Some comparison on whole-proteome phylogeny of large dsDNA viruses based on dynamical language approach and feature frequency profiles method

There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among them, CVTree method, feature frequency profiles method and dynamical language approach were used to investigate the whole-proteome phylogeny of large dsDNA viruses. Using the data set of large dsDNA viruses from Gao and Qi (BMC Evol. Biol. 2007), the phylogenetic results based on the CVTree method and the dynamical language approach were compared in Yu et al. (BMC Evol. Biol. 2010). In this paper, we first apply dynamical language approach to the data set of large dsDNA viruses from Wu et al. (Proc. Natl. Acad. Sci. USA 2009) and compare our phylogenetic results with those based on the feature frequency profiles method. Then we construct the whole-proteome phylogeny of the larger dataset combining the above two data sets. According to the report of The International Committee on the Taxonomy of Viruses (ICTV), the trees from our analyses are in good agreement to the latest classification of large dsDNA viruses.

A high performance liquid chromatography and electrospray ionization mass spectrometry method for the analysis of the natural medicine, Forsythia suspensa

Samples of Forsythia suspensa from raw (Laoqiao) and ripe (Qingqiao) fruit were analyzed with the use of HPLC-DAD and the EIS-MS techniques. Seventeen peaks were detected, and of these, twelve were identified. Most were related to the glucopyranoside molecular fragment. Samples collected from three geographical areas (Shanxi, Henan and Shandong Provinces), were discriminated with the use of hierarchical clustering analysis (HCA), discriminant analysis (DA), and principal component analysis (PCA) models, but only PCA was able to provide further information about the relationships between objects and loadings; eight peaks were related to the provinces of sample origin. The supervised classification models-K-nearest neighbor (KNN), least squares support vector machines (LS-SVM), and counter propagation artificial neural network (CP-ANN) methods, indicated successful classification but KNN produced 100% classification rate. Thus, the fruit were discriminated on the basis of their places of origin.

Fully validated LC–MS/MS method for quantification of homocysteine concentrations in samples of human serum : a new approach

Reported homocysteine (HCY) concentrations in human serum show poor concordance amongst laboratories due to endogenous HCY in the matrices used for assay calibrators and QCs. Hence, we have developed a fully validated LC–MS/MS method for measurement of HCY concentrations in human serum samples that addresses this issue by minimising matrix effects. We used small volumes (20 μL) of 2% Bovine Serum Albumin (BSA) as surrogate matrix for making calibrators and QCs with concentrations adjusted for the endogenous HCY concentration in the surrogate matrix using the method of standard additions. To aliquots (20 μL) of human serum samples, calibrators or QCs, were added HCY-d4 (internal standard) and tris-(2-carboxyethyl) phosphine hydrochloride (TCEP) as reducing agent. After protein precipitation, diluted supernatants were injected into the LC–MS/MS. Calibration curves were linear; QCs were accurate (5.6% deviation from nominal), precise (CV% ≤ 9.6%), stable for four freeze–thaw cycles, and when stored at room temperature for 5 h or at −80 °C (27 days). Recoveries from QCs in surrogate matrix or pooled human serum were 91.9 and 95.9%, respectively. There was no matrix effect using 6 different individual serum samples including one that was haemolysed. Our LC–MS/MS method has satisfied all of the validation criteria of the 2012 EMA guideline.

The impact of socialisation on graduates’ public service motivation : a mixed method study

The need to attract and retain a high calibre cadre of public servants today has resulted in a renaissance of interest in public service motivation (PSM) within public management literature. This article outlines a study of PSM with graduate employees within an Australian public sector. The study extends our understanding of PSM by adopting a longitudinal, mixed method design, including surveys and individual interviews, to consider the effects of socialisation on levels of PSM. Results show an organisation's mission and values do not affect individual PSM while work type and communication style is vital and organisational socialisation can provide a negative influence.

Doing whitefella research in blackfella communities in Australia : decolonizing method in sports related research

There is much for non-Indigenous researchers to consider when researching in Indigenous contexts. This paper is a story of discovery for two researchers working on a project with the Indigenous Sports Program section of the Australian Sports Commission. It documents the slow, meticulous and sometimes clumsy steps taken to gain access to communities and conduct research guided by a social justice ethic. The research was successful in that eventually it was possible to develop the trust of individuals and some of the Indigenous communities more broadly, so that information could be gathered and given within the context of shared understandings and mutual interest. However, it is the turbulent journey, filled as it is, with latent tendencies, privileged assumptions and eventually reflexive readings of the data, which remains the focus of this paper. Tentative recommendations are offered to those wishing to advance this politically and epistemologically challenging approach to culturally based research

Moving forwards with the aim of going backwards fast : high performance rowing as a learning environment

Background and Purpose: - This paper focuses on the learning culture within the high performance levels of rowing. In doing so, we explore the case of an individual’s learning as he moves across athletic, coaching and administrative functions. This exploration draws on a cultural learning framework and complementary theorisings related to reflexivity. Method - This study makes use of an intellectually, morally and collaboratively challenging approach whereby one member of the research team was also the sole participant of this study. The participant’s careers as a high performance athlete, coach and administrator, coupled with his experience in conducting empirical research presented a rare opportunity to engage in collaborative research (involving degrees of insider and outsider status for each of the research team). We acknowledge that others have looked to combine roles of coach / athlete / administrator with that of researcher however few (if any) have attempted to combine them all in one project. Moreover, coupled with the approach to reflexivity adopted in this study and the authorship contributions we consider this scholarly direction uncommon. Data were comprised of recorded research conversations, a subsequently constructed learning narrative, reflections on the narrative, a stimulated reflective piece from the participant, and a final (re)construction of the participant’s story. Accordingly, data were integrated through an iterative process of thematic analysis. Results - The cultural (i.e., the ways things get done) and structural (e.g., the rules and regulations) properties of high performance rowing were found to shape both the opportunities to be present (e.g., secure a place in the crew) and to learn (e.g., learn the skills required to perform at an Olympic level). However, the individual’s personal properties were brought to bear on re-shaping the constraints such that many limitations could be overcome. In keeping with the theory of learning cultures, the culture of rowing was found to position individuals (a coxswain in this case) differentially. In a similar manner, a range of structural features was found to be important in shaping the cultural and personal elements in performance contexts. For example, the ‘field of play’ was found to be important as a structural feature (i.e., inability of coach to communicate with athletes) in shaping the cultural and personal elements of learning in competition (e.g., positioning the coxswain as an in-boat coach and trusted crewmate). Finally, the cultural and structural elements in rowing appeared to be activated by the participant’s personal elements, most notably his orientation towards quality performance. Conclusion - The participant in this study was found to be driven by the project that he cares about most and at each turn he has bent his understanding of his sport back on itself to see if he can find opportunities to learn and subsequently explore ways to improve performance. The story here emphasises the importance of learner agency, and this is an aspect that has often been missing in recent theorising about learning. In this study, we find an agent using his ‘personal emergent powers to activate the resources in the culture and structure of his sport in an attempt to improve performance. We conclude from this account that this particular high performance rowing culture is one that provided support but nonetheless encouraged those involved, to ‘figure things out’ for themselves – be it as athletes, coaches and/or administrators.

Practice as Method : The Ex/centric Fixations Project

In this chapter, I consider the efficacy of creative practice as a research method, concentrating specifically on its applications in the performing arts, using one of my own recent projects, The Ex/centric Fixations Project (2009), as an example.