Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

Development and validation of the Diabetes Numeracy Test (DNT)

<p>Abstract</p> <p>Background</p> <p>Low literacy and numeracy skills are common. Adequate numeracy skills are crucial in the management of diabetes. Diabetes patients use numeracy skills to interpret glucose meters, administer medications, follow dietary guidelines and other tasks. Existing literacy scales may not be adequate to assess numeracy skills. This paper describes the development and psychometric properties of the Diabetes Numeracy Test (DNT), the first scale to specifically measure numeracy skills used in diabetes.</p> <p>Methods</p> <p>The items of the DNT were developed by an expert panel and refined using cognitive response interviews with potential respondents. The final version of the DNT (43 items) and other relevant measures were administered to a convenience sample of 398 patients with diabetes. Internal reliability was determined by the Kuder-Richardson coefficient (KR-20). An <it>a priori </it>hypothetical model was developed to determine construct validity. A shortened 15-item version, the DNT15, was created through split sample analysis.</p> <p>Results</p> <p>The DNT had excellent internal reliability (KR-20 = 0.95). The DNT was significantly correlated (p < 0.05) with education, income, literacy and math skills, and diabetes knowledge, supporting excellent construct validity. The mean score on the DNT was 61% and took an average of 33 minutes to complete. The DNT15 also had good internal reliability (KR-20 = 0.90 and 0.89). In split sample analysis, correlations of the DNT-15 with the full DNT in both sub-samples was high (rho = 0.96 and 0.97, respectively).</p> <p>Conclusion</p> <p>The DNT is a reliable and valid measure of diabetes related numeracy skills. An equally adequate but more time-efficient version of the DNT, the DNT15, can be used for research and clinical purposes to evaluate diabetes related numeracy.</p

Towards computerizing intensive care sedation guidelines: design of a rule-based architecture for automated execution of clinical guidelines

<p>Abstract</p> <p>Background</p> <p>Computerized ICUs rely on software services to convey the medical condition of their patients as well as assisting the staff in taking treatment decisions. Such services are useful for following clinical guidelines quickly and accurately. However, the development of services is often time-consuming and error-prone. Consequently, many care-related activities are still conducted based on manually constructed guidelines. These are often ambiguous, which leads to unnecessary variations in treatments and costs.</p> <p>The goal of this paper is to present a semi-automatic verification and translation framework capable of turning manually constructed diagrams into ready-to-use programs. This framework combines the strengths of the manual and service-oriented approaches while decreasing their disadvantages. The aim is to close the gap in communication between the IT and the medical domain. This leads to a less time-consuming and error-prone development phase and a shorter clinical evaluation phase.</p> <p>Methods</p> <p>A framework is proposed that semi-automatically translates a clinical guideline, expressed as an XML-based flow chart, into a Drools Rule Flow by employing semantic technologies such as ontologies and SWRL. An overview of the architecture is given and all the technology choices are thoroughly motivated. Finally, it is shown how this framework can be integrated into a service-oriented architecture (SOA).</p> <p>Results</p> <p>The applicability of the Drools Rule language to express clinical guidelines is evaluated by translating an example guideline, namely the sedation protocol used for the anaesthetization of patients, to a Drools Rule Flow and executing and deploying this Rule-based application as a part of a SOA. The results show that the performance of Drools is comparable to other technologies such as Web Services and increases with the number of decision nodes present in the Rule Flow. Most delays are introduced by loading the Rule Flows.</p> <p>Conclusions</p> <p>The framework is an effective solution for computerizing clinical guidelines as it allows for quick development, evaluation and human-readable visualization of the Rules and has a good performance. By monitoring the parameters of the patient to automatically detect exceptional situations and problems and by notifying the medical staff of tasks that need to be performed, the computerized sedation guideline improves the execution of the guideline.</p

Oxidative discolouration in whole-head and cut lettuce: biochemical and environmental influences on a complex phenotype and potential breeding strategies to improve shelf-life

Lettuce discolouration is a key post-harvest trait. The major enzyme controlling oxidative discolouration has long been considered to be polyphenol oxidase (PPO) however, levels of PPO and subsequent development of discolouration symptoms have not always correlated. The predominance of a latent state of the enzyme in plant tissues combined with substrate activation and contemporaneous suicide inactivation mechanisms are considered as potential explanations for this phenomenon. Leaf tissue physical properties have been associated with subsequent discolouration and these may be influenced by variation in nutrient availability, especially excess nitrogen and head maturity at harvest. Mild calcium and irrigation stress has also been associated with a reduction in subsequent discolouration, although excess irrigation has been linked to increased discolouration potentially through leaf physical properties. These environmental factors, including high temperature and UV light intensities, often have impacts on levels of phenolic compounds linking the environmental responses to the biochemistry of the PPO pathway. Breeding strategies targeting the PALand PPOpathway biochemistry and environmental response genes are discussed as a more cost-effective method of mitigating oxidative discolouration then either modified atmosphere packaging or post-harvest treatments, although current understanding of the biochemistry means that such programs are likely to be limited in nature and it is likely that they will need to be deployed alongside other methods for the foreseeable future

Lifelogging: Privacy and Empowerment with Memories for Life

The growth of information acquisition, storage and retrieval capacity has led to the development of the practice of lifelogging, the undiscriminating collection of information concerning one’s life and behaviour. There are potential problems in this practice, but equally it could be empowering for the individual, and provide a new locus for the construction of an online identity. In this paper we look at the technological possibilities and constraints for lifelogging tools, and set out some of the most important privacy, identity and empowerment-related issues. We argue that some of the privacy concerns are overblown, and that much research and commentary on lifelogging has made the unrealistic assumption that the information gathered is for private use, whereas, in a more socially-networked online world, much of it will have public functions and will be voluntarily released into the public domain