Mining SOM expression portraits: Feature selection and integrating concepts of molecular function

Background: 
Self organizing maps (SOM) enable the straightforward portraying of high-dimensional data of large sample collections in terms of sample-specific images. The analysis of their texture provides so-called spot-clusters of co-expressed genes which require subsequent significance filtering and functional interpretation. We address feature selection in terms of the gene ranking problem and the interpretation of the obtained spot-related lists using concepts of molecular function.

Results: 
Different expression scores based either on simple fold change-measures or on regularized Students t-statistics are applied to spot-related gene lists and compared with special emphasis on the error characteristics of microarray expression data. The spot-clusters are analyzed using different methods of gene set enrichment analysis with the focus on overexpression and/or overrepresentation of predefined sets of genes. Metagene-related overrepresentation of selected gene sets was mapped into the SOM images to assign gene function to different regions. Alternatively we estimated set-related overexpression profiles over all samples studied using a gene set enrichment score. It was also applied to the spot-clusters to generate lists of enriched gene sets. We used the tissue body index data set, a collection of expression data of human tissues, as an illustrative example. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. In addition, we display special sets of housekeeping and of consistently weak and highly expressed genes using SOM data filtering. 

Conclusions:
The presented methods allow the comprehensive downstream analysis of SOM-transformed expression data in terms of cluster-related gene lists and enriched gene sets for functional interpretation. SOM clustering implies the ability to define either new gene sets using selected SOM spots or to verify and/or to amend existing ones

Model-based groupware solution for distributed real-time collaborative 4D planning via teamwork

Construction planning plays a fundamental role in construction project management that requires team working among planners from a diverse range of disciplines and in geographically dispersed working situations. Model-based four-dimensional (4D) computer-aided design (CAD) groupware, though considered a possible approach to supporting collaborative planning, is still short of effective collaborative mechanisms for teamwork due to methodological, technological and social challenges. Targeting this problem, this paper proposes a model-based groupware solution to enable a group of multidisciplinary planners to perform real-time collaborative 4D planning across the Internet. In the light of the interactive definition method, and its computer-supported collaborative work (CSCW) design analysis, the paper discusses the realization of interactive collaborative mechanisms from software architecture, application mode, and data exchange protocol. These mechanisms have been integrated into a groupware solution, which was validated by a planning team in a truly geographically dispersed condition. Analysis of the validation results revealed that the proposed solution is feasible for real-time collaborative 4D planning to gain a robust construction plan through collaborative teamwork. The realization of this solution triggers further considerations about its enhancement for wider groupware applications

Towards a teacher-centric approach for multi-touch surfaces in classrooms

The potential of tabletops to enable simultaneous interaction and face-to-face collaboration can provide novel learning opportunities. Despite significant research in the area of collaborative learning around tabletops, little attention has been paid to the integration of multi-touch surfaces into classroom layouts and how to employ this technology to facilitate teacher-learner dialogue and teacher-led activities across multi-touch surfaces. While most existing techniques focus on the collaboration between learners, this work aims to gain a better understanding of practical challenges that need to be considered when integrating multi-touch surfaces into classrooms. It presents a multi-touch interaction technique, called TablePortal, which enables teachers to manage and monitor collaborative learning on students' tables. Early observations of using the proposed technique within a novel classroom consisting of networked

A qualitative study of active participation in sport and exercise for individuals with multiple sclerosis

Objective: The aim of this study was to explore the experience of participation in sport and exercise for individuals with multiple sclerosis (MS) with minimal disability. The objectives were to gain an understanding of key factors that influence participation in sport and exercise and to determine support required by individuals with MS to participate in their choice of sport and exercise for as long as possible. Methods: A qualitative, descriptive study utilizing three focus groups was conducted. Data were analysed thematically aided by NVivo software. Participants were individuals with MS who had an Expanded Disability Status Scale score of 0–4, indicating full ambulation. All participants were living in northern Queensland, Australia. Results Sixteen individuals participated; 63% of whom regularly participated in sport or exercise. All participants viewed sport and exercise positively and identified inherent benefits of exercise. Five key themes emerged to describe the experience of participating in sport and exercise: “personally engaging with exercise,” “influencing barriers and enablers of exercise,” “sustaining independence,” “integrating exercise into lifestyle,” and “getting the balance right.” Most participants felt that advice and guidance from health professionals about the optimum mode and dose (how much and how often) of exercise was lacking. Conclusions: Participation in sport and exercise was valued by individuals with MS with minimal disability for sustaining independence and an active lifestyle. Personalized exercise advice from health professionals was the key support identified by participants to assist them to maintain an active lifestyle for as long as possible

Global morphogenetic flow is accurately predicted by the spatial distribution of myosin motors.

During embryogenesis tissue layers undergo morphogenetic flow rearranging and folding into specific shapes. While developmental biology has identified key genes and local cellular processes, global coordination of tissue remodeling at the organ scale remains unclear. Here, we combine in toto light-sheet microscopy of the Drosophila embryo with quantitative analysis and physical modeling to relate cellular flow with the patterns of force generation during the gastrulation process. We find that the complex spatio-temporal flow pattern can be predicted from the measured meso-scale myosin density and anisotropy using a simple, effective viscous model of the tissue, achieving close to 90% accuracy with one time dependent and two constant parameters. Our analysis uncovers the importance of a) spatial modulation of myosin distribution on the scale of the embryo and b) the non-locality of its effect due to mechanical interaction of cells, demonstrating the need for the global perspective in the study of morphogenetic flow

Developing Theory Through Integrating Human and Machine Pattern Recognition

New forms of digital trace data are becoming ubiquitous. Traditional methods of qualitative research that aim at developing theory, however, are often overwhelmed by the sheer volume of such data. To remedy this situation, qualitative researchers can engage not only with digital traces, but also with computational tools that are increasingly able to model digital trace data in ways that support the process of developing theory. To facilitate such research, this paper crafts a research design framework based on the philosophical tradition of pragmatism, which provides intellectual tools for dealing with multifaceted digital trace data, and offers an abductive analysis approach suitable for leveraging both human and machine pattern recognition. This framework provides opportunities for researchers to engage with digital traces and computational tools in a way that is sensitive to qualitative researchers’ concerns about theory development. The paper concludes by showing how this framework puts human imaginative capacities at the center of the push for qualitative researchers to engage with computational tools and digital trace

Using treemaps for variable selection in spatio-temporal visualisation

We demonstrate and reflect upon the use of enhanced treemaps that incorporate spatial and temporal ordering for exploring a large multivariate spatio-temporal data set. The resulting data-dense views summarise and simultaneously present hundreds of space-, time-, and variable-constrained subsets of a large multivariate data set in a structure that facilitates their meaningful comparison and supports visual analysis. Interactive techniques allow localised patterns to be explored and subsets of interest selected and compared with the spatial aggregate. Spatial variation is considered through interactive raster maps and high-resolution local road maps. The techniques are developed in the context of 42.2 million records of vehicular activity in a 98 km(2) area of central London and informally evaluated through a design used in the exploratory visualisation of this data set. The main advantages of our technique are the means to simultaneously display hundreds of summaries of the data and to interactively browse hundreds of variable combinations with ordering and symbolism that are consistent and appropriate for space- and time- based variables. These capabilities are difficult to achieve in the case of spatio-temporal data with categorical attributes using existing geovisualisation methods. We acknowledge limitations in the treemap representation but enhance the cognitive plausibility of this popular layout through our two-dimensional ordering algorithm and interactions. Patterns that are expected (e.g. more traffic in central London), interesting (e.g. the spatial and temporal distribution of particular vehicle types) and anomalous (e.g. low speeds on particular road sections) are detected at various scales and locations using the approach. In many cases, anomalies identify biases that may have implications for future use of the data set for analyses and applications. Ordered treemaps appear to have potential as interactive interfaces for variable selection in spatio-temporal visualisation. Information Visualization (2008) 7, 210-224. doi: 10.1057/palgrave.ivs.950018