Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy

A whole-genome scan was conducted to map quantitative trait loci (QTL) for BSE resistance or susceptibility. Cows from four half-sib families were included and 173 microsatellite markers were used to construct a 2835-cM (Kosambi) linkage map covering 29 autosomes and the pseudoautosomal region of the sex chromosome. Interval mapping by linear regression was applied and extended to a multiple-QTL analysis approach that used identified QTL on other chromosomes as cofactors to increase mapping power. In the multiple-QTL analysis, two genome-wide significant QTL (BTA17 and X/Y ps) and four genome-wide suggestive QTL (BTA1, 6, 13, and 19) were revealed. The QTL identified here using linkage analysis do not overlap with regions previously identified using TDT analysis. One factor that may explain the disparity between the results is that a more extensive data set was used in the present study. Furthermore, methodological differences between TDT and linkage analyses may affect the power of these approaches.

Power of QTL detection using association tests with family controls

The power of testing for a population-wide association between a biallelic quantitative trait locus and a linked biallelic marker locus is predicted both empirically and deterministically for several tests. The tests were based on the analysis of variance (ANOVA) and on a number of transmission disequilibrium tests (TDT). Deterministic power predictions made use of family information, and were functions of population parameters including linkage disequilibrium, allele frequencies, and recombination rate. Deterministic power predictions were very close to the empirical power from simulations in all scenarios considered in this study. The different TDTs had very similar power, intermediate between one-way and nested ANOVAs. One-way ANOVA was the only test that was not robust against spurious disequilibrium. Our general framework for predicting power deterministically can be used to predict power in other association tests. Deterministic power calculations are a powerful tool for researchers to plan and evaluate experiments and obviate the need for elaborate simulation studies.

Genome-wide search for markers associated with bovine spongiform encephalopathy

A genome-wide search for markers associated with BSE incidence was performed by using Transmission-Disequilibrium Tests (TDTs). Significant segregation distortion, i.e., unequal transmission probabilities of alleles within a locus, was found for three marker loci on Chromosomes (Chrs) 5, 10, and 20. Although TDTs are robust to false associations owing to hidden population substructures, it cannot distinguish segregation distortion caused by a true association between a marker and bovine spongiform encephalopathy (BSE) from a population-wide distortion. An interaction test and a segregation distortion analysis in half-sib controls were used to disentangle these two alternative hypotheses. None of the markers showed any significant interaction between allele transmission rates and disease status, and only the marker on Chr 10 showed a significant segregation distortion in control individuals. Nevertheless, the control group may have been a mixture of resistant and susceptible but unchallenged individuals. When new genotypes were generated in the vicinity of these three markers, evidence for an association with BSE was confirmed for the locus on Chr 5.

A vibrational spectroscopic study of philipsbornite PbAl3(AsO4)2(OH)5⋅H2O-molecular structural implications and relationship to the crandallite subgroup arsenates

The presence of arsenic in the environment is a hazard. The accumulation of arsenate by a range of cations in the formation of minerals provides a mechanism for the remediation of arsenate contamination. The formation of the crandallite group of minerals provides a mechanism for arsenate accumulation. Among the crandallite minerals are philipsbornite, arsenocrandallite and arsenogoyazite. Raman spectroscopy complimented with infrared spectroscopy has enabled aspects of the structure of philipsbornite to be studied. The Raman spectrum of philipsbornite displays an intense band at around 840 cm−1 attributed to the overlap of the symmetric and antisymmetric stretching modes. Raman bands observed at 325, 336, 347, 357, 376 and 399 cm−1 are assigned to the ν2 (AsO4)3− symmetric bending vibration (E) and to the ν4 bending vibration (F2). The observation of multiple bending modes supports the concept of a reduction in symmetry of the arsenate anion in philipsbornite. Evidence for phosphate in the mineral is provided. By using an empirical formula, hydrogen bond distances for the OH units in philipsbornite of 2.8648 Å, 2.7864 Å, 2.6896 Å cm−1 and 2.6220 were calculated.

A vibrational spectroscopic study of the phosphate mineral zanazziite - Ca2(MgFe2+)(MgFe2+Al)4Be4(PO4)6⋅6(H2O)

Zanazziite is the magnesium member of a complex beryllium calcium phosphate mineral group named roscherite. The studied samples were collected from the Ponte do Piauí mine, located in Itinga, Minas Gerais. The mineral was studied by electron microprobe, Raman and infrared spectroscopy. The chemical formula can be expressed as Ca2.00(Mg3.15,Fe0.78,Mn0.16,Zn0.01,Al0.26,Ca0.14)Be4.00(PO4)6.09(OH)4.00⋅5.69(H2O) and shows an intermediate member of the zanazziite–greinfeinstenite series, with predominance of zanazziite member. The molecular structure of the mineral zanazziite has been determined using a combination of Raman and infrared spectroscopy. A very intense Raman band at 970 cm−1 is assigned to the phosphate symmetric stretching mode whilst the Raman bands at 1007, 1047, 1064 and 1096 cm−1 are attributed to the phosphate antisymmetric stretching mode. The infrared spectrum is broad and the antisymmetric stretching bands are prominent. Raman bands at 559, 568, 589 cm−1 are assigned to the ν4 out of plane bending modes of the PO4 and HPO4 units. The observation of multiple bands supports the concept that the symmetry of the phosphate unit in the zanazziite structure is reduced in symmetry. Raman bands at 3437 and 3447 cm−1 are attributed to the OH stretching vibrations; Raman bands at 3098 and 3256 are attributed to water stretching vibrations. The width and complexity of the infrared spectral profile in contrast to the well resolved Raman spectra, proves that the pegmatitic phosphates are better studied with Raman spectroscopy.

The molecular structure of matioliite – NaMgAl5(PO4)4(OH)6·2(H2O) : a pegmatite mineral from Minas Gerais, Brazil

Detailed spectroscopic and chemical investigation of matioliite, including infrared and Raman spectroscopy, scanning electron microscopy and electron probe microanalysis has been carried out on homogeneous samples from the Gentil pegmatite, Mendes Pimentel, Minas Gerais, Brazil. The chemical composition is (wt.%): FeO 2.20, CaO 0.05, Na2O 1.28, MnO 0.06, Al2O3 39.82, P2O5 42.7, MgO 4.68, F 0.02 and H2O 9.19; total 100.00. The mineral crystallize in the monoclinic crystal system, C2/c space group, with a = 25.075(1) Å, b = 5.0470(3) Å, c = 13.4370(7) Å, β = 110.97(3)°, V = 1587.9(4) Å3, Z = 4. Raman spectroscopy coupled with infrared spectroscopy supports the concept of phosphate, hydrogen phosphate and dihydrogen phosphate units in the structure of matioliite. Infrared and Raman bands attributed to water and hydroxyl stretching modes are identified. Vibrational spectroscopy adds useful information to the molecular structure of matioliite.

Developing intercultural competence in pre-service teachers from Australia and Malaysia : insights from the “Patches” programme

Developing intercultural competence in pre-service teachers from Australia and Malaysia: Insights from a Patches program. Innovative pedagogies can offer pre-service teachers the opportunity to develop their intercultural competence and take up more globalised viewpoints. One such innovation is the Patches program which brought together Malaysian and Australian pre-service teachers who were studying at the same university in Brisbane, Australia, to actively explore issues of cultural and linguistic difference. The participants were 14 Australian fourth-year pre-service teachers who were enrolled in a program on inclusive education, and 58 Malaysian pre-service teachers who had recently arrived at the university in Brisbane to commence their second year of an international education program. In peer groupings, these domestic and international pre-service teachers engaged in a series of interactive tasks and reflective writing workshops exploring intercultural experiences, over a period of ten weeks. Each element or ‘patch’ in the program was designed to build up into a mosaic of intercultural learning. The flexible structuring of the Patches Program provided a supportive framework for participant interaction whilst allowing the groups to decide for themselves the nature and extent of their involvement in a series of community-related tasks. The process of negotiating and implementing these activities formed the basis for establishing meaningful relationships between the participants. The development of the participants’ intercultural competence is traced through their reflective narratives and focus group discussions, drawing on Byram’s concept of the five savoirs. Explaining aspects of Australian culture to their newly arrived Malaysian peers, allowed the Australian pre-service teachers to take a perspective of outsideness towards their own familiar social practices. In addition, being unusually positioned as the linguistic other amongst a group of Bahasa Melayu speakers, highlighted for the Australian pre-service teachers the importance of being inclusive. For the Malaysian pre-service teachers, participation in the Patches program helped to extend intercultural understandings, establish social networks with local students, and build a sense of community in their new learning environment. Both groups of pre-service teachers noted the power of “learning directly by interacting rather than through books”. In addition to interacting interculturally, the process of reflecting on these intercultural experiences is seen as integral to the development of intercultural competence.

Transnational field experience : making the familiar strange

This study explores the impact of field experience in Australian primary classrooms on the developing professional identities of Malaysian pre-service teachers. This group of 24 Malaysian students are undertaking their Bachelor of Education in Teaching English as a Foreign Language (BEd TESL) at an Australian university, as part of a transnational twinning program. The globalisation of education has seen an increase in such transnational school experiences for pre-service teachers, with the aim of extending professional experience and intercultural competence by engaging in communities of practice beyond the local (Tsui 2005, Luke 2004). Despite overseas governments, such as Malaysia, having sponsored multimillion dollar twinning programs for their pre-service teachers, there is a lack of research regarding the outcomes of transnational professional practice within such programs. This study adopts a qualitative approach focusing on participants’ narratives as revealed in their reflective writing and through semi-structured interviews. Adopting a Bakhtinian framework, this research uses the concept of ‘voice’ to explore how pre-service teachers negotiate their identities as EFL teachers in response to their lived professional experiences (Bakhtin 1981, 1986). Encountering different cultural and educational practices in their transnational field experiences can lead pre-service teachers to question taken-for-granted practices that they have grown up with. This has been described as a process of making the familiar strange, and can lead to a shift in professional understandings. This study investigates how such questioning occurs and how the transnational field experience is perceived by the participants as contributing to their developing professional identities.

Parent and adolescent perceptions of family functioning : a comparison of clinic and non-clinic families

In this paper two studies are reported which compare (a) the perceptions of family functioning held by clinic and non-clinic adolescents, and (b) the perceptions of family functioning held by adolescents and their mothers in clinic and non-clinic families. In Study 1, matched group of clinic and non-clinic adolescents were compared on their responses to a 30-item scale (ICPS) designed to measure three factors of family functioning: Intimacy (high vs. low), Parenting Style (democratic vs. controlled) and Conflict (high vs. low). Clinic and non-clinic adolescents were also compared on their responses to a multi-dimensional measure of adolescent self-concept. Although there was little difference between the two groups of adolescents in terms of their perceptions of family functioning, there were strong relationships between the self-concept variables and the family functioning variables. In Study 2, comparisons were made between the perceptions of family functioning held by mothers and adolescents for both clinical and non-clinic families. There were no differences between the two groups of adolescents in terms of their perceptions of family functioning, although there were clear differences between the two groups of mothers. In addition, clinic adolescents and their mothers did not differ in their perceptions of the family, whereas adolescents in the non-clinic group saw their families significantly as less intimate and more conflicted than did their mothers.

An evaluation of corpus-driven measures of medical concept similarity for information retrieval

Measures of semantic similarity between medical concepts are central to a number of techniques in medical informatics, including query expansion in medical information retrieval. Previous work has mainly considered thesaurus-based path measures of semantic similarity and has not compared different corpus-driven approaches in depth. We evaluate the effectiveness of eight common corpus-driven measures in capturing semantic relatedness and compare these against human judged concept pairs assessed by medical professionals. Our results show that certain corpus-driven measures correlate strongly (approx 0.8) with human judgements. An important finding is that performance was significantly affected by the choice of corpus used in priming the measure, i.e., used as evidence from which corpus-driven similarities are drawn. This paper provides guidelines for the implementation of semantic similarity measures for medical informatics and concludes with implications for medical information retrieval.

From movie screens to moving screens : mapping qualities of new urban interactions

Next generation screens of diverse dimensions such as the Pebble e-paper watch, Google’s Project Glass, Microsoft’s Kinect and IllumiRoom, and large-scale multi-touch screen surface areas, increasingly saturate and diversify the urban mediascape. This paper seeks to contribute to media architecture and interaction design theory by starting to critically examine how these different screen formats are creating a ubiquitous screen mediascape across the city. We introduce next generation personal, domestic, and public screens. The paper critically challenges conventional dichotomies such as local / global, online / offline, private / public, large / small, mobile / static, that have been created in the past to describe some of the qualities and characteristics of interfaces and their usage. More and more scholars recognise that the black and white nature of these dichotomies does not adequately represent the fluid and agile capabilities of many new screen interfaces. With this paper, we hope to illustrate the more nuanced ‘trans-scalar’ qualities of these new urban interactions, that is, ways in which they provide a range functionality, without being locked into either end of a scale.

Use of concept maps in reforming teaching Family and Consumer Sciences in Kuwait

This paper addresses the professional development of Kuwaiti teachers in the use of concept maps to teach Family and Consumer Science. A key aim of the study was to evaluate the degree to which the use of concept maps would influence the way Kuwaiti teachers approach and teach Family and Consumer Studies (FCS) subjects and the degree to which concept maps empower students to critically identify and express their knowledge of the subject being taught. A case study methodology was adopted to follow the implementation of lessons using concept maps by four teachers of middle years. An analysis of the data revealed the positive impact that student-centred teaching tools can have on the reformation of traditional teaching environments. For all teachers, the primary strengths of using concept maps were the ability to generate student interest, to motivate student participation and to enhance student understanding of content. Although a case study design may limit the generalisation and comparative value of the study, the findings of this study remain important to the planning of future professional development programs and the use of concept maps within Kuwait’s FCS curriculum area.

The enactment of formative assessment in English language classrooms in two Chinese universities : teacher and student responses

The College English Curriculum Requirements (CECR), announced by the Chinese Ministry of Education in 2007, recommended the inclusion of formative assessment into the existing summative assessment framework of College English. This policy had the potential to fundamentally change the nature of assessment and its role in the teaching and learning of English in Chinese universities. In order to document and analyse these changes, case studies involving English language teachers and learners were undertaken in two Chinese Universities: one a Key university in the national capital; the other a non-Key university in a western province. The case study design incorporated classroom observations and interviews with English language teachers and their students. The type and focus of feedback and the engagement of students in assessment were analysed in the two contexts. Fundamental to the analysis was the concept of enactment, with the focus of this study on the ways that policy ideas and principles were enacted in the practices of the Chinese university classroom. Understandings of formative assessment as applied in contexts other than the predominantly Western, Anglophone contexts from where many of its principles derive, are offered.

Which cultural values matter to business process management? Results from a global Delphi study

Purpose – Business process management (BPM) requires a holistic perspective that includes managing the culture of an organization to achieve objectives of efficient and effective business processes. Still, the specifics of a BPM-supportive organizational culture have not been examined so far. Thus, the purpose of this paper is to identify the characteristics of a cultural setting supportive of BPM objectives. Design/methodology/approach – The paper examines the constituent values of a BPM-supportive cultural setting through a global Delphi study with BPM experts from academia and practice and explore these values in a cultural value framework. Findings – The paper empirically identifies and defines four key cultural values supporting BPM, viz., customer orientation, excellence, responsibility, and teamwork. The paper discusses the relationships between these values and identifies a particular challenge in managing these seemingly competing values. Research limitations/implications – The identification and definition of these values represents a first step towards the operationalization (and empirical analysis) of what has been identified as the concept of BPM culture, i.e. a culture supportive of achieving BPM objectives. Practical implications – Identifying these cultural values provides the basis for developing an instrument that can measure how far an existing cultural context is supportive of BPM. This, in turn, is fundamental for identifying measures towards achieving a BPM culture as a necessary, yet not sufficient means to obtain BPM success. Originality/value – The paper examines which cultural values create an environment receptive for BPM and, thus, specifies the important theoretical construct BPM culture. In addition, the paper raises awareness for realizing these values in a BPM context.