Factors associated with the isolation of Nontuberculous mycobacteria (NTM) from a large municipal water system in Brisbane, Australia

Background Nontuberculous mycobacteria (NTM) are normal inhabitants of a variety of environmental reservoirs including natural and municipal water. The aim of this study was to document the variety of species of NTM in potable water in Brisbane, QLD, with a specific interest in the main pathogens responsible for disease in this region and to explore factors associated with the isolation of NTM. One-litre water samples were collected from 189 routine collection sites in summer and 195 sites in winter. Samples were split, with half decontaminated with CPC 0.005%, then concentrated by filtration and cultured on 7H11 plates in MGIT tubes (winter only). Results Mycobacteria were grown from 40.21% sites in Summer (76/189) and 82.05% sites in winter (160/195). The winter samples yielded the greatest number and variety of mycobacteria as there was a high degree of subculture overgrowth and contamination in summer. Of those samples that did yield mycobacteria in summer, the variety of species differed from those isolated in winter. The inclusion of liquid media increased the yield for some species of NTM. Species that have been documented to cause disease in humans residing in Brisbane that were also found in water include M. gordonae, M. kansasii, M. abscessus, M. chelonae, M. fortuitum complex, M. intracellulare, M. avium complex, M. flavescens, M. interjectum, M. lentiflavum, M. mucogenicum, M. simiae, M. szulgai, M. terrae. M. kansasii was frequently isolated, but M. avium and M. intracellulare (the main pathogens responsible for disease is QLD) were isolated infrequently. Distance of sampling site from treatment plant in summer was associated with isolation of NTM. Pathogenic NTM (defined as those known to cause disease in QLD) were more likely to be identified from sites with narrower diameter pipes, predominantly distribution sample points, and from sites with asbestos cement or modified PVC pipes. Conclusions NTM responsible for human disease can be found in large urban water distribution systems in Australia. Based on our findings, additional point chlorination, maintenance of more constant pressure gradients in the system, and the utilisation of particular pipe materials should be considered.

Data innovation and open access [Blog]

After nearly fifteen years of the open access (OA) movement and its hard-fought struggle for a more open scholarly communication system, publishers are realizing that business models can be both open and profitable. Making journal articles available on an OA license is becoming an accepted strategy for maximizing the value of content to both research communities and the businesses that serve them. The first blog in this two-part series celebrating Data Innovation Day looks at the role that data-innovation is playing in the shift to open access for journal articles.

Enterovirus71 (EV71) utilise host microRNAs to mediate host immune system enhancing survival during infection

Hand, Foot and Mouth Disease (HFMD) is a self-limiting viral disease that mainly affects infants and children. In contrast with other HFMD causing enteroviruses, Enterovirus71 (EV71) has commonly been associated with severe clinical manifestation leading to death. Currently, due to a lack in understanding of EV71 pathogenesis, there is no antiviral therapeutics for the treatment of HFMD patients. Therefore the need to better understand the mechanism of EV71 pathogenesis is warranted. We have previously reported a human colorectal adenocarcinoma cell line (HT29) based model to study the pathogenesis of EV71. Using this system, we showed that knockdown of DGCR8, an essential cofactor for microRNAs biogenesis resulted in a reduction of EV71 replication. We also demonstrated that there are miRNAs changes during EV71 pathogenesis and EV71 utilise host miRNAs to attenuate antiviral pathways during infection. Together, data from this study provide critical information on the role of miRNAs during EV71 infection.

QUT Library advances the use of open public tools to navigate genetic inventions and builds research networks

Many emerging economies are dangling the patent system to stimulate bio-technological innovations with the ultimate premise that these will improve their economic and social growth. The patent system mandates full disclosure of the patented invention in exchange of a temporary exclusive patent right. Recently, however, patent offices have fallen short of complying with such a mandate, especially for genetic inventions. Most patent offices provide only static information about disclosed patent sequences and even some do not keep track of the sequence listing data in their own database. The successful partnership of QUT Library and Cambia exemplifies advocacy in Open Access, Open Innovation and User Participation. The library extends its services to various departments within the university, builds and encourages research networks to complement skills needed to make a contribution in the real world.

The politics of open-access publishing : M/C Journal, Public Intellectualism, and Academic Discourses of Legitimacy

This article investigates the discourses of academic legitimacy that surround the production, consumption, and accreditation of online scholarship. Using the web-based media and cultural studies journal (http://journal.media-culture.org.au) as a case study, it examines how online scholarly journals often position themselves as occupying a space between the academic and the popular and as having a functional advantage over print-based media in promoting a spirit of public intellectualism. The current research agenda of both government and academe prioritises academic research that is efficient, self-promoting, and relevant to the public. Yet, although the cost-effectiveness and public-intellectual focus of online scholarship speak to these research priorities, online journals such as M/C Journal have occupied, and continue to occupy, an unstable position in relation to the perceived academic legitimacy of their content. Although some online scholarly journals have achieved a limited form of recognition within a system of accreditation that still privileges print-based scholarship, I argue that this, nevertheless, points to the fact that traditional textual notions of legitimate academic work continue to pervade the research agenda of an academe that increasingly promotes flexible delivery of teaching and online research initiatives.

Identity, addressing, authenticity and audit requirements for trust in ERP, analytics and big/open data in a “Cloud” computing environment : a review and proposal

Enterprises, both public and private, have rapidly commenced using the benefits of enterprise resource planning (ERP) combined with business analytics and “open data sets” which are often outside the control of the enterprise to gain further efficiencies, build new service operations and increase business activity. In many cases, these business activities are based around relevant software systems hosted in a “cloud computing” environment. “Garbage in, garbage out”, or “GIGO”, is a term long used to describe problems in unqualified dependency on information systems, dating from the 1960s. However, a more pertinent variation arose sometime later, namely “garbage in, gospel out” signifying that with large scale information systems, such as ERP and usage of open datasets in a cloud environment, the ability to verify the authenticity of those data sets used may be almost impossible, resulting in dependence upon questionable results. Illicit data set “impersonation” becomes a reality. At the same time the ability to audit such results may be an important requirement, particularly in the public sector. This paper discusses the need for enhancement of identity, reliability, authenticity and audit services, including naming and addressing services, in this emerging environment and analyses some current technologies that are offered and which may be appropriate. However, severe limitations to addressing these requirements have been identified and the paper proposes further research work in the area.

Trust in merged ERP and open data schemes in the “Cloud”

Enterprise resource planning (ERP) systems are rapidly being combined with “big data” analytics processes and publicly available “open data sets”, which are usually outside the arena of the enterprise, to expand activity through better service to current clients as well as identifying new opportunities. Moreover, these activities are now largely based around relevant software systems hosted in a “cloud computing” environment. However, the over 50- year old phrase related to mistrust in computer systems, namely “garbage in, garbage out” or “GIGO”, is used to describe problems of unqualified and unquestioning dependency on information systems. However, a more relevant GIGO interpretation arose sometime later, namely “garbage in, gospel out” signifying that with large scale information systems based around ERP and open datasets as well as “big data” analytics, particularly in a cloud environment, the ability to verify the authenticity and integrity of the data sets used may be almost impossible. In turn, this may easily result in decision making based upon questionable results which are unverifiable. Illicit “impersonation” of and modifications to legitimate data sets may become a reality while at the same time the ability to audit any derived results of analysis may be an important requirement, particularly in the public sector. The pressing need for enhancement of identity, reliability, authenticity and audit services, including naming and addressing services, in this emerging environment is discussed in this paper. Some current and appropriate technologies currently being offered are also examined. However, severe limitations in addressing the problems identified are found and the paper proposes further necessary research work for the area. (Note: This paper is based on an earlier unpublished paper/presentation “Identity, Addressing, Authenticity and Audit Requirements for Trust in ERP, Analytics and Big/Open Data in a ‘Cloud’ Computing Environment: A Review and Proposal” presented to the Department of Accounting and IT, College of Management, National Chung Chen University, 20 November 2013.)

Parental perceptions of the learner driver log book system in two Australian states

Objective While many jurisdictions internationally now require learner drivers to complete a specified number of hours of supervised driving practice before being able to drive unaccompanied, very few require learner drivers to complete a log book to record this practice and then present it to the licensing authority. Learner drivers in most Australian jurisdictions must complete a log book that records their practice thereby confirming to the licensing authority that they have met the mandated hours of practice requirement. These log books facilitate the management and enforcement of minimum supervised hours of driving requirements. Method Parents of learner drivers in two Australian states, Queensland and New South Wales, completed an online survey assessing a range of factors, including their perceptions of the accuracy of their child’s learner log book and the effectiveness of the log book system. Results The study indicates that the large majority of parents believe that their child’s learner log book is accurate. However, they generally report that the log book system is only moderately effective as a system to measure the number of hours of supervised practice a learner driver has completed. Conclusions The results of this study suggest the presence of a paradox with many parents possibly believing that others are not as diligent in the use of log books as they are or that the system is too open to misuse. Given that many parents report that their child’s log book is accurate, this study has important implications for the development and ongoing monitoring of hours of practice requirements in graduated driver licensing systems.

Beyond online preprints : formalization of open initiatives in China

A growing number of online journals and academic platforms are adopting light peer review or 'publish then filter' models of scholarly communication. These approaches have the advantage of enabling instant exchanges of knowledge between academics and are part of a wider search for alternatives to traditional peer review and certification processes in scholarly publishing. However, establishing credibility and identifying the correct balance between communication and scholarly rigour remains an important challenge for digital communication platforms targeting academic communities. This paper looks at a highly influential, government-backed, open publishing platform in China: Science Paper Online, which is using transparent post-publication peer-review processes to encourage innovation and address systemic problems in China's traditional academic publishing system. There can be little doubt that the Chinese academic publishing landscape differs in important ways from counterparts in the United States and Western Europe. However, this article suggests that developments in China also provide important lessons about the potential of digital technology and government policy to facilitate a large-scale shift towards more open and networked models of scholarly communication.

Efficiently capturing large, complex cultural heritage sites with a handheld mobile 3D laser mapping system

Accurate three-dimensional representations of cultural heritage sites are highly valuable for scientific study, conservation, and educational purposes. In addition to their use for archival purposes, 3D models enable efficient and precise measurement of relevant natural and architectural features. Many cultural heritage sites are large and complex, consisting of multiple structures spatially distributed over tens of thousands of square metres. The process of effectively digitising such geometrically complex locations requires measurements to be acquired from a variety of viewpoints. While several technologies exist for capturing the 3D structure of objects and environments, none are ideally suited to complex, large-scale sites, mainly due to their limited coverage or acquisition efficiency. We explore the use of a recently developed handheld mobile mapping system called Zebedee in cultural heritage applications. The Zebedee system is capable of efficiently mapping an environment in three dimensions by continually acquiring data as an operator holding the device traverses through the site. The system was deployed at the former Peel Island Lazaret, a culturally significant site in Queensland, Australia, consisting of dozens of buildings of various sizes spread across an area of approximately 400 × 250 m. With the Zebedee system, the site was scanned in half a day, and a detailed 3D point cloud model (with over 520 million points) was generated from the 3.6 hours of acquired data in 2.6 hours. We present results demonstrating that Zebedee was able to accurately capture both site context and building detail comparable in accuracy to manual measurement techniques, and at a greatly increased level of efficiency and scope. The scan allowed us to record derelict buildings that previously could not be measured because of the scale and complexity of the site. The resulting 3D model captures both interior and exterior features of buildings, including structure, materials, and the contents of rooms.

A contextualised general systems theory

A system is something that can be separated from its surrounds, but this definition leaves much scope for refinement. Starting with the notion of measurement, we explore increasingly contextual system behaviour, and identify three major forms of contextuality that might be exhibited by a system: (a) between components; (b) between system and experimental method, and; (c) between a system and its environment. Quantum Theory is shown to provide a highly useful formalism from which all three forms of contextuality can be analysed, offering numerous tests for contextual behaviour, as well as modelling possibilities for systems that do indeed display it. I conclude with the introduction of a Contextualised General Systems Theory based upon an extension of this formalism.

Implementation and evaluation of open source unified communications for SMBs

Unified Communication (UC) is the integration of two or more real time communication systems into one platform. Integrating core communication systems into one overall enterprise level system delivers more than just cost saving. These real-time interactive communication services and applications over Internet Protocol (IP) have become critical in boosting employee accessibility and efficiency, improving customer support and fostering business agility. However, some small and medium-sized businesses (SMBs) are far from implementing this solution due to the high cost of initial deployment and ongoing support. In this paper, we will discuss and demonstrate an open source UC solution, viz. “Asterisk” for use by SMBs, and report on some performance tests using SIPp. The contribution from this research is the provision of technical advice to SMBs in deploying UC, which is manageable in terms of cost, ease of deployment and support.

Hardware design and implementation of a MAVLink interface for an FPGA-based autonomous UAV flight control system

This paper details the initial design and planning of a Field Programmable Gate Array (FPGA) implemented control system that will enable a path planner to interact with a MAVLink based flight computer. The design is aimed at small Unmanned Aircraft Vehicles (UAV) under autonomous operation which are typically subject to constraints arising from limited on-board processing capabilities, power and size. An FPGA implementation for the de- sign is chosen for its potential to address such limitations through low power and high speed in-hardware computation. The MAVLink protocol offers a low bandwidth interface for the FPGA implemented path planner to communicate with an on-board flight computer. A control system plan is presented that is capable of accepting a string of GPS waypoints generated on-board from a previously developed in- hardware Genetic Algorithm (GA) path planner and feeding them to the open source PX4 autopilot, while simultaneously respond- ing with flight status information.

Discovery of a lipid synthesising organ in the auditory system of an insect

Weta possess typical Ensifera ears. Each ear comprises three functional parts: two equally sized tympanal membranes, an underlying system of modified tracheal chambers, and the auditory sensory organ, the crista acustica. This organ sits within an enclosed fluid-filled channel-previously presumed to be hemolymph. The role this channel plays in insect hearing is unknown. We discovered that the fluid within the channel is not actually hemolymph, but a medium composed principally of lipid from a new class. Three-dimensional imaging of this lipid channel revealed a previously undescribed tissue structure within the channel, which we refer to as the olivarius organ. Investigations into the function of the olivarius reveal de novo lipid synthesis indicating that it is producing these lipids in situ from acetate. The auditory role of this lipid channel was investigated using Laser Doppler vibrometry of the tympanal membrane, which shows that the displacement of the membrane is significantly increased when the lipid is removed from the auditory system. Neural sensitivity of the system, however, decreased upon removal of the lipid-a surprising result considering that in a typical auditory system both the mechanical and auditory sensitivity are positively correlated. These two results coupled with 3D modelling of the auditory system lead us to hypothesize a model for weta audition, relying strongly on the presence of the lipid channel. This is the first instance of lipids being associated with an auditory system outside of the Odentocete cetaceans, demonstrating convergence for the use of lipids in hearing.

A Likelihood-Maximizing Framework for Enhanced In-Car Speech Recognition Based on Speech Dialog System Interaction

Speech recognition in car environments has been identified as a valuable means for reducing driver distraction when operating noncritical in-car systems. Under such conditions, however, speech recognition accuracy degrades significantly, and techniques such as speech enhancement are required to improve these accuracies. Likelihood-maximizing (LIMA) frameworks optimize speech enhancement algorithms based on recognized state sequences rather than traditional signal-level criteria such as maximizing signal-to-noise ratio. LIMA frameworks typically require calibration utterances to generate optimized enhancement parameters that are used for all subsequent utterances. Under such a scheme, suboptimal recognition performance occurs in noise conditions that are significantly different from that present during the calibration session – a serious problem in rapidly changing noise environments out on the open road. In this chapter, we propose a dialog-based design that allows regular optimization iterations in order to track the ever-changing noise conditions. Experiments using Mel-filterbank noise subtraction (MFNS) are performed to determine the optimization requirements for vehicular environments and show that minimal optimization is required to improve speech recognition, avoid over-optimization, and ultimately assist with semireal-time operation. It is also shown that the proposed design is able to provide improved recognition performance over frameworks incorporating a calibration session only.