A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models.

Insurance and trust : lessons from the Christchurch Cathedral

This article examines important insurance and trust law issues that may confront trustees charged with the governance and protection of unique properties with broad community and heritage significance. Often trustee roles are assumed by community leaders without full appreciation of the potential difficulties and consequences when unforeseen circumstances arise. Three recent New Zealand court decisions in relation to the deconstruction and repair of the Christchurch Cathedral and to the interim construction of a transitional"cardboard Cathedral" highlight how difficult - and legally exposed - the role of trustee can be. The Cathedral cases go to the heart of defining the core purpose for which a Trust is created and examine the scope of discretion in fulfilling this charge its Trustees carry. Arising in the wake of the devastating Christchurch earthquakes, the Cathedral's Trustees were called upon to consider the best directions forward for a criplled and dangerous building subject to potential demolition, the wellbeing of the Cathedral's direct community, and the broader heritage and identity factors that this 'heart' of Christchurch represented. In the context of a seemingly grossly underinsured material damage cover - and faced with broader losses across the Diocese's holdings - the Trustees found that their sense of mission failed to gel with that of a community-based heritage buildings preservation trust. The High Court had to consider how monies received under the material damage policy could be applied by the Trustee in deconstructing, reinstating or repairing the Cathedral and if monies could be partly deployed to create an interim solution in the former of a transitional cathedral - all this in the context of the site-specific purpose of the Cathedral trust. The cases emphasise further the need to assess professionally the nature and quantum of cover effected to protect against various risks. In addition, in the case of historic or unusual buildings extra care must be exercised to take account additional costs associated with reinstatement so as to substantially retain the character and intrinsic value of such properties.

Social water assessment protocol : a step towards connecting mining, water and human rights

The human right to water has recently been recognised by both the United Nations General Assembly and the Human Rights Council. As the mining industry interacts with water on multiple levels, it is important that these interactions respect the human right to water. Currently, a disconnect exists between mine site water management practices and the recognition of water from a human rights perspective. The Minerals Council of Australia (MCA) Water Accounting Framework (WAF) has previously been used to strengthen the connection between water management and human rights. This article extends this connection through the use of a Social Water Assessment Protocol (SWAP). The SWAP is scoping tool consisting of a set of questions classified into taxonomic themes under leading topics with suggested sources of data that enable mine sites to better understand the local water context in which they operate. Three of the themes contained in the SWAP – gender, Indigenous peoples and health – are discussed to demonstrate how the protocol may be useful in assisting mining companies to consider their impacts on the human right to water.

The road we're on

The creative development and direction of THE ROAD WE'RE ON (Book by Stephen Carleton, Music by Scott Saunders), commissioned by the Queensland Music Festival and the Murweh Shire Council. The was a site-specific, community-driven music theatre production produced and performed in Charleville and involved over 100 local artists and the communities of western Queensland.

Guardians of hidden universes

“Guardians of Hidden Universes” is a playful story for experiencing on your phone in the street. You’re a Guardian of Hidden Universes, and when you check your Communication Terminal you find the Guild has made a terrible mistake they need you to repair. The experience lasts about 15-25 minutes, and takes you around whatever city you happen to be in. That’s right – you can play it in any city in the world! The app was launched at Popup Playground‘s 2013 Fresh Air Festival – a new pervasive gaming festival in Melbourne, Australia. This playful story is inspired by the idea of creating a locative-experience that is not site-specific. How can we have an experience than engages with the environment that also can work worldwide? The story is also playing with the idea of engaging with a character and a space and intuition within a short period of time. The short and playful experience is a Universe Creation 101 production. It was conceived, written, and designed by Christy Dena; with artwork, coding, and interface design by Elroy.

The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone

Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

Identification of genes important for growth of asymptomatic bacteriuria Escherichia coli in urine

Escherichia coli is the most important etiological agent of urinary tract infections (UTIs). Unlike uropathogenic E. coli, which causes symptomatic infections, asymptomatic bacteriuria (ABU) E. coli strains typically lack essential virulence factors and colonize the bladder in the absence of symptoms. While ABU E. coli can persist in the bladder for long periods of time, little is known about the genetic determinants required for its growth and fitness in urine. To identify such genes, we have employed a transposon mutagenesis approach using the prototypic ABU E. coli strain 83972 and the clinical ABU E. coli strain VR89. Six genes involved in the biosynthesis of various amino acids and nucleobases were identified (carB, argE, argC, purA, metE, and ilvC), and site-specific mutants were subsequently constructed in E. coli 83972 and E. coli VR89 for each of these genes. In all cases, these mutants exhibited reduced growth rates and final cell densities in human urine. The growth defects could be complemented in trans as well as by supplementation with the appropriate amino acid or nucleobase. When assessed in vivo in a mouse model, E. coli 83972carAB and 83972argC showed a significantly reduced competitive advantage in the bladder and/or kidney during coinoculation experiments with the parent strain, whereas 83972metE and 83972ilvC did not. Taken together, our data have identified several biosynthesis pathways as new important fitness factors associated with the growth of ABU E. coli in human urine.

Comparative analysis of FimB and FimE recombinase activity

FimB and FimE are site-specific recombinases, part of the λ integrase family, and invert a 314 bp DNA switch that controls the expression of type 1 fimbriae in Escherichia coli. FimB and FimE differ in their activity towards the fim switch, with FimB catalysing inversion in both directions in comparison to the higher-frequency but unidirectional on-to-off recombination catalysed by FimE. Previous work has demonstrated that FimB, but not FimE, recombination is completely inhibited in vitro and in vivo by a regulator, PapB, expressed from a distinct fimbrial locus. The aim of this work was to investigate differences between FimB and FimE activity by exploiting the differential inhibition demonstrated by PapB. The research focused on genetic changes to the fim switch that alter recombinase binding and its structural context. FimB and FimE still recombined a switch in which the majority of fimS DNA was replaced with a larger region of non-fim DNA. This demonstrated a minimal requirement for FimB and FimE recombination of the Fim binding sites and associated inverted repeats. With the original leucine-responsive regulatory protein (Lrp) and integration host factor (IHF)-dependent structure removed, PapB was now able to inhibit both recombinases. The relative affinities of FimB and FimE were determined for the four ‘half sites’. This analysis, along with the effect of extensive swaps and duplications of the half sites on recombination frequency, demonstrated that FimB recruitment and therefore subsequent activity was dependent on a single half site and its context, whereas FimE recombination was less stringent, being able to interact initially with two half sites with equally high affinity. While increasing FimB recombination frequencies failed to overcome PapB repression, mutations made in recombinase binding sites resulted in inhibition of FimE recombination by PapB. Overall, the data support a model in which the recombinases differ in loading order and co-operative interactions. PapB exploits this difference and FimE becomes susceptible when its normal loading is restricted or changed.

Collective coverings, communal skin

Collective Coverings, Communal Skin is a large-scale site-specific installation that grows with community contributions created for the 2012 Liverpool Biennial. The work involves transforming objects used in conflict (second hand hunting and camouflage t-shirts) into objects of comfort (hula hoop rag mats) . Many of the shirts were either donated or purchased from thrift stores in Los Angeles and Liverpool. With the massive help of the Liverpool community we transformed individual t-shirts through weaving them into a communal skin that covers the existing internal architecture. There was a workshop space with instruction video, inside the installation where visitors could sit and work on patchwork body-pillows. During structured workshops I talked with the community about meditating while they weave so as to contemplate the spiritual and conceptual dimension of the project. The hula-hoop weavings grew throughout the space for the duration of the 10-week Biennial. The community contributed 770 weavings. This project was funded by the Australia Council for the Arts and FACT.

Development of a flexible design approach for the deflection zone behind road safety barriers

Flexible design practices broadly permit that design values outside the normal range can be accepted as appropriate for a site-specific context providing that the risk is evaluated and is tolerable. Execution of flexible design demands some evaluation of risk. In restoration projects, it may be the case that an immovable object exists within the zone of the expected deflection of a road safety barrier system. Only by design exception can the situation be determined to be acceptable. However, the notion of using flexible design for road safety barrier design is not well developed. The existence of a diminishing return relationship between safety benefits and provision of increased clear zone has been established previously. This paper proposes that a similar rationale might reasonably apply for the deflection zone behind road safety barriers and describes how the risk associated with road safety barriers might be quantified in order that defensible road safety barrier design can exist below the lower bounds of normal design standards. As such, the methodology described in this paper may provide some basis to enable road authorities to make informed design decisions, particularly for restoration, or “Brownfield”, projects.

Soil moisture variability in a temperate deciduous forest: insights from electrical resistivity and throughfall data

Hydrogeophysics is a growing discipline that holds significant promise to help elucidate details of dynamic processes in the near surface, built on the ability of geophysical methods to measure properties from which hydrological and geochemical variables can be derived. For example, bulk electrical conductivity is governed by, amongst others, interstitial water content, fluid salinity, and temperature, and can be measured using a range of geophysical methods. In many cases, electrical resistivity tomography (ERT) is well suited to characterize these properties in multiple dimensions and to monitor dynamic processes, such as water infiltration and solute transport. In recent years, ERT has been used increasingly for ecosystem research in a wide range of settings; in particular to characterize vegetation-driven changes in root-zone and near-surface water dynamics. This increased popularity is due to operational factors (e.g., improved equipment, low site impact), data considerations (e.g., excellent repeatability), and the fact that ERT operates at scales significantly larger than traditional point sensors. Current limitations to a more widespread use of the approach include the high equipment costs, and the need for site-specific petrophysical relationships between properties of interest. In this presentation we will discuss recent equipment advances and theoretical and methodological aspects involved in the accurate estimation of soil moisture from ERT results. Examples will be presented from two studies in a temperate climate (Michigan, USA) and one from a humid tropical location (Tapajos, Brazil).

Source characterisation of urban road surface pollutants for enhanced water quality predictions

This study developed a comprehensive research methodology for identification and quantification of sources responsible for pollutant build-up and wash-off from urban road surfaces. The study identified soil and asphalt wear, and non-combusted diesel fuel as the most influential sources for metal and hydrocarbon pollution respectively. The study also developed mathematical models to relate contributions from identified sources to underlying site specific factors such as land use and traffic. Developed mathematical model will play a key role in urban planning practices, enabling the implementation of effective water pollution control strategies.

Towards a theoretical framework for online professional discussions

Online interactions are becoming commonplace for a multitude of educational purposes. Each context presents a unique and dynamic mix of variables that combine to shape the practice and the identities of those involved. In this article, sociocultural theories of learning and sociocultural theories of technology are explored as a way to view and to map the complex interactions that can occur. The case of synchronous online moderation meetings are used as an example of the combination of variables that can impact on the development of shared understandings of a practice. Online moderation can involve teachers from geographically diverse areas discussing and negotiating their judgement decisions. These discussions represent an intersection of a national curriculum, standards-referenced assessment, moderation protocols, site-specific practices and understandings, and individual teachers’ knowledges and histories. It is suggested that the proposed theoretical combination addresses some of the limitations of each of the theories when investigating such a dynamic context. As higher education moves into increasing use of online modes of communication and a higher level of accountability the relevance of this discussion to higher education is evident.

Terra Preta (Agriculture+Art+Algorithm)

Terra Preta is a site-specific bio-energy project which aims to create a synergy between the public and the pre-existing engineered landscape of Freshkills Park on Staten Island, New York. The project challenges traditional paradigms of public space by proposing a dynamic and ever-changing landscape. The initiative allows the publuc to self-organise the landscape and to engage in 'algorithmic processes' of growth, harvest and space creation.

Black Nectar

Black Nectar is a site-specific light & sound installation, that asks audiences to take slow, sensory walks through the inky-blackness of Bundanon’s forests at night, charting personal courses through seasons of change, animality and imagination – far beyond the blinding lights and howling tones of our contemporary existence. Gathering during a time Europeans once named as ‘spring’ audiences will leave the comfy lights and sounds of Bundanon’s homestead area, to take powerful, personal, silent journeys into the long darks of night, heading ultimately towards the place of ‘Black Nectar’. This most unusual of walks begins with impending darkness, and yet ultimately ends with the faintest, sweetest of glimmers – an en-lightening, re-sounding of our seasonal futures?