Independent component analysis of microarray data in the study of endometrial cancer.

Gene microarray technology is highly effective in screening for differential gene expression and has hence become a popular tool in the molecular investigation of cancer. When applied to tumours, molecular characteristics may be correlated with clinical features such as response to chemotherapy. Exploitation of the huge amount of data generated by microarrays is difficult, however, and constitutes a major challenge in the advancement of this methodology. Independent component analysis (ICA), a modern statistical method, allows us to better understand data in such complex and noisy measurement environments. The technique has the potential to significantly increase the quality of the resulting data and improve the biological validity of subsequent analysis. We performed microarray experiments on 31 postmenopausal endometrial biopsies, comprising 11 benign and 20 malignant samples. We compared ICA to the established methods of principal component analysis (PCA), Cyber-T, and SAM. We show that ICA generated patterns that clearly characterized the malignant samples studied, in contrast to PCA. Moreover, ICA improved the biological validity of the genes identified as differentially expressed in endometrial carcinoma, compared to those found by Cyber-T and SAM. In particular, several genes involved in lipid metabolism that are differentially expressed in endometrial carcinoma were only found using this method. This report highlights the potential of ICA in the analysis of microarray data.

Air quality and public health impacts of UK airports. Part I: Emissions

The potential adverse human health and climate impacts of emissions from UK airports have become a significant political issue, yet the emissions, air quality impacts and health impacts attributable to UK airports remain largely unstudied. We produce an inventory of UK airport emissions - including aircraft landing and takeoff (LTO) operations and airside support equipment - with uncertainties quantified. The airports studied account for more than 95% of UK air passengers in 2005. We estimate that in 2005, UK airports emitted 10.2 Gg [-23 to +29%] of NOx, 0.73 Gg [-29 to +32%] of SO2, 11.7 Gg [-42 to +77%] of CO, 1.8 Gg [-59 to +155%] of HC, 2.4 Tg [-13 to +12%] of CO2, and 0.31 Gg [-36 to +45%] of PM2.5. This translates to 2.5 Tg [-12 to +12%] CO2-eq using Global Warming Potentials for a 100-year time horizon. Uncertainty estimates were based on analysis of data from aircraft emissions measurement campaigns and analyses of aircraft operations.The First-Order Approximation (FOA3) - currently the standard approach used to estimate particulate matter emissions from aircraft - is compared to measurements and it is shown that there are discrepancies greater than an order of magnitude for 40% of cases for both organic carbon and black carbon emissions indices. Modified methods to approximate organic carbon emissions, arising from incomplete combustion and lubrication oil, and black carbon are proposed. These alterations lead to factor 8 and a 44% increase in the annual emissions estimates of black and organic carbon particulate matter, respectively, leading to a factor 3.4 increase in total PM2.5 emissions compared to the current FOA3 methodology. Our estimates of emissions are used in Part II to quantify the air quality and health impacts of UK airports, to assess mitigation options, and to estimate the impacts of a potential London airport expansion. © 2011 Elsevier Ltd.

Improving data quality in DSM modelling: A structural comparison approach

The Dependency Structure Matrix (DSM) has proved to be a useful tool for system structure elicitation and analysis. However, as with any modelling approach, the insights gained from analysis are limited by the quality and correctness of input information. This paper explores how the quality of data in a DSM can be enhanced by elicitation methods which include comparison of information acquired from different perspectives and levels of abstraction. The approach is based on comparison of dependencies according to their structural importance. It is illustrated through two case studies: creation of a DSM showing the spatial connections between elements in a product, and a DSM capturing information flows in an organisation. We conclude that considering structural criteria can lead to improved data quality in DSM models, although further research is required to fully explore the benefits and limitations of our proposed approach.

Civil and Environmental Engineering Challenges for Data Sensing and Analysis

The objective of this study was to identify challenges in civil and environmental engineering that can potentially be solved using data sensing and analysis research. The challenges were recognized through extensive literature review in all disciplines of civil and environmental engineering. The literature review included journal articles, reports, expert interviews, and magazine articles. The challenges were ranked by comparing their impact on cost, time, quality, environment and safety. The result of this literature review includes challenges such as improving construction safety and productivity, improving roof safety, reducing building energy consumption, solving traffic congestion, managing groundwater, mapping and monitoring the underground, estimating sea conditions, and solving soil erosion problems. These challenges suggest areas where researchers can apply data sensing and analysis research.

Generalized power method for sparse principal component analysis

In this paper we develop a new approach to sparse principal component analysis (sparse PCA). We propose two single-unit and two block optimization formulations of the sparse PCA problem, aimed at extracting a single sparse dominant principal component of a data matrix, or more components at once, respectively. While the initial formulations involve nonconvex functions, and are therefore computationally intractable, we rewrite them into the form of an optimization program involving maximization of a convex function on a compact set. The dimension of the search space is decreased enormously if the data matrix has many more columns (variables) than rows. We then propose and analyze a simple gradient method suited for the task. It appears that our algorithm has best convergence properties in the case when either the objective function or the feasible set are strongly convex, which is the case with our single-unit formulations and can be enforced in the block case. Finally, we demonstrate numerically on a set of random and gene expression test problems that our approach outperforms existing algorithms both in quality of the obtained solution and in computational speed. © 2010 Michel Journée, Yurii Nesterov, Peter Richtárik and Rodolphe Sepulchre.

Geometric optimization methods for independent component analysis applied on gene expression data

DNA microarrays provide a huge amount of data and require therefore dimensionality reduction methods to extract meaningful biological information. Independent Component Analysis (ICA) was proposed by several authors as an interesting means. Unfortunately, experimental data are usually of poor quality- because of noise, outliers and lack of samples. Robustness to these hurdles will thus be a key feature for an ICA algorithm. This paper identifies a robust contrast function and proposes a new ICA algorithm. © 2007 IEEE.

Energy performance certification as a signal of workplace quality

Energy performance labelling and certification have been introduced widely to address market failures affecting the uptake of energy efficient technologies, by providing a signal to support decision making during contracting processes. The UK has recently introduced the Energy Performance Certificate (EPC) as a signal of building energy performance. The aims of this article are: to evaluate how valid EPC's are signals of occupier satisfaction with office facilities; and to understand whether occupant attitudes towards environmental issues have affected commercial office rental values. This was achieved by surveying occupant satisfaction with their workplaces holistically using a novel multi-item rating scale which gathered 204 responses. Responses to this satisfaction scale were matched with the corresponding EPC and rental value of occupier's workplaces. The satisfaction scale was found to be both a reliable and valid measure. The analysis found that EPC asset rating correlates significantly with occupant satisfaction with all facility attributes. Therefore, EPC ratings may be considered valid signals of overall facility satisfaction within the survey sample. Rental value was found to correlate significantly only with facility aesthetics. No evidence suggests rental value has been affected by occupants' perceptions towards the environmental impact of facilities. © 2013 The Authors.

Articulating current service development practices: a qualitative analysis of eleven mental health projects.

BACKGROUND: The utilisation of good design practices in the development of complex health services is essential to improving quality. Healthcare organisations, however, are often seriously out of step with modern design thinking and practice. As a starting point to encourage the uptake of good design practices, it is important to understand the context of their intended use. This study aims to do that by articulating current health service development practices. METHODS: Eleven service development projects carried out in a large mental health service were investigated through in-depth interviews with six operation managers. The critical decision method in conjunction with diagrammatic elicitation was used to capture descriptions of these projects. Stage-gate design models were then formed to visually articulate, classify and characterise different service development practices. RESULTS: Projects were grouped into three categories according to design process patterns: new service introduction and service integration; service improvement; service closure. Three common design stages: problem exploration, idea generation and solution evaluation - were then compared across the design process patterns. Consistent across projects were a top-down, policy-driven approach to exploration, underexploited idea generation and implementation-based evaluation. CONCLUSIONS: This study provides insight into where and how good design practices can contribute to the improvement of current service development practices. Specifically, the following suggestions for future service development practices are made: genuine user needs analysis for exploration; divergent thinking and innovative culture for idea generation; and fail-safe evaluation prior to implementation. Better training for managers through partnership working with design experts and researchers could be beneficial.