The Time Machine: A Simulation Approach for Stochastic Trees

In the following paper we consider a simulation technique for stochastic trees. One of the most important areas in computational genetics is the calculation and subsequent maximization of the likelihood function associated to such models. This typically consists of using importance sampling (IS) and sequential Monte Carlo (SMC) techniques. The approach proceeds by simulating the tree, backward in time from observed data, to a most recent common ancestor (MRCA). However, in many cases, the computational time and variance of estimators are often too high to make standard approaches useful. In this paper we propose to stop the simulation, subsequently yielding biased estimates of the likelihood surface. The bias is investigated from a theoretical point of view. Results from simulation studies are also given to investigate the balance between loss of accuracy, saving in computing time and variance reduction.Comment: 22 Pages, 5 Figure

Understanding decision making about major surgery: protocol for a qualitative study of shared decision making by high-risk patients and their clinical teams.

INTRODUCTION: Surgical treatments are being offered to more patients than ever before, and increasingly to high-risk patients (typically multimorbid and over 75). Shared decision making is seen as essential practice. However, little is currently known about what 'good' shared decision making involves nor how it applies in the context of surgery for high-risk patients. This new study aims to identify how high-risk patients, their families and clinical teams negotiate decision making for major surgery. METHODS AND ANALYSIS: Focusing on major joint replacement, colorectal and cardiac surgery, we use qualitative methods to explore how patients, their families and clinicians negotiate decision making (including interactional, communicative and informational aspects and the extent to which these are perceived as shared) and reflect back on the decisions they made. Phase 1 involves video recording 15 decision making encounters about major surgery between patients, their carers/families and clinicians; followed by up to 90 interviews (with the same patient, carer and clinician participants) immediately after a decision has been made and again 3-6 months later. Phase 2 involves focus groups with a wider group of (up to 90) patients and (up to 30) clinicians to test out emerging findings and inform development of shared decision making scenarios (3-5 summary descriptions of how decisions are made). ETHICS AND DISSEMINATION: The study forms the first part in a 6-year programme of research, Optimising Shared decision-makIng for high-RIsk major Surgery (OSIRIS). Ethical challenges around involving patients at a challenging time in their lives will be overseen by the programme steering committee, which includes strong patient representation and a lay chair. In addition to academic outputs, we will produce a typology of decision making scenarios for major surgery to feed back to patients, professionals and service providers and inform subsequent work in the OSIRIS programme

An Adaptive Interacting Wang-Landau Algorithm for Automatic Density Exploration

While statisticians are well-accustomed to performing exploratory analysis in the modeling stage of an analysis, the notion of conducting preliminary general-purpose exploratory analysis in the Monte Carlo stage (or more generally, the model-fitting stage) of an analysis is an area which we feel deserves much further attention. Towards this aim, this paper proposes a general-purpose algorithm for automatic density exploration. The proposed exploration algorithm combines and expands upon components from various adaptive Markov chain Monte Carlo methods, with the Wang-Landau algorithm at its heart. Additionally, the algorithm is run on interacting parallel chains -- a feature which both decreases computational cost as well as stabilizes the algorithm, improving its ability to explore the density. Performance is studied in several applications. Through a Bayesian variable selection example, the authors demonstrate the convergence gains obtained with interacting chains. The ability of the algorithm's adaptive proposal to induce mode-jumping is illustrated through a trimodal density and a Bayesian mixture modeling application. Lastly, through a 2D Ising model, the authors demonstrate the ability of the algorithm to overcome the high correlations encountered in spatial models.Comment: 33 pages, 20 figures (the supplementary materials are included as appendices

Beryllium abundances in stars hosting giant planets

We have derived beryllium abundances in a wide sample of stars hosting planets, with spectral types in the range F7V-K0V, aimed at studying in detail the effects of the presence of planets on the structure and evolution of the associated stars. Predictions from current models are compared with the derived abundances and suggestions are provided to explain the observed inconsistencies. We show that while still not clear, the results suggest that theoretical models may have to be revised for stars with Teff<5500K. On the other hand, a comparison between planet host and non-planet host stars shows no clear difference between both populations. Although preliminary, this result favors a ``primordial'' origin for the metallicity ``excess'' observed for the planetary host stars. Under this assumption, i.e. that there would be no differences between stars with and without giant planets, the light element depletion pattern of our sample of stars may also be used to further investigate and constraint Li and Be depletion mechanisms.Comment: A&A in press -- accepted on the 22/02/2002 (11 pages, 6 figures included

Are beryllium abundances anomalous in stars with giant planets?

In this paper we present beryllium (Be) abundances in a large sample of 41 extra-solar planet host stars, and for 29 stars without any known planetary-mass companion, spanning a large range of effective temperatures. The Be abundances were derived through spectral synthesis done in standard Local Thermodynamic Equilibrium, using spectra obtained with various instruments. The results seem to confirm that overall, planet-host stars have ``normal'' Be abundances, although a small, but not significant, difference might be present. This result is discussed, and we show that this difference is probably not due to any stellar ``pollution'' events. In other words, our results support the idea that the high-metal content of planet-host stars has, overall, a ``primordial'' origin. However, we also find a small subset of planet-host late-F and early-G dwarfs that might have higher than average Be abundances. The reason for the offset is not clear, and might be related either to the engulfment of planetary material, to galactic chemical evolution effects, or to stellar-mass differences for stars of similar temperature.Comment: 15 pages, 9 figures, accepted for publication in Astronomy & Astrophysic

Toileting Abilities Survey as a surrogate outcome measure for cognitive function : findings from neuronopathic mucopolysaccharidosis II patients treated with idursulfase and intrathecal idursulfase

An outcome measure of toileting skills, the Toileting Abilities Survey or TAS, with sensitivity to detect change in a neurodegenerative disorder such as MPS II, was developed. The TAS was used in a research study of patients (n = 86) with the neuronopathic form of MPS II to measure treatment benefit of intrathecal idursulfase. Treatment with idursulfase and intrathecal idursulfase is associated with significantly higher individual and overall toileting skills versus treatment with idursulfase alone.http://www.elsevier.com/locate/ymgmrpm2020Paediatrics and Child Healt

Designing a complex intervention for dementia case management in primary care

Background: Community-based support will become increasingly important for people with dementia, but currently services are fragmented and the quality of care is variable. Case management is a popular approach to care co-ordination, but evidence to date on its effectiveness in dementia has been equivocal. Case management interventions need to be designed to overcome obstacles to care co-ordination and maximise benefit. A successful case management methodology was adapted from the United States (US) version for use in English primary care, with a view to a definitive trial. Medical Research Council guidance on the development of complex interventions was implemented in the adaptation process, to capture the skill sets, person characteristics and learning needs of primary care based case managers. Methods: Co-design of the case manager role in a single NHS provider organisation, with external peer review by professionals and carers, in an iterative technology development process. Results: The generic skills and personal attributes were described for practice nurses taking up the case manager role in their workplaces, and for social workers seconded to general practice teams, together with a method of assessing their learning needs. A manual of information material for people with dementia and their family carers was also created using the US intervention as its source. Conclusions: Co-design produces rich products that have face validity and map onto the complexities of dementia and of health and care services. The feasibility of the case manager role, as described and defined by this process, needs evaluation in ‘real life’ settings

Geographically touring the eastern bloc: British geography, travel cultures and the Cold War

This paper considers the role of travel in the generation of geographical knowledge of the eastern bloc by British geographers. Based on oral history and surveys of published work, the paper examines the roles of three kinds of travel experience: individual private travels, tours via state tourist agencies, and tours by academic delegations. Examples are drawn from across the eastern bloc, including the USSR, Poland, Romania, East Germany and Albania. The relationship between travel and publication is addressed, notably within textbooks, and in the Geographical Magazine. The study argues for the extension of accounts of cultures of geographical travel, and seeks to supplement the existing historiography of Cold War geography

Artificial drainage of peatlands: hydrological and hydrochemical process and wetland restoration

Peatlands have been subject to artificial drainage for centuries. This drainage has been in response to agricultural demand, forestry, horticultural and energy properties of peat and alleviation of flood risk. However, the are several environmental problems associated with drainage of peatlands. This paper describes the nature of these problems and examines the evidence for changes in hydrological and hydrochemical processes associated with these changes. Traditional black-box water balance approaches demonstrate little about wetland dynamics and therefore the science of catchment response to peat drainage is poorly understood. It is crucial that a more process-based approach be adopted within peatland ecosystems. The environmental problems associated with peat drainage have led, in part, to a recent reversal in attitudes to peatlands and we have seen a move towards wetland restoration. However, a detailed understanding of hydrological, hydrochemical and ecological process-interactions will be fundamental if we are to adequately restore degraded peatlands, preserve those that are still intact and understand the impacts of such management actions at the catchment scale

High resolution global climate modelling; the UPSCALE project, a large simulation campaign

The UPSCALE (UK on PRACE: weather-resolving Simulations of Climate for globAL Environmental risk) project constructed and ran an ensemble of HadGEM3 (Hadley Centre Global Environment Model 3) atmosphere only global climate simulations over the period 1985–2011, at resolutions of N512 (25 km), N216 (60 km) and N96 (130 km) as used in current global weather forecasting, seasonal prediction and climate modelling respectively. Alongside these present climate simulations a parallel ensemble looking at extremes of future climate was run, using a timeslice methodology to consider conditions at the end of this century. These simulations were primarily performed using a 144 million core hour, single year grant of computing time from PRACE (the Partnership for Advanced Computing in Europe) in 2012, with additional resources supplied by the Natural Environment Research Council (NERC) and the Met Office. Almost 400 terabytes of simulation data were generated on the HERMIT supercomputer at the High Performance Computing Center Stuttgart (HLRS), and transferred to the JASMIN super-data cluster provided by the Science and Technology Facilities Council Centre for Data Archival (STFC CEDA) for analysis and storage. In this paper we describe the implementation of the project, present the technical challenges in terms of optimisation, data output, transfer and storage that such a project involves and include details of the model configuration and the composition of the UPSCALE data set. This data set is available for scientific analysis to allow assessment of the value of model resolution in both present and potential future climate conditions