Statistical search space reduction and two-dimensional data display approaches for UPLC-MS in biomarker discovery and pathway analysis

A new analytical strategy for biomarker recovery from directly coupled ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC Tof MS) data on biofluids is presented and exemplified using a study on hydrazine-induced liver toxicity. A key step in the strategy involves a novel procedure for reducing the spectroscopic search space by differential analysis of cohorts of normal and pathological samples using an orthogonal projection to latent structures discriminant analysis (O-PLS-DA). This efficiently sorts principal discriminators of toxicity from the background of thousands of metabolic features commonly observed in data sets generated by UPLC-MS analysis of biological fluids and is thus a powerful tool for biomarker discovery.     

The social construction of housing management

Although housing management as an occupational role has existed for over a century it has never received an adequate definition, and its scope and emphasis have varied over time. This paper locates housing management within the debates on the nature of the professions and bureaucracy, and suggests that these analyses are inadequate. It is proposed that a more fruitful approach in understanding the nature of housing management is derived from a consideration of its ‘social construction’. In support of this interpretation material from qualitative empirical research with practitioners is presented and analysed. Key respondents were identified as people working at the boundaries of housing management, such as in a caring or support role, since it was felt that the perceptions of such boundaries were important in defining the limits and limitations of housing management. In conclusion it is suggested that this is a critical moment for housing management in terms of achieving a more rigorous definition of its activities, and of seeking to resolve the conflict between the pressures to organise around commercial objectives and to provide a welfare service. Meanwhile there remains a somewhat paradoxical situation in that whilst the lack of consistent practice within housing management weakens its claims to occupational strength and legitimacy, these same inconsistencies permit individual practitioners the flexibility to offer a more responsive service to those in need.     

Molecular approaches to study probiotic bacteria

Functional foods comprising probiotic bacteria are receiving increasing attention from the scientific community and science funding agencies [1]. An essential aspect relating to the functionality of probiotic-based foods is to develop molecular methods to determine the presence, activity and viability of probiotic bacteria in the human gastrointestinal (GI) tract [2]. The GI tract is composed of a complex ecosystem of various microbial habitats colonized by numerous different commensal micro-organisms. This indigenous gut microbiota is essential to the overall health of the host by performing important physiological functions. In particular, they protect against pathogenic bacteria and drive the development of the immune system during neonatal life. Further metabolic activities of the GI microbiota that beneficially affect the host include continued degradation of food components, vitamin production, and production of short chain fatty acids that feed the colonic mucosa. It is clear that factors such as diet, sickness, stress, or medication can result in loss of well-being of the host, and it is assumed that some of these symptoms are due to perturbation of what is termed the normal balance of the gut microbiota. Knowledge of the structure and function of the standard microbiota, and its response to diet, genetic background and lifetime of the host must be taken into account when designing probiotic-based functional foods. The application of molecular techniques for detection and identification of microbes has provided a major breakthrough in the analysis of microbial ecosystems and their function [3]. The successful application and further potential of these molecular methods to study probiotic bacteria and their impact on the standard GI microbiota is discussed below.     

Interactive Mechanical Design Variation for Haptics and CAD

A fast design variation technique for mechanical systems is presented. It is used to interactively optimize mechanical characteristics while "self-assembling" or satisfying large systems of mechanical constraints. The high speed method is central to providing inverse dynamics force feedback in haptics and control applications. Performance advantages with the use of augmented coordinates for inverse dynamics of closed loop topologies are also noted. The interaction framework allows manipulation of complex assemblies while maintaining kinematically admissible configurations though linkage and joint limit constraints. Furthermore, design variables such as link length can be treated as free variables and optimized to meet design criteria such as assembly dexterity. Assemblies with flexible bodies fit naturally within this framework. Thus, the contribution of this paper is the advancement of techniques in augmented coordinates for the kinematic and force feedback interaction with virtual mechanical assembly design optimization at force control rates.     

Enhancing the biofiltration of geosmin by seeding sand filter columns with a consortium of geosmin-degrading bacteria

Geosmin is a secondary metabolite that can be produced by many species of cyanobacteria and Actinomycetes. It imparts a musty/earthy taste and odour to drinking water which can result in consumer complaints and a general perception that there is a problem with the water quality. As geosmin is recalcitrant to conventional water treatment, processes are sought to ensure effective removal of this compound from potable water. Biological filtration (biofiltration) is an attractive option for geosmin removal as this compound has been shown to be biodegradable. However, effective biofiltration of geosmin can be site specific as it is highly dependent upon the types of organism present and there is often an extended acclimation period before efficient removals are achieved. We report here, a novel approach to enhance the biofiltration of geosmin by seeding sand filter columns with a bacterial consortium previously shown to be capable of effectively degrading geosmin. Geosmin removals of up to 75% were evident through sand columns which had been inoculated with the geosmin-degrading bacteria, when compared with non-inoculated sand columns where geosmin removals were as low as 25%. These low geosmin removals through the non-inoculated sand columns are consistent with previous studies and were attributed to physical/abiotic losses. The presence of an existing biofilm was shown to influence geosmin removal, as the biofilm allowed for greater attachment of the geosmin-degrading consortium (as determined by an ATP assay), and enhanced removals of geosmin. Minimal difference in geosmin removal was observed when the geosmin-degrading bacteria were inoculated into the sand columns containing either an active or inactive biofilm.     

Occupational exposure to paint, lacquer and solvents, and cancer risk in the area of the upper aero-digestive tract

So far, only few studies exist that have investigated the influence of occupational exposure to paint and lacquer on the risk of cancer in the upper aerodigestive tract. Based on data from the Heidelberg case control study which enrolled 369 patients with carcinomas of the upper aerodigestive tract and 1476 randomized control subjects, the relative risk of head and neck cancer in patients exposed to paint, lacquer and varnish was analyzed. The relative risk (RR) of squamous cell cancer (after adjustment for possible alcohol and tobacco effects) was significantly increased for the larynx (RR = 2.3) and the oral cavity (RR = 3.6). However, this risk was not increased for the pharynx. Our findings and a critical analysis of the literature provide evidence that chronic exposure to paint, varnish and lacquer is a definite risk factor for cancer of the upper aerodigestive tract. Further studies are required to confirm these findings, and to identify more precisely toxic substances encountered in the workplace.     

Good-bye and happy holidays! [From the Editor]

This is my last issue as editor-inchief of IEEE Engineering in Medicine and Biology Magazine. It has been a wonderful experience for me to work with the readers of themagazine, column writers, IEEE staff, guest editors, and the authors. Michael Neuman is the new editor-in-chief, and I wish him the very best of luck.