StaRProtein: a web server for prediction of stability of repeat proteins

Repeat proteins have become increasingly important due to their capability to bind to almost any proteins and the potential as alternative therapy to monoclonal antibodies. In the past decade repeat proteins have been designed to mediate specific protein-protein interactions. The tetratricopeptide and ankyrin repeat proteins are two classes of helical repeat proteins that form different binding pockets to accommodate various partners. It is important to understand the factors that define folding and stability of repeat proteins in order to prioritize the most stable designed repeat proteins to further explore their potential binding affinities. Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency in predicting the stability of repeat proteins. We demonstrated that the repeat-specific statistical potentials based on these two classes of repeat proteins showed paramount accuracy compared with non-specific statistical potentials in: 1) discriminate correct vs. incorrect models 2) rank the stability of designed repeat proteins. In particular, the statistical scores correlate closely with the equilibrium unfolding free energies of repeat proteins and therefore would serve as a novel tool in quickly prioritizing the designed repeat proteins with high stability. StaRProtein web server was developed for predicting the stability of repeat proteins.

The first major step in the peace process’? Exploring the impact of the Anglo-Irish Agreement on Irish Republican thinking

This article supports interpretations of the Anglo-Irish Agreement of 1985 as a significant factor contributing to the development of the Northern Ireland peace process. However, it also emphasises a certain serendipity in the Agreement's effect on northern nationalist, and more specifically republican, politics in the region. In particular, it stresses that a specific interpretation of the Agreement promoted by the Social Democratic and Labour Party inspired a dialogue with republicanism, encouraging an ongoing reappraisal within the latter about the nature of Britain's role in Northern Ireland. This, the article argues, reinforced the movement towards a more political approach that republicans had begun in the 1980s, and encouraged their eventual embrace of a constitutional strategy in the 1990s. However, in advancing this argument, the article notes that such an outcome was far from the minds of the British and Irish officials who negotiated the Anglo-Irish Agreement. The Agreement was intended to marginalise rather than accommodate republicans. Despite this, it provided an inadvertent incentive to draw militant republicanism into the democratic process in Northern Ireland.

The first major step in the peace process’? Exploring the impact of the Anglo-Irish Agreement on Irish republican thinking

This article supports interpretations of the Anglo-Irish Agreement of 1985 as a significant factor contributing towards the development of the Northern Ireland peace process. However, it also emphasises a certain serendipity in the Agreement’s effect on northern nationalist, and more specifically republican, politics in the region. In particular, it stresses that a specific interpretation of the Agreement promoted by the SDLP inspired a dialogue with republicanism, encouraging an ongoing re-appraisal within the latter about the nature of Britain’s role in Northern Ireland. This, the article argues, reinforced the movement towards a more political approach that republicans had begun in the 1980s, and encouraged their eventual embrace of a constitutional strategy in the 1990s. However, in advancing this argument, the article notes that such an outcome was far from the minds of the British and Irish officials who negotiated the Anglo-Irish Agreement. The Agreement was intended to marginalise rather than accommodate republicans. Despite this, it provided an inadvertent incentive to draw militant republicanism into the democratic process in Northern Ireland.

Urban high-density construction sites and their surrounding community:issues encountered and strategiesadopted by contractors

Inner city developments are a common feature within many urban environments. Where these construction sites are not managed effectively, they can negatively impact their surrounding community. The aim of this paper is to identify and document, in an urban context, the numerous issues encounter and subsequent strategies adopted by on-site contractors and local people, in the mitigation of factors which negatively impact their surrounding community. The objectives in achieving this aim are to identify what effect, if any, an urban construction site has on its surrounding environment, the issues and resulting strategies adopted by contractors on the factors identified, and also what measures are put in place to minimise such disturbances to the local community. In order to meet the requirements, a mixed methodology is adopted culminating in a literature review, case study analysis, contractor and community interviews, concluding in the development of two specific questions for both perspectives in question. The data is assessed using severity indices based on mean testing in the development of key findings. The results indicate that the main forms of disturbance to the local community from an urban development include noise, dust and traffic congestion. With respect to a contractor on-site, the key issues include damaging surrounding buildings, noise control and off-site parking. The resulting strategies identified in the mitigation of such issues include the implementation of noise and dust containment measures and minimising disruption to local infrastructure. It is envisaged that the results of this study will provide contractors operating in such environments, with the required information which can assist in minimising disruption and therefore, avoiding disputes with the local community members. By consulting with and surveying those most affected, this research will illustrate to on-site management, the difficulties faced by those who accommodate such developments within their living environment.

The Muslim Brotherhood: the Arab Spring its Future Face

The Muslim Brotherhood is the most significant and enduring Sunni Islamist organization of the contemporary era. Its roots lie in the Middle East but it has grown into both a local and global movement, with its well-placed branches reacting effectively to take the opportunities for power and electoral competition offered by the Arab Spring.

Regarded by some as a force of moderation among Islamists, and by others as a façade hiding a terrorist fundamentalist threat, the potential influence of the Muslim Brotherhood on Middle Eastern politics remains ambiguous.The Muslim Brotherhood: The Arab Spring and its Future Face provides an essential insight into the organisation, with chapters devoted to specific cases where the Brotherhood has important impacts on society, the state and politics. Key themes associated with the Brotherhood, such as democracy, equality, pan-Islamism, radicalism, reform, the Palestine issue and gender, are assessed to reveal an evolutionary trend within the movement since its founding in Egypt in 1928 to its manifestation as the largest Sunni Islamist movement in the Middle East in the 21st century. The book addresses the possible future of the Muslim Brotherhood; whether it can surprise sceptics and effectively accommodate democracy and secular trends, and how its ascension to power through the ballot box might influence Western policy debates on their engagement with this manifestation of political Islam.

Drawing on a wide range of sources, this book presents a comprehensive study of a newly resurgent movement and is a valuable resource for students, scholars and policy makers focused on Middle Eastern Politics.

Hierarchical energy management system for multi-source multi-product microgrids

This paper proposes a hierarchical energy management system for multi-source multi-product (MSMP) microgrids. Traditional energy hub based scheduling method is combined with a hierarchical control structure to incorporate transient characteristics of natural gas flow and dynamics of energy converters in microgrids. The hierarchical EMS includes a supervisory control layer, an optimizing control layer, and an execution control layer. In order to efficiently accommodate the systems multi time-scale characteristics, the optimizing control layer is decomposed into three sub-layers: slow, medium and fast. Thermal, gas and electrical management systems are integrated into the slow, medium, and fast control layer, respectively. Compared with wind energy, solar energy is easier to integrate and more suitable for the microgrid environment, therefore, potential impacts of the hierarchical EMS on MSMP microgrids is investigated based on a building energy system integrating photovoltaic and microturbines. Numerical studies indicate that by using a hierarchical EMS, MSMP microgrids can be economically operated. Also, interactions among thermal, gas, and electrical system can be effectively managed.

A Reliability Assessment Approach for the Urban Energy System and Its Application in Energy Hub Planning

With the increasing utilization of combined heat and power plants (CHP), electrical, gas, and thermal systems are becoming tightly integrated in the urban energy system (UES). However, the three systems are usually planned and operated separately, ignoring their interactions and coordination. To address this issue, the coupling point of different systems in the UES is described by the energy hub model. With this model, an integrated load curtailment method is proposed for the UES. Then a Monte Carlo simulation based approach is developed to assess the reliability of coordinated energy supply systems. Based on this approach, a reliability-optimal energy hub planning method is proposed to accommodate higher renewable energy penetration. Numerical studies indicate that the proposed approach is able to quantify the UES reliability with different structures. Also, optimal energy hub planning scheme can be determined to ensure the reliability of the UES with high renewable penetration.

A constructive approach for examination timetabling based on adaptive decomposition and ordering

In this study, we investigate an adaptive decomposition and ordering strategy that automatically divides examinations into difficult and easy sets for constructing an examination timetable. The examinations in the difficult set are considered to be hard to place and hence are listed before the ones in the easy set in the construction process. Moreover, the examinations within each set are ordered using different strategies based on graph colouring heuristics. Initially, the examinations are placed into the easy set. During the construction process, examinations that cannot be scheduled are identified as the ones causing infeasibility and are moved forward in the difficult set to ensure earlier assignment in subsequent attempts. On the other hand, the examinations that can be scheduled remain in the easy set.

Within the easy set, a new subset called the boundary set is introduced to accommodate shuffling strategies to change the given ordering of examinations. The proposed approach, which incorporates different ordering and shuffling strategies, is explored on the Carter benchmark problems. The empirical results show that the performance of our algorithm is broadly comparable to existing constructive approaches.

Factors that impact on the use of mechanical ventilation weaning protocols in critically ill adults and children: a qualitative-evidence synthesis

Background:
Prolonged mechanical ventilation is associated with a longer intensive care unit (ICU) length of stay and higher mortality. Consequently, methods to improve ventilator weaning processes have been sought. Two recent Cochrane systematic reviews in ICU adult and paediatric populations concluded that protocols can be effective in reducing the duration of mechanical ventilation, but there was significant heterogeneity in study findings. Growing awareness of the benefits of understanding the contextual factors impacting on effectiveness has encouraged the integration of qualitative evidence syntheses with effectiveness reviews, which has delivered important insights into the reasons underpinning (differential) effectiveness of healthcare interventions.

Objectives:
1. To locate, appraise and synthesize qualitative evidence concerning the barriers and facilitators of the use of protocols for weaning critically-ill adults and children from mechanical ventilation;

2. To integrate this synthesis with two Cochrane effectiveness reviews of protocolized weaning to help explain observed heterogeneity by identifying contextual factors that impact on the use of protocols for weaning critically-ill adults and children from mechanical ventilation;

3. To use the integrated body of evidence to suggest the circumstances in which weaning protocols are most likely to be used.

Search methods:
We used a range of search terms identified with the help of the SPICE (Setting, Perspective, Intervention, Comparison, Evaluation) mnemonic. Where available, we used appropriate methodological filters for specific databases. We searched the following databases: Ovid MEDLINE, Embase, OVID, PsycINFO, CINAHL Plus, EBSCOHost, Web of Science Core Collection, ASSIA, IBSS, Sociological Abstracts, ProQuest and LILACS on the 26th February 2015. In addition, we searched: the grey literature; the websites of professional associations for relevant publications; and the reference lists of all publications reviewed. We also contacted authors of the trials included in the effectiveness reviews as well as of studies (potentially) included in the qualitative synthesis, conducted citation searches of the publications reporting these studies, and contacted content experts.

We reran the search on 3rd July 2016 and found three studies, which are awaiting classification.

Selection criteria:
We included qualitative studies that described: the circumstances in which protocols are designed, implemented or used, or both, and the views and experiences of healthcare professionals either involved in the design, implementation or use of weaning protocols or involved in the weaning of critically-ill adults and children from mechanical ventilation not using protocols. We included studies that: reflected on any aspect of the use of protocols, explored contextual factors relevant to the development, implementation or use of weaning protocols, and reported contextual phenomena and outcomes identified as relevant to the effectiveness of protocolized weaning from mechanical ventilation.

Data collection and analysis:
At each stage, two review authors undertook designated tasks, with the results shared amongst the wider team for discussion and final development. We independently reviewed all retrieved titles, abstracts and full papers for inclusion, and independently extracted selected data from included studies. We used the findings of the included studies to develop a new set of analytic themes focused on the barriers and facilitators to the use of protocols, and further refined them to produce a set of summary statements. We used the Confidence in the Evidence from Reviews of Qualitative Research (CERQual) framework to arrive at a final assessment of the overall confidence of the evidence used in the synthesis. We included all studies but undertook two sensitivity analyses to determine how the removal of certain bodies of evidence impacted on the content and confidence of the synthesis. We deployed a logic model to integrate the findings of the qualitative evidence synthesis with those of the Cochrane effectiveness reviews.

Main results:
We included 11 studies in our synthesis, involving 267 participants (one study did not report the number of participants). Five more studies are awaiting classification and will be dealt with when we update the review.

The quality of the evidence was mixed; of the 35 summary statements, we assessed 17 as ‘low’, 13 as ‘moderate’ and five as ‘high’ confidence. Our synthesis produced nine analytical themes, which report potential barriers and facilitators to the use of protocols. The themes are: the need for continual staff training and development; clinical experience as this promotes felt and perceived competence and confidence to wean; the vulnerability of weaning to disparate interprofessional working; an understanding of protocols as militating against a necessary proactivity in clinical practice; perceived nursing scope of practice and professional risk; ICU structure and processes of care; the ability of protocols to act as a prompt for shared care and consistency in weaning practice; maximizing the use of protocols through visibility and ease of implementation; and the ability of protocols to act as a framework for communication with parents.

Authors' conclusions:
There is a clear need for weaning protocols to take account of the social and cultural environment in which they are to be implemented. Irrespective of its inherent strengths, a protocol will not be used if it does not accommodate these complexities. In terms of protocol development, comprehensive interprofessional input will help to ensure broad-based understanding and a sense of ‘ownership’. In terms of implementation, all relevant ICU staff will benefit from general weaning as well as protocol-specific training; not only will this help secure a relevant clinical knowledge base and operational understanding, but will also demonstrate to others that this knowledge and understanding is in place. In order to maximize relevance and acceptability, protocols should be designed with the patient profile and requirements of the target ICU in mind. Predictably, an under-resourced ICU will impact adversely on protocol implementation, as staff will prioritize management of acutely deteriorating and critically-ill patients.

Parker Morris and the Fordist House

6.00 pm. If people like watching T.V. while they are eating their evening meal, space for a low table is needed (Ministry of Housing and Local Government, Space in the Home, 1963, p. 4).

This paper re-examines the 1961 Parker Morris report on housing standards in Britain. It explores the origins, scope, text and iconography of the report and suggests that these not only express a particularly modernist conception of space but one which presupposed very specific economic conditions and geographies.

Also known as Homes for Today and Tomorrow Parker Morris attempted, through the application of scientific principles, to define the minimum living space standards needed to accommodate household activities. But while early modernist research into notions of existenzminimum were the work of avant-garde architects and thinkers, Homes for Today and Tomorrow and its sister design manual Space in the Home were commissioned by the British State. This normalization of scientific enquiry into space can be considered not only as a response to new conditions in the mass production of housing – economies of scale, prefabrication, system-building and modular coordination – but also to the post-war boom in consumer goods. In this, it is suggested that the domestic interior was assigned a key role as a privileged site of mass consumption as the production and micro-management of space in Britain became integral to the development of a planned national economy underpinned by Fordist principles. Parker Morris, therefore, sought to accommodate activities which were pre-determined not so much by traditional social or familial ties but rather by recently introduced commodities such as the television set, white goods, table tennis tables and train sets. This relationship between the domestic interior and the national economy are emblematized by the series of placeless and scale-less diagrams executed by Gordon Cullen in Space in the Home. Here, walls dissolve as space flows from inside to outside in a homogenized and ephemeral landscape whose limits are perhaps only the boundaries of the nation state and the circuits of capital.

In Britain, Parker Morris was the last explicit State-sponsored attempt to prescribe a normative spatial programme for national living. The calm neutral efficiency of family-life expressed in its diagrams was almost immediately problematised by the rise of 1960s counter-culture, the feminist movement and the oil crisis of 1972 which altered perhaps forever the spatial, temporal and economic conditions it had taken for granted. The debate on space-standards, however, continues.

Initiating advance care planning on end-of-life issues in dementia: Ambiguity among UK and Dutch physicians

Background
In dementia, advance care planning (ACP) of end-of-life issues may start as early as possible in view of the patient’s decreasing ability to participate in decision making. We aimed to assess whether practicing physicians in the Netherlands and the United Kingdom who provide most of the end-of-life care, differ in finding that ACP in dementia should start at diagnosis.

Methods
In a cross-sectional study, we surveyed 188 Dutch elderly care physicians who are on the staff of nursing homes and 133 general practitioners from Northern Ireland. We compared difference by country in the outcome (perception of ACP timing), rated on a 1–5 agreement scale. Regression analyses examined whether a country difference can be explained by contrasts in demographics, presence, exposure and role perceptions.

Results
There was wide variability in agreement with the initiation of ACP at dementia diagnosis, in particular in the UK but also in the Netherlands (60.8% agreed, 25.3% disagreed and 14.0% neither agreed, nor disagreed). Large differences in physician characteristics (Dutch physicians being more present, exposed and adopting a stronger role perception) hardly explained the modest country difference. The perception that the physician should take the initiative was independently associated with agreeing with ACP at diagnosis.

Conclusions
There is considerable ambiguity about initiating ACP in dementia at diagnosis among physicians practicing in two different European health care systems and caring for different patient populations. ACP strategies should accommodate not only variations in readiness to engage in ACP early among patient and families, but also among physicians.