Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Background Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study. Results In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics. Conclusions CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.

Integrating Intangible Cultural Heritage elements and learning strategy : a case study

Tanzania has a rich and diverse cultural history based on community cultural life. However, at present, young people have limited opportunity to exploit this richness of creative expressions and engage in creative jobs as their future career. Hence, the significant challenge remains: how to integrate Intangible cultural heritage elements and learning strategy as a means of promoting creative jobs for youth. This paper presents a case study on 'Strategies for youth employment in Tanzania: A creative industries approach'. The case study employed mixed methods incorporating questionnaires, interviews and focus groups and was held in Dar-Es-Salaam, Mwanza, Dodoma, Lindi and Morogoro from July to October, 2012. This paper discusses some of the issues and argues that there is no virtual utilization of the intangible cultural heritage knowledge and skills in 'putting education to work' (UNESCO, 2012) for the better prospects of youth. Although the discussion is specific to Tanzania, the case may also apply to other developing countries.

A framework to better understand emotional experiences with portable interactive devices : preliminary trial

Two longitudinal experiments were conducted exploring emotional experiences with PIDs over six months including media and medial Portable Interactive Devices (PIDs). Results identifying the impact of negative social and personal interactions on the overall emotional experience as well as different task categories (Features, Functional, Mediation and Auxiliary) and their corresponding emotional responses have previously been reported [2,3,4,5]. This paper builds on these findings and presents the Designing for Evolving Emotional Experience (DE3) framework promoting positive (and deals with negative) emotional experiences with PIDs including a set of principles to better understand emotional experiences. To validate the DE3 framework a preliminary trial was conducted with five practicing industrial designers. The trial required them to consider initial design concepts using the DE3 framework followed by a questionnaire asking about their use of the framework for concept development. The trial aimed to analyse the effectiveness, efficiency and usefulness of the framework in assisting in the development of initial concepts for PIDs taking into account emotional experiences. Common themes regarding the framework are outlined including the ease of use, the effectiveness in focusing on the personal and social contexts and positive ratings regarding its use. Overall the feedback from the preliminary trial was encouraging with responses suggesting that the framework was accessible, rated highly and most importantly permitted designers to consider emotional experiences during concept development. The paper concludes with a discussion regarding the future development of the DE3 framework and the potential implications to design theory and the design discipline.

Reconstructing places and spaces in blended work integrated learning

This paper considers the emergence and ongoing development of an embedded, studentnegotiated work placement model of Work Integrated Learning (WIL) in the engineering and built environment disciplines at an Australian metropolitan university. The characteristics of the model and a continuous improvement strategy are provided. The model is characterised by large student cohorts independently sourcing and negotiating relevant work placements and completing at least one, mandatory credit-bearing WIL unit. Through ongoing analyses and evaluation of the model more experiential and collaborative learning approaches have been adopted. This has included the creation of blended learning spaces using technology. The paper focuses on the five year journey travelled by the teaching team as they embarked on ways to improve curriculum, pedagogy, administrative processes and assessment - effectively relocating much of their interaction with students online. The insights derived from this rich, single case study should be of interest to others considering alternative ways of responding to increasing student enrolments in WIL and the impact of blended learning in this context.

Converse consumption : the converse blank canvas project

Research background For almost 80 years the Chuck Taylor (or Chuck T's) All Star basketball shoe has been an iconic item of fashion apparel. The Chuck T's were first designed in 1921 by Converse, an American shoe company and over the decades they became a popular item not purely for sports and athletic purposes but rather evolved into the shoe of choice for many subcultural groups as a fashion item. In some circles the Chuck Taylor is still seen as the "coolest" sneaker of all time - one which will never go out of fashion regardless of changing trends. With over 600 millions pairs sold all over the world since its release, the Converse shoe is representative of not only a fashion culture - but also of a consumption culture - that evolved as the driving force behind the massive growth of the Western economic system during the 20th Century. Artisan Gallery (Brisbane), in conjunction with the exhibition Reboot: Function, Fashion and the Sneaker, a history of the sneaker, selected 20 designers to customise and re-design the classic Converse Chuck Taylor All Stars shoe and in doing so highlighted the diversity of forms possible for creative outcomes. As Artisan Gallery Curator Kirsten Fitzpatrick states “We were expecting people to draw and paint on them. Instead, we had shoes... mounted as trophies.." referring to the presentation of "Converse Consumption". The exhibition ran from 21 June – 16 August 2012: Research question The Chuck T’s is one of many overwhelmingly commercially successful designs of the last century. Nowadays we are faced with the significant problems of overconsumption and the stress this causes on the natural ecosystem; and on people as a result. As an active member of the industrial design fraternity – a discipline that sits at the core of this problem - how can I use this opportunity to comment on the significant issue of consumption? An effective way to do this was to associate consumption of goods with consumption of sugar. There are significant similarities between our ceaseless desires to consume products and our fervent need to consume indulgent sweet foods. Artisan Statement Delicious, scrumptious, delectable... your pupils dilate, your blood pressure spikes, your liver goes into overdrive. Immediately, your brain cuts off the adenosine receptors, preventing drowsiness. Your body increases dopamine production, in-turn stimulating the pleasure receptors in your brain. Your body absorbs all the sweetness and turns it into fat – while all the nutrients that you actually require are starting to be destroyed, about to be expelled. And this is only after one bite! After some time though, your body comes crashing back to earth. You become irritable and begin to feel sluggish. Your eyelids seem heavy while your breathing pattern changes. Your body has consumed all the energy and destroyed all available nutrients. You literally begin to shut down. These are the physiological effects of sugar consumption. A perfect analogy for our modern day consumer driven world. Enjoy your dessert! Research contribution “Converse Consumption” contributes to the conversation regarding over-consumption by compelling people to reflect on their consumption behaviour through the reconceptualising of the deconstructed Chuck T’s in an attractive edible form. By doing so the viewer has to deal with the desire to consume the indulgent looking dessert with the contradictory fact that it is comprised of a pair of shoes. The fact that the shoes are Chuck T’s make the effect even more powerful due to their iconic status. These clashing motivations are what make “Converse Consumption” a bizarre yet memorable experience. Significance The exhibition was viewed by an excess of 1000 people and generated exceptional media coverage and public exposure/impact. As Artisan Gallery Curator Kirsten Fitzpatrick states “20 of Brisbane's best designers were given the opportunity to customise their own Converse Sneakers, with The Converse Blank Canvas Project.” And to be selected in this category demonstrates the calibre of importance for design prominence.

Meta-analysis of individual patient data from randomized trials of chemotherapy plus cetuximab as first-line treatment for advanced non-small cell lung cancer

OBJECTIVES: Four randomized phase II/III trials investigated the addition of cetuximab to platinum-based, first-line chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). A meta-analysis was performed to examine the benefit/risk ratio for the addition of cetuximab to chemotherapy. MATERIALS AND METHODS: The meta-analysis included individual patient efficacy data from 2018 patients and individual patient safety data from 1970 patients comprising respectively the combined intention-to-treat and safety populations of the four trials. The effect of adding cetuximab to chemotherapy was measured by hazard ratios (HRs) obtained using a Cox proportional hazards model and odds ratios calculated by logistic regression. Survival rates at 1 year were calculated. All applied models were stratified by trial. Tests on heterogeneity of treatment effects across the trials and sensitivity analyses were performed for all endpoints. RESULTS: The meta-analysis demonstrated that the addition of cetuximab to chemotherapy significantly improved overall survival (HR 0.88, p=0.009, median 10.3 vs 9.4 months), progression-free survival (HR 0.90, p=0.045, median 4.7 vs 4.5 months) and response (odds ratio 1.46, p<0.001, overall response rate 32.2% vs 24.4%) compared with chemotherapy alone. The safety profile of chemotherapy plus cetuximab in the meta-analysis population was confirmed as manageable. Neither trials nor patient subgroups defined by key baseline characteristics showed significant heterogeneity for any endpoint. CONCLUSION: The addition of cetuximab to platinum-based, first-line chemotherapy for advanced NSCLC significantly improved outcome for all efficacy endpoints with an acceptable safety profile, indicating a favorable benefit/risk ratio.

A participatory framework for researching and evaluating communication for development and social change

The growing dominance of project planning cycles and results-based management in development over the past 20 years has significant implications for the effective evaluation of communication for development and social change and the sustainability of these processes. These approaches to development and evaluation usually give priority to the linear, logical framework (or log frame) approach promoted by many development institutions. This tends to emphasize upward accountability approaches to development and its evaluation, so that development is driven by exogenous rather than endogenous models of development and social change. Such approaches are underpinned by ideas of preplanning, and predetermination of what successful out -comes look like. In this way, outcomes of complex interventions tend to be reduced to simple, cause-effect processes and the categorization of things, including people (Chambers and Pettit 2004; Eyben 2011). This runs counter to communication for development approaches, which prioritize engagement, relationships, empowerment and dialogue as important components for positive social change.

Beyond BIM: It’s not the end of the road!

Over several decades, academics around the world have investigated the necessary tools, techniques, and conditions which would allow BIM (building information modeling) to become a positive force in the world of construction. As the research results matured, BIM started to become commercially available. Researchers and many in industry soon realized that BIM, as a technological innovation, was, in and of itself, not the end point in the journey. The technical adoption of BIM has to be supported by process and culture change within organizations to make a real impact on a project (for example, see AECbytes Viewpoint #35 by Chuck Eastman, Paul Teicholz, Rafael Sacks and Kathleen Liston). Current academic research aims to understand the steps beyond BIM, which will help chart the future of our industry over the coming decades. This article describes an international research effort in this area, coordinated by the Integrated Design and Delivery Solutions (IDDS) initiative of the CIB (International Council for Research and Innovation in Building and Construction). We hope that it responds to and extends the discussion initiated by Brian Lighthart in AECbytes Viewpoint #56, which asked about who is charting future BIM directions.

The Interaction of lean and building information modeling in construction

Lean construction and building information modeling (BIM) are quite different initiatives, but both are having profound impacts on the construction industry. A rigorous analysis of the myriad specific interactions between them indicates that a synergy exists which, if properly understood in theoretical terms, can be exploited to improve construction processes beyond the degree to which it might be improved by application of either of these paradigms independently. Using a matrix that juxtaposes BIM functionalities with prescriptive lean construction principles, 56 interactions have been identified, all but four of which represent constructive interaction. Although evidence for the majority of these has been found, the matrix is not considered complete but rather a framework for research to explore the degree of validity of the interactions. Construction executives, managers, designers, and developers of information technology systems for construction can also benefit from the framework as an aid to recognizing the potential synergies when planning their lean and BIM adoption strategies.

Analysis framework for the interaction between lean construction and building information modelling

Building with Building Information Modelling (BIM) changes design and production processes. But can BIM be used to support process changes designed according to lean production and lean construction principles? To begin to answer this question we provide a conceptual analysis of the interaction of lean construction and BIM for improving construction. This was investigated by compiling a detailed listing of lean construction principles and BIM functionalities which are relevant from this perspective. These were drawn from a detailed literature survey. A research framework for analysis of the interaction between lean and BIM was then compiled. The goal of the framework is to both guide and stimulate research; as such, the approach adopted up to this point is constructive. Ongoing research has identified 55 such interactions, the majority of which show positive synergy between the two.

Autonomy in technology design

Issues of autonomy impact motivation, the user experience and even psychological wellbeing, yet many questions surrounding design for autonomy remain unanswered. This workshop will explore theory, issues and design strategies related to autonomy drawing on theoretical frameworks available in psychology and looking at autonomy from multiple levels. These include user autonomy within the context of software environments, technologies that increase autonomy in daily life, and how technologies might foster autonomy as a component of psychological development.

The type I collagen induction of MT1-MMP-mediated MMP-2 activation is repressed by αVβ3 integrin in human breast cancer cells

The influence of αVβ3 integrin on MT1-MMP functionality was studied in human breast cancer cells of differing β3 integrin status. Overexpression of β3 integrin caused increased cell surface expression of αV integrin and increased cellular adhesion to extracellular matrix (ECM) substrates in BT-549, MDA-MB-231 and MCF-7 cells. β3 integrin expression also enhanced the migration of breast cancer cells on ECM substrates and enhanced collagen gel contraction. In vivo, αVβ3 cooperated with MT1-MMP to increase the growth of MCF-7 cells after orthotopic inoculation in immunocompromised mice, but had no influence on in vitro proliferation. Despite these stimulatory effects, overexpression of β3 integrin suppressed the type I collagen (Col I) induced MMP-2 activation in all breast cancer cell lines analyzed. This was also evident in extracts from the MCF-7 tumors in vivo, where MMP-2 activation was stimulated by MT1-MMP transfection, but attenuated with β3 integrin expression. Although our studies confirm important biological effects of αVβ3 integrin on enhancing cell adhesion and migration, ECM remodeling and tumor growth, β3 integrin caused reduced MMP-2 activation in response to Col I in vitro, which appears to be physiologically relevant, as it was also seen in tumor xenografts in vivo. The reduction of MMP-2 activation (and thus MT1-MMP activity) by αVβ3 in response to Col I may be important in scenarios where cells which are activated for matrix degradation need to preserve some pericellular collagen, perhaps as a substrate for cell adhesion and migration, thus maintaining a balanced level of proteolysis required for efficient tumor growth.

Beyond Wearables : Experiences and Trends in Design of Portable Medical Devices

The use of Portable Medical Devices (PMDs) has become increasingly widespread over the last few years. A combination of factors; including advances in technology, the pressure to reduce public health costs and the desire to make health solutions accessible to a wider patient base are contributing to the growth in the PMD market. Design has a clear role to play in the current and future context of the PMD landscape. In this paper, we identify emerging trends in the design of PMDs; including changes in the form, purpose and mode of use, and explore how these trends are likely to fundamentally impact the nature of healthcare and the patient experience from an experience design perspective. We conclude by identifying a research opportunity for design within the healthcare and PMD context.

The influence of atmospheric conditions on the leakage current of ceramic insulators on the Colombian Caribbean coast

The contamination of electrical insulators is one of the major contributors to the risk of operation outages in electrical substations, especially in coastal zones with high salinity levels and atmospheric pollution. By using the measurement of leakage-currents, which is one of the main indicators of contamination in insulators, this work seeks to the determine the correlation with climatic variables, such as ambient temperature, relative humidity, solar irradiance, atmospheric pressure, and wind speed and direction. The results obtained provide an input to the behaviour of the leakage current under atmospheric conditions that are particular to the Caribbean coast of Colombia. Spearman’s rank correlation coefficients and principal component analysis are utilised to determine the significant relationships among the different variables under consideration. The necessary information for the study was obtained via historical databases of both atmospheric variables and the leakage current measured in over a period of one year in a 220-kV potential transformer insulator. We identified the influencing factors of temperature, humidity, radiation, wind speed and direction on the magnitude of the leakage current as the most relevant.