A Comparison of Two Shallow Water Models with Non-Conforming Adaptive Grids: classical tests

In an effort to study the applicability of adaptive mesh refinement (AMR) techniques to atmospheric models an interpolation-based spectral element shallow water model on a cubed-sphere grid is compared to a block-structured finite volume method in latitude-longitude geometry. Both models utilize a non-conforming adaptation approach which doubles the resolution at fine-coarse mesh interfaces. The underlying AMR libraries are quad-tree based and ensure that neighboring regions can only differ by one refinement level. The models are compared via selected test cases from a standard test suite for the shallow water equations. They include the advection of a cosine bell, a steady-state geostrophic flow, a flow over an idealized mountain and a Rossby-Haurwitz wave. Both static and dynamics adaptations are evaluated which reveal the strengths and weaknesses of the AMR techniques. Overall, the AMR simulations show that both models successfully place static and dynamic adaptations in local regions without requiring a fine grid in the global domain. The adaptive grids reliably track features of interests without visible distortions or noise at mesh interfaces. Simple threshold adaptation criteria for the geopotential height and the relative vorticity are assessed.Comment: 25 pages, 11 figures, preprin

Molecular subtyping of bladder cancer using Kohonen self-organizing maps

Kohonen self-organizing maps (SOMs) are unsupervised Artificial Neural Networks (ANNs) that are good for low-density data visualization. They easily deal with complex and nonlinear relationships between variables. We evaluated molecular events that characterize high- and low-grade BC pathways in the tumors from 104 patients. We compared the ability of statistical clustering with a SOM to stratify tumors according to the risk of progression to more advanced disease. In univariable analysis, tumor stage (log rank P = 0.006) and grade (P < 0.001), HPV DNA (P < 0.004), Chromosome 9 loss (P = 0.04) and the A148T polymorphism (rs 3731249) in CDKN2A (P = 0.02) were associated with progression. Multivariable analysis of these parameters identified that tumor grade (Cox regression, P = 0.001, OR.2.9 (95% CI 1.6–5.2)) and the presence of HPV DNA (P = 0.017, OR 3.8 (95% CI 1.3–11.4)) were the only independent predictors of progression. Unsupervised hierarchical clustering grouped the tumors into discreet branches but did not stratify according to progression free survival (log rank P = 0.39). These genetic variables were presented to SOM input neurons. SOMs are suitable for complex data integration, allow easy visualization of outcomes, and may stratify BC progression more robustly than hierarchical clustering

Physics–Dynamics Coupling in weather, climate and Earth system models: Challenges and recent progress

This is the final version. Available from American Meteorological Society via the DOI in this record.Numerical weather, climate, or Earth system models involve the coupling of components. At a broad level, these components can be classified as the resolved fluid dynamics, unresolved fluid dynamical aspects (i.e., those represented by physical parameterizations such as subgrid-scale mixing), and nonfluid dynamical aspects such as radiation and microphysical processes. Typically, each component is developed, at least initially, independently. Once development is mature, the components are coupled to deliver a model of the required complexity. The implementation of the coupling can have a significant impact on the model. As the error associated with each component decreases, the errors introduced by the coupling will eventually dominate. Hence, any improvement in one of the components is unlikely to improve the performance of the overall system. The challenges associated with combining the components to create a coherent model are here termed physics–dynamics coupling. The issue goes beyond the coupling between the parameterizations and the resolved fluid dynamics. This paper highlights recent progress and some of the current challenges. It focuses on three objectives: to illustrate the phenomenology of the coupling problem with references to examples in the literature, to show how the problem can be analyzed, and to create awareness of the issue across the disciplines and specializations. The topics addressed are different ways of advancing full models in time, approaches to understanding the role of the coupling and evaluation of approaches, coupling ocean and atmosphere models, thermodynamic compatibility between model components, and emerging issues such as those that arise as model resolutions increase and/or models use variable resolutions.Natural Environment Research Council (NERC)National Science FoundationDepartment of Energy Office of Biological and Environmental ResearchPacific Northwest National Laboratory (PNNL)DOE Office of Scienc

Multimodality imaging: Bird’s eye view from The European Society of Cardiology Congress 2015 London, August 29-September 2, 2015

Cardiolog

Impact of gastroesophageal reflux disease on patients' daily lives: a European observational study in the primary care setting

<p>Abstract</p> <p>Background</p> <p>The impact of gastroesophageal reflux disease (GERD) on the daily lives of patients managed in primary care is not well known. We report the burden of GERD in a large population of patients managed in primary care, in terms of symptoms and impact on patients' daily lives.</p> <p>Methods</p> <p>RANGE (<it>R</it>etrospective <it>AN</it>alysis of <it>GE</it>RD) was an observational study that was conducted at 134 primary care sites across six European countries. All adult subjects who had consulted their primary care physician (PCP) during a 4-month identification period were screened retrospectively and those consulting at least once for GERD-related reasons were identified. From this population, a random sample of patients was selected to enter the study and attended a follow-up appointment, during which the Reflux Disease Questionnaire (RDQ), the GERD Impact Scale (GIS) and an extra-esophageal symptoms questionnaire were self-administered. Based on medical records, data were collected on demographics, history of GERD, its diagnostic work-up and therapy.</p> <p>Results</p> <p>Over the 4-month identification period, 373,610 subjects consulted their PCP and 12,815 (3.4%) did so for GERD-related reasons. From 2678 patients interviewed (approximately 75% of whom reported taking medication for GERD symptoms), symptom recurrence following a period of remission was the most common reason for consultation (35%). At the follow-up visit, with regard to RDQ items (score range 0–5, where high score = worse status), mean Heartburn dimension scores ranged from 0.8 (Sweden) to 1.2 (UK) and mean Regurgitation dimension scores ranged from 1.0 (Norway) to 1.4 (Germany). Mean overall GIS scores (range 1–4, where low score = worse status) ranged from 3.3 (Germany) to 3.5 (Spain). With regard to extra-esophageal symptoms, sleep disturbance was common in all countries in terms of both frequency and intensity.</p> <p>Conclusion</p> <p>In this large European observational study, GERD was associated with a substantial impact on the daily lives of affected individuals managed in the primary care setting.</p