Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

DREAM is an initiative that allows researchers to assess how well their methods or approaches can describe and predict networks of interacting molecules [1]. Each year, recently acquired datasets are released to predictors ahead of publication. Researchers typically have about three months to predict the masked data or network of interactions, using any predictive method. Predictions are assessed prior to an annual conference where the best predictions are unveiled and discussed. Here we present the strategy we used to make a winning prediction for the DREAM3 phosphoproteomics challenge. We used Amelia II, a multiple imputation software method developed by Gary King, James Honaker and Matthew Blackwell[2] in the context of social sciences to predict the 476 out of 4624 measurements that had been masked for the challenge. To chose the best possible multiple imputation parameters to apply for the challenge, we evaluated how transforming the data and varying the imputation parameters affected the ability to predict additionally masked data. We discuss the accuracy of our findings and show that multiple imputations applied to this dataset is a powerful method to accurately estimate the missing data. We postulate that multiple imputations methods might become an integral part of experimental design as a mean to achieve cost savings in experimental design or to increase the quantity of samples that could be handled for a given cost.

Geometry and physics of catenanes applied to the study of DNA replication.

The concept of ideal geometric configurations was recently applied to the classification and characterization of various knots. Different knots in their ideal form (i.e., the one requiring the shortest length of a constant-diameter tube to form a given knot) were shown to have an overall compactness proportional to the time-averaged compactness of thermally agitated knotted polymers forming corresponding knots. This was useful for predicting the relative speed of electrophoretic migration of different DNA knots. Here we characterize the ideal geometric configurations of catenanes (called links by mathematicians), i.e., closed curves in space that are topologically linked to each other. We demonstrate that the ideal configurations of different catenanes show interrelations very similar to those observed in the ideal configurations of knots. By analyzing literature data on electrophoretic separations of the torus-type of DNA catenanes with increasing complexity, we observed that their electrophoretic migration is roughly proportional to the overall compactness of ideal representations of the corresponding catenanes. This correlation does not apply, however, to electrophoretic migration of certain replication intermediates, believed up to now to represent the simplest torus-type catenanes. We propose, therefore, that freshly replicated circular DNA molecules, in addition to forming regular catenanes, may also form hemicatenanes.

Understanding the Economics of Investments in the Social Determinants of Health

Briefing 9 - Understanding the economics of investments in the social determinants of health This document, commissioned by Public Health England, and written by the UCL Institute of Health Equity, examines how to use measures of economic investment to improve and increase local investment in the social determinants of health. The paper provides information to support decision-making on actions to address the social determinants of health and the development of business cases for investment. It supplements the evidence reviews in this series, which include information on the economic impacts of actions on health inequalities, and should help the reader to be an intelligent customer and commissioner of economic analyses and to understand their limitations. The paper covers: - The rationale for understanding, measuring and taking into account the economic impact of decisions and interventions that impact on the social determinants of health.- The benefits and limitations of various ‘economic measures of impact’ – commonly used terms which can be confusing, sometimes leading to misinterpretation of which measure of economic impact is appropriate for what purpose.- What is currently known about the economic impact of intervening in the social determinants of health.- Good practice and further resources which will support better decisions. The briefing is available to download above. This document is part of a series. An overview document which provides an introduction to this and other documents in the series, and links to the other topic areas, is available on the ‘Local Action on health inequalities’ project page. A video of Michael Marmot introducing the work is also available on our videos page.

Putting children first: The role of health psychology in applied child/youth research

Overview Part One • Background/context  – defining and thinking about health • The role of the health psychologist • Promoting the psychosocial well being of children and young people • Early intervention and prevention in Ireland • Intervening in the lives of children with emotional and behavioural difficulties   Part Two • Case-study  – The Incredible Years Ireland Study: theory, practice and research   Part Three • Some key considerations in intervention science for research, policy and practice with children and young people   Sinead McGilloway: Putting children first. The role of health psychology

An Introduction to Health Economics & Economic Evaluations

- Overview of Economic Evaluation - Stages in Economic Evaluation  

Introduction to Evaluation and Health Economics

A video summary by Orla Doyle

New imaging techniques applied to Paleogene radiolaria

A simple and time efficient technique to illustrate specimens is described and demonstrated with Paleogene radiolarians. This method produces Scanning Electron Microscope (SEM) and composite focal depth Transmitted Light Microscope (TLM) images for single radiolarian specimens. We propose the use of this technique to clarify radiolarian taxonomy. This technique has distinct advantages over previously published time consuming techniques that can also require toxic materials.

U.S. National Parks and "The Tragedy of the Commons" : A contribution to the characterization of U.S. mountain guides' professional practice

This paper aims at presenting the stakes related to the access to protected land in the United States and to its conservation, through the analysis of the professional practice of U.S. mountain guides. From a methodological standpoint, this research is based both on a theoretical analysis grounded in the field of environmental economics and on an empirical study. The authors' starting point is Garrett Hardin's paper, "The Tragedy of the Commons" (Science, 1968), even if it introduces some confusion on the notion of common goods. So as to avoid this confusion, the authors use two theoretical tools pertaining to a typology of common goods and the different property rights that can be applied in National Parks. Finally, they apply this framework to the observations made on the field in Colorado in July 2009.

Quantitative paleoparasitology applied to archaeological sediments

Three techniques to extract parasite remains from archaeological sediments were tested. The aim was to improve the sensibility of recommended paleoparasitological techniques applied in archaeological remains. Sediment collected from the pelvic girdle of a human body found in Cabo Vírgenes, Santa Cruz, Argentina, associated to a Spanish settlement founded in 1584 known as Nombre de Jesús, was used to search for parasites. Sediment close to the skull was used as control. The techniques recommended by Jones, Reinhard, and Dittmar and Teejen were used and compared with the modified technique presented here, developed to improve the sensibility to detect parasite remains. Positive results were obtained only with the modified technique, resulting in the finding of Trichuris trichiura eggs in the sediment.

Response of Triatoma infestans to pour-on cypermethrin applied to chickens under laboratory conditions

This article reports the effects of a pour-on formulation of cypermethrin (6% active ingredient) applied to chickens exposed to Triatoma infestans, the main vector of Chagas disease in rural houses of the Gran Chaco Region of South America. This study was designed as a completely random experiment with three experimental groups and five replicates. Third instar nymphs were fed on chickens treated with 0, 1 and 2 cc of the formulation. Nymphs were allowed to feed on the chickens at different time intervals after the insecticide application. Third-instar nymphs fed on treated chickens showed a higher mortality, took less blood during feeding and had a lower moulting rate. The mortality rate was highest seven days after the insecticide solution application and blood intake was affected until 30 days after the application of the solution.

Knowledge integration within an applied mobile robot summer course

This paper presents the use of a mobile robot platform as an innovative educational tool in order to promote and integrate different curriculum knowledge. Hence, it is presented the acquired experience within a summer course named ldquoapplied mobile roboticsrdquo. The main aim of the course is to integrate different subjects as electronics, programming, architecture, perception systems, communications, control and trajectory planning by using the educational open mobile robot platform PRIM. The summer course is addressed to a wide range of student profiles. However, it is of special interests to the students of electrical and computer engineering around their final academic year. The summer course consists of the theoretical and laboratory sessions, related to the following topics: design & programming of electronic devices, modelling and control systems, trajectory planning and control, and computer vision systems. Therefore, the clues for achieving a renewed path of progress in robotics are the integration of several knowledgeable fields, such as computing, communications, and control sciences, in order to perform a higher level reasoning and use decision tools with strong theoretical base