Integrated Bayesian network frameworks for modelling complex ecological issues

Ecological problems are typically multi faceted and need to be addressed from a scientific and a management perspective. There is a wealth of modelling and simulation software available, each designed to address a particular aspect of the issue of concern. Choosing the appropriate tool, making sense of the disparate outputs, and taking decisions when little or no empirical data is available, are everyday challenges facing the ecologist and environmental manager. Bayesian Networks provide a statistical modelling framework that enables analysis and integration of information in its own right as well as integration of a variety of models addressing different aspects of a common overall problem. There has been increased interest in the use of BNs to model environmental systems and issues of concern. However, the development of more sophisticated BNs, utilising dynamic and object oriented (OO) features, is still at the frontier of ecological research. Such features are particularly appealing in an ecological context, since the underlying facts are often spatial and temporal in nature. This thesis focuses on an integrated BN approach which facilitates OO modelling. Our research devises a new heuristic method, the Iterative Bayesian Network Development Cycle (IBNDC), for the development of BN models within a multi-field and multi-expert context. Expert elicitation is a popular method used to quantify BNs when data is sparse, but expert knowledge is abundant. The resulting BNs need to be substantiated and validated taking this uncertainty into account. Our research demonstrates the application of the IBNDC approach to support these aspects of BN modelling. The complex nature of environmental issues makes them ideal case studies for the proposed integrated approach to modelling. Moreover, they lend themselves to a series of integrated sub-networks describing different scientific components, combining scientific and management perspectives, or pooling similar contributions developed in different locations by different research groups. In southern Africa the two largest free-ranging cheetah (Acinonyx jubatus) populations are in Namibia and Botswana, where the majority of cheetahs are located outside protected areas. Consequently, cheetah conservation in these two countries is focussed primarily on the free-ranging populations as well as the mitigation of conflict between humans and cheetahs. In contrast, in neighbouring South Africa, the majority of cheetahs are found in fenced reserves. Nonetheless, conflict between humans and cheetahs remains an issue here. Conservation effort in South Africa is also focussed on managing the geographically isolated cheetah populations as one large meta-population. Relocation is one option among a suite of tools used to resolve human-cheetah conflict in southern Africa. Successfully relocating captured problem cheetahs, and maintaining a viable free-ranging cheetah population, are two environmental issues in cheetah conservation forming the first case study in this thesis. The second case study involves the initiation of blooms of Lyngbya majuscula, a blue-green algae, in Deception Bay, Australia. L. majuscula is a toxic algal bloom which has severe health, ecological and economic impacts on the community located in the vicinity of this algal bloom. Deception Bay is an important tourist destination with its proximity to Brisbane, Australia’s third largest city. Lyngbya is one of several algae considered to be a Harmful Algal Bloom (HAB). This group of algae includes other widespread blooms such as red tides. The occurrence of Lyngbya blooms is not a local phenomenon, but blooms of this toxic weed occur in coastal waters worldwide. With the increase in frequency and extent of these HAB blooms, it is important to gain a better understanding of the underlying factors contributing to the initiation and sustenance of these blooms. This knowledge will contribute to better management practices and the identification of those management actions which could prevent or diminish the severity of these blooms.

A Bayesian network approach to modelling temporal behaviour of Lyngbya majuscula bloom initiation

Lyngbya majuscula is a cyanobacterium (blue-green algae) occurring naturally in tropical and subtropical coastal areas worldwide. Deception Bay, in Northern Moreton Bay, Queensland, has a history of Lyngbya blooms, and forms a case study for this investigation. The South East Queensland (SEQ) Healthy Waterways Partnership, collaboration between government, industry, research and the community, was formed to address issues affecting the health of the river catchments and waterways of South East Queensland. The Partnership coordinated the Lyngbya Research and Management Program (2005-2007) which culminated in a Coastal Algal Blooms (CAB) Action Plan for harmful and nuisance algal blooms, such as Lyngbya majuscula. This first phase of the project was predominantly of a scientific nature and also facilitated the collection of additional data to better understand Lyngbya blooms. The second phase of this project, SEQ Healthy Waterways Strategy 2007-2012, is now underway to implement the CAB Action Plan and as such is more management focussed. As part of the first phase of the project, a Science model for the initiation of a Lyngbya bloom was built using Bayesian Networks (BN). The structure of the Science Bayesian Network was built by the Lyngbya Science Working Group (LSWG) which was drawn from diverse disciplines. The BN was then quantified with annual data and expert knowledge. Scenario testing confirmed the expected temporal nature of bloom initiation and it was recommended that the next version of the BN be extended to take this into account. Elicitation for this BN thus occurred at three levels: design, quantification and verification. The first level involved construction of the conceptual model itself, definition of the nodes within the model and identification of sources of information to quantify the nodes. The second level included elicitation of expert opinion and representation of this information in a form suitable for inclusion in the BN. The third and final level concerned the specification of scenarios used to verify the model. The second phase of the project provides the opportunity to update the network with the newly collected detailed data obtained during the previous phase of the project. Specifically the temporal nature of Lyngbya blooms is of interest. Management efforts need to be directed to the most vulnerable periods to bloom initiation in the Bay. To model the temporal aspects of Lyngbya we are using Object Oriented Bayesian networks (OOBN) to create ‘time slices’ for each of the periods of interest during the summer. OOBNs provide a framework to simplify knowledge representation and facilitate reuse of nodes and network fragments. An OOBN is more hierarchical than a traditional BN with any sub-network able to contain other sub-networks. Connectivity between OOBNs is an important feature and allows information flow between the time slices. This study demonstrates more sophisticated use of expert information within Bayesian networks, which combine expert knowledge with data (categorized using expert-defined thresholds) within an expert-defined model structure. Based on the results from the verification process the experts are able to target areas requiring greater precision and those exhibiting temporal behaviour. The time slices incorporate the data for that time period for each of the temporal nodes (instead of using the annual data from the previous static Science BN) and include lag effects to allow the effect from one time slice to flow to the next time slice. We demonstrate a concurrent steady increase in the probability of initiation of a Lyngbya bloom and conclude that the inclusion of temporal aspects in the BN model is consistent with the perceptions of Lyngbya behaviour held by the stakeholders. This extended model provides a more accurate representation of the increased risk of algal blooms in the summer months and show that the opinions elicited to inform a static BN can be readily extended to a dynamic OOBN, providing more comprehensive information for decision makers.

Brucite Microbialites in Living Coral Skeletons: Indicators of Extreme Microenvironments in Shallow-Marine Settings

Brucite [Mg(OH)2] microbialites occur in vacated interseptal spaces of living scleractinian coral colonies (Acropora, Pocillopora, Porites) from subtidal and intertidal settings in the Great Barrier Reef, Australia, and subtidal Montastraea from the Florida Keys, United States. Brucite encrusts microbial filaments of endobionts (i.e., fungi, green algae, cyanobacteria) growing under organic biofilms; the brucite distribution is patchy both within interseptal spaces and within coralla. Although brucite is undersaturated in seawater, its precipitation was apparently induced in the corals by lowered pCO2 and increased pH within microenvironments protected by microbial biofilms. The occurrence of brucite in shallow-marine settings highlights the importance of microenvironments in the formation and early diagenesis of marine carbonates. Significantly, the brucite precipitates discovered in microenvironments in these corals show that early diagenetic products do not necessarily reflect ambient seawater chemistry. Errors in environmental interpretation may arise where unidentified precipitates occur in microenvironments in skeletal carbonates that are subsequently utilized as geochemical seawater proxies.

Does a high UV environment ensure adequate vitamin D status?

This study assesses the Vitamin D status of 126 healthy free-living adults aged 18–87 years, in southeast Queensland, Australia (27°S) at the end of the 2006 winter. Participants provided blood samples for analysis of 25(OH)D (the measure of an individual’s Vitamin D status), PTH, Calcium, Phosphate, and Albumin, completed a questionnaire on sun-protective/sun-exposure behaviours, and were assessed for phenotypic characteristics such as skin/hair/eye colour and BMI. We found that 10.2% of the participants had serum 25(OH)D levels below 25 nmol/l (considered deficient) and a further 32.3% had levels between 25 nmol/l and 50 nmol/l (considered insufficient). Our results show that low levels of 25(OH)D can occur in a substantial proportion of the population at the end of winter, even in a sunny climate. 25(OH)D levels were higher amongst those who spent more time in the sun and lower among obese participants (BMI > 30) than those who were not obese (BMI < 30). 25(OH)D levels were also lower in participants who had black hair, dark/olive skin, or brown eyes, when compared with participants who had brown or fair hair, fair skin, or blue/green eyes. No associations were found between 25(OH)D status and age, gender, smoking status, or the use of sunscreen.

Workers’ UV exposure and the subsequent impact on skin

Introduction: Excessive exposure to ultraviolet (UV) radiation from sunlight is a causative factor in the development of skin damage and skin cancer. Little research has been undertaken into assessing the sun exposure linking to skin damage inside buildings or behind window glass. This project directly addressed this issue by aiming to assess the role that UV exposure has on skin damage for indoor workers and drivers. Methods: Measurements of personal UV exposure using UV sensitive polymer dosimeters were undertaken of 41 indoor workers and 3 professional drivers. Physical measurements of skin characteristics including skin pigmentation and UV induced skin photoaging were also determined. In addition, demographic information along with phenotypic characteristics, sun exposure and sun protection practice history, and history of skin damage were assessed through a questionnaire. Results: Indoor workers typically received low doses of UV radiation. However, one driver received a high dose (13J/cm2 UVA and 4.99 MED UVB on the arm). Age and years residing in Australia had a positive correlation with UV induced skin pigmentation. The number of major sunburns before 18 years was a risk factor for skin damage in adults. Those participants with fair skin, non-black hair and blue/green /blue-grey eye were more likely to have skin damage related to sun exposure. Conclusions: A person’s age, years residing in Australia, numbers of major sunburn, skin colour, hair colour and eye colour are important factors associated with the development of sun-related skin damage in workers. ‘Real World’ implications: 1. The number of major sunburns before 18 years was a risk factor for skin damage in adults. This clearly confirms the importance of early prevention. To protect the skin from extensive sun exposure for your generation should have significance for further prevention of skin damage. 2. It is unsurprising that age and years residing in Australia were associated with skin damage related UV radiation. Therefore, the general public should reinforce their sun protective measures and check skin regularly. 3. Drivers should take sun protective measures during their working hours between sunrise and sunset.

Particle wave

“Particle Wave” is comprised of six lenticular panels hung in an even, horizontal sequence. Each panel alternates between two solid colour fields as you move past it. There are six colours in total, with each colour represented twice in the spectrum. From left to right, the panels move through yellow, orange, magenta, violet, blue, green and back to yellow. The work’s title refers to the two competing theories of light, which can be understood as either paradoxical or complementary. Like these theories, the experience of viewing the work catches us in a double bind. While we can orient ourselves to see solid colour fields one by one, we are never able to fully capture them all at once. In fact, it is only through our continual movement, and the subsequent transitioning of visible colours that we register the complete spectrum. Through this viewing experience, “Particle Wave” actively engages with our peripheral vision and the transitory nature of perception. It plays with the fundamental pleasures of colour and vision, and the uneasy seduction of being unable to grasp multiple phenomena simultaneously.

Grandiflora : Recent Paintings by Daniel Mafe

Grandiflora: Recent Paintings by Daniel Mafe The paintings of Grandiflora are improvised around a range of different flower motifs culled from medieval textiles and botanical illustrations. Each of the paintings is constructed upon a ground of flat, palely luminous yellow occasionally supplemented by additional areas of high-keyed pastel. Pink, blue, green and mauve together with the yellow, generate a shimmering and even incandescent glow. The graphic images of the flowers with the flat colour areas are then contrasted and worked over with richly sensual, abstract gestures of paint. Within the work there is a pronounced almost rococo-esque opticality as it operates between these different visual codes of flat colour, recognizable floral forms, and gesture. These codes combine to produce a definite visceral impact on the viewer, a pronounced and tactile sense of the experience and ambiguity inherent in perceiving. This ambiguity is interestingly at odds with the apparently clean and crisp quality each painting demonstrates as an integrated whole. Indeed each piece goes on to reveal, despite the use of overt figurative quotations, a sense of the purely abstract which in its turn concretely establishes the ornamental.

Assessment of the molecular structure of the borate mineral boracite Mg3B7O13Cl using vibrational spectroscopy

Boracite is a magnesium borate mineral with formula: Mg3B7O13Cl and occurs as blue green, colorless, gray, yellow to white crystals in the orthorhombic – pyramidal crystal system. An intense Raman band at 1009 cm−1 was assigned to the BO stretching vibration of the B7O13 units. Raman bands at 1121, 1136, 1143 cm−1 are attributed to the in-plane bending vibrations of trigonal boron. Four sharp Raman bands observed at 415, 494, 621 and 671 cm−1 are simply defined as trigonal and tetrahedral borate bending modes. The Raman spectrum clearly shows intense Raman bands at 3405 and 3494 cm−1, thus indicating that some Cl anions have been replaced with OH units. The molecular structure of a natural boracite has been assessed by using vibrational spectroscopy.

Structure, magnetism and colour in simple bis­(phosphine)nickel(II) dihalide complexes : an experimental and theoretical investigation

The complex [1,2-bis­(di-tert-butyl­phosphan­yl)ethane-[kappa]2P,P']di­iodido­nickel(II), [NiI2(C18H40P2] or (dtbpe-[kappa]2P)NiI2, [dtbpe is 1,2-bis­(di-tert-butyl­phosphan­yl)ethane], is bright blue-green in the solid state and in solution, but, contrary to the structure predicted for a blue or green nickel(II) bis­(phos­phine) complex, it is found to be close to square planar in the solid state. The solution structure is deduced to be similar, because the optical spectra measured in solution and in the solid state contain similar absorptions. In solution at room temperature, no 31P{1H} NMR resonance is observed, but the very small solid-state magnetic moment at temperatures down to 4 K indicates that the weak paramagnetism of this nickel(II) complex can be ascribed to temperature independent paramagnetism, and that the complex has no unpaired electrons. The red [1,2-bis­(di-tert-butyl­phosphan­yl)ethane-[kappa]2P,P']di­chlorido­nickel(II), [NiCl2(C18H40P2] or (dtbpe-[kappa]2P)NiCl2, is very close to square planar and very weakly paramagnetic in the solid state and in solution, while the maroon [1,2-bis­(di-tert-butyl­phosphan­yl)ethane-[kappa]2P,P']di­bromido­nickel(II), [NiBr2(C18H40P2] or (dtbpe-[kappa]2P)NiBr2, is isostructural with the diiodide in the solid state, and displays paramagnetism inter­mediate between that of the dichloride and the diiodide in the solid state and in solution. Density functional calculations demonstrate that distortion from an ideal square plane for these complexes occurs on a flat potential energy surface. The calculations reproduce the observed structures and colours, and explain the trends observed for these and similar complexes. Although theoretical investigation identified magnetic-dipole-allowed excitations that are characteristic for temperature-independent paramagnetism (TIP), theory predicts the mol­ecules to be diamagnetic.

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants (∼200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots. © 2006 Federation of European Biochemical Societies.

Electron-accepting conjugated materials based on 2-Vinyl-4,5- dicyanoimidazoles for application in organic electronics

We report the Heck coupling of 2-vinyl-4,5-dicyanoimidazole (vinazene) with selected di- and trihalo aromatics in an effort to prepare linear and branched electron-accepting conjugated materials for application in organic electronics. By selecting the suitable halo-aromatic moiety, it is possible to tune the HOMO - LUMO energy levels, absorption, and emission properties for a specific application. In this regard, materials with strong photoluminescence from blue → green → red are reported that may have potential application in organic light-emitting diodes (OLEDs). Furthermore, derivatives with strong absorption in the visible spectrum, coupled with favorable HOMO-LUMO levels, have been used to prepare promising organic photovoltaic devices (OPVs) when combined with commercially available semiconducting donor polymers.

4-hexylbithieno[3,2-b:2′3′-e]pyridine: An efficient electron-accepting unit in fluorene and indenofluorene copolymers for light-emitting devices

4-Hexylbithienopyridine has been prepared as a novel electron-accepting monomer for conjugated polymers. To test its electronic properties, alternating copolymers with fluorene and indenofluorene polymers have been prepared. The copolymers displayed reduction potentials about 0.5 V lower than for the corresponding fluorene and indenofluorene homopolymers, indicating much improved electron-accepting properties. Analysis of the microscopic morphology of thin films of the copolymers by AFM shows that they lack the extensive supramolecular order seen with the homopolymers, which is attributed to the bithienopyridine units disrupting the π-stacking. LEDs using these polymers as the emitting layer produce blue-green emission with low turn-on voltages with aluminum electrodes confirming their improved electron affinity. The indenofluorene copolymer displayed an irreversible red shift in emission at high voltages, which is attributed to oxidation of the indenofluorene units. This red shift occurred at higher potentials than for indenofluorene homopolymers in LEDs, suggesting that the heterocyclic moieties offer some protection against electrically promoted oxidation.

Optimising ketocarotenoid production in potato tubers : effect of genetic background, transgene combinations and environment

Astaxanthin is a high value carotenoid produced by some bacteria, a few green algae, several fungi but only a limited number of plants from the genus Adonis. Astaxanthin has been industrially exploited as a feed supplement in poultry farming and aquaculture. Consumption of ketocarotenoids, most notably astaxanthin, is also increasingly associated with a wide range of health benefits,as demonstrated in numerous clinical studies. Currently astaxanthin is produced commercially by chemical synthesis or from algal production systems. Several studies have used a metabolic engineering approach to produce astaxanthin in transgenic plants. Previous attempts to produce transgenic potato tubers biofortified with astaxanthin have met with limited success. In this study we have investigated approaches to optimising tuber astaxanthin content. It is demonstrated that the selection of appropriate parental genotype for transgenic approaches and stacking carotenoid biosynthetic pathway genes with the cauliflower Or gene result in enhanced astaxanthin content, to give six-fold higher tuber astaxanthin content than has been achieved previously. Additionally we demonstrate the effects of growth environment on tuber carotenoid content in both wild type and astaxanthin-producing transgenic lines and describe the associated transcriptome and metabolome restructuring.

The effect of light on cognitive performance of partially sleep-deprived young drivers

Sleepiness remains a primary cause of road crashes, the major cause of death in young adults. Light is known to produce a direct alerting effect, but little is known about its effects on sleepy drivers. This study aimed to compare the effect of blue-green light and caffeine on young drivers’ cognitive performance after chronic-partial sleep loss.

Green fireballs and ball lightning

This paper presents evidence of an apparent connection between ball lightning and a green fireball. On the evening of the 16th May 2006 at least three fireballs were seen by many people in the skies of Queensland, Australia. One of the fireballs was seen passing over the Great Divide about 120 km west of Brisbane, and soon after, a luminous green ball about 30 cm in diameter was seen rolling down the slope of the Great Divide. A detailed description given by a witness indicates that the phenomenon was probably a highly luminous form of ball lightning. An hypothesis presented in this paper is that the passage of the Queensland fireball meteor created an electrically conductive path between the ionosphere and ground, providing energy for the ball lightning phenomenon. A strong similarity is noted between the Queensland fireball and the Pasamonte fireball seen in New Mexico in 1933. Both meteors exhibit a twist in the tail that could be explained by hydrodynamic forces. The possibility that multiple sightings of fireballs across South East Queensland were produced owing to fragments from comet 73P Schwassmann-Wachmann 3 is discussed.