The predictive science of community ecology

Body mass measures provide a tantalizing tool for explaining both variation in emergent community-level patterns and as a mechanistic basis for fundamental processes such as metabolism, consumption and competition. The unification of body mass, abundance and food web (ecological network) structure in community ecology is an effective way to explore future scenarios of environmental change. However, constraints over the availability of data against which to validate model predictions limit the application of size-based approaches. Here, I explore issues over the use of body size for predicting interaction strengths and hence the dynamics of natural ecosystems. The advantages, disadvantages, opportunities and limitations of such approaches are explored. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society.

The forgiving tree: a self-healing distributed data structure

We consider the problem of self-healing in peer-to-peer networks that are under repeated attack by an omniscient adversary. We assume that the following process continues for up to n rounds where n is the total number of nodes initially in the network: the adversary deletesan arbitrary node from the network, then the network responds by quickly adding a small number of new edges.

We present a distributed data structure that ensures two key properties. First, the diameter of the network is never more than O(log Delta) times its original diameter, where Delta is the maximum degree of the network initially. We note that for many peer-to-peer systems, Delta is polylogarithmic, so the diameter increase would be a O(loglog n) multiplicative factor. Second, the degree of any node never increases by more than 3 over its original degree. Our data structure is fully distributed, has O(1) latency per round and requires each node to send and receive O(1) messages per round. The data structure requires an initial setup phase that has latency equal to the diameter of the original network, and requires, with high probability, each node v to send O(log n) messages along every edge incident to v. Our approach is orthogonal and complementary to traditional topology-based approaches to defending against attack.

Picking up the Pieces: Self-Healing in reconfigurable networks

We consider the problem of self-healing in networks that are reconfigurable in the sense that they can change their topology during an attack. Our goal is to maintain connectivity in these networks, even in the presence of repeated adversarial node deletion, by carefully adding edges after each attack. We present a new algorithm, DASH, that provably ensures that: 1) the network stays connected even if an adversary deletes up to all nodes in the network; and 2) no node ever increases its degree by more than 2 log n, where n is the number of nodes initially in the network. DASH is fully distributed; adds new edges only among neighbors of deleted nodes; and has average latency and bandwidth costs that are at most logarithmic in n. DASH has these properties irrespective of the topology of the initial network, and is thus orthogonal and complementary to traditional topology- based approaches to defending against attack. We also prove lower-bounds showing that DASH is asymptotically optimal in terms of minimizing maximum degree increase over multiple attacks. Finally, we present empirical results on power-law graphs that show that DASH performs well in practice, and that it significantly outperforms naive algorithms in reducing maximum degree increase.

DNA hypermethylation and DNA hypomethylation is present at different loci in chronic kidney disease

Genetic risk factors for chronic kidney disease (CKD) are being identified through international collaborations. By comparison, epigenetic risk factors for CKD have only recently been considered using population-based approaches. DNA methylation is a major epigenetic modification that is associated with complex diseases, so we investigated methylome-wide loci for association with CKD. A total of 485,577 unique features were evaluated in 255 individuals with CKD (cases) and 152 individuals without evidence of renal disease (controls). Following stringent quality control, raw data were quantile normalized and β values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls with resultant P values adjusted for multiple testing. Genes with significantly increased and decreased levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways in Partek Genomics Suite. Twenty-three genes, where more than one CpG per loci was identified with Padjusted < 10−8, demonstrated significant methylation changes associated with CKD and additional support for these associated loci was sought from published literature. Strong biological candidates for CKD that showed statistically significant differential methylation include CUX1, ELMO1, FKBP5, INHBA-AS1, PTPRN2, and PRKAG2 genes; several genes are differentially methylated in kidney tissue and RNA-seq supports a functional role for differential methylation in ELMO1 and PRKAG2 genes. This study reports the largest, most comprehensive, genome-wide quantitative evaluation of DNA methylation for association with CKD. Evidence confirming methylation sites influence development of CKD would stimulate research to identify epigenetic therapies that might be clinically useful for CKD.

Predictive Maintenance for Improved Sustainability - An Ion Beam Etch Endpoint Detection System Use Case

In modern semiconductor manufacturing facilities maintenance strategies are increasingly shifting from traditional preventive maintenance (PM) based approaches to more efficient and sustainable predictive maintenance (PdM) approaches. This paper describes the development of such an online PdM module for the endpoint detection system of an ion beam etch tool in semiconductor manufacturing. The developed system uses optical emission spectroscopy (OES) data from the endpoint detection system to estimate the RUL of lenses, a key detector component that degrades over time. Simulation studies for historical data for the use case demonstrate the effectiveness of the proposed PdM solution and the potential for improved sustainability that it affords.

ZIL: An Energy-Efficient Indoor Localization System Using ZigBee Radio to Detect WiFi Fingerprints

In existing WiFi-based localization methods, smart mobile devices consume quite a lot of power as WiFi interfaces need to be used for frequent AP scanning during the localization process. In this work, we design an energy-efficient indoor localization system called ZigBee assisted indoor localization (ZIL) based on WiFi fingerprints via ZigBee interference signatures. ZIL uses ZigBee interfaces to collect mixed WiFi signals, which include non-periodic WiFi data and periodic beacon signals. However, WiFi APs cannot be identified from these WiFi signals by ZigBee interfaces directly. To address this issue, we propose a method for detecting WiFi APs to form WiFi fingerprints from the signals collected by ZigBee interfaces. We propose a novel fingerprint matching algorithm to align a pair of fingerprints effectively. To improve the localization accuracy, we design the K-nearest neighbor (KNN) method with three different weighted distances and find that the KNN algorithm with the Manhattan distance performs best. Experiments show that ZIL can achieve the localization accuracy of 87%, which is competitive compared to state-of-the-art WiFi fingerprint-based approaches, and save energy by 68% on average compared to the approach based on WiFi interface.

Knowledge translation in men’s health research: development and delivery of content for use online

Background: Men can be hard to reach with face-to-face health-related information, while increasingly, research shows that they are seeking health information from online sources. Recognizing this trend, there is merit in developing innovative online knowledge translation (KT) strategies capable of translating research on men’s health into engaging health promotion materials. While the concept of KT has become a new mantra for researchers wishing to bridge the gap between research evidence and improved health outcomes, little is written about the process, necessary skills, and best practices by which researchers can develop online knowledge translation.
Objective: Our aim was to illustrate some of the processes and challenges involved in, and potential value of, developing research knowledge online to promote men’s health.

Methods: We present experiences of KT across two case studies of men’s health. First, we describe a study that uses interactive Web apps to translate knowledge relating to Canadian men’s depression. Through a range of mechanisms, study findings were repackaged with the explicit aim of raising awareness and reducing the stigma associated with men’s depression and/or help-seeking. Second, we describe an educational resource for teenage men about unintended pregnancy, developed for delivery in the formal Relationship and Sexuality Education school curricula of Ireland, Northern Ireland (United Kingdom), and South Australia. The intervention is based around a Web-based interactive film drama entitled “If I Were Jack”.

Results: For each case study, we describe the KT process and strategies that aided development of credible and well-received online content focused on men’s health promotion. In both case studies, the original research generated the inspiration for the interactive online content and the core development strategy was working with a multidisciplinary team to develop this material through arts-based approaches. In both cases also, there is an acknowledgment of the need for gender and culturally sensitive information. Both aimed to engage men by disrupting stereotypes about men, while simultaneously addressing men through authentic voices and faces. Finally, in both case studies we draw attention to the need to think beyond placement of content online to delivery to target audiences from the outset.

Conclusions: The case studies highlight some of the new skills required by academics in the emerging paradigm of translational research and contribute to the nascent literature on KT. Our approach to online KT was to go beyond dissemination and diffusion to actively repackage research knowledge through arts-based approaches (videos and film scripts) as health promotion tools, with optimal appeal, to target male audiences. Our findings highlight the importance of developing a multidisciplinary team to inform the design of content, the importance of adaptation to context, both in terms of the national implementation context and consideration of gender-specific needs, and an integrated implementation and evaluation framework in all KT work.

Genomics and the impact of new technologies on the management of colorectal cancer

High-throughput genomic technologies have the potential to have a major impact on preclinical and clinical drug development and the selection and stratification of patients in clinical trials. These technologies, which are at varying stages of commercialization, include array-based comparative genomic hybridization, single-nucleotide polymorphism arrays, and (the most mature example) expression-based arrays. One of the rate-limiting steps in the routine clinical application of expression array-based technology is the need for suitable clinical samples. One of the major challenges moving forward, therefore, relates to the ability to use formalin-fixed, paraffin-embedded--derived tissue in expression profiling-based approaches.

The Imagined Contact Hypothesis

Imagined intergroup contact (Crisp & Turner, 2009) is a new indirect contact strategy for promoting tolerance and more positive intergroup relations. Research has shown that mentally simulating a positive interaction with an outgroup member can elicit more favorable explicit and implicit outgroup attitudes, less stereotyping, and enhance intentions to engage in future contact. This review documents the range of benefits that accrue from imagined contact, the processes through which it operates, and the conditions that limit or enhance its effectiveness. Studies have shown when, how, and why imagining contact reduces prejudice against a range of different target groups, and how it can be integrated with existing contact-based approaches to provide maximally effective strategies for improving intergroup relations. The approach is not without its critics, and this review addresses the controversies and debates stimulated by imagined contact theory and research. The review concludes with a discussion of the value that imagery techniques can bring to implementations of contact theory, and how the approach offers a new, flexible, and effective tool for practitioners and policy makers in their efforts to promote, encourage, and enhance more harmonious intergroup relations.

Foreign Direct Investment and Country Risk::Is There Evidence of 'Malign Investment in the Former Soviet States'

This paper examines the relationship between concepts of MNE bargaining power and broader concepts of political power. It notes that the analysis of MNE bargaining power presents a number of puzzles from the perspective of political theory. These puzzles arise, in part, from the fact that the overlap between traditional concepts of MNE bargaining power and broader concepts of political power is only a partial one. Despite these problems, it is suggested that political- theory-based approaches can add realism to our understanding of bargaining power.

(223)Ra and other bone-targeting radiopharmaceuticals-the translation of radiation biology into clinical practice

Osseous metastases are a source of significant morbidity for patients with a variety of cancers. Radiotherapy is well established as an effective means of palliating symptoms associated with such metastases. The role of external beam radiotherapy is limited where sites of metastases are numerous and widespread. Low linear energy transfer (LET) radionuclides have been utilized to allow targeted delivery of radiotherapy to disparate sites of disease, with evidence of palliative benefit. More recently, the bone targeting, high LET radionuclide (223)Ra has been shown to not only have a palliative effect but also a survival prolonging effect in metastatic, castration-resistant prostate cancer with bone metastases. This article reviews the different radionuclide-based approaches for targeting bone metastases, with an emphasis on (223)Ra, and key elements of the underlying radiobiology of these that will impact their clinical effectiveness. Consideration is given to the remaining unknowns of both the basic radiobiological and applied clinical effects of (223)Ra as targets for future research.

Simulating reinforced concrete members. Part 1: partial interaction properties

Reinforced concrete members are extremely complex under loading because of localised deformations in the concrete (cracks, sliding planes) and between the reinforcement and concrete (slip). An ideal model for simulating behaviour of reinforced concrete members should incorporate both global behaviour and the localised behaviours that are seen and measured in practice; these localised behaviours directly affect the global behaviour. Most commonly used models do not directly simulate these localised behaviours that can be seen or measured in real members; instead, they overcome these limitations by using empirically or semi-empirically derived strain-based pseudo properties such as the use of effective flexural rigidities for deflection; plastic hinge lengths for strength and ductility; and energy-based approaches for both concrete softening in compression and concrete softening after tensile cracking to allow for tension stiffening. Most reinforced concrete member experimental testing is associated with deriving these pseudo properties for use in design and analysis, and this component of development is thus costly. The aim of the present research is to reduce this cost substantially. In this paper, localised material behaviours and the mechanisms they induce are described. Their incorporation into reinforced concrete member behaviour without the need for empirically derived pseudo properties is described in a companion paper.

Chromatin immunoprecipitation (ChIP) methodology and readouts

The identification of direct nuclear hormone receptor gene targets provides clues to their contribution to both development and cancer progression. Until recently, the identification of such direct target genes has relied on a combination of expression analysis and in silico searches for consensus binding motifs in gene promoters. Consensus binding motifs for transcription factors are often defined using in vitro DNA binding strategies. Such in vitro strategies fail to account for the many factors that contribute significantly to target selection by transcription factors in cells beyond the recognition of these short consensus DNA sequences. These factors include DNA methylation, chromatin structure, posttranslational modifications of transcription factors, and the cooperative recruitment of transcription factor complexes. Chromatin immunoprecipitation (ChIP) provides a means of isolating transcription factor complexes in the context of endogenous chromatin, allowing the identification of direct transcription factor targets. ChIP can be combined with site-specific PCR for candidate binding sites or alternatively with cloning, genomic microarrays or more recently direct high throughput sequencing to identify novel genomic targets. The application of ChIP-based approaches has redefined consensus binding motifs for transcription factors and provided important insights into transcription factor biology.

Experiencing Youth Justice: Process, Meaning and Legitimacy

Reform of the youth justice system, including the wide incorporation of restorative justice approaches, was a central component of the Criminal Justice Review (2000). Following the devolution of policing and justice powers to the Assembly, the Youth Justice Review (2011) made a series of recommendations for further reforms. These included proposals for the introduction of a statutory time limit in youth cases to tackle avoidable delay. Strengthening legitimacy and advancing rights-based approaches are key themes underpinning the recommendations of Youth Justice Review (2011). Young people’s views of justice within the system are critical to our understanding of how such aims can be achieved. This presentation is based on findings from a longitudinal qualitative study exploring young people’s experiences of transitions into and from custody in the Juvenile Justice Centre. Using a life-history approach young people’s experiences of justice at various stages of the criminal justice process and in the wider context of their lives is explored. Key issues such as social contexts, legitimacy and perceptions of fairness are highlighted and the implications of this for system reform are critically examined.