Improving model quality through foundational ontologies: Two contrasting approaches to the representation of roles

Several foundational ontologies have been developed recently. We examine two of these from the point of view of their quality in representing temporal changes, focusing on the example of roles. We discuss how these are modelled in two foundational ontologies: the Unified Foundational Ontology and the BORO foundational ontology. These exhibit two different approaches, endurantist and perdurantist respectively. We illustrate the differences using a running example in the university student domain, wherein one individual is not only a registered student but also, for part of this period, was elected the President of the Student Union. The metaphysical choices made by UFO and BORO lead to different representations of roles. Two key differences which affect the way roles are modelled are exemplified in this paper: (1) different criteria of identity and (2) differences in the way individual objects extend over time and possible worlds. These differences impact upon the quality of the models produced in terms of their respective explanatory power. The UFO model concentrates on the notion of validity in “all possible worlds” and is unable to accurately represent the way particulars are extended in time. The perdurantist approach is best able to describe temporal changes wherein roles are spatio-temporal extents of individuals

Sexual reproduction is the null hypothesis for life cycles of rust fungi

Sexual reproduction, mutation, and reassortment of nuclei increase genotypic diversity in rust fungi. Sexual reproduction is inherent to rust fungi, coupled with their coevolved plant hosts in native pathosystems. Rust fungi are hypothesised to exchange nuclei by somatic hybridisation with an outcome of increased genotypic diversity, independent of sexual reproduction. We provide criteria to demonstrate whether somatic exchange has occurred, including knowledge of parental haplotypes and rejection of fertilisation in normal rust life cycles

Genetic diversity and recombination between turnip yellows virus strains in Australia

Disease outbreaks caused by turnip yellows virus (TuYV), a member of the genus Polerovirus, family Luteoviridae, regularly occur in canola and pulse crops throughout Australia. To understand the genetic diversity of TuYV for resistance breeding and management, genome sequences of 28 TuYV isolates from different hosts and locations were determined using high-throughput sequencing (HTS). We aimed to identify the parts of the genome that were most variable and clarify the taxonomy of viruses related to TuYV. Poleroviruses contain seven open reading frames (ORFs): ORF 0–2, 3a, and 3–5. Phylogenetic analysis based on the genome sequences, including isolates of TuYV and brassica yellows virus (BrYV) from the GenBank database, showed that most genetic variation among isolates occurred in ORF 5, followed by ORF 0 and ORF 3a. Phylogenetic analysis of ORF 5 revealed three TuYV groups; P5 group 1 and group 3 shared 45–49% amino acid sequence identity, and group 2 is a recombinant between the other two. Phylogenomic analysis of the concatenated ORFs showed that TuYV is paraphyletic with respect to BrYV, and together these taxa form a well-supported monophyletic group. Our results support the hypothesis that TuYV and BrYV belong to the same species and that the phylogenetic topologies of ORF 0, 3a and 5 are incongruent and may not be informative for species demarcation. A number of beet western yellow virus (BWYV)- and TuYV-associated RNAs (aRNA) were also identified by HTS for the first time in Australia

High-Density Support Matrices: Key to the Deep Borehole Disposal of Spent Nuclear Fuel

Abstract Deep (4-5 km) boreholes are emerging as a safe, secure, environmentally sound and potentially cost-effective option for disposal of high-level radioactive wastes, including plutonium. One reason this option has not been widely accepted for spent fuel is because stacking the containers in a borehole could create load stresses threatening their integrity with potential for releasing highly mobile radionuclides like 129 I before the borehole is filled and sealed. This problem can be overcome by using novel high-density support matrices deployed as fine metal shot along with the containers. Temperature distributions in and around the disposal are modelled to show how decay heat from the fuel can melt the shot within weeks of disposal to give a dense liquid in which the containers are almost weightless. Finally, within a few decades, this liquid will cool and solidify, entombing the waste containers in a base metal sarcophagus sealed into the host rock

Action research in physical education: focusing beyond myself through cooperative learning

This paper reports on the pedagogical changes that I experienced as a teacher engaged in an action research project in which I designed and implemented an indirect, developmentally appropriate and child‐centred approach to my teaching. There have been repeated calls to expunge – or at least rationalise – the use of traditional, teacher‐led practice in physical education. Yet despite the advocacy of many leading academics there is little evidence that such a change of approach is occurring. In my role as teacher‐as‐researcher I sought to implement a new pedagogical approach, in the form of cooperative learning, and bring about a positive change in the form of enhanced pupil learning. Data collection included a reflective journal, post‐teaching reflective analysis, pupil questionnaires, student interviews, document analysis, and non‐participant observations. The research team analysed the data using inductive analysis and constant comparison. Six themes emerged from the data: teaching and learning, reflections on cooperation, performance, time, teacher change, and social interaction. The paper argues that cooperative learning allowed me to place social and academic learning goals on an even footing, which in turn placed a focus on pupils’ understanding and improvement of skills in athletics alongside their interpersonal development

Bias in protein and potassium intake collected with 24-h recalls (EPIC-Soft) is rather comparable across European populations

Purpose: We investigated whether group-level bias of a 24-h recall estimate of protein and potassium intake, as compared to biomarkers, varied across European centers and whether this was influenced by characteristics of individuals or centers. Methods: The combined data from EFCOVAL and EPIC studies included 14 centers from 9 countries (n = 1,841). Dietary data were collected using a computerized 24-h recall (EPIC-Soft). Nitrogen and potassium in 24-h urine collections were used as reference method. Multilevel linear regression analysis was performed, including individual-level (e.g., BMI) and center-level (e.g., food pattern index) variables. Results: For protein intake, no between-center variation in bias was observed in men while it was 5.7% in women. For potassium intake, the between-center variation in bias was 8.9% in men and null in women. BMI was an important factor influencing the biases across centers (p <0.01 in all analyses). In addition, mode of administration (p = 0.06 in women) and day of the week (p = 0.03 in men and p = 0.06 in women) may have influenced the bias in protein intake across centers. After inclusion of these individual variables, between-center variation in bias in protein intake disappeared for women, whereas for potassium, it increased slightly in men (to 9.5%). Center-level variables did not influence the results. Conclusion: The results suggest that group-level bias in protein and potassium (for women) collected with 24-h recalls does not vary across centers and to a certain extent varies for potassium in men. BMI and study design aspects, rather than center-level characteristics, affected the biases across center