Insights into a multidrug resistant Escherichia coli pathogen of the globally disseminated ST131 lineage : genome analysis and virulence mechanisms

Escherichia coli strains causing urinary tract infection (UTI) are increasingly recognized as belonging to specific clones. E. coli clone O25b:H4-ST131 has recently emerged globally as a leading multi-drug resistant pathogen causing urinary tract and bloodstream infections in hospitals and the community. While most molecular studies to date examine the mechanisms conferring multi-drug resistance in E. coli ST131, relatively little is known about their virulence potential. Here we examined E. coli ST131 clinical isolates from two geographically diverse collections, one representing the major pathogenic lineages causing UTI across the United Kingdom and a second representing UTI isolates from patients presenting at two large hospitals in Australia. We determined a draft genome sequence for one representative isolate, E. coli EC958, which produced CTX-M-15 extended-spectrum β-lactamase, CMY-23 type AmpC cephalosporinase and was resistant to ciprofloxacin. Comparative genome analysis indicated that EC958 encodes virulence genes commonly associated with uropathogenic E. coli (UPEC). The genome sequence of EC958 revealed a transposon insertion in the fimB gene encoding the activator of type 1 fimbriae, an important UPEC bladder colonization factor. We identified the same fimB transposon insertion in 59% of the ST131 UK isolates, as well as 71% of ST131 isolates from Australia, suggesting this mutation is common among E. coli ST131 strains. Insertional inactivation of fimB resulted in a phenotype resembling a slower off-to-on switching for type 1 fimbriae. Type 1 fimbriae expression could still be induced in fimB-null isolates; this correlated strongly with adherence to and invasion of human bladder cells and bladder colonisation in a mouse UTI model. We conclude that E. coli ST131 is a geographically widespread, antibiotic resistant clone that has the capacity to produce numerous virulence factors associated with UTI.

Evolution of brain size in the palaeognath lineage, with an emphasis on New Zealand ratites

Brain size in vertebrates varies principally with body size. Although many studies have examined the variation of brain size in birds, there is little information on Palaeognaths, which include the ratite lineage of kiwi, emu, ostrich and extinct moa, as well as the tinamous. Therefore, we set out to determine to what extent the evolution of brain size in Palaeognaths parallels that of other birds, i. e., Neognaths, by analyzing the variation in the relative sizes of the brain and cerebral hemispheres of several species of ratites and tinamous. Our results indicate that the Palaeognaths possess relatively smaller brains and cerebral hemispheres than the Neognaths, with the exception of the kiwi radiation (Apteryx spp.). The external morphology and relatively large size of the brain of Apteryx, as well as the relatively large size of its telencephalon, contrast with other Palaeognaths, including two species of historically sympatric moa, suggesting that unique selective pressures towards increasing brain size accompanied the evolution of kiwi. Indeed, the size of the cerebral hemispheres with respect to total brain size of kiwi is rivaled only by a handful of parrots and songbirds, despite a lack of evidence of any advanced behavioral/ cognitive abilities such as those reported for parrots and crows. In addition, the enlargement in brain and telencephalon size of the kiwi occurs despite the fact that this is a precocial bird. These findings form an exception to, and hence challenge, the current rules that govern changes in relative brain size in birds. Copyright (c) 2007 S. Karger AG, Basel.

Mesenchymal stem cells as mediators of the neuronal cell niche

This study examined the role of heparan sulfate proteoglycans (HSPGs) in neural lineage differentiation of human mesenchymal stem cells (hMSCs). Several HSPGs were identified as potential new targets controlling neural fate specification and may be applied to the development of improved models to examine and repair brain damage. hMSCs were characterised throughout extended in vitro expansion for neural lineage potential (neurons, astrocytes, oligodendrocytes) and differentiated using terminal differentiation and intermediate sphere formation. Brain damage and neurological disorders caused by injury or disease affect a large number of people often resulting in lifelong disabilities. Multipotent mesenchymal stem cells have a large capacity for self-renewal and provide an excellent model to examine the regulation and contribution of both stem cells and their surrounding microenvironment to the repair of neural tissue damage.

Product-library-derived specification parameters in building information models augmentation

This paper conceptualizes a framework for bridging the BIM (building information modelling)-specifications divide through augmenting objects within BIM with specification parameters derived from a product library. We demonstrate how model information, enriched with data at various LODs (levels of development), can evolve simultaneously with design and construction using different representation of a window object embedded in a wall as lifecycle phase exemplars at different levels of granularity. The conceptual standpoint is informed by the need for exploring a methodological approach which extends beyond current limitations of current modelling platforms in enhancing the information content of BIM models. Therefore, this work demonstrates that BIM objects can be augmented with construction specification parameters leveraging product libraries.

Phylogenetic lineage and pilus protein Spb1/SAN1518 affect opsonin-independent phagocytosis and intracellular survival of Group B Streptococcus

Opsonin-independent phagocytosis of Group B Streptococcus (GBS) is important in defense against neonatal GBS infections. A recent study indicated a role for GBS pilus in macrophage phagocytosis (Maisey et al Faseb J 22 2008 1715-24). We studied 163 isolates from different phylogenetic backgrounds and those possessing or lacking the gene encoding the pilus backbone protein, Spb1 (SAN1518, PI-2b) and spb1-deficient mutants of wild-type (WT) serotype III-3 GBS 874391 in non-opsonic phagocytosis assays using J774A.1 macrophages. Numbers of GBS phagocytosed differed up to 23-fold depending on phylogenetic background; isolates possessing spb1 were phagocytosed more than isolates lacking spb1. Comparing WT GBS and isogenic spb1-deficient mutants showed WT was phagocytosed better compared to mutants; Spb1 also enhanced intracellular survival as mutants were killed more efficiently. Complementation of mutants restored phagocytosis and resistance to killing in J774A.1 macrophages. Spb1 antiserum revealed surface expression in WT GBS and spatial distribution relative to capsular polysaccharide. spb1 did not affect macrophage nitric oxide and TNF-alpha responses; differences in phagocytosis did not correlate with N-acetyl d-glucosamine (from GBS cell-wall) according to enzyme-linked lectin-sorbent assay. Together, these findings support a role for phylogenetic lineage and Spb1 in opsonin-independent phagocytosis and intracellular survival of GBS in J774A.1 macrophages.

Human mesenchymal stem cells retain multilineage differentiation capacity including neural marker expression after extended in vitro expansion

The suitability of human mesenchymal stem cells (hMSCs) in regenerative medicine relies on retention of their proliferative expansion potential in conjunction with the ability to differentiate toward multiple lineages. Successful utilisation of these cells in clinical applications linked to tissue regeneration requires consideration of biomarker expression, time in culture and donor age, as well as their ability to differentiate towards mesenchymal (bone, cartilage, fat) or non-mesenchymal (e.g., neural) lineages. To identify potential therapeutic suitability we examined hMSCs after extended expansion including morphological changes, potency (stemness) and multilineage potential. Commercially available hMSC populations were expanded in vitro for > 20 passages, equating to > 60 days and > 50 population doublings. Distinct growth phases (A-C) were observed during serial passaging and cells were characterised for stemness and lineage markers at representative stages (Phase A: P+5, approximately 13 days in culture; Phase B: P+7, approximately 20 days in culture; and Phase C: P+13, approximately 43 days in culture). Cell surface markers, stem cell markers and lineage-specific markers were characterised by FACS, ICC and Q-PCR revealing MSCs maintained their multilineage potential, including neural lineages throughout expansion. Co-expression of multiple lineage markers along with continued CD45 expression in MSCs did not affect completion of osteogenic and adipogenic specification or the formation of neurospheres. Improved standardised isolation and characterisation of MSCs may facilitate the identification of biomarkers to improve therapeutic efficacy to ensure increased reproducibility and routine production of MSCs for therapeutic applications including neural repair.

A large-scale computing infrastructure for design education

Most departmental computing infrastructure reflects the state of networking technology and available funds at the time of construction, which converge in a preconceived notion of homogeneity of network architecture and usage patterns. The DMAN (Digital Media Access Network) project, a large-scale server and network foundation for the Hong Kong Polytechnic University's School of Design was created as a platform that would support a highly complex academic environment while giving maximum freedom to students, faculty and researchers through simplicity and ease of use. As a centralized multi-user computation backbone, DMAN faces an extremely hetrogeneous user and application profile, exceeding implementation and maintenance challenges of typical enterprise, and even most academic server set-ups. This paper sumarizes the specification, implementation and application of the system while describing its significance for design education in a computational context.

Abstracting and correlating heterogeneous events to detect complex scenarios

The research presented in this thesis addresses inherent problems in signaturebased intrusion detection systems (IDSs) operating in heterogeneous environments. The research proposes a solution to address the difficulties associated with multistep attack scenario specification and detection for such environments. The research has focused on two distinct problems: the representation of events derived from heterogeneous sources and multi-step attack specification and detection. The first part of the research investigates the application of an event abstraction model to event logs collected from a heterogeneous environment. The event abstraction model comprises a hierarchy of events derived from different log sources such as system audit data, application logs, captured network traffic, and intrusion detection system alerts. Unlike existing event abstraction models where low-level information may be discarded during the abstraction process, the event abstraction model presented in this work preserves all low-level information as well as providing high-level information in the form of abstract events. The event abstraction model presented in this work was designed independently of any particular IDS and thus may be used by any IDS, intrusion forensic tools, or monitoring tools. The second part of the research investigates the use of unification for multi-step attack scenario specification and detection. Multi-step attack scenarios are hard to specify and detect as they often involve the correlation of events from multiple sources which may be affected by time uncertainty. The unification algorithm provides a simple and straightforward scenario matching mechanism by using variable instantiation where variables represent events as defined in the event abstraction model. The third part of the research looks into the solution to address time uncertainty. Clock synchronisation is crucial for detecting multi-step attack scenarios which involve logs from multiple hosts. Issues involving time uncertainty have been largely neglected by intrusion detection research. The system presented in this research introduces two techniques for addressing time uncertainty issues: clock skew compensation and clock drift modelling using linear regression. An off-line IDS prototype for detecting multi-step attacks has been implemented. The prototype comprises two modules: implementation of the abstract event system architecture (AESA) and of the scenario detection module. The scenario detection module implements our signature language developed based on the Python programming language syntax and the unification-based scenario detection engine. The prototype has been evaluated using a publicly available dataset of real attack traffic and event logs and a synthetic dataset. The distinct features of the public dataset are the fact that it contains multi-step attacks which involve multiple hosts with clock skew and clock drift. These features allow us to demonstrate the application and the advantages of the contributions of this research. All instances of multi-step attacks in the dataset have been correctly identified even though there exists a significant clock skew and drift in the dataset. Future work identified by this research would be to develop a refined unification algorithm suitable for processing streams of events to enable an on-line detection. In terms of time uncertainty, identified future work would be to develop mechanisms which allows automatic clock skew and clock drift identification and correction. The immediate application of the research presented in this thesis is the framework of an off-line IDS which processes events from heterogeneous sources using abstraction and which can detect multi-step attack scenarios which may involve time uncertainty.

Building Information Modelling for FM at Sydney Opera House

“SOH see significant benefit in digitising its drawings and operation and maintenance manuals. Since SOH do not currently have digital models of the Opera House structure or other components, there is an opportunity for this national case study to promote the application of Digital Facility Modelling using standardized Building Information Models (BIM)”. The digital modelling element of this project examined the potential of building information models for Facility Management focusing on the following areas: • The re-usability of building information for FM purposes • BIM as an Integrated information model for facility management • Extendibility of the BIM to cope with business specific requirements • Commercial facility management software using standardised building information models • The ability to add (organisation specific) intelligence to the model • A roadmap for SOH to adopt BIM for FM The project has established that BIM – building information modelling - is an appropriate and potentially beneficial technology for the storage of integrated building, maintenance and management data for SOH. Based on the attributes of a BIM, several advantages can be envisioned: consistency in the data, intelligence in the model, multiple representations, source of information for intelligent programs and intelligent queries. The IFC – open building exchange standard – specification provides comprehensive support for asset and facility management functions, and offers new management, collaboration and procurement relationships based on sharing of intelligent building data. The major advantages of using an open standard are: information can be read and manipulated by any compliant software, reduced user “lock in” to proprietary solutions, third party software can be the “best of breed” to suit the process and scope at hand, standardised BIM solutions consider the wider implications of information exchange outside the scope of any particular vendor, information can be archived as ASCII files for archival purposes, and data quality can be enhanced as the now single source of users’ information has improved accuracy, correctness, currency, completeness and relevance. SOH current building standards have been successfully drafted for a BIM environment and are confidently expected to be fully developed when BIM is adopted operationally by SOH. There have been remarkably few technical difficulties in converting the House’s existing conventions and standards to the new model based environment. This demonstrates that the IFC model represents world practice for building data representation and management (see Sydney Opera House – FM Exemplar Project Report Number 2005-001-C-3, Open Specification for BIM: Sydney Opera House Case Study). Availability of FM applications based on BIM is in its infancy but focussed systems are already in operation internationally and show excellent prospects for implementation systems at SOH. In addition to the generic benefits of standardised BIM described above, the following FM specific advantages can be expected from this new integrated facilities management environment: faster and more effective processes, controlled whole life costs and environmental data, better customer service, common operational picture for current and strategic planning, visual decision-making and a total ownership cost model. Tests with partial BIM data – provided by several of SOH’s current consultants – show that the creation of a SOH complete model is realistic, but subject to resolution of compliance and detailed functional support by participating software applications. The showcase has demonstrated successfully that IFC based exchange is possible with several common BIM based applications through the creation of a new partial model of the building. Data exchanged has been geometrically accurate (the SOH building structure represents some of the most complex building elements) and supports rich information describing the types of objects, with their properties and relationships.

Trip to Sunshine Coast Queensland, September 2004 visit to bridge and foreshore

A trip was undertaken to look at concerns of Public Works and Main Roads Departments of Queensland. David Paterson and Wayne Ganther from CSIRO travelled to the Sunshine Coast with Alan Carse of Queensland Department of Main Roads and Michael Ball of Queensland Department of Public Works. We were also joined for part of the visits by Ed Bowers of QBuild which is a commercial unit of Public Works responsible for maintenance of Public Works. During the trip we visited a bridge on the David Low Way at Sunrise Beach near Noosa. This bridge was in a serve marine environment with high salt content in the concrete and corrosion of the galvanised guardrails and barriers. Also the foreshore at Coolum was visited and the use of stainless steel was examined. This is discussed in this report. Most problems stemmed from incorrect specification due to lack of awareness of the severity of the environment. The companion report Visit to Schools Report 2002-059-B No 7. covers the visit to four schools north of Caloundra.

Experimental methodology report

In architectural design and the construction industry, there is insufficient evidence about the way designers collaborate in their normal working environments using both traditional and digital media. It is this gap in empirical evidence that the CRC project, “Team Collaboration in High Bandwidth Virtual Environments” addresses. The project is primarily, but not exclusively, concerned with the conceptual stages of design carried out by professional designers working in different offices. The aim is to increase opportunities for communication and interaction between people in geographically distant locations in order to improve the quality of collaboration. In order to understand the practical implications of introducing new digital tools on working practices, research into how designers work collaboratively using both traditional and digital media is being undertaken. This will involve a series of empirical studies in the work places of the industry partners in the project. The studies of collaboration processes will provide empirical results that will lead to more effective use of virtual environments in design and construction processes. The report describes the research approach, the industry study, the methods for data collection and analysis and the foundation research methodologies. A distinctive aspect is that the research has been devised to enable field studies to be undertaken in a live industrial environment where the participant designers carry out real projects alongside their colleagues and in familiar locations. There are two basic research objectives: one is to obtain evidence about design practice that will inform the architecture and construction industries about the impact and potential benefit of using digital collaboration technologies; the second is to add to long term research knowledge of human cognitive and behavioural processes based on real world data. In order to achieve this, the research methods must be able to acquire a rich and heterogeneous set of data from design activities as they are carried out in the normal working environment. This places different demands upon the data collection and analysis methods to those of laboratory studies where controlled conditions are required. In order to address this, the research approach that has been adopted is ethnographic in nature and case study-based. The plan is to carry out a series of indepth studies in order to provide baseline results for future research across a wider community of user groups. An important objective has been to develop a methodology that will produce valid, significant and transferable results. The research will contribute to knowledge about how architectural design and the construction industry may benefit from the introduction of leading edge collaboration technologies. The outcomes will provide a sound foundation for the production of guidelines for the assessment of high bandwidth tools and their future deployment. The knowledge will form the basis for the specification of future collaboration products and collaboration processes. This project directly addresses the industry-identified focus on cultural change, image, e-project management, and innovative methods.

High quality indoor environments for sustainable office buildings

The quality of office indoor environments is considered to consist of those factors that impact occupants according to their health and well-being and (by consequence) their productivity. Indoor Environment Quality (IEQ) can be characterized by four indicators: • Indoor air quality indicators • Thermal comfort indicators • Lighting indicators • Noise indicators. Within each indicator, there are specific metrics that can be utilized in determining an acceptable quality of an indoor environment based on existing knowledge and best practice. Examples of these metrics are: indoor air levels of pollutants or odorants; operative temperature and its control; radiant asymmetry; task lighting; glare; ambient noise. The way in which these metrics impact occupants is not fully understood, especially when multiple metrics may interact in their impacts. While the potential cost of lost productivity from poor IEQ has been estimated to exceed building operation costs, the level of impact and the relative significance of the above four indicators are largely unknown. However, they are key factors in the sustainable operation or refurbishment of office buildings. This paper presents a methodology for assessing indoor environment quality (IEQ) in office buildings, and indicators with related metrics for high performance and occupant comfort. These are intended for integration into the specification of sustainable office buildings as key factors to ensure a high degree of occupant habitability, without this being impaired by other sustainability factors. The assessment methodology was applied in a case study on IEQ in Australia’s first ‘six star’ sustainable office building, Council House 2 (CH2), located in the centre of Melbourne. The CH2 building was designed and built with specific focus on sustainability and the provision of a high quality indoor environment for occupants. Actual IEQ performance was assessed in this study by field assessment after construction and occupancy. For comparison, the methodology was applied to a 30 year old conventional building adjacent to CH2 which housed the same or similar occupants and activities. The impact of IEQ on occupant productivity will be reported in a separate future paper

Extending the advanced forensic format to accommodate multiple data sources, logical evidence, arbitrary information and forensic workflow

Forensic analysis requires the acquisition and management of many different types of evidence, including individual disk drives, RAID sets, network packets, memory images, and extracted files. Often the same evidence is reviewed by several different tools or examiners in different locations. We propose a backwards-compatible redesign of the Advanced Forensic Formatdan open, extensible file format for storing and sharing of evidence, arbitrary case related information and analysis results among different tools. The new specification, termed AFF4, is designed to be simple to implement, built upon the well supported ZIP file format specification. Furthermore, the AFF4 implementation has downward comparability with existing AFF files.

Interoperable Standards Development : Final Report

Since 1995 the buildingSMART International Alliance for Interoperability (buildingSMART)has developed a robust standard called the Industry Foundation Classes (IFC). IFC is an object oriented data model with related file format that has facilitated the efficient exchange of data in the development of building information models (BIM). The Cooperative Research Centre for Construction Innovation has contributed to the international effort in the development of the IFC standard and specifically the reinforced concrete part of the latest IFC 2x3 release. Industry Foundation Classes have been endorsed by the International Standards Organisation as a Publicly Available Specification (PAS) under the ISO label ISO/PAS 16739. For more details, go to http://www.tc184- sc4.org/About_TC184-SC4/About_SC4_Standards/ The current IFC model covers the building itself to a useful level of detail. The next stage of development for the IFC standard is where the building meets the ground (terrain) and with civil and external works like pavements, retaining walls, bridges, tunnels etc. With the current focus in Australia on infrastructure projects over the next 20 years a logical extension to this standard was in the area of site and civil works. This proposal recognises that there is an existing body of work on the specification of road representation data. In particular, LandXML is recognised as also is TransXML in the broader context of transportation and CityGML in the common interfacing of city maps, buildings and roads. Examination of interfaces between IFC and these specifications is therefore within the scope of this project. That such interfaces can be developed has already been demonstrated in principle within the IFC for Geographic Information Systems (GIS) project. National road standards that are already in use should be carefully analysed and contacts established in order to gain from this knowledge. The Object Catalogue for the Road Transport Sector (OKSTRA) should be noted as an example. It is also noted that buildingSMART Norway has submitted a proposal

Formative and reflective measurement and validation mismatch in survey research : an archival analysis of information systems success constructs 1985-2007

The generic IS-success constructs first identified by DeLone and McLean (1992) continue to be widely employed in research. Yet, recent work by Petter et al (2007) has cast doubt on the validity of many mainstream constructs employed in IS research over the past 3 decades; critiquing the almost universal conceptualization and validation of these constructs as reflective when in many studies the measures appear to have been implicitly operationalized as formative. Cited examples of proper specification of the Delone and McLean constructs are few, particularly in light of their extensive employment in IS research. This paper introduces a four-stage formative construct development framework: Conceive > Operationalize > Respond > Validate (CORV). Employing the CORV framework in an archival analysis of research published in top outlets 1985-2007, the paper explores the extent of possible problems with past IS research due to potential misspecification of the four application-related success dimensions: Individual-Impact, Organizational-Impact, System-Quality and Information-Quality. Results suggest major concerns where there is a mismatch of the Respond and Validate stages. A general dearth of attention to the Operationalize and Respond stages in methodological writings is also observed.