Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen

Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen. © 2008 SGM.

Melting, ablation, and vapor phase condensation during atmospheric passage of the Bjurbole Meteorite

A detailed study of the Bjurbole fusion crust using scanning electron microscopy (SEM) and energy dispersive analysis (EDS) shows that filamentary crystals and ablation spheres may form on the meteoroid surface. Filamentary crystals, hollow spheres, and porous regions of the surface point to a period of intense vapor phase activity during atmospheric passage. Filamentary crystals can be divided into three categories on the basis of bulk composition and morphology. Two types of filamentary crystals are vapor phase condensation products formed during atmospheric entry of the meteoroid. The other type forms by the interaction of seawater with the fusion surface. The density and composition of ablation spheres varies with the flight orientation of the meteorite. The size range and composition of iron-nickel spheres on the surface of Bjurbole are similar to spheres collected in the stratosphere. A comparison of stratospheric dust collections with meteorite surfaces may provide further insight into the mechanisms of meteoroid entry into planetary atmospheres.

Grain size distributions of Magneli phases and metallic titanium in chondritic porous interplanetary dust particles

A mineralogical survey of chondritic interplanetary dust particles (IDPs)showed that these micrometeorites differ significantly in form and texture from components of carbonaceous chondrites and contain some mineral assemblages which do not occur in any meteorite class1. Models of chondritic IDP mineral evolution generally ignore the typical (ultra-) fine grain size of consituent minerals which range between 0.002-0.1µm in size2. The chondritic porous (CP) subset of chondritic IDPs is probably debris from short period comets although evidence for a cometary origin is still circumstantial3. If CP IDPs represent dust from regions of the Solar System in which comet accretion occurred, it can be argued that pervasive mineralogical evolution of IDP dust has been arrested due to cryogenic storage in comet nuclei. Thus, preservation in CP IDPs of "unusual meteorite minerals", such as oxides of tin, bismuth and titanium4, should not be dismissed casually. These minerals may contain specific information about processes that occurred in regions of the solar nebula, and early Solar System, which spawned the IDP parent bodies such as comets and C, P and D asteroids6. It is not fully appreciated that the apparent disparity between the mineralogy of CP IDPs and carbonaceous chondrite matrix may also be caused by the choice of electron-beam techniques with different analytical resolution. For example, Mg-Si-Fe distributions of Cl matrix obtained by "defocussed beam" microprobe analyses are displaced towards lower Fe-values when using analytical electron microscope (AEM)data which resolve individual mineral grains of various layer silicates and magnetite in the same matrix6,7. In general, "unusual meteorite minerals" in chondritic IDPs, such as metallic titanium, Tin01-n(Magneli phases) and anatase8 add to the mineral data base of fine-grained Solar System materials and provide constraints on processes that occurred in the early Solar System.

Coexistence of stable spots and fronts in a three-component FitzHugh-Nagumo system

We investigate regions of bistability between different travelling and stationary structures in a planar singularly-perturbed three-component reaction-diffusion system that arises in the context of gas discharge systems. In previous work, we delineated the existence and stabil-ity regions of stationary localized spots in this system. Here, we complement this analysis by establishing the stability regions of planar travelling fronts and stationary stripes. Taken together, these results imply that stable fronts and spots can coexist in three-component systems. Numerical simulations indicate that the stable fronts never move towards stable spots but instead move away from them.

A critical regionalist approach to housing design in Vietnam : socio-environmental organisation of living spaces in pre- and post-reform houses

Vietnam has a unique culture which is revealed in the way that people have built and designed their traditional housing. Vietnamese dwellings reflect occupants’ activities in their everyday lives, while adapting to tropical climatic conditions impacted by seasoning monsoons. It is said that these characteristics of Vietnamese dwellings have remained unchanged until the economic reform in 1986, when Vietnam experienced an accelerated development based on the market-oriented economy. New housing types, including modern shop-houses, detached houses, and apartments, have been designed in many places, especially satisfying dwellers’ new lifestyles in Vietnamese cities. The contemporary housing, which has been mostly designed by architects, has reflected rules of spatial organisation so that occupants’ social activities are carried out. However, contemporary housing spaces seem unsustainable in relation to socio-cultural values because they has been influenced by globalism that advocates the use of homogeneous spatial patterns, modern technologies, materials and construction methods. This study investigates the rules of spaces in Vietnamese houses that were built before and after the reform to define the socio-cultural implications in Vietnamese housing design. Firstly, it describes occupants’ views of their current dwellings in terms of indoor comfort conditions and social activities in spaces. Then, it examines the use of spaces in pre-reform Vietnamese housing through occupants’ activities and material applications. Finally, it discusses the organisation of spaces in both pre- and post-reform housing to understand how Vietnamese housing has been designed for occupants to live, act, work, and conduct traditional activities. Understanding spatial organisation is a way to identify characteristics of the lived spaces of the occupants created from the conceived space, which is designed by designers. The characteristics of the housing spaces will inform the designers the way to design future Vietnamese housing in response to cultural contexts. The study applied an abductive approach for the investigation of housing spaces. It used a conceptual framework in relation to Henri Lefebvre’s (1991) theory to understand space as the main factor constituting the language of design, and the principles of semiotics to examine spatial structure in housing as a language used in the everyday life. The study involved a door-knocking survey to 350 households in four regional cities of Vietnam for interpretation of occupancy conditions and levels of occupants’ comfort. A statistical analysis was applied to interpret the survey data. The study also required a process of data selection and collection of fourteen cases of housing in three main climatic regions of the country for analysing spatial organisation and housing characteristics. The study found that there has been a shift in the relationship of spaces from the pre- to post-reform Vietnamese housing. It also indentified that the space for guest welcoming and family activity has been the central space of the Vietnamese housing. Based on the relationships of the central space with the others, theoretical models were proposed for three types of contemporary Vietnamese housing. The models will be significant in adapting to Vietnamese conditions to achieve socioenvironmental characteristics for housing design because it was developed from the occupants’ requirements for their social activities. Another contribution of the study is the use of methodological concepts to understand the language of living spaces. Further work will be needed to test future Vietnamese housing designs from the applications of the models.

Preliminary reliability and validity testing of a self-efficacy questionnaire for Chinese family caregivers

Objectives: To develop and test preliminary reliability and validity of a Self-Efficacy Questionnaire for Chinese Family Caregivers (SEQCFC). Methods: A cross-sectional survey of 196 family caregivers (CGs) of people with dementia (CGs) was conducted to determine the factor structure of a SEQCFC of people with dementia. Following factor analyses, preliminary testing was performed, including internal consistency, 4-week test retest reliability, and construct and convergent validity. Results: Factor analyses with direct oblimin rotation were performed. Eight items were removed and five subscales(selfefficacy for gathering information about treatment, symptoms and health care; obtaining support; responding to behaviour disturbances; managing household, personal and medical care; and managing distress associated with caregiving) were identified. The Cronbach’s alpha coefficients for the whole scale and for each subscale were all over 0.80. The 4-week testretest reliabilities for the whole scale and for each subscale ranged from 0.64 to 0.85. The convergent validity was acceptable. Conclusions: Evidence for the preliminary testing of the SEQCFC was encouraging. A future follow-up study using confirmatory factor analysis with a new sample from different recruitment centres in Shanghai will be conducted. Future psychometric property testings of the questionnaire will be required for CGs from other regions of mainland China.

Anatomical MR imaging of long bones : comparative performance of MRI at 1.5 T and 3 T

The current gold standard for the design of orthopaedic implants is 3D models of long bones obtained using computed tomography (CT). However, high-resolution CT imaging involves high radiation exposure, which limits its use in healthy human volunteers. Magnetic resonance imaging (MRI) is an attractive alternative for the scanning of healthy human volunteers for research purposes. Current limitations of MRI include difficulties of tissue segmentation within joints and long scanning times. In this work, we explore the possibility of overcoming these limitations through the use of MRI scanners operating at a higher field strength. We quantitatively compare the quality of anatomical MR images of long bones obtained at 1.5 T and 3 T and optimise the scanning protocol of 3 T MRI. FLASH images of the right leg of five human volunteers acquired at 1.5 T and 3 T were compared in terms of signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). The comparison showed a relatively high CNR and SNR at 3 T for most regions of the femur and tibia, with the exception of the distal diaphyseal region of the femur and the mid diaphyseal region of the tibia. This was accompanied by an ~65% increase in the longitudinal spin relaxation time (T1) of the muscle at 3 T compared to 1.5 T. The results suggest that MRI at 3 T may be able to enhance the segmentability and potentially improve the accuracy of 3D anatomical models of long bones, compared to 1.5 T. We discuss how the total imaging times at 3 T can be kept short while maximising the CNR and SNR of the images obtained.

Time-varying bispectral analysis of visually evoked multi-channel EEG

Theoretical foundations of higher order spectral analysis are revisited to examine the use of time-varying bicoherence on non-stationary signals using a classical short-time Fourier approach. A methodology is developed to apply this to evoked EEG responses where a stimulus-locked time reference is available. Short-time windowed ensembles of the response at the same offset from the reference are considered as ergodic cyclostationary processes within a non-stationary random process. Bicoherence can be estimated reliably with known levels at which it is significantly different from zero and can be tracked as a function of offset from the stimulus. When this methodology is applied to multi-channel EEG, it is possible to obtain information about phase synchronization at different regions of the brain as the neural response develops. The methodology is applied to analyze evoked EEG response to flash visual stimulii to the left and right eye separately. The EEG electrode array is segmented based on bicoherence evolution with time using the mean absolute difference as a measure of dissimilarity. Segment maps confirm the importance of the occipital region in visual processing and demonstrate a link between the frontal and occipital regions during the response. Maps are constructed using bicoherence at bifrequencies that include the alpha band frequency of 8Hz as well as 4 and 20Hz. Differences are observed between responses from the left eye and the right eye, and also between subjects. The methodology shows potential as a neurological functional imaging technique that can be further developed for diagnosis and monitoring using scalp EEG which is less invasive and less expensive than magnetic resonance imaging.

Pulling apart the mid to late Cenozoic magmatic record of the Gulf of California : no room for the Comondú Arc

Understanding the link between tectonic-driven extensional faulting and volcanism is crucial from a hazard perspective in active volcanic environments, while ancient volcanic successions provide records on how volcanic eruption styles, compositions, magnitudes and frequencies can change in response to extension timing, distribution and intensity. Significantly, incorrect tectonic interpretations can be made when the spatial-temporal-compositional trends of, and source contributions to magmatism are not properly considered. This study draws on intimate relationships of volcanism and extension preserved in the Sierra Madre Occidental (SMO) and Gulf of California (GoC) regions of western Mexico. Here, a major Oligocene rhyolitic ignimbrite “flare-up” (>300,000 km3) switched to a dominantly bimodal and mixed effusive-explosive volcanic phase in the Early Miocene (~100,000 km3), associated with distributed extension and opening of numerous grabens. Rhyolitic dome fields were emplaced along graben edges and at intersections of cross-graben and graben-parallel structures during early stages of graben development. Concomitant with this change in rhyolite eruption style was a change in crustal source as revealed by zircon chronochemistry with rapid rates of rhyolite magma generation due to remelting of mid- to upper crustal, highly differentiated igneous rocks emplaced during earlier SMO magmatism. Extension became more focused ~18 Ma resulting in volcanic activity being localised along the site of GoC opening. This localised volcanism (known as the Comondú “arc”) was dominantly effusive and andesite-dacite in composition. This compositional change resulted from increased mixing of basaltic and rhyolitic magmas rather than fluid flux melting of the mantle wedge above the subducting Guadalupe Plate. A poor understanding of space-time relationships of volcanism and extension has thus led to incorrect past tectonic interpretations of Comondú-age volcanism.

Faster Monte Carlo simulation of radiotherapy geometries

Using Monte Carlo simulation for radiotherapy dose calculation can provide more accurate results when compared to the analytical methods usually found in modern treatment planning systems, especially in regions with a high degree of inhomogeneity. These more accurate results acquired using Monte Carlo simulation however, often require orders of magnitude more calculation time so as to attain high precision, thereby reducing its utility within the clinical environment. This work aims to improve the utility of Monte Carlo simulation within the clinical environment by developing techniques which enable faster Monte Carlo simulation of radiotherapy geometries. This is achieved principally through the use new high performance computing environments and simpler alternative, yet equivalent representations of complex geometries. Firstly the use of cloud computing technology and it application to radiotherapy dose calculation is demonstrated. As with other super-computer like environments, the time to complete a simulation decreases as 1=n with increasing n cloud based computers performing the calculation in parallel. Unlike traditional super computer infrastructure however, there is no initial outlay of cost, only modest ongoing usage fees; the simulations described in the following are performed using this cloud computing technology. The definition of geometry within the chosen Monte Carlo simulation environment - Geometry & Tracking 4 (GEANT4) in this case - is also addressed in this work. At the simulation implementation level, a new computer aided design interface is presented for use with GEANT4 enabling direct coupling between manufactured parts and their equivalent in the simulation environment, which is of particular importance when defining linear accelerator treatment head geometry. Further, a new technique for navigating tessellated or meshed geometries is described, allowing for up to 3 orders of magnitude performance improvement with the use of tetrahedral meshes in place of complex triangular surface meshes. The technique has application in the definition of both mechanical parts in a geometry as well as patient geometry. Static patient CT datasets like those found in typical radiotherapy treatment plans are often very large and present a significant performance penalty on a Monte Carlo simulation. By extracting the regions of interest in a radiotherapy treatment plan, and representing them in a mesh based form similar to those used in computer aided design, the above mentioned optimisation techniques can be used so as to reduce the time required to navigation the patient geometry in the simulation environment. Results presented in this work show that these equivalent yet much simplified patient geometry representations enable significant performance improvements over simulations that consider raw CT datasets alone. Furthermore, this mesh based representation allows for direct manipulation of the geometry enabling motion augmentation for time dependant dose calculation for example. Finally, an experimental dosimetry technique is described which allows the validation of time dependant Monte Carlo simulation, like the ones made possible by the afore mentioned patient geometry definition. A bespoke organic plastic scintillator dose rate meter is embedded in a gel dosimeter thereby enabling simultaneous 3D dose distribution and dose rate measurement. This work demonstrates the effectiveness of applying alternative and equivalent geometry definitions to complex geometries for the purposes of Monte Carlo simulation performance improvement. Additionally, these alternative geometry definitions allow for manipulations to be performed on otherwise static and rigid geometry.

Characterisation of atmospheric deposited particles during a dust storm in urban areas of Eastern Australia

The characteristics of dust particles deposited during the 2009 dust storm in the Gold Coast and Brisbane regions of Australia are discussed in this paper. The study outcomes provide important knowledge in relation to the potential impacts of dust storm related pollution on ecosystem health in the context that the frequency of dust storms is predicted to increase due to anthropogenic desert surface modifications and climate change impacts. The investigated dust storm contributed a large fraction of fine particles to the environment with an increased amount of total suspended solids, compared to dry deposition under ambient conditions. Although the dust storm passed over forested areas, the organic carbon content in the dust was relatively low. The primary metals present in the dust storm deposition were aluminium, iron and manganese, which are common soil minerals in Australia. The dust storm deposition did not contain significant loads of nickel, cadmium, copper and lead, which are commonly present in the urban environment. Furthermore, the comparison between the ambient and dust storm chromium and zinc loads suggested that these metals were contributed to the dust storm by local anthropogenic sources. The potential ecosystem health impacts of the 2009 dust storm include, increased fine solids deposition on ground surfaces resulting in an enhanced capacity to adsorb toxic pollutants as well as increased aluminium, iron and manganese loads. In contrast, the ecosystem health impacts related to organic carbon and other metals from dust storm atmospheric deposition are not considered to be significant.

Assessing the long term viability of leasehold rural land in Queensland

Rural land holdings in a number of states in Australia can be freehold or leasehold. The actual type and tenure of the leasehold varies according to each state, but the underlying principles of ownership, transferability and farming and grazing rights are reasonably similar. There are rural areas that are all leasehold title such as the western lands in NSW, while rural land in some states and areas can be a mix of both freehold and lease hold rural property. Over the years many rural farming areas that were originally developed or granted as leasehold land have been converted to freehold title. In many instances the cost of purchasing perpetual leasehold property is similar to the equivalent freehold property despite the fact that an additional rental charge is applied to this form of ownership. Many of the current leasehold rural holdings are located in the more arid regions of the state and the prevailing agricultural farming system is either cattle or sheep grazing.

Fractional models for the migration of biological cells in complex spatial domains

Travelling wave phenomena are observed in many biological applications. Mathematical theory of standard reaction-diffusion problems shows that simple partial differential equations exhibit travelling wave solutions with constant wavespeed and such models are used to describe, for example, waves of chemical concentrations, electrical signals, cell migration, waves of epidemics and population dynamics. However, as in the study of cell motion in complex spatial geometries, experimental data are often not consistent with constant wavespeed. Non-local spatial models have successfully been used to model anomalous diffusion and spatial heterogeneity in different physical contexts. In this paper, we develop a fractional model based on the Fisher-Kolmogoroff equation and analyse it for its wavespeed properties, attempting to relate the numerical results obtained from our simulations to experimental data describing enteric neural crest-derived cells migrating along the intact gut of mouse embryos. The model proposed essentially combines fractional and standard diffusion in different regions of the spatial domain and qualitatively reproduces the behaviour of neural crest-derived cells observed in the caecum and the hindgut of mouse embryos during in vivo experiments.

Detection of dugongs from unmanned aerial vehicles

Monitoring and estimation of marine populations is of paramount importance for the conservation and management of sea species. Regular surveys are used to this purpose followed often by a manual counting process. This paper proposes an algorithm for automatic detection of dugongs from imagery taken in aerial surveys. Our algorithm exploits the fact that dugongs are rare in most images, therefore we determine regions of interest partially based on color rarity. This simple observation makes the system robust to changes in illumination. We also show that by applying the extended-maxima transform on red-ratio images, submerged dugongs with very fuzzy edges can be detected. Performance figures obtained here are promising in terms of degree of confidence in the detection of marine species, but more importantly our approach represents a significant step in automating this type of surveys.

Molecular genetics of migraine

Migraine is a common neurological disorder with a significantly heritable component. It is a complex disease and despite numerous molecular genetic studies, the exact pathogenesis causing the neurological disturbance remains poorly understood. Although several known molecular mechanisms have been associated with an increased risk for developing migraine, there remains significant scope for future studies. The majority of studies have investigated the most plausible candidate genes involved in common migraine pathogenesis utilising criteria that takes into account a combination of physiological functionality in conjunction with regions of genomic association. Thus, far genes involved in neurological, vascular or hormonal pathways have been identified and investigated on this basis. Genome-wide association studies (GWAS) studies have helped to identify novel regions that may be associated with migraine and have aided in providing the basis for further molecular investigations. However, further studies utilising sequencing technologies are required to characterise the genetic basis for migraine.