Improvement of the GenTHREADER method for genomic fold recognition

Motivation: In order to enhance genome annotation, the fully automatic fold recognition method GenTHREADER has been improved and benchmarked. The previous version of GenTHREADER consisted of a simple neural network which was trained to combine sequence alignment score, length information and energy potentials derived from threading into a single score representing the relationship between two proteins, as designated by CATH. The improved version incorporates PSI-BLAST searches, which have been jumpstarted with structural alignment profiles from FSSP, and now also makes use of PSIPRED predicted secondary structure and bi-directional scoring in order to calculate the final alignment score. Pairwise potentials and solvation potentials are calculated from the given sequence alignment which are then used as inputs to a multi-layer, feed-forward neural network, along with the alignment score, alignment length and sequence length. The neural network has also been expanded to accommodate the secondary structure element alignment (SSEA) score as an extra input and it is now trained to learn the FSSP Z-score as a measurement of similarity between two proteins. Results: The improvements made to GenTHREADER increase the number of remote homologues that can be detected with a low error rate, implying higher reliability of score, whilst also increasing the quality of the models produced. We find that up to five times as many true positives can be detected with low error rate per query. Total MaxSub score is doubled at low false positive rates using the improved method.

Improvement of 3D protein models using multiple templates guided by single-template model quality assessment

Motivation: Modelling the 3D structures of proteins can often be enhanced if more than one fold template is used during the modelling process. However, in many cases, this may also result in poorer model quality for a given target or alignment method. There is a need for modelling protocols that can both consistently and significantly improve 3D models and provide an indication of when models might not benefit from the use of multiple target-template alignments. Here, we investigate the use of both global and local model quality prediction scores produced by ModFOLDclust2, to improve the selection of target-template alignments for the construction of multiple-template models. Additionally, we evaluate clustering the resulting population of multi- and single-template models for the improvement of our IntFOLD-TS tertiary structure prediction method. Results: We find that using accurate local model quality scores to guide alignment selection is the most consistent way to significantly improve models for each of the sequence to structure alignment methods tested. In addition, using accurate global model quality for re-ranking alignments, prior to selection, further improves the majority of multi-template modelling methods tested. Furthermore, subsequent clustering of the resulting population of multiple-template models significantly improves the quality of selected models compared with the previous version of our tertiary structure prediction method, IntFOLD-TS.

Why the home region matters: location and regional multinationals

Much of the literature in international business analysing the multinational enterprise uses the country as the relevant environmental parameter. This paper presents both theoretical and empirical evidence to demonstrate that country-level analysis now needs to be augmented by analysis at the ‘regional’ level of the broad triad markets of Europe, North America and the Asia Pacific. The great majority of the world's 500 largest firms concentrate their activities within their home region of the triad. This study uses variance component analysis and finds that this home region effect outperforms the country effect. Together, the regional and industry effects explain most of the geographic expansion of multinational enterprises (MNEs), whereas country, firm and year effects are very minor. The new data and variance component analysis on the activities of large MNEs reported here suggest that new thinking is required about the importance of large regions of the triad as the relevant unit of analysis for business strategy to supplement the conventional focus on the country.

Energy consumption feedback in perspective: integrating Australian data to meta-analyses on in home displays

Providing homeowners with real-time feedback on their electricity consumption through a dedicated display device has been shown to reduce consumption by approximately 6-10%. However, recent advances in smart grid technology have enabled larger sample sizes and more representative sample selection and recruitment methods for display trials. By analyzing these factors using data from current studies, this paper argues that a realistic, large-scale conservation effect from feedback is in the range of 3-5%. Subsequent analysis shows that providing real-time feedback may not be a cost effective strategy for reducing carbon emissions in Australia, but that it may enable additional benefits such as customer retention and peak-load shift.

Home-ownership for future generations

This paper constructs a housing market model to analyse conditions for different generations of households in the UK. Previous policy work has suggested that baby-boomers have benefitted at the expense of younger generations. The model relies on a form of financial accelerator in which existing homeowners reinvest a proportion of the capital gains on moving home. The model is extended to look at homeownership probabilities. It also explains why an increasing share of mortgages has gone to existing owners, despite market liberalisation and securitisation. In addition, the model contributes to the explanation of volatility.

Higher education as a portfolio investment: students’ choices about studying, term time employment, leisure, and loans

Recent UK changes in the number of students entering higher education, and in the nature of financial support, highlight the complexity of students’ choices about human capital investments. Today’s students have to focus not on the relatively narrow issue of how much academic effort to invest, but instead on the more complicated issue of how to invest effort in pursuit of ‘employability skills’, and how to signal such acquisitions in the context of a highly competitive graduate jobs market. We propose a framework aimed specifically at students’ investment decisions, which encompasses corner solutions for both borrowing and employment while studying.

Portals to the world: technological extensions to the boundaries of the home

This article examines the ways that technological objects inside the home are viewed and productively used by a group of older people to extend their access to environments beyond the home. Beginning with a discussion of types of domestic object, we highlight appliances and gadgets, and focus our attentions on the latter. The changes in life brought on by ageing, in particular a reduction in mobility, provide the context for our study, in which access to the outside world becomes increasingly difficult. Recognising their changing circumstances led our participants to actively and selectively engage with these objects, mitigating the shrinking of their accessible environment by using them as a gateway to the many virtual worlds now available. We coin the term ‘portal objects’ to describe the potential that this type of technological object provides, and suggest that the investigation of interiors can be enriched by recognising and including the worlds outside that become integral to occupation inside.

The embodied use of the material home: an affordance approach

This paper examines the relationship between embodied individuals and the home that they inhabit. Although there has been some work on both the embodied practices in the home and on the material nature of the home itself, this has not been integrated with the majority of research on home which has focused on meaning. It is argued that there is a lack of a unifying framework that can incorporate both use and meaning elements of home. A way of incorporating these elements through adoption of the concept of affordances is put forward. However, the affordance approach needs to be developed to achieve this. The paper does this first by incorporating the concept of intentionality of actions and then through the use of the concept of well‐being. Debates about housing for people with a physical disability and the practical help provided to this group of people are used to illustrate how the approach could work.

What determines the out-of-home placement of children in the USA?

Using NCANDS data of US child maltreatment reports for 2009, logistic regression, probit analysis, discriminant analysis and an artificial neural network are used to determine the factors which explain the decision to place a child in out-of-home care. As well as developing a new model for 2009, a previous study using 2005 data is replicated. While there are many small differences, the four estimation techniques give broadly the same results, demonstrating the robustness of the results. Similarly, apart from age and sexual abuse, the 2005 and 2009 results are roughly similar. For 2009, child characteristics (particularly child emotional problems) are more important than the nature of the abuse and the situation of the household; while caregiver characteristics are the least important. All these models have low explanatory power.

Mobility based energy efficient and multi-sink algorithms for consumer home networks

With the fast development of the Internet, wireless communications and semiconductor devices, home networking has received significant attention. Consumer products can collect and transmit various types of data in the home environment. Typical consumer sensors are often equipped with tiny, irreplaceable batteries and it therefore of the utmost importance to design energy efficient algorithms to prolong the home network lifetime and reduce devices going to landfill. Sink mobility is an important technique to improve home network performance including energy consumption, lifetime and end-to-end delay. Also, it can largely mitigate the hot spots near the sink node. The selection of optimal moving trajectory for sink node(s) is an NP-hard problem jointly optimizing routing algorithms with the mobile sink moving strategy is a significant and challenging research issue. The influence of multiple static sink nodes on energy consumption under different scale networks is first studied and an Energy-efficient Multi-sink Clustering Algorithm (EMCA) is proposed and tested. Then, the influence of mobile sink velocity, position and number on network performance is studied and a Mobile-sink based Energy-efficient Clustering Algorithm (MECA) is proposed. Simulation results validate the performance of the proposed two algorithms which can be deployed in a consumer home network environment.

A conceptual valuation framework (VF) for home telecare system devices

Purpose – The aim of this paper is to present a conceptual valuation framework to allow telecare service stakeholders to assess telecare devices in the home in terms of their social, psychological and practical effects. The framework enables telecare service operators to more effectively engage with the social and psychological issues resulting from telecare technology deployment in the home and to design and develop appropriate responses as a result. Design/methodology/approach – The paper provides a contextual background for the need for sociologically pitched tools that engage with the social and cultural feelings of telecare service users before presenting the valuation framework and how it could be used. Findings – A conceptual valuation framework is presented for potential development/use. Research limitations/implications – The valuation framework has yet to be extensively tested or verified. Practical implications – The valuation framework needs to be tested and deployed by a telecare service operator but the core messages of the paper are valid and interesting for readership. Social implications – In addressing the social and cultural perspectives of telecare service stakeholders, the paper makes a link between the technologies in the home, the feelings and orientations of service users (e.g. residents, emergency services, wardens, etc.) and the telecare service operator. Originality/value – The paper is an original contribution to the field as it details how the sociological orientations of telecare technology service users should be valued and addressed by service operators. It has a value through the conceptual arguments made and through valuation framework presented.

Knowledge-based clinical pathway for medical quality improvement

Clinical pathways have been adopted for various diseases in clinical departments for quality improvement as a result of standardization of medical activities in treatment process. Using knowledge-based decision support on the basis of clinical pathways is a promising strategy to improve medical quality effectively. However, the clinical pathway knowledge has not been fully integrated into treatment process and thus cannot provide comprehensive support to the actual work practice. Therefore this paper proposes a knowledgebased clinical pathway management method which contributes to make use of clinical knowledge to support and optimize medical practice. We have developed a knowledgebased clinical pathway management system to demonstrate how the clinical pathway knowledge comprehensively supports the treatment process. The experiences from the use of this system show that the treatment quality can be effectively improved by the extracted and classified clinical pathway knowledge, seamless integration of patient-specific clinical pathway recommendations with medical tasks and the evaluating pathway deviations for optimization.

Integrated clinical pathway management for medical quality improvement-based on a semiotically inspired systems architecture

Clinical pathway is an approach to standardise care processes to support the implementations of clinical guidelines and protocols. It is designed to support the management of treatment processes including clinical and non-clinical activities, resources and also financial aspects. It provides detailed guidance for each stage in the management of a patient with the aim of improving the continuity and coordination of care across different disciplines and sectors. However, in the practical treatment process, the lack of knowledge sharing and information accuracy of paper-based clinical pathways burden health-care staff with a large amount of paper work. This will often result in medical errors, inefficient treatment process and thus poor quality medical services. This paper first presents a theoretical underpinning and a co-design research methodology for integrated pathway management by drawing input from organisational semiotics. An approach to integrated clinical pathway management is then proposed, which aims to embed pathway knowledge into treatment processes and existing hospital information systems. The capability of this approach has been demonstrated through the case study in one of the largest hospitals in China. The outcome reveals that medical quality can be improved significantly by the classified clinical pathway knowledge and seamless integration with hospital information systems.

Cortical thickness changes in the non-lesioned hemisphere associated with non-paretic arm immobilization in modified CI therapy

Recent evidence suggests that immobilization of the upper limb for 2–3 weeks induces changes in cortical thickness as well as motor performance. In constraint induced (CI) therapy, one of the most effective interventions for hemiplegia, the non-paretic arm is constrained to enforce the use of the paretic arm in the home setting. With the present study we aimed to explore whether non-paretic arm immobilization in CI therapy induces structural changes in the non-lesioned hemisphere, and how these changes are related to treatment benefit. 31 patients with chronic hemiparesis participated in CI therapy with (N = 14) and without (N = 17) constraint. Motor ability scores were acquired before and after treatment. Diffusion tensor imaging (DTI) data was obtained prior to treatment. Cortical thickness was measured with the Freesurfer software. In both groups cortical thickness in the contralesional primary somatosensory cortex increased and motor function improved with the intervention. However the cortical thickness change was not associated with the magnitude of motor function improvement. Moreover, the treatment effect and the cortical thickness change were not significantly different between the constraint and the non-constraint groups. There was no correlation between fractional anisotropy changes in the non-lesioned hemisphere and treatment outcome. CI therapy induced cortical thickness changes in contralesional sensorimotor regions, but this effect does not appear to be driven by the immobilization of the non-paretic arm, as indicated by the absence of differences between the constraint and the non-constraint groups. Our data does not suggest that the arm immobilization used in CI therapy is associated with noticeable cortical thinning.

Home, meaning and identity: learning from the English model of shared ownership

This article explores the problematic nature of the label “home ownership” through a case study of the English model of shared ownership, one of the methods used by the UK government to make home ownership affordable. Adopting a legal and socio-legal analysis, the article considers whether shared ownership is capable of fulfilling the aspirations households have for home ownership. To do so, the article considers the financial and nonfinancial meanings attached to home ownership and suggests that the core expectation lies in ownership of the value. The article demonstrates that the rights and responsibilities of shared owners are different in many respects from those of traditional home owners, including their rights as regards ownership of the value. By examining home ownership through the lens of shared ownership the article draws out lessons of broader significance to housing studies. In particular, it is argued that shared ownership shows the limitations of two dichotomies commonly used in housing discourse: that between private and social housing; and the classification of tenure between owner-occupiers and renters. The article concludes that a much more nuanced way of referring to home ownership is required, and that there is a need for a change of expectations amongst consumers as to what sharing ownership means.