Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.

Discrete choice modelling of combined mode and departure time

Typical daily decision-making process of individuals regarding use of transport system involves mainly three types of decisions: mode choice, departure time choice and route choice. This paper focuses on the mode and departure time choice processes and studies different model specifications for a combined mode and departure time choice model. The paper compares different sets of explanatory variables as well as different model structures to capture the correlation among alternatives and taste variations among the commuters. The main hypothesis tested in this paper is that departure time alternatives are also correlated by the amount of delay. Correlation among different alternatives is confirmed by analyzing different nesting structures as well as error component formulations. Random coefficient logit models confirm the presence of the random taste heterogeneity across commuters. Mixed nested logit models are estimated to jointly account for the random taste heterogeneity and the correlation among different alternatives. Results indicate that accounting for the random taste heterogeneity as well as inter-alternative correlation improves the model performance.

A preliminary examination of the effects of changes in motorcycle licensing in Queensland

Several sets of changes have been made to motorcycle licensing in Queensland since 2007, with the aim of improving the safety of novice riders. These include a requirement that a motorcycle learner licence applicant must have held a provisional or open car licence for 12 months, and imposing a 3 year limit for learner licence renewal. Additionally, a requirement to hold an RE (250 cc limited) class licence for a period of 12 months prior to progressing to an R class licence was introduced for Q-RIDE. This paper presents analyses of licensing transaction data that examine the effects of the licensing changes on the duration that the learner licence was held, factors affecting this duration and the extent to which the demographic characteristics of learner licence holders changed. The likely safety implications of the observed changes are discussed.

Towards a unified method for the knowledge based urban development framework

Purpose–The growing debate in the literature indicates that the initiative to implement Knowledge Based Urban Development (KBUD) approaches in urban development process is neither simple nor quick. Many research efforts has therefore, been put forward to the development of appropriate KBUD framework and KBUD practical approaches. But this has lead to a fragmented and incoherent methodological approach. This paper outlines and compares a few most popular KBUD frameworks selected from the literature. It aims to identify some key and common features in the effort to achieve a unified method of KBUD framework. Design/methodology/approach–This paper reviews, examines and identifies various popular KBUD frameworks discussed in the literature from urban planners’ viewpoint. It employs a content analysis technique i.e. a research tool used to determine the presence of certain words or concepts within texts or sets of texts. Originality/value–The paper reports on the key and common features of a few selected most popular KBUD frameworks. The synthesis of the results is based from a perspective of urban planners. The findings which encompass a new KBUD framework incorporating the key and common features will be valuable in setting a platform to achieve a unified method of KBUD. Practical implications –The discussion and results presented in this paper should be significant to researchers and practitioners and to any cities and countries that are aiming for KBUD. Keywords – Knowledge based urban development, Knowledge based urban development framework, Urban development and knowledge economy

Inter-and Intra-Site Genetic Diversity of Natural Field Populations of Rice Tungro Bacilliform Virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations within and between growing sites was analyzed in a collection of natural field isolates from different rice varieties grown in eight tungro-endemic sites of the Philippines. Total DNA extracts from 345 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV, a procedure shown in preliminary experiments capable of revealing high levels of polymorphism in RTBV field isolates. In the total population, 17 distinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isabela and North Cotabato provinces suggesting a geographic isolation of virus populations. However, among the sites in each province, there were few significant differences in the genotype compositions of virus populations. The number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from season to season indicating a genetic stability for the local virus population. Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no apparent selection pressures. Insect transmission experiments on selected RTBV field isolates showed that dramatic shifts in genotype and phenotype distributions can occur in response to host /environmental shifts.

Good practice for enhancing the engagement and success of commencing students

There is widespread recognition that higher education institutions (HEIs) must actively support commencing students to ensure equity in access to the opportunities afforded by higher education. This role is particularly critical for students who because of educational, cultural or financial disadvantage or because they are members of social groups currently under-represented in higher education, may require additional transitional support to “level the playing field.” The challenge faced by HEIs is to provide this “support” in a way that is integrated into regular teaching and learning practices and reaches all commencing students. The Student Success Program (SSP) is an intervention in operation at the Queensland University of Technology (QUT) designed to identify and support those students deemed to be at risk of disengaging from their learning and their institution. Two sets of evidence of the impact of the SSP are presented: First, its expansion (a) from a one-faculty pilot project (Nelson, Duncan & Clarke, 2009) to all faculties and (b) into a variety of applications mirroring the student life cycle; and second, an evaluation of the impact of the SSP on students exposed to it. The outcomes suggest that: the SSP is an example of good practice that can be successfully applied to a variety of learning contexts and student enrolment situations; and the impact of the intervention on student persistence is sustained for at least 12 months and positively influences student retention. It is claimed that the good practice evidenced by the SSP is dependent on its integration into the broader First Year Experience Program at QUT as an example of transition pedagogy in action.

Modeling circulation of train-set with multiple routing

Planning on utilization of train-set is one of the key tasks of transport organization for passenger dedicated railway in China. It also has strong relationships with timetable scheduling and operation plans at a station. To execute such a task in a railway hub pooling multiple railway lines, the characteristics of multiple routing for train-set is discussed in term of semicircle of train-sets' turnover. In programming the described problem, the minimum dwell time is selected as the objectives with special derive constraints of the train-set's dispatch, the connecting conditions, the principle of uniqueness for train-sets, and the first plus for connection in the same direction based on time tolerance σ. A compact connection algorithm based on time tolerance is then designed. The feasibility of the model and the algorithm is proved by the case study. The result indicates that the circulation model and algorithm about multiple routing can deal with the connections between the train-sets of multiple directions, and reduce the train's pulling in or leaving impact on the station's throat.

Similarity metrics within a point of view

In vector space based approaches to natural language processing, similarity is commonly measured by taking the angle between two vectors representing words or documents in a semantic space. This is natural from a mathematical point of view, as the angle between unit vectors is, up to constant scaling, the only unitarily invariant metric on the unit sphere. However, similarity judgement tasks reveal that human subjects fail to produce data which satisfies the symmetry and triangle inequality requirements for a metric space. A possible conclusion, reached in particular by Tversky et al., is that some of the most basic assumptions of geometric models are unwarranted in the case of psychological similarity, a result which would impose strong limits on the validity and applicability vector space based (and hence also quantum inspired) approaches to the modelling of cognitive processes. This paper proposes a resolution to this fundamental criticism of of the applicability of vector space models of cognition. We argue that pairs of words imply a context which in turn induces a point of view, allowing a subject to estimate semantic similarity. Context is here introduced as a point of view vector (POVV) and the expected similarity is derived as a measure over the POVV's. Different pairs of words will invoke different contexts and different POVV's. Hence the triangle inequality ceases to be a valid constraint on the angles. We test the proposal on a few triples of words and outline further research.

Impact of traffic oscillations on freeway crash occurrences

Traffic oscillations are typical features of congested traffic flow that are characterized by recurring decelerations followed by accelerations (stop-and-go driving). The negative environmental impacts of these oscillations are widely accepted, but their impact on traffic safety has been debated. This paper describes the impact of freeway traffic oscillations on traffic safety. This study employs a matched case-control design using high-resolution traffic and crash data from a freeway segment. Traffic conditions prior to each crash were taken as cases, while traffic conditions during the same periods on days without crashes were taken as controls. These were also matched by presence of congestion, geometry and weather. A total of 82 cases and about 80,000 candidate controls were extracted from more than three years of data from 2004 to 2007. Conditional logistic regression models were developed based on the case-control samples. To verify consistency in the results, 20 different sets of controls were randomly extracted from the candidate pool for varying control-case ratios. The results reveal that the standard deviation of speed (thus, oscillations) is a significant variable, with an average odds ratio of about 1.08. This implies that the likelihood of a (rear-end) crash increases by about 8% with an additional unit increase in the standard deviation of speed. The average traffic states prior to crashes were less significant than the speed variations in congestion.

Drivers of supply chain collaboration among Finnish manufacturers

This paper focuses on data exchange relationships and ways to improve collaboration in the supply chain. Initially, the paper examines the information needs and alternatives in supply chain management. In the second part, the paper identifies different sets of factors that are likely to influence information sharing with suppliers, from the manufacturers’ point of view. Results from a Finnish Manufacturing industry survey show that manufacturers provided substantial information on demand data, production schedules, and inventories to their suppliers. Respondents perceived delivery performance measured by the timeliness, accuracy, and defect rate of deliveries as the primary incentives for supplier collaboration. On the other hand, supplier image and the market in which the supplier operates were found to be less relevant in determining the intensity of collaboration.

Managing Wetlands Sustainably as Ecosystems: The Contribution of the Law (Part 2)

In this Part 2 attention is turned towards the legal arrangements in nation states for managing wetlands. These national arrangements have effect within the international arrangements already mentioned and any regional arrangements that are relevant. However, each national system is a reflection of its own historical, cultural, political and constitutional background. It is the purpose of this Part 2 to review and assess the national approaches to wetlands management. This involves an analysis of a range of instruments. These are: constitutional rules; strategic rules; regulatory rules; and management rules. Each of these sets of rules performs different functions, assumes different forms and is differentially capable of enforcement.

Spectroscopic and structural characterization of pascoite

Pascoite mineral having yellow-orange colour of Colorado, USA origin has been characterized by EPR, optical and NIR spectroscopy. The colour dark red-orange to yellow-orange colour of the pascoite indicates that the mineral contain mixed valency of vanadium. The optical spectrum exhibits a number of electronic bands due to presence of VO(II) ions in the mineral. From EPR studies, the parameters of g, A are evaluated and the data confirm that the ion is in distorted octahedron. Optical absorption studies reveal that two sets of VO(II) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules.

Numerical exploration of plastic deformation mechanisms of copper nanowires with surface defects

Based on the molecular dynamics simulation, plastic deformation mechanisms associated with the zigzag stress curves in perfect and surface defected copper nanowires under uniaxial tension are studied. In our previous study, it has found that the surface defect exerts larger influence than the centro-plane defect, and the 45o surface defect appears as the most influential surface defect. Hence, in this paper, the nanowire with a 45o surface defect is chosen to investigate the defect’s effect to the plastic deformation mechanism of nanowires. We find that during the plastic deformation of both perfect and defected nanowires, decrease regions of the stress curve are accompanied with stacking faults generation and migration activities, but during stress increase, the structure of the nanowire appears almost unchanged. We also observe that surface defects have obvious influence on the nanowire’s plastic deformation mechanisms. In particular, only two sets of slip planes are found to be active and twins are also observed in the defected nanowire.

Systemic inflammatory responses to maximal versus submaximal lengthening contractions of the elbow flexors

We compared changes in markers of muscle damage and systemic inflammation after submaximal and maximal lengthening muscle contractions of the elbow flexors. Using a cross-over design, 10 healthy young men not involved in resistance training completed a submaximal trial (10 sets of 60 lengthening contractions at 10% maximum isometric strength, 1 min rest between sets), followed by a maximal trial (10 sets of three lengthening contractions at 100% maximum isometric strength, 3 min rest between sets). Lengthening contractions were performed on an isokinetic dynamometer. Opposite arms were used for the submaximal and maximal trials, and the trials were separated by a minimum of two weeks. Blood was sampled before, immediately after, 1 h, 3 h, and 1-4 d after each trial. Total leukocyte and neutrophil numbers, and the serum concentration of soluble tumor necrosis factor-alpha receptor 1 were elevated after both trials (P < 0.01), but there were no differences between the trials. Serum IL-6 concentration was elevated 3 h after the submaximal contractions (P < 0.01). The concentrations of serum tumor necrosis factor-alpha, IL-1 receptor antagonist, IL-10, granulocyte-colony stimulating factor and plasma C-reactive protein remained unchanged following both trials. Maximum isometric strength and range of motion decreased significantly (P < 0.001) after both trials, and were lower from 1-4 days after the maximal contractions compared to the submaximal contractions. Plasma myoglobin concentration and creatine kinase activity, muscle soreness and upper arm circumference all increased after both trials (P < 0.01), but were not significantly different between the trials. Therefore, there were no differences in markers of systemic inflammation, despite evidence of greater muscle damage following maximal versus submaximal lengthening contractions of the elbow flexors.

On a Syntactic Characterization of Classification with a Mind Change Bound

Most learning paradigms impose a particular syntax on the class of concepts to be learned; the chosen syntax can dramatically affect whether the class is learnable or not. For classification paradigms, where the task is to determine whether the underlying world does or does not have a particular property, how that property is represented has no implication on the power of a classifier that just outputs 1’s or 0’s. But is it possible to give a canonical syntactic representation of the class of concepts that are classifiable according to the particular criteria of a given paradigm? We provide a positive answer to this question for classification in the limit paradigms in a logical setting, with ordinal mind change bounds as a measure of complexity. The syntactic characterization that emerges enables to derive that if a possibly noncomputable classifier can perform the task assigned to it by the paradigm, then a computable classifier can also perform the same task. The syntactic characterization is strongly related to the difference hierarchy over the class of open sets of some topological space; this space is naturally defined from the class of possible worlds and possible data of the learning paradigm.