On multiple solutions of the Grad–Shafranov equation

The Grad-Shafranov equation (GSE) for axisymmetric MHD equilibria is a nonlinear, scalar PDE which in principle can have zero, one or more non-trivial solutions. The conditions for the existence of multiple solutions has been little explored in the literature so far. We develop a simple analytic model to calculate multiple solutions in the large aspect ratio limit. We compare the results to the recently developed deflated continuation method to find multiple solutions in a realistic geometry and right-hand side of the GSE using the finite element method. The analytic model is surprisingly accurate in calculating multiple solutions of the GSE for given boundary conditions and the two methods agree well in limiting cases. We examine the effect of plasma shaping and aspect ratio on the multiple solutions and show that shaping generally does not alter the number of solutions. We discuss implications for predictive modelling, equilibrium reconstruction, plasma stability and disruptions

A domain-specific language for the hybridization and static condensation of finite element methods

In this paper, we introduce a domain-specific language (DSL) for concisely expressing localized linear algebra on finite element tensors and its integration within a code-generation framework. This DSL is general enough to facilitate the automatic generation of element-based dense linear algebra kernels necessary for the implementation of static condensation methods and local solvers for a variety of problems. We demonstrate its use for the static condensation of continuous Galerkin problems, and systems arising from hybridizing finite element discretizations. We also describe how this DSL can be used to execute local post-processing procedures to construct superconvergent approximations to mixed problems. This work also features high-level implementations of static condensation and hybrid-mixed methods as preconditioners conforming to PETSc's interface for solving linear systems. These preconditioning interfaces provide reduced operators, which are obtained from locally assembled expressions, with the necessary context to specify full solver configurations on the resulting linear systems. We validate our implementations within the context of model second-order elliptic problems. Finally, we conclude with a performance comparison highlighting the use of a hybrid-mixed method as an efficient preconditioner in a semi-implicit method for the nonlinear rotating shallow water equations

Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

Gene network approach reveals co-expression patterns in nasal and bronchial epithelium

© 2019, The Author(s). Nasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate 2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking

The impact of Cochrane Systematic Reviews : a mixed method evaluation of outputs from Cochrane Review Groups supported by the UK National Institute for Health Research

© 2014 Bunn et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: There has been a growing emphasis on evidence-informed decision making in health care. Systematic reviews, such as those produced by the Cochrane Collaboration, have been a key component of this movement. The UK National Institute for Health Research (NIHR) Systematic Review Programme currently supports 20 Cochrane Review Groups (CRGs). The aim of this study was to identify the impacts of Cochrane reviews published by NIHR funded CRGs during the years 2007-11. Methods: We sent questionnaires to CRGs and review authors, interviewed guideline developers and used bibliometrics and documentary review to get an overview of CRG impact and to evaluate the impact of a sample of 60 Cochrane reviews. We used a framework with four categories (knowledge production, research targeting, informing policy development, and impact on practice/services). Results: A total of 1502 new and updated reviews were produced by the 20 NIHR funded CRGs between 2007-11. The clearest impacts were on policy with a total of 483 systematic reviews cited in 247 sets of guidance; 62 were international, 175 national (87 from the UK) and 10 local. Review authors and CRGs provided some examples of impact on practice or services, for example safer use of medication, the identification of new effective drugs or treatments and potential economic benefits through the reduction in the use of unproven or unnecessary procedures. However, such impacts are difficult to objectively document and the majority of reviewers were unsure if their review had produced specific impacts. Qualitative data suggested that Cochrane reviews often play an instrumental role in informing guidance although a poor fit with guideline scope or methods, reviews being out of date and a lack of communication between CRGs and guideline developers were barriers to their use. Conclusions: Health and economic impacts of research are generally difficult to measure. We found that to be the case with this evaluation. Impacts on knowledge production and clinical guidance were easier to identify and substantiate than those on clinical practice. Questions remain about how we define and measure impact and more work is needed to develop suitable methods for impact analysis.Peer reviewe

Weight management interventions in adults with intellectual disabilities and obesity: a systematic review of the evidence

o evaluate the clinical effectiveness of weight management interventions in adults with intellectual disabilities (ID) and obesity using recommendations from current clinical guidelines for the first line management of obesity in adults. Full papers on lifestyle modification interventions published between 1982 to 2011 were sought by searching the Medline, Embase, PsycINFO and CINAHL databases. Studies were evaluated based on 1) intervention components, 2) methodology, 3) attrition rate 4) reported weight loss and 5) duration of follow up. Twenty two studies met the inclusion criteria. The interventions were classified according to inclusion of the following components: behaviour change alone, behaviour change plus physical activity, dietary advice or physical activity alone, dietary plus physical activity advice and multi-component (all three components). The majority of the studies had the same methodological limitations: no sample size justification, small heterogeneous samples, no information on randomisation methodologies. Eight studies were classified as multi-component interventions, of which one study used a 600 kilocalorie (2510 kilojoule) daily energy deficit diet. Study durations were mostly below the duration recommended in clinical guidelines and varied widely. No study included an exercise program promoting 225–300 minutes or more of moderate intensity physical activity per week but the majority of the studies used the same behaviour change techniques. Three studies reported clinically significant weight loss (≥ 5%) at six months post intervention. Current data indicate weight management interventions in those with ID differ from recommended practice and further studies to examine the effectiveness of multi-component weight management interventions for adults with ID and obesity are justified

Climate change, the Great Barrier Reef and the response of Australians

© 2016, Palgrave Macmillan Ltd. All rights reserved. Inspiration, aspirations, attitudes, and perception of threats play a pivotal role in the way that individuals associate themselves with natural environments. These sentiments affect how people connect to natural places, including their behaviours, perceived responsibility, and the management interventions they support. World Heritage Areas hold an important place in the lives of people who visit, aspire to visit, or derive a sense of security and well-being from their existence. Yet, the connection between people and special places is rarely quantified and policymakers find it difficult to incorporate these human dimensions into decision-making processes. Here we describe the personal concern and connection that Australians have with the Great Barrier Reef and discuss how the results may help with its management. We utilize a statistically representative sample of Australian residents (n = 2,002) and show empirically that climate change is perceived to be the biggest threat to the Great Barrier Reef, and that the Great Barrier Reef inspires Australians, promotes pride, and instills a sense of individual identity and collective responsibility to protect it. An increased understanding of the high levels of personal connection to iconic natural resources may help managers to enhance public support for protecting climate-sensitive systems within Australia and around the world

Evapotranspiration and crop coefficients of rice (Oryza sativa L.) under sprinkler irrigation in a semiarid climate determined by the surface renewal method

The evapotranspiration (ETc) of sprinkler-irrigated rice was determined for the semiarid conditions of NE Spain during 2001, 2002 and 2003. The surface renewal method, after calibration against the eddy covariance method, was used to obtain values of sensible heat flux (H) from high-frequency temperature readings. Latent heat flux values were obtained by solving the energy balance equation. Finally, lysimeter measurements were used to validate the evapotranspiration values obtained with the surface renewal method. Seasonal rice evapotranspiration was about 750–800 mm. Average daily ETc for mid-season (from 90 to 130 days after sowing) was 5.1, 4.5 and 6.1 mm day−1 for 2001, 2002 and 2003, respectively. The experimental weekly crop coefficients fluctuated in the range of 0.83–1.20 for 2001, 0.81–1.03 for 2002 and 0.84–1.15 for 2003. The total growing season was about 150–160 days. In average, the crop coefficients for the initial (Kcini), mid-season (Kcmid) and late-season stages (Kcend) were 0.92, 1.06 and 1.03, respectively, the length of these stages being about 55, 45 and 25 days, respectively

The epidemiology and patterns of acute and chronic toxicity associated with recreational ketamine use

Ketamine was originally synthesised for use as a dissociative anaesthetic, and it remains widely used legitimately for this indication. However, there is increasing evidence of non-medical recreational use of ketamine, particularly in individuals who frequent the night-time economy. The population-level and sub-population (clubbers) prevalence of recreational use of ketamine is not known but is likely to be similar, or slightly lower than, that of other recreational drugs such as cocaine, MDMA, and amphetamine