A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Motivation: Microarray experiments generate a high data volume. However, often due to financial or experimental considerations, e.g. lack of sample, there is little or no replication of the experiments or hybridizations. These factors combined with the intrinsic variability associated with the measurement of gene expression can result in an unsatisfactory detection rate of differential gene expression (DGE). Our motivation was to provide an easy to use measure of the success rate of DGE detection that could find routine use in the design of microarray experiments or in post-experiment assessment.

An assessment of the earth pressure coefficient in overconsolidated clays

The determination of the earth pressure coefficient K 0 in a natural clay deposit is a problem of considerable significance in geotechnical engineering. While the methods for evaluation of K 0 are reliable for normally consolidated soils, significant difficulties still exist in evaluating K 0 in overconsolidated clays, given that it is influenced by the stress history of the material, together with the age, structure, mineralogical composition and depositional environment. Indeed, some of these factors are responsible for the soil becoming anisotropic. The existing framework for prediction of K 0 in overconsolidated soils does not account for any influences caused by anisotropy. The work reported in this paper evaluates the validity of a revised relationship between K 0oc and OCR (overconsolidation ratio) using data obtained from laboratory investigations. The tests were performed on reconstituted and undisturbed samples of Belfast Upper Boulder Clay, London Clay and Gault Clay. Tests were also performed on reconstituted samples of kaolin. The values of K 0oc were determined using various approaches, including on-sample measurements. The results have confirmed that reliable predictions of K 0oc can be made using the proposed relationship.

Assessment of fighting ability in animal contests

Selection should favour accurate information gathering regarding the likely costs and benefits of continued conflict. Here we consider how variation in the abilities of contestants to assess resource-holding potential (RHP) influences fights. This has been examined in various game theory models. However, discriminating between assessment strategies has proven difficult and has resulted in confusion. To add clarity, we group existing models into three main types that differ in the information about RHP that contestants are presumed to gather: (1) pure self-assessment, (2) cumulative assessment and (3) mutual assessment. Within this framework we outline methods advocated to discriminate successfully between the three main assessment models. We discuss support for each model, before highlighting a number of conflicting and inconclusive studies, leading us to consider alternative approaches to investigate assessment. Furthermore, we examine support for newly emerging concepts such as 'varying degrees of assessment', 'switching assessment' strategies and the possibility of contestants adopting different assessment strategies within a fight involving distinctive roles. We suggest future studies will benefit by judicious use of a battery of techniques to determine how animals settle contests. Finally, we highlight difficulties with current game theory models, and raise concerns regarding the use of certain behavioural criteria to accept or reject a model, particularly since this may conflict with evidence for a given assessment strategy. Furthermore, the failure of existing models to account for newly emerging concepts points to limitations of their use and leads us to challenge game theoreticians to develop upon them. (C) 2009 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Framework for Establishing Limits of Tabular Aerodynamic Models for Flight Dynamics Analysis

This paper describes the use of the Euler equations for the generation and testing of tabular aerodynamic models for flight dynamics analysis. Maneuvers for the AGARD Standard Dynamics Model sharp leading-edge wind-tunnel geometry are considered as a test case. Wind-tunnel data is first used to validate the prediction of static and dynamic coefficients at both low and high angles, featuring complex vortical flow, with good agreement obtained at low to moderate angles of attack. Then the generation of aerodynamic tables is described based on a data fusion approach. Time-optimal maneuvers are generated based on these tables, including level flight trim, pull-ups at constant and varying incidence, and level and 90 degrees turns. The maneuver definition includes the aircraft states and also the control deflections to achieve the motion. The main point of the paper is then to assess the validity of the aerodynamic tables which were used to define the maneuvers. This is done by replaying them, including the control surface motions, through the time accurate computational fluid dynamics code. The resulting forces and moments are compared with the tabular values to assess the presence of inadequately modeled dynamic or unsteady effects. The agreement between the tables and the replay is demonstrated for slow maneuvers. Increasing rate maneuvers show discrepancies which are ascribed to vortical flow hysteresis at the higher rate motions. The framework is suitable for application to more complex viscous flow models, and is powerful for the assessment of the validity of aerodynamics models of the type currently used for studies of flight dynamics.

Retrofit versus new-build house using life-cycle assessment

This paper reports the findings of research on the environmental performance of two case-study houses, a retrofit and new build. The retrofit was completed to a Passivhaus standard while the new build was completed to current Irish building regulations. Environmental performance of the retrofit and new build was measured using life-cycle assessments, examining the assembly, operational and end-of-life stage over life spans of 50 and 80 years. Using primary information, life-cycle assessment software and life-cycle assessment databases the environmental impacts of each stage were modelled. The operational stage of both case studies was found to be the source of the most significant environmental damage, followed by the assembly and the end-of-life stage respectively. The relative importance of the assembly and end-of-life stage decreased as the life span increased. It was found that the retrofit house studied outperformed the new build in the assembly and operational stage, whereas the new build performed better in the end-of-life stage; however, this is highly sensitive, depending on the standards to which both are completed. Operational energy savings pre- and post-retrofit were significant, indicating the future potential for adoption of high-quality retrofitting practices.

A virtual inspection framework for precision manufacturing of aerofoil components

The finite element method plays an extremely important role in forging process design as it provides a valid means to quantify forging errors and thereby govern die shape modification to improve the dimensional accuracy of the component. However, this dependency on process simulation could raise significant problems and present a major drawback if the finite element simulation results were inaccurate. This paper presents a novel approach to assess the dimensional accuracy and shape quality of aeroengine blades formed from finite element hot-forging simulation. The proposed virtual inspection system uses conventional algorithms adopted by modern coordinate measurement processes as well as the latest free-form surface evaluation techniques to provide a robust framework for virtual forging error assessment. Established techniques for the physical registration of real components have been adapted to localise virtual models in relation to a nominal Design Coordinate System. Blades are then automatically analysed using a series of intelligent routines to generate measurement data and compute dimensional errors. The results of a comparison study indicate that the virtual inspection results and actual coordinate measurement data are highly comparable, validating the approach as an effective and accurate means to quantify forging error in a virtual environment. Consequently, this provides adequate justification for the implementation of the virtual inspection system in the virtual process design, modelling and validation of forged aeroengine blades in industry.

Critical assessment of two-qubit post-Markovian master equations

A post-Markovian master equation has been recently proposed as a tool to describe the evolution of a system coupled to a memory-keeping environment [A. Shabani and D. A. Lidar, Phys. Rev. A 71, 020101 ( R) ( 2005)]. For a single qubit affected by appropriately chosen environmental conditions, the corresponding dynamics is always legitimate and physical. Here we extend such a situation to the case of two qubits, only one of which experiences the environmental effects. We show how, despite the innocence of such an extension, the introduction of the second qubit should be done cum grano salis to avoid consequences such as the breaking of the positivity of the associated dynamical map. This hints at the necessity of using care when adopting phenomenologically derived models for evolutions occurring outside the Markovian framework.

A Risky Business: An Examination of Irish Probation Officers Attitudes and Work Practices Regarding Risk Assessment

This article examines recent research on risk assessment and probation practice in Ireland and relates the findings to the ongoing debate regarding risk management practices in probation. The piece discusses current theoretical arguments on the influence of risk in criminal justice and outlines the impact of risk discourse on probation practice in Ireland and England and Wales. Using a mix of qualitative and quantitative methods, Irish probation officers’ attitudes are examined in order to highlight key issues facing probation officers when making risk decisions. These findings are compared and contrasted to other research results from England and Wales. All the conclusions identify both positive and negative consequences of adopting risk tools and point to the continued salience of clinical judgment over actuarial methods of risk assessment. It is argued that the research highlights the role of ‘resistance’ by criminal justice professionals in mediating the effects of the ‘new penology’ at the level of implementation. The idea of resistance holds particular relevance for probation practice in Ireland where professional discretion is maintained within the National Standards framework. Despite this, to date there has been an uncritical approach taken to risk assessment which may ignore the dangers of risk inflation/deflation and the need to take into account local factors in assessing risk of reoffending

Educational assessment policy and practice - a matter of ethics

Long-standing concerns within the field of educational assessment consider the impact of assessment policy and practice as matters of equity, inequality and social justice.Yet educational assessment policy and practice continues to have powerful social consequences for key users such as children and young people.This paper re-positions these consequences as a matter of ethics.It uses the work of Messick to frame how ethical matters extend beyond test instruments into the realm of uses and impact. A case study of the 11+ school transfer system in Northern Ireland is presented to illustrate ethical dilemmas emerging as a consequence of actions and decisions of using assessment systems for particular purposes.In looking forward to how we might attend to ethical matters in assessment policy and practice, a consideration of a children’s rights approach is outlined that may provide a moral and legal framework for action.

Climate change adaptation : a decision support framework to encourage environmentally responsible behaviour

Structured Abstract:
Purpose: Very few studies investigate environmentally responsible behaviour (ERB). This paper presents a new 'Awareness Behaviour Intervention Action' (ABIA) Decision Support Framework to sustain ERB.

Design/methodology/approach: Previous ERB programmes have failed to deliver lasting results; they have not appropriately understood and provided systems to address ERB (Costanzo et al., 1986). These programmes were based on assumptions (Moloney et al., 2010), which this paper addresses. The ABIA Framework has been developed through a case study of social housing tenants waiting for low or zero carbon homes.

Findings: The ABIA Framework enables a better understanding of current attitudes to environmental issues and provides support for ERB alongside technological interventions employed to promote and sustain carbon reduction.

Research limitations/implications: The ABIA Framework should be tested on individuals and communities in a variety of socio-economic, political and cultural contexts. This will help unpack how it can impact on the behaviours of individuals and communities including stakeholders.

Practical implications: This type of research and the ABIA Framework developed from it are crucial if the UK pledge to become the first country in the World where all new homes from 2016 are to be zero carbon.

Social implications: The Framework encourages both individual and community discussion and solving of sustainability issues.

Originality/value: There are few, if any, studies that have developed a framework which can be used to support behavioural change for adaptation to sustainable living in low or zero carbon homes.

Temporary tattoos:a novel OSCE assessment tool

Background: There are many issues regarding the use of real patients in objective structured clinical examinations (OSCEs). In dermatology OSCE stations, standardised patients (SPs) with clinical photographs are often used. Temporary transfer tattoos can potentially simulate skin lesions when applied to an SP. This study aims to appraise the use of temporary malignant melanoma tattoos within an OSCE framework. Method: Within an 11-station OSCE, a temporary malignant melanoma tattoo was developed and applied to SPs in a 'skin lesion' OSCE station. A questionnaire captured the opinions of the candidate, SP and examiners, and the degree of perceived realism of each station was determined. Standard post hoc OSCE analysis determined the psychometric reliability of the stations. Results: The response rates were 95.9 per cent of candidates and 100 per cent of the examiners and SPs. The 'skin lesion' station achieved the highest realism score compared with other stations: 89.0 per cent of candidates felt that the skin lesion appeared realistic; only 28 per cent of candidates had ever seen a melanoma before in training. The psychometric performance of the melanoma station was comparable with, and in many instances better than, other OSCE stations. Discussion: Transfer tattoo technology facilitates a realistic dermatology OSCE station encounter. Temporary tattoos, alongside trained SPs, provide an authentic, standardised and reliable experience, allowing the assessment of integrated dermatology clinical skills.

CoWiSMoN: A Framework for Cognitive Wireless Sensor Mobile Network System for Emergency Rescue Management

One of the crucial aspects of disaster management of emergency situations is the early assessment of needs and damages. In most disaster situations, higher fatality and increased casualty results from lack of access to timely available emergency services rather than the initial disaster itself. This is usually caused by lack of access to the affected area in order to properly assess the situation for relevant and urgent measures. Cognitive wireless sensor networks provide an opportunity to overcome this situation especially through interconnection via mobile systems. This paper presents a cognitive wireless sensor mobile networks-based framework (CoWiSMoN), designed to offer real-time emergency services to victims and rescue personnel in event of disasters. Critical issues underlying the implementation of such a system are discussed and analyzed.

Food web indicators under the Marine Strategy Framework Directive: From complexity to simplicity?

The Marine Strategy Framework Directive (MSFD) requires that European Union Member States achieve "Good Environmental Status" (GES) in respect of 11 Descriptors of the marine environment by 2020. Of those, Descriptor 4, which focuses on marine food webs, is perhaps the most challenging to implement since the identification of simple indicators able to assess the health of highly dynamic and complex interactions is difficult. Here, we present the proposed food web criteria/indicators and analyse their theoretical background and applicability in order to highlight both the current knowledge gaps and the difficulties associated with the assessment of GES. We conclude that the existing suite of indicators gives variable focus to the three important food web properties: structure, functioning and dynamics, and more emphasis should be given to the latter two and the general principles that relate these three properties. The development of food web indicators should be directed towards more integrative and process-based indicators with an emphasis on their responsiveness to multiple anthropogenic pressures. (C) 2013 Elsevier Ltd. All rights reserved.

A new statistical framework for the quantification of covariate associations with species distributions

Identifying processes that shape species geographical ranges is a prerequisite for understanding environmental change. Currently, species distribution modelling methods do not offer credible statistical tests of the relative influence of climate factors and typically ignore other processes (e.g. biotic interactions and dispersal limitation). We use a hierarchical model fitted with Markov Chain Monte Carlo to combine ecologically plausible niche structures using regression splines to describe unimodal but potentially skewed response terms. We apply spatially explicit error terms that account for (and may help identify) missing variables. Using three example distributions of European bird species, we map model results to show sensitivity to change in each covariate. We show that the overall strength of climatic association differs between species and that each species has considerable spatial variation in both the strength of the climatic association and the sensitivity to climate change. Our methods are widely applicable to many species distribution modelling problems and enable accurate assessment of the statistical importance of biotic and abiotic influences on distributions.