Comprehensive evaluation of DNA barcoding for the molecular species identification of forensically important Australian Sarcophagidae (Diptera)

Carrion-breeding Sarcophagidae (Diptera) can be used to estimate the post-mortem interval (PMI) in forensic cases. Difficulties with accurate morphological identifications at any life stage and a lack of documented thermobiological profiles have limited their current usefulness of these flies. The molecular-based approach of DNA barcoding, which utilises a 648-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, was previously evaluated in a pilot study for the discrimination between 16 Australian sarcophagids. The current study comprehensively evaluated DNA barcoding on a larger taxon set of 588 adult Australian sarcophagids. A total of 39 of the 84 known Australian species were represented by 580 specimens, which includes 92% of potentially forensically important species. A further eight specimens could not be reliably identified, but included as six unidentifable taxa. A neighbour-joining phylogenetic tree was generated and nucleotide sequence divergences were calculated using the Kimura-two-parameter distance model. All species except Sarcophaga (Fergusonimyia) bancroftorum, known for high morphological variability, were resolved as reciprocally monophyletic (99.2% of cases), with most having bootstrap support of 100. Excluding S. bancroftorum, the mean intraspecific and interspecific variation ranged from 0.00-1.12% and 2.81-11.23%, respectively, allowing for species discrimination. DNA barcoding was therefore validated as a suitable method for the molecular identification of the Australian Sarcophagidae, which will aid in the implementation of this fauna in forensic entomology.

Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces

The three genera of smut fungi, Ustilago, Sporisorium and Macalpinomyces, form a complex that has eluded resolution by morphology (Langdon & Fullerton 1975, Vánky 1991, Piepenbring et al. 1998) and molecular phylogenetic analysis (Stoll et al. 2003, 2005). Two suggestions to reconcile the taxonomy of the complex have been proposed. The first was to break up the current taxa into several smaller genera and subgenera, and the second to unify the three genera into a single genus, Ustilago (Vánky 2002, Piepenbring 2004). The former solution is dependent on finding morphological synapomorphies that can delimit the genera, and the latter solution dismisses the wide morphological diversity within the group (McTaggart et al. 2012b). Synapomorphic morphological characters and host plant classification delimited clades in the Ustilago-Sporisorium-Macalpinomyces complex (McTaggart et al. 2012a). The current study defines these synapomorphic characters and proposes a new classification for many species currently placed in Ustilago, Sporisorium and Macalpinomyces. This approach preserves the well-known genera Ustilago, Sporisorium and Macalpinomyces, and enables the classification to reflect morphological diversity in the complex.

A review of the Ustilago-Sporisorium-Macalpinomyces complex

The fungal genera Ustilago, Sporisorium and Macalpinomyces represent an unresolved complex. Taxa within the complex often possess characters that occur in more than one genus, creating uncertainty for species placement. Previous studies have indicated that the genera cannot be separated by morphology alone. Here we chronologically review the history of the Ustilago-Sporisorium-Macalpinomyces complex, argue for its resolution and suggest methods to accomplish a stable taxonomy. A combined molecular and morphological approach is required to identify synapomorphic characters that underpin a new classification. Ustilago, Sporisorium and Macalpinomyces require explicit re-description and new genera, based on monophyletic groups, are needed to accommodate taxa that no longer fit the emended descriptions. A resolved classification will end the taxonomic confusion that surrounds generic placement of these smut fungi.

Crowdsourcing information systems : definition, typology and design

Crowdsourcing has become a popular approach for capitalizing on the potential of large and open crowds of people external to the organization. While crowdsourcing as a phenomenon is studied in a variety of fields, research mostly focuses on isolated aspects and little is known about the integrated design of crowdsourcing efforts. We introduce a socio-technical systems perspective on crowdsourcing, which provides a deeper understanding of the components and relationships in crowdsourcing systems. By considering the function of crowdsourcing systems within their organizational context, we develop a typology of four distinct system archetypes. We analyze the characteristics of each type and derive a number of design requirements for the respective system components. The paper lays a foundation for IS-based crowdsourcing research, channels related academic work, and helps guiding the study and design of crowdsourcing information systems.

Design and analysis of key management schemes for distributed wireless sensor networks

Secure communications in distributed Wireless Sensor Networks (WSN) operating under adversarial conditions necessitate efficient key management schemes. In the absence of a priori knowledge of post-deployment network configuration and due to limited resources at sensor nodes, key management schemes cannot be based on post-deployment computations. Instead, a list of keys, called a key-chain, is distributed to each sensor node before the deployment. For secure communication, either two nodes should have a key in common in their key-chains, or they should establish a key through a secure-path on which every link is secured with a key. We first provide a comparative survey of well known key management solutions for WSN. Probabilistic, deterministic and hybrid key management solutions are presented, and they are compared based on their security properties and re-source usage. We provide a taxonomy of solutions, and identify trade-offs in them to conclude that there is no one size-fits-all solution. Second, we design and analyze deterministic and hybrid techniques to distribute pair-wise keys to sensor nodes before the deployment. We present novel deterministic and hybrid approaches based on combinatorial design theory and graph theory for deciding how many and which keys to assign to each key-chain before the sensor network deployment. Performance and security of the proposed schemes are studied both analytically and computationally. Third, we address the key establishment problem in WSN which requires key agreement algorithms without authentication are executed over a secure-path. The length of the secure-path impacts the power consumption and the initialization delay for a WSN before it becomes operational. We formulate the key establishment problem as a constrained bi-objective optimization problem, break it into two sub-problems, and show that they are both NP-Hard and MAX-SNP-Hard. Having established inapproximability results, we focus on addressing the authentication problem that prevents key agreement algorithms to be used directly over a wireless link. We present a fully distributed algorithm where each pair of nodes can establish a key with authentication by using their neighbors as the witnesses.

Six theories of Neoliberalism

This paper takes as its starting point the observation that neoliberalism is a concept that is ‘oft-invoked but ill-defined’ (Mudge 2008: 703). It provides a taxonomy of uses of the term neoliberalism to include: (1) an all-purpose denunciatory category; (2) ‘the way things are’; (3) a particular institutional framework characterizing Anglo-American forms of national capitalism; (4) a dominant ideology of global capitalism; (5) a form of governmentality and hegemony; and (6) a variant within the broad framework of liberalism as both theory and policy discourse. It is argued that this sprawling set of definitions are not mutually compatible, and that uses of the term need to be dramatically narrowed from its current association with anything and everything that a particular author may find objectionable. In particular, it is argued that the uses of the term by Michel Foucault in his 1978-79 lectures, found in The Birth of Biopolitics (Foucault, 2008) are not particularly compatible with its more recent status as a variant of dominant ideology or hegemony theories.

A revision of Calyptochloa C.E.Hubb. (Poaceae), with two new species and a new subspecies

Thompson, E.J. & Simon, B.K. (2012). A revision of Calyptochloa C.E.Hubb. (Poaceae), with two new species and a new subspecies. Austrobaileya 8(4): 634–652. Two new species of Calyptochloa C.E.Hubb. (Calyptochloa cylindrosperma E.J.Thomps. & B.K.Simon and C. johnsoniana E.J.Thomps. & B.K.Simon) endemic to central Queensland, and a new subspecies of Calyptochloa gracillima C.E.Hubb. (C. gracillima subsp. ipsviciensis E.J.Thomps. & B.K.Simon) endemic to southeast Queensland are described and illustrated.

A critical assessment of the Australian OHS accreditation system's "Body of Knowledge (BoK)"

In response to an increasing perception of poor OHS consultancy quality amongst the Australian public, regulator and OHS professionals, the Safety Institute Australia (SIA) was tasked by the Victorian government to establish an accreditation process for OHS professionals. The OHS accreditation board decided to base its accreditation on a core "body of knowledge" (BoK), against which applicants are assesssed. While the foundation and structure of the BoK is unclear, the BoK consists of a collection of essays from a variety of invited authors. The BoK comprises about 811 pages in 34 chapters, with significant redundancy and considerable subjective components. The SIA BoK is benchmarked against two international best-practices, the German "Core Definition, Object Catalog and Research Domains of Labour Science (Ergonomics)" (Luzcak, Volpert, Raeithel & Schwier, 1989)(100 pages) and the American "Core Competency Model" for the "Master's Degree in Public Health" (Association of Schools of Public Health, 2006) (21 pages). Both "core definition" and "core competency model" are on a comparative level to the BoK. While the German expert panel consisted of 14 eminent professors, the American panel consisted of 135 members, organized in 6 groups chaired by discipline leading academics. The Australian approach employed a broad approach, where 137 professionals, consultants, emerging academics and academics contributed to 8 workshops. Both the German and the American panels maintained an open communication amongst members and with the discipline community throughout the process, whereas SIA applied an open and directed peer-review process. Moreover, the German process involved an analysis of all congress content and journal publications in the scientific domain in a set timeframe, which were then systematically clustered. These results were further expanded by structured interviews with 38 professors in the discpline, grasping their research and teaching practice. The American workgroup however assumed core scientific areas, underlying the domain. Based upon the a-priori assumption, they then established well defined competencies across all areas using a modified Delphi process. Although the BoK attempts to explore the knowledge in the OHS domain without an imposed structure in a bottom-up approach, it does not result in a structured systematic of the science. We conclude that the outcome of the German, rigorous academic approach, and the US American democratic approach under unambiguous academic leadership both outperform the Australian advocacy group approach. This product was determined for both structure and content of the taxonomy delivered through the processes.

Passenger experience at airports : An activity-centred approach

This project has provided a new understanding of the passenger experience in Australian international airport departure terminals. A novel understanding of the passenger experience developed by observing the activities passengers carried out on their day of travel, and interviewing passengers and staff members. The development of the Taxonomy of Passenger Activities (TOPA) has been an important outcome of this research. It provides a new understanding of the airport passenger experience at departure. The Taxonomy of Passenger Activities identifies the activities that improve the experience of passengers and the processing efficiency of the airport terminal.

The evolving emotional experience with portable interactive devices

Emotions play a significant role in people’s lives, including interactions with portable devices. The research aimed to understand the evolving emotional experience between people and portable interactive devices (PIDs). Activity Theory was the theoretical framework used to contextualise the research approach and findings. Two longitudinal experiments were conducted investigating emotional experiences with PIDs over six months. Experiment 1 focused on media / entertainment PIDs while Experiment 2 focused on medical / health PIDs. Mixed research methods consisting of diaries, interviews and codiscovery sessions were used to collect data. Results identified that more social interactions were experienced with media PIDs than medical PIDs. Different Task Categories, and their emotional responses, were also revealed including Features, Functional, Mediation and Auxiliary Categories. Functional and Mediation categories were characterised as overall positive while Features and Auxiliary Categories were characterised as overall negative. Further, the consequences of Negative Personal and Social interactions on the overall emotional experience were determined. For media PIDs, Negative Social experiences adversely impacted the evolving emotional experience. For medical PIDs, both Negative Social and Negative Personal experiences adversely impacted the evolving emotional experience. As a result of the findings the Designing for Evolving Emotional Experience framework was developed, outlining principles to promote positive, and avoid negative, emotional experiences with PIDs. Contributions to knowledge from the research include methodological contributions, advancing understanding of emotional experiences with PIDs, expanding the taxonomy of emotional interactions with PIDs and broadening emotion design theory and principles. The thesis concludes with an outline of implications to design research, design and related fields, future research potentials, as well as the positive contributions to designing for meaningful and enjoyable experiences in everyday life.

The linking of plate tectonics and evolutionary divergence

It is exciting to be living at a time when the big questions in biology can be investigated using modern genetics and computing [1]. Bauzà-Ribot et al.[2] take on one of the fundamental drivers of biodiversity, the effect of continental drift in the formation of the world’s biota 3 and 4, employing next-generation sequencing of whole mitochondrial genomes and modern Bayesian relaxed molecular clock analysis. Bauzà-Ribot et al.[2] conclude that vicariance via plate tectonics best explains the genetic divergence between subterranean metacrangonyctid amphipods currently found on islands separated by the Atlantic Ocean. This finding is a big deal in biogeography, and science generally [3], as many other presumed biotic tectonic divergences have been explained as probably due to more recent transoceanic dispersal events [4]. However, molecular clocks can be problematic 5 and 6 and we have identified three issues with the analyses of Bauzà-Ribot et al.[2] that cast serious doubt on their results and conclusions. When we reanalyzed their mitochondrial data and attempted to account for problems with calibration 5 and 6, modeling rates across branches 5 and 7 and substitution saturation [5], we inferred a much younger date for their key node. This implies either a later trans-Atlantic dispersal of these crustaceans, or more likely a series of later invasions of freshwaters from a common marine ancestor, but either way probably not ancient tectonic plate movements.

A phylogenetic analysis and taxonomic revision of the oribatid mite family Malaconothridae (Acari: Oribatida), with new species of Tyrphonothrus and Malaconothrus from Australia

Hitherto, the Malaconothridae contained Malaconothrus Berlese, 1904 and Trimalaconothrus Berlese, 1916, defined by the possession of one pre-tarsal claw (monodactyly) or by three claws (tridactyly) respectively. However, monodactyly is a convergent apomorphy within the Oribatida and an unreliable character for a classification. Therefore we undertook a phylogenetic analysis of 102 species as the basis for a taxonomic review of the Malaconothridae. We identified two major clades, equivalent to the genera Tyrphonothrus Knülle, 1957 and Malaconothrus. These genera are redefined. Trimala-conothrus becomes the junior subjective synonym of Malaconothrus. Some 42 species of Trimalaconothrus are recom-bined to Malaconothrus and 15 species to Tyrphonothrus. Homonyms created by the recombinations are rectified. The replacement name M. hammerae nom. nov. is proposed for M. angulatus Hammer, 1958, the junior homonym of M. an-gulatus (Willmann, 1931) and the replacement name M. luxtoni nom. nov. is proposed for M. scutatus Luxton, 1987, the junior homonym of M. scutatus Mihelč ič, 1959. Trimalaconothrus iteratus Subías, 2004 is an unnecessary replacement name and is a junior objective synonym of Malaconothrus longirostrum (Hammer 1966). Malaconothrus praeoccupatus Subías, 2004 is a junior objective synonym of M. machadoi Balogh & Mahunka, 1969. Malaconothrus obsessus (Subías, 2004), an unnecessary replacement name for Trimalaconothrus albulus Hammer 1966 sensu Tseng 1982, becomes an available name for what is in fact a previously-undescribed species of Malaconothrus. We describe four new species of Tyrphonothrus: T. gnammaensis sp. nov. from Western Australia, T. gringai sp. nov. and T. maritimus sp. nov. from New South Wales, and T. taylori sp. nov. from Queensland. We describe six new species of Malaconothrus: M. beecroftensis sp. nov., M. darwini sp. nov. M. gundungurra sp. nov. and M. knuellei sp. nov. from New South Wales, M. jowettae sp. nov. from Norfolk Island, and M. talaitae sp. nov. from Victoria.

Approaches to reducing the most important patient errors in primary health care : patient and professional perspectives

We have previously reported a preliminary taxonomy of patient error. However, approaches to managing patients' contribution to error have received little attention in the literature. This paper aims to assess how patients and primary care professionals perceive the relative importance of different patient errors as a threat to patient safety. It also attempts to suggest what these groups believe may be done to reduce the errors, and how. It addresses these aims through original research that extends the nominal group analysis used to generate the error taxonomy. Interviews were conducted with 11 purposively selected groups of patients and primary care professionals in Auckland, New Zealand, during late 2007. The total number of participants was 83, including 64 patients. Each group ranked the importance of possible patient errors identified through the nominal group exercise. Approaches to managing the most important errors were then discussed. There was considerable variation among the groups in the importance rankings of the errors. Our general inductive analysis of participants' suggestions revealed the content of four inter-related actions to manage patient error: Grow relationships; Enable patients and professionals to recognise and manage patient error; be Responsive to their shared capacity for change; and Motivate them to act together for patient safety. Cultivation of this GERM of safe care was suggested to benefit from 'individualised community care'. In this approach, primary care professionals individualise, in community spaces, population health messages about patient safety events. This approach may help to reduce patient error and the tension between personal and population health-care.

A data mining framework for relevance feature discovery

This thesis is a study for automatic discovery of text features for describing user information needs. It presents an innovative data-mining approach that discovers useful knowledge from both relevance and non-relevance feedback information. The proposed approach can largely reduce noises in discovered patterns and significantly improve the performance of text mining systems. This study provides a promising method for the study of Data Mining and Web Intelligence.

Personalized ontology learning for enhancing text mining effectiveness

Over the last decade, the majority of existing search techniques is either keyword- based or category-based, resulting in unsatisfactory effectiveness. Meanwhile, studies have illustrated that more than 80% of users preferred personalized search results. As a result, many studies paid a great deal of efforts (referred to as col- laborative filtering) investigating on personalized notions for enhancing retrieval performance. One of the fundamental yet most challenging steps is to capture precise user information needs. Most Web users are inexperienced or lack the capability to express their needs properly, whereas the existent retrieval systems are highly sensitive to vocabulary. Researchers have increasingly proposed the utilization of ontology-based tech- niques to improve current mining approaches. The related techniques are not only able to refine search intentions among specific generic domains, but also to access new knowledge by tracking semantic relations. In recent years, some researchers have attempted to build ontological user profiles according to discovered user background knowledge. The knowledge is considered to be both global and lo- cal analyses, which aim to produce tailored ontologies by a group of concepts. However, a key problem here that has not been addressed is: how to accurately match diverse local information to universal global knowledge. This research conducts a theoretical study on the use of personalized ontolo- gies to enhance text mining performance. The objective is to understand user information needs by a \bag-of-concepts" rather than \words". The concepts are gathered from a general world knowledge base named the Library of Congress Subject Headings. To return desirable search results, a novel ontology-based mining approach is introduced to discover accurate search intentions and learn personalized ontologies as user profiles. The approach can not only pinpoint users' individual intentions in a rough hierarchical structure, but can also in- terpret their needs by a set of acknowledged concepts. Along with global and local analyses, another solid concept matching approach is carried out to address about the mismatch between local information and world knowledge. Relevance features produced by the Relevance Feature Discovery model, are determined as representatives of local information. These features have been proven as the best alternative for user queries to avoid ambiguity and consistently outperform the features extracted by other filtering models. The two attempt-to-proposed ap- proaches are both evaluated by a scientific evaluation with the standard Reuters Corpus Volume 1 testing set. A comprehensive comparison is made with a num- ber of the state-of-the art baseline models, including TF-IDF, Rocchio, Okapi BM25, the deploying Pattern Taxonomy Model, and an ontology-based model. The gathered results indicate that the top precision can be improved remarkably with the proposed ontology mining approach, where the matching approach is successful and achieves significant improvements in most information filtering measurements. This research contributes to the fields of ontological filtering, user profiling, and knowledge representation. The related outputs are critical when systems are expected to return proper mining results and provide personalized services. The scientific findings have the potential to facilitate the design of advanced preference mining models, where impact on people's daily lives.