenated-Hb + deoxygenated-Hb) determined by near-infrared spectroscopy (NIRS). The biceps brachii muscle of 10 healthy men (23–39 years) was electrically stimulated at high frequency (75 Hz) via surface electrodes to evoke 50 intermittent (4-s contraction, 15-s relaxation) isometric contractions at maximum tolerated current level (EMS session). The contralateral arm performed 50 intermittent (4-s contraction, 15-s relaxation) maximal voluntary isometric contractions (VOL session) in a counterbalanced order separated by 2–3 weeks. Results indicated that although the torque produced during EMS was approximately 50% of VOL (P<0Æ05), there was no significant difference in the changes in TOI amplitude or TOI slope between EMS and VOL over the 50 contractions. However, the TOI amplitude divided by peak torque was approximately 50% lower for EMS than VOL (P<0Æ05), which indicates EMS was less efficient than VOL. This seems likely because of the difference in the muscles involved in the force production between conditions. Mean decrease in tHb amplitude during the contraction phases was significantly (P<0Æ05) greater for EMS than VOL from the 10th contraction onwards, suggesting that the muscle blood volume was lower in EMS than VOL. It is concluded that local oxygen demand of the biceps brachii sampled by NIRS is similar between VOL and EMS.

Full circle : the future of sustainable fashion manufacturing in New Zealand

Many fashion businesses in New Zealand have followed a global trend towards inexpensive off shore manufacturing. The transfer of the production of garments to overseas workers has had consequences for the wellbeing of local businesses, fashion designers and garment makers. The gradual decline of fashion manufacturing also appears to have resulted in a local fashion scene where many garments look the same in style, colour, fabric, cut and fit. The excitement of the past, where the majority of fashion designers established their own individuality through the cut and shape of the garments that they produced, may have been inadvertently lost in an effort to take advantage of cost savings achieved through mass production and manufacturing methods which are now largely unavailable in New Zealand. Consequently, a sustainable local fashion and manufacturing industry, with design integrity, seems further out of reach. This paper is focussed upon the thesis that the design and manufacture of a fashion garment, bearing in mind certain economic and practical restrictions at its inception, can contribute to a more sustainable fashion manufacturing industry in New Zealand.

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.

Electrospraying a reproducible method for production of polymeric microspheres for biomedical applications

The ability to reproducibly load bioactive molecules into polymeric microspheres is a challenge. Traditional microsphere fabrication methods typically provide inhomogeneous release profiles and suffer from lack of batch to batch reproducibility, hindering their potential to up-scale and their translation to the clinic. This deficit in homogeneity is in part attributed to broad size distributions and variability in the morphology of particles. It is thus desirable to control morphology and size of non-loaded particles in the first instance, in preparation for obtaining desired release profiles of loaded particles in the later stage. This is achieved by identifying the key parameters involved in particle production and understanding how adapting these parameters affects the final characteristics of particles. In this study, electrospraying was presented as a promising technique for generating reproducible particles made of polycaprolactone, a biodegradable, FDA-approved polymer. Narrow size distributions were obtained by the control of electrospraying flow rate and polymer concentration, with average particle sizes ranging from 10 to 20 um. Particles were shown to be spherical with a homogenous embossed texture, determined by the polymer entanglement regime taking place during electrospraying. No toxic residue was detected by this process based on preliminary cell work using DNA quantification assays, validating this method as suitable for further loading of bioactive components.

Essays on irrigation development, farm production and unaccounted costs : theory and empirical evidence

A review of the literature related to issues involved in irrigation induced agricultural development (IIAD) reveals that: (1) the magnitude, sensitivity and distribution of social welfare of IIAD is not fully analysed; (2) the impacts of excessive pesticide use on farmers’ health are not adequately explained; (3) no analysis estimates the relationship between farm level efficiency and overuse of agro-chemical inputs under imperfect markets; and (4) the method of incorporating groundwater extraction costs is misleading. This PhD thesis investigates these issues by using primary data, along with secondary data from Sri Lanka. The overall findings of the thesis can be summarised as follows. First, the thesis demonstrates that Sri Lanka has gained a positive welfare change as a result of introducing new irrigation technology. The change in the consumer surplus is Rs.48,236 million, while the change in the producer surplus is Rs. 14,274 millions between 1970 and 2006. The results also show that the long run benefits and costs of IIAD depend critically on the magnitude of the expansion of the irrigated area, as well as the competition faced by traditional farmers (agricultural crowding out effects). The traditional sector’s ability to compete with the modern sector depends on productivity improvements, reducing production costs and future structural changes (spillover effects). Second, the thesis findings on pesticides used for agriculture show that, on average, a farmer incurs a cost of approximately Rs. 590 to 800 per month during a typical cultivation period due to exposure to pesticides. It is shown that the value of average loss in earnings per farmer for the ‘hospitalised’ sample is Rs. 475 per month, while it is approximately Rs. 345 per month for the ‘general’ farmers group during a typical cultivation season. However, the average willingness to pay (WTP) to avoid exposure to pesticides is approximately Rs. 950 and Rs. 620 for ‘hospitalised’ and ‘general’ farmers’ samples respectively. The estimated percentage contribution for WTP due to health costs, lost earnings, mitigating expenditure, and disutility are 29, 50, 5 and 16 per cent respectively for hospitalised farmers, while they are 32, 55, 8 and 5 per cent respectively for ‘general’ farmers. It is also shown that given market imperfections for most agricultural inputs, farmers are overusing pesticides with the expectation of higher future returns. This has led to an increase in inefficiency in farming practices which is not understood by the farmers. Third, it is found that various groundwater depletion studies in the economics literature have provided misleading optimal water extraction quantity levels. This is due to a failure to incorporate all production costs in the relevant models. It is only by incorporating quality changes to quantity deterioration, that it is possible to derive socially optimal levels. Empirical results clearly show that the benefits per hectare per month considering both the avoidance costs of deepening agro-wells by five feet from the existing average, as well as the avoidance costs of maintaining the water salinity level at 1.8 (mmhos/Cm), is approximately Rs. 4,350 for farmers in the Anuradhapura district and Rs. 5,600 for farmers in the Matale district.

The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing : a finite element study based on sheep experiments

During secondary fracture healing, various tissue types including new bone are formed. The local mechanical strains play an important role in tissue proliferation and differentiation. To further our mechanobiological understanding of fracture healing, a precise assessment of local strains is mandatory. Until now, static analyses using Finite Elements (FE) have assumed homogenous material properties. With the recent quantification of both the spatial tissue patterns (Vetter et al., 2010) and the development of elastic modulus of newly formed bone during healing (Manjubala et al., 2009), it is now possible to incorporate this heterogeneity. Therefore, the aim of this study is to investigate the effect of this heterogeneity on the strain patterns at six successive healing stages. The input data of the present work stemmed from a comprehensive cross-sectional study of sheep with a tibial osteotomy (Epari et al., 2006). In our FE model, each element containing bone was described by a bulk elastic modulus, which depended on both the local area fraction and the local elastic modulus of the bone material. The obtained strains were compared with the results of hypothetical FE models assuming homogeneous material properties. The differences in the spatial distributions of the strains between the heterogeneous and homogeneous FE models were interpreted using a current mechanobiological theory (Isakson et al., 2006). This interpretation showed that considering the heterogeneity of the hard callus is most important at the intermediate stages of healing, when cartilage transforms to bone via endochondral ossification.

Local adjustment and global adaptation of control periods for QoC management of control systems

Linking real-time schedulability directly to the Quality of Control (QoC), the ultimate goal of a control system, a hierarchical feedback QoC management framework with the Fixed Priority (FP) and the Earliest-Deadline-First (EDF) policies as plug-ins is proposed in this paper for real-time control systems with multiple control tasks. It uses a task decomposition model for continuous QoC evaluation even in overload conditions, and then employs heuristic rules to adjust the period of each of the control tasks for QoC improvement. If the total requested workload exceeds the desired value, global adaptation of control periods is triggered for workload maintenance. A sufficient stability condition is derived for a class of control systems with delay and period switching of the heuristic rules. Examples are given to demonstrate the proposed approach.