Bulldust, flat tyres and roadkill: a disorderly decolonising fieldwork journey through remote Aboriginal and Torres Strait Islander Australia

The purpose of this paper is to discuss the iterations and outcomes of a doctoral fieldwork experience where the Aboriginal and Torres Strait Islander participants challenged me to radically adapt my constructivist grounded theory methodology and commence decolonising data gathering and analysis while in the field. The starting point for the research was a discourse of defeatism in the literature around mature-age Aboriginal and Torres Strait Islander university graduates and students, which the participants, my doctoral supervisors and I perceived as unjust and unjustifiable. The aim of the ongoing research, therefore, is to explore and explicate an alternative discourse, beginning with the emic perspectives of mature- age Aboriginal and Torres Strait Islander university graduates. In the context of the remote Aboriginal and Torres Strait Islander field, I detail the early and some- what disorderly enactment of decolonising methodology — disorderly because I was unprepared for the extent to which the participants would take control of both the research agenda and methods. Disorder also partly characterised our collabora- tive methodological adaptation, in that it was initially more intuitive than deliber- ate. I discuss how the participants shifted the post-graduation narrative from one of personal and professional uplift to one they dubbed ‘the blessings and burdens of being an educated black’. This narrative unequivocally challenges the notion of Australia as a postcolonial society and positions the participants as activists in the fight for indigenous self-determination. I reflect on mistakes made and lessons learned, and articulate pragmatic and achievable fieldwork research methods that privilege participants as knowledge producers and custodians. The paper concludes by discussing the next stages of the decolonising constructivist grounded theory project, which necessitated a return to the field to test and refine the emerging conceptual categories with the participants, most of whom have remained active partners in the research

Bringing Feedback in From the Outback via a Generic and Preference-Sensitive Instrument for Course Quality Assessment

Background: Much effort and many resources have been put into developing ways of eliciting valid and informative student feedback on courses in medical, nursing, and other health professional schools. Whatever their motivation, items, and setting, the response rates have usually been disappointingly low, and there seems to be an acceptance that the results are potentially biased. Objective: The objective of the study was to look at an innovative approach to course assessment by students in the health professions. This approach was designed to make it an integral part of their educational experience, rather than a marginal, terminal, and optional add-on as feedback . It becomes a weighted, but ungraded, part of the course assignment requirements. Methods: A ten-item, two-part Internet instrument, MyCourseQuality (MCQ-10D), was developed following a purposive review of previous instruments. Shorthand labels for the criteria are: Content, Organization, Perspective, Presentations, Materials, Relevance, Workload, Support, Interactivity, and Assessment. The assessment is unique in being dually personalized. In part 1, at the beginning of the course, the student enters their importance weights for the ten criteria. In part 2, at its completion, they rate the course on the same criteria. Their ratings and weightings are combined in a simple expected-value calculation to produce their dually personalized and decomposable MCQ score. Satisfactory (technical) completion of both parts contributes 10% of the marks available in the course. Providers are required to make the relevant characteristics of the course fully transparent at enrollment, and the course is to be rated as offered. A separate item appended to the survey allows students to suggest changes to what is offered. Students also complete (anonymously) the standard feedback form in the setting concerned. Results: Piloting in a medical school and health professional school will establish the organizational feasibility and acceptability of the approach (a version of which has been employed in one medical school previously), as well as its impact on provider behavior and intentions, and on student engagement and responsiveness. The priorities for future improvements in terms of the specified criteria are identified at both individual and group level. The group results from MCQ will be compared with those from the standard feedback questionnaire, which will also be completed anonymously by the same students (or some percentage of them). Conclusions: We present a protocol for the piloting of a student-centered, dually personalized course quality instrument that forms part of the assignment requirements and is therefore an integral part of the course. If, and how, such an essentially formative Student-Reported Outcome or Experience Measure can be used summatively, at unit or program level, remains to be determined, and is not our concern here

Equipping future teachers with innovative strategies that increase physical activity in the classroom : A hybrid implementation trial across three Australian universities

Introduction: TransformEd targets initial teacher education (ITE) to equip future teachers with innovative strategies that increase physical activity in the Primary school classroom. Methods: This hybrid implementation-effectiveness trial investigated the effects of the TransformEd program when embedded in ITE degrees at two Australian universities (University 1 Single Unit offering; University 2 Dual Unit offering) over a 12-week period, on pre-service teachers’ perceived competence, confidence, and willingness to deliver active pedagogies, in comparison with a third ‘usual practice’ control university. Results: There was a favourable intervention effect on the total teacher perceptions score among pre-service teachers in University 1 compared to the control group pre-service teachers. Further, there was a significant intervention effect on reduced perceived barriers to active strategies in University 1, and a significant increase in perceived effects of active strategies on Primary school student outcomes in University 2. Qualitative data suggested the program strengthened the connection between theory and practice (i.e., how pre-service teachers are educated in university and the way they teach in Primary schools). The program was motivating to both lecturers and pre-service teachers, resulted in them reflecting on their own teaching practice, and helped with pre-service teacher engagement. Discussion: Recommendations for improvement included stronger and more explicit alignment with the Australian Professional Standards for Teachers

A systematic review of tools designed for teacher proxy-report of children’s physical literacy or constituting elements

Abstract Background Physical literacy (PL) in childhood is essential for a healthy active lifestyle, with teachers playing a critical role in guiding its development. Teachers can assist children to acquire the skills, confidence, and creativity required to perform diverse movements and physical activities. However, to detect and directly intervene on the aspects of children’s PL that are suboptimal, teachers require valid and reliable measures. This systematic review critically evaluates the psychometric properties of teacher proxy-report instruments for assessing one or more of the 30 elements within the four domains (physical, psychological, cognitive, social) of the Australian Physical Literacy Framework (APLF), in children aged 5–12 years. Secondary aims were to: examine alignment of each measure (and relevant items) with the APLF and provide recommendations for teachers in assessing PL. Methods Seven electronic databases (Academic Search Complete, CINAHL Complete, Education Source, Global Health, MEDLINE Complete, PsycINFO, and SPORTDiscus) were systematically searched originally in October 2019, with an updated search in April 2021. Eligible studies were peer-reviewed English language publications that sampled a population of children with mean age between 5 and 12 years and focused on developing and evaluating at least one psychometric property of a teacher proxy-report instrument for assessing one or more of the 30 APLF elements. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidance was followed for the conduct and reporting of this review. The methodological quality of included studies and quality of psychometric properties of identified tools were evaluated using the COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) guidance. Alignment of each measure (and relevant items) with the APLF domains and 30 elements was appraised. Results Database searches generated 61,412 citations; reduced to 41 studies that evaluated the psychometric properties of 24 teacher proxy-report tools. Six tools were classified as single domain measures (i.e. assessing a single domain of the APLF), eleven as dual-domain measures, and seven as tri-domain measures. No single tool captured all four domains and 30 elements of the APLF. Tools contained items that aligned with all physical, psychological, and social elements; however, four cognitive elements were not addressed by any measure. No tool was assessed for all nine psychometric properties outlined by COSMIN. Included studies reported a median of 3 out of nine psychometric properties. Most reported psychometric properties were construct validity (n = 32; 78% of studies), structural validity (n = 26; 63% of studies), and internal consistency (n = 25; 61% of studies). There was underreporting of content validity, cross-cultural validity, measurement error, and responsiveness. Psychometric data across tools were mostly indeterminate for construct validity, structural validity, and internal consistency. Conclusions There is limited evidence to fully support the use of a specific teacher proxy-report tool in practice. Further psychometric testing and detailed reporting of methodological aspects in future validity and reliability studies is needed. Tools have been designed to assess some elements of the framework. However, no comprehensive teacher proxy-report tool exists to assess all 30 elements of the APLF, demonstrating the need for a new tool. It is our recommendation that such tools be developed and psychometrically tested. Trial registration This systematic review was registered in the PROSPERO international prospective register of systematic reviews, with registration number CRD42019130936

Characteristics of transposable element exonization within human and mouse

Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.Comment: 11 pages, 4 figure

A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data

Motivation: Copy Number Variants (CNVs) are important genetic factors for studying human diseases. While high-throughput whole genome re-sequencing provides multiple lines of evidence for detecting CNVs, computational algorithms need to be tailored for different type or size of CNVs under different experimental designs. Results: To achieve optimal power and resolution of detecting CNVs at low depth of coverage, we implemented a Hidden Markov Model that integrates both depth of coverage and mate-pair relationship. The novelty of our algorithm is that we infer the likelihood of carrying a deletion jointly from multiple mate pairs in a region without the requirement of a single mate pairs being obvious outliers. By integrating all useful information in a comprehensive model, our method is able to detect medium-size deletions (200-2000bp) at low depth (<10× per sample). We applied the method to simulated data and demonstrate the power of detecting medium-size deletions is close to theoretical values. Availability: A program implemented in Java, Zinfandel, is available at http://www.cs.columbia.edu/~itsik/zinfandel

Widespread horizontal transfer of mitochondrial genes in flowering plants

Horizontal gene transfer - the exchange of genes across mating barriers - is recognized as a major force in bacterial evolution(1,2). However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes(3-5). Although the human genome was initially reported(6) to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted(7,8). Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements(9-12). Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62688/1/nature01743.pd

Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data

It is well known that Affymetrix microarrays are widely used to predict genome-wide gene expression and genome-wide genetic polymorphisms from RNA and genomic DNA hybridization experiments, respectively. It has recently been proposed to integrate the two predictions by use of RNA microarray data only. Although the ability to detect single feature polymorphisms (SFPs) from RNA microarray data has many practical implications for genome study in both sequenced and unsequenced species, it raises enormous challenges for statistical modelling and analysis of microarray gene expression data for this objective. Several methods are proposed to predict SFPs from the gene expression profile. However, their performance is highly vulnerable to differential expression of genes. The SFPs thus predicted are eventually a reflection of differentially expressed genes rather than genuine sequence polymorphisms. To address the problem, we developed a novel statistical method to separate the binding affinity between a transcript and its targeting probe and the parameter measuring transcript abundance from perfect-match hybridization values of Affymetrix gene expression data. We implemented a Bayesian approach to detect SFPs and to genotype a segregating population at the detected SFPs. Based on analysis of three Affymetrix microarray datasets, we demonstrated that the present method confers a significantly improved robustness and accuracy in detecting the SFPs that carry genuine sequence polymorphisms when compared to its rivals in the literature. The method developed in this paper will provide experimental genomicists with advanced analytical tools for appropriate and efficient analysis of their microarray experiments and biostatisticians with insightful interpretation of Affymetrix microarray data