Locality-sensitive hashing for protein classification

Determination of sequence similarity is a central issue in computational biology, a problem addressed primarily through BLAST, an alignment based heuristic which has underpinned much of the analysis and annotation of the genomic era. Despite their success, alignment-based approaches scale poorly with increasing data set size, and are not robust under structural sequence rearrangements. Successive waves of innovation in sequencing technologies – so-called Next Generation Sequencing (NGS) approaches – have led to an explosion in data availability, challenging existing methods and motivating novel approaches to sequence representation and similarity scoring, including adaptation of existing methods from other domains such as information retrieval. In this work, we investigate locality-sensitive hashing of sequences through binary document signatures, applying the method to a bacterial protein classification task. Here, the goal is to predict the gene family to which a given query protein belongs. Experiments carried out on a pair of small but biologically realistic datasets (the full protein repertoires of families of Chlamydia and Staphylococcus aureus genomes respectively) show that a measure of similarity obtained by locality sensitive hashing gives highly accurate results while offering a number of avenues which will lead to substantial performance improvements over BLAST..

The ethics, aesthetics and practical politics of ownership in co-creative media

What is ‘best practice’ when it comes to managing intellectual property rights in participatory media content? As commercial media and entertainment business models have increasingly come to rely upon the networked productivity of end-users (Banks and Humphreys 2008) this question has been framed as a problem of creative labour made all the more precarious by changing employment patterns and work cultures of knowledge-intensive societies and globalising economies (Banks, Gill and Taylor 2014). This paper considers how the problems of ownership are addressed in non-commercial, community-based arts and media contexts. Problems of labour are also manifest in these contexts (for example, reliance on volunteer labour and uncertain economic reward for creative excellence). Nonetheless, managing intellectual property rights in collaborative creative works that are created in community media and arts contexts is no less challenging or complex than in commercial contexts. This paper takes as its focus a particular participatory media practice known as ‘digital storytelling’. The digital storytelling method, formalised by the Centre for Digital Storytelling (CDS) from the mid-1990s, has been internationally adopted and adapted for use in an open-ended variety of community arts, education, health and allied services settings (Hartley and McWilliam 2009; Lambert 2013; Lundby 2008; Thumin 2012). It provides a useful point of departure for thinking about a range of collaborative media production practices that seek to address participation ‘gaps’ (Jenkins 2006). However the outputs of these activities, including digital stories, cannot be fully understood or accurately described as user-generated content. For this reason, digital storytelling is taken here to belong to a category of participatory media activity that has been described as ‘co-creative’ media (Spurgeon 2013) in order to improve understanding of the conditions of mediated and mediatized participation (Couldry 2008). This paper reports on a survey of the actual copyrighting practices of cultural institutions and community-based media arts practitioners that work with digital storytelling and similar participatory content creation methods. This survey finds that although there is a preference for Creative Commons licensing a great variety of approaches are taken to managing intellectual property rights in co-creative media. These range from the use of Creative Commons licences (for example, Lambert 2013, p.193) to retention of full copyrights by storytellers, to retention of certain rights by facilitating organisations (for example, broadcast rights by community radio stations and public service broadcasters), and a range of other shared rights arrangements between professional creative practitioners, the individual storytellers and communities with which they collaborate, media outlets, exhibitors and funders. This paper also considers how aesthetic and ethical considerations shape responses to questions of intellectual property rights in community media arts contexts. For example, embedded in the CDS digital storytelling method is ‘a critique of power and the numerous ways that rank is unconsciously expressed in engagements between classes, races and gender’ (Lambert 117). The CDS method privileges the interests of the storyteller and, through a transformative workshop process, aims to generate original individual stories that, in turn, reflect self-awareness of ‘how much the way we live is scripted by history, by social and cultural norms, by our own unique journey through a contradictory, and at times hostile, world’ (Lambert 118). Such a critical approach is characteristic of co-creative media practices. It extends to a heightened awareness of the risks of ‘story theft’ and the challenges of ownership and informs ideas of ‘best practice’ amongst creative practitioners, teaching artists and community media producers, along with commitments to achieving equitable solutions for all participants in co-creative media practice (for example, Lyons-Reid and Kuddell nd.). Yet, there is surprisingly little written about the challenges of managing intellectual property produced in co-creative media activities. A dialogic sense of ownership in stories has been identified as an indicator of successful digital storytelling practice (Hayes and Matusov 2005) and is helpful to grounding the more abstract claims of empowerment for social participation that are associated with co-creative methods. Contrary to the ‘change from below’ philosophy that underpins much thinking about co-creative media, however, discussions of intellectual property usually focus on how methods such as digital storytelling contribute to the formation of copyright law-compliant subjects, particularly when used in educational settings (for example, Ohler nd.). This also exposes the reliance of co-creative methods on the creative assets storytellers (rather than on the copyrighted materials of the media cultures of storytellers) as a pragmatic response to the constraints that intellectual property right laws impose on the entire category of participatory media. At the level of practical politics, it also becomes apparent that co-creative media practitioners and storytellers located in copyright jurisdictions governed by ‘fair use’ principles have much greater creative flexibility than those located in jurisdictions governed by ‘fair dealing’ principles.

Biologically inspired SLAM using Wi-Fi

Wi-Fi is a commonly available source of localization information in urban environments but is challenging to integrate into conventional mapping architectures. Current state of the art probabilistic Wi-Fi SLAM algorithms are limited by spatial resolution and an inability to remove the accumulation of rotational error, inherent limitations of the Wi-Fi architecture. In this paper we leverage the low quality sensory requirements and coarse metric properties of RatSLAM to localize using Wi-Fi fingerprints. To further improve performance, we present a novel sensor fusion technique that integrates camera and Wi-Fi to improve localization specificity, and use compass sensor data to remove orientation drift. We evaluate the algorithms in diverse real world indoor and outdoor environments, including an office floor, university campus and a visually aliased circular building loop. The algorithms produce topologically correct maps that are superior to those produced using only a single sensor modality.

SHM through flexible vibration sensing technologies and robust safety evaluation paradigm

This research has successfully developed a novel synthetic structural health monitoring system model that is cost-effective and flexible in sensing and data acquisition; and robust in the structural safety evaluation aspect for the purpose of long-term and frequent monitoring of large-scale civil infrastructure during their service lives. Not only did it establish a real-world structural monitoring test-bed right at the heart of QUT Gardens Point Campus but it can also facilitate reliable and prompt protection for any built infrastructure system as well as the user community involved.

Text recognition approaches for indoor robotics : a comparison

This paper evaluates the performance of different text recognition techniques for a mobile robot in an indoor (university campus) environment. We compared four different methods: our own approach using existing text detection methods (Minimally Stable Extremal Regions detector and Stroke Width Transform) combined with a convolutional neural network, two modes of the open source program Tesseract, and the experimental mobile app Google Goggles. The results show that a convolutional neural network combined with the Stroke Width Transform gives the best performance in correctly matched text on images with single characters whereas Google Goggles gives the best performance on images with multiple words. The dataset used for this work is released as well.

Experiencing archives at universities : archivists, librarians, understanding, and collaboration

Collaboration is one of the top trends in academic librarianship in the United States as noted by the Association of College and Research Libraries (ACRL), and is likely to be a growing trend in other countries as well (Association of College and Research Libraries [ACRL] Research Planning and Review Committee, 2014). While ACRL is focusing on library participation in various initiatives and projects on campus that are external to the library, this trend can be broadened to include the possibility for further collaboration within many academic libraries between the librarians and archivists.

An efficient tagging data interpretation and representation scheme for item recommendation

A tag-based item recommendation method generates an ordered list of items, likely interesting to a particular user, using the users past tagging behaviour. However, the users tagging behaviour varies in different tagging systems. A potential problem in generating quality recommendation is how to build user profiles, that interprets user behaviour to be effectively used, in recommendation models. Generally, the recommendation methods are made to work with specific types of user profiles, and may not work well with different datasets. In this paper, we investigate several tagging data interpretation and representation schemes that can lead to building an effective user profile. We discuss the various benefits a scheme brings to a recommendation method by highlighting the representative features of user tagging behaviours on a specific dataset. Empirical analysis shows that each interpretation scheme forms a distinct data representation which eventually affects the recommendation result. Results on various datasets show that an interpretation scheme should be selected based on the dominant usage in the tagging data (i.e. either higher amount of tags or higher amount of items present). The usage represents the characteristic of user tagging behaviour in the system. The results also demonstrate how the scheme is able to address the cold-start user problem.

Old mastheads and new media : newspapers striving to adapt in Australia and South-east Asia

As a key element in their response to new media forcing transformations in mass media and media use, newspapers have deployed various strategies to not only establish online and mobile products, and develop healthy business plans, but to set out to be dominant portals. Their response to change was the subject of an early investigation by one of the present authors (Keshvani 2000). That was part of a set of short studies inquiring into what impact new software applications and digital convergence might have on journalism practice (Tickle and Keshvani 2000), and also looking for demonstrations of the way that innovations, technologies and protocols then under development might produce a “wireless, streamlined electronic news production process (Tickle and Keshvani 2001).” The newspaper study compared the online products of The Age in Melbourne and the Straits Times in Singapore. It provided an audit of the Singapore and Australia Information and Communications Technology (ICT) climate concentrating on the state of development of carrier networks, as a determining factor in the potential strength of the two services with their respective markets. In the outcome, contrary to initial expectations, the early cable roll-out and extensive ‘wiring’ of the city in Singapore had not produced a level of uptake of Internet services as strong as that achieved in Melbourne by more ad hoc and varied strategies. By interpretation, while news websites and online content were at an early stage of development everywhere, and much the same as one another, no determining structural imbalance existed to separate these leading media participants in Australia and South-east Asia. The present research revisits that situation, by again studying the online editions of the two large newspapers in the original study, and one other, The Courier Mail, (recognising the diversification of types of product in this field, by including it as a representative of Newscorp, now a major participant). The inquiry works through the principle of comparison. It is an exercise in qualitative, empirical research that establishes a comparison between the situation in 2000 as described in the earlier work, and the situation in 2014, after a decade of intense development in digital technology affecting the media industries. It is in that sense a follow-up study on the earlier work, although this time giving emphasis to content and style of the actual products as experienced by their users. It compares the online and print editions of each of these three newspapers; then the three mastheads as print and online entities, among themselves; and finally it compares one against the other two, as representing a South-east Asian model and Australian models. This exercise is accompanied by a review of literature on the developments in ICT affecting media production and media organisations, to establish the changed context. The new study of the online editions is conducted as a systematic appraisal of the first level, or principal screens, of the three publications, over the course of six days (10-15.2.14 inclusive). For this, categories for analysis were made, through conducting a preliminary examination of the products over three days in the week before. That process identified significant elements of media production, such as: variegated sourcing of materials; randomness in the presentation of items; differential production values among media platforms considered, whether text, video or stills images; the occasional repurposing and repackaging of top news stories of the day and the presence of standard news values – once again drawn out of the trial ‘bundle’ of journalistic items. Reduced in this way the online artefacts become comparable with the companion print editions from the same days. The categories devised and then used in the appraisal of the online products have been adapted to print, to give the closest match of sets of variables. This device, to study the two sets of publications on like standards -- essentially production values and news values—has enabled the comparisons to be made. This comparing of the online and print editions of each of the three publications was set up as up the first step in the investigation. In recognition of the nature of the artefacts, as ones that carry very diverse information by subject and level of depth, and involve heavy creative investment in the formulation and presentation of the information; the assessment also includes an open section for interpreting and commenting on main points of comparison. This takes the form of a field for text, for the insertion of notes, in the table employed for summarising the features of each product, for each day. When the sets of comparisons as outlined above are noted, the process then becomes interpretative, guided by the notion of change. In the context of changing media technology and publication processes, what substantive alterations have taken place, in the overall effort of news organisations in the print and online fields since 2001; and in their print and online products separately? Have they diverged or continued along similar lines? The remaining task is to begin to make inferences from that. Will the examination of findings enforce the proposition that a review of the earlier study, and a forensic review of new models, does provide evidence of the character and content of change --especially change in journalistic products and practice? Will it permit an authoritative description on of the essentials of such change in products and practice? Will it permit generalisation, and provide a reliable base for discussion of the implications of change, and future prospects? Preliminary observations suggest a more dynamic and diversified product has been developed in Singapore, well themed, obviously sustained by public commitment and habituation to diversified online and mobile media services. The Australian products suggest a concentrated corporate and journalistic effort and deployment of resources, with a strong market focus, but less settled and ordered, and showing signs of limitations imposed by the delay in establishing a uniform, large broadband network. The scope of the study is limited. It is intended to test, and take advantage of the original study as evidentiary material from the early days of newspaper companies’ experimentation with online formats. Both are small studies. The key opportunity for discovery lies in the ‘time capsule’ factor; the availability of well-gathered and processed information on major newspaper company production, at the threshold of a transformational decade of change in their industry. The comparison stands to identify key changes. It should also be useful as a reference for further inquiries of the same kind that might be made, and for monitoring of the situation in regard to newspaper portals on line, into the future.

Factors influencing robustness and effectiveness of conditional random fields in active learning frameworks

Active learning approaches reduce the annotation cost required by traditional supervised approaches to reach the same effectiveness by actively selecting informative instances during the learning phase. However, effectiveness and robustness of the learnt models are influenced by a number of factors. In this paper we investigate the factors that affect the effectiveness, more specifically in terms of stability and robustness, of active learning models built using conditional random fields (CRFs) for information extraction applications. Stability, defined as a small variation of performance when small variation of the training data or a small variation of the parameters occur, is a major issue for machine learning models, but even more so in the active learning framework which aims to minimise the amount of training data required. The factors we investigate are a) the choice of incremental vs. standard active learning, b) the feature set used as a representation of the text (i.e., morphological features, syntactic features, or semantic features) and c) Gaussian prior variance as one of the important CRFs parameters. Our empirical findings show that incremental learning and the Gaussian prior variance lead to more stable and robust models across iterations. Our study also demonstrates that orthographical, morphological and contextual features as a group of basic features play an important role in learning effective models across all iterations.

Preparing Queensland pharmacists to vaccinate – Australia’s first pharmacists immunisation pilot

In November 2013, the Queensland Department of Health announced its intention to pilot pharmacists vaccination for influenza in the 2014 Flu season. The Pharmaceutical Society of Australia Queensland Branch was tasked with development of an appropriate training program for the pilot.

Australia’s first Pharmacist Immunisation Pilot - who did pharmacists inject?

The Queensland Pharmacist Immunisation Pilot is Australia’s first to allow pharmacists vaccination. The pilot ran between April 1st 2014 and August 31st 2014, with pharmacists administering influenza vaccination during the flu season. METHODS Participant demographics and previous influenza vaccination experiences were recorded using GuildCare software. Participants also completed a ‘post-vaccination satisfaction survey’ following their influenza vaccination. RESULTS A total of 11,475 participant records were analysed. Females accounted for 63% of participants, with the majority of participants aged between 45 – 64 years (53%). Overall, 49% of participants had been vaccinated before, the majority at a GP clinic (60%). Most participants reported receiving their previous influenza vaccination from a nurse (61%). Interestingly, 1% thought a pharmacist had administered their previous vaccination, while 7% were unsure which health professional had administer it. It was also of note that approximately 10% of all participants were eligible to receive a free vaccination from the National Immunisation Program, but still opted to receive their vaccine in a pharmacy. Over 8,000 participants took part in the post-vaccination survey, 93% were happy to receive their vaccination from a pharmacy in the future while 94% would recommend this service to other people. The remaining 7% and 6% respectively had omitted to fill in those questions. DISCUSSION Participants were overwhelmingly positive in their response to the pharmacist vaccination pilot. These findings have helped pave the way for expanding the scope of practice for pharmacists with the aim to increase vaccination rates across the state.

Australia’s first Allied Health Prescribing Program – exploring participants' understanding and confidence in clinical therapy choices for patient management

BACKGROUND Globally there are emerging trends for non-medical health professionals to expand their scope of practice into prescribing. The NPS Prescribing Competencies Framework and the Health Professionals Prescribing Pathway Program are recent initiatives to assist with implementation of prescribing for allied health professionals (AHPs). For AHPs to become prescribers, training programmes must be designed to extend their knowledge of medicines information and medicine management principles with the aim of optimising medicines related outcomes for patients. AIM To explore the understanding and confidence in clinical therapeutic choices for patient management of those AHPs enrolled in the Allied Health Prescribing Training Program Module One: Introduction to clinical therapeutics for prescribers, delivered by Queensland University of Technology, Brisbane. METHOD A pre-post survey was developed to explore key themes around understanding and confidence in selecting therapeutic choices for patients with varying complexities of conditions. Data were collected from participants in week one and 13 of the module via an online survey using a five-point Likert scale (1 = Strongly Agree (SA) to 5 = Strongly Disagree (SD)). RESULTS In the pre-Module survey the AHPs had a limited degree (D/SD) of understanding and confidence regarding the safe and effective use of medicines and appropriate therapeutic choices for managing patients, particularly with complex patients. This improved significantly in the post Module survey (A/SA).

Delivering crushed tablets using thickened fluids : is drug diffusion into gastric fluids restricted?

Solid medications are often crushed and mixed with food or thickened water to aid drug delivery for those who cannot or prefer not to swallow whole tablets or capsules. Dysphagic patients have the added problem of being unable to safely swallow thin fluids so water thickened with polysaccharides is used to deliver crushed medications and ensure safe swallowing. It is postulated that these polysaccharide systems may restrict drug release by reducing the diffusion of the drug into gastric fluids. METHODS By using a vertical diffusion cell separated with a synthetic membrane, the diffusion of a model drug (atenolol) was studied from a donor system containing the drug dispersed into thickened water with xanthan gum (concentration range from 0.005%-2.2%) into a receptor system containing simulated gastric fluid (SGF) at 37°C. The amount of drug transferred was measured over 8 hours and diffusion coefficients estimated using the Higuchi model approach. RESULTS Atenolol diffusion decreased with increasing xanthan gum concentration up to 1.0%, above which diffusion remained around 300 μ2s-1. The rheological measurements captured the influence of the structure and conformation of the polysaccharide in water on the movement and availability of the drug in SGF. DISCUSSION Dose form administration for dysphagic patients’ needs special attention from general practitioners, pharmacist and patients. Improving drug release of crushed tablets from thickening agents requires a reduction in the diffusion pathway (e.g. by decreasing drop size radius). This approach could make the drug available in SGF in a short time without compromising the mechanical aspects of thickening agents that guarantee safe swallowing.

Delivering crushed paracetamol tablets using thickened fluids : does it alter the pharmacokinetics?

Dysphagia, often associated with conditions such as stroke, Parkinson’s disease, multiple sclerosis, and dementia, causes patients to have difficulty with swallowing food and/or liquids. These patients require their fluids to be thickened using gum-based thickening powders in order to facilitate safe swallowing. These thickened fluids are also used as a vehicle for delivery of crushed medicines. Our in vitro measurements suggest that thickened fluids can delay and reduce the dissolution of a number of medications. This study was conducted to assess the impact of the use of thickened fluids on the clinical pharmacokinetics of oral paracetamol. METHODS 20 Healthy volunteers were administered a single oral dose (1g) of paracetamol as either whole tablets, crushed with water, crushed with semi-solid jam, or crushed with thickened fluid according to a randomised, crossover design. Saliva samples were collected periodically over 8 hr and paracetamol concentration analysed by HPLC-UV. Non-compartmental pharmacokinetic analysis was conducted using Winnonlin®. RESULTS The mean peak concentration (Cmax) of paracetamol ranged between 5.62 – 8.00 μg/mL. Comparison between the crushed paracetamol with thickened water (Level 900) and other treatment options (whole, crushed with water, and crushed with jam) showed there was a significant difference in Cmax at 90% CI (p < 0.05). Also, whole tablet had a significant difference in Cmax between crushed with water and crushed with jam. There was no significant difference in AUC irrespective of the treatment. DISCUSSION The use of thickened water resulted in alteration in the absorption kinetics of paracetamol. Given this interaction, co-administration with thickened fluids may have important clinical implications for medications with a narrow therapeutic index.