Shared Memory Pipelined Parareal

For the parallel-in-time integration method Parareal, pipelining can be used to hide some of the cost of the serial correction step and improve its efficiency. The paper introduces an OpenMP implementation of pipelined Parareal and compares it to a standard MPI-based variant. Both versions yield almost identical runtimes, but, depending on the compiler, the OpenMP variant consumes about 7% less energy and has a significantly smaller memory footprint. However, its higher implementation complexity might make it difficult to use in legacy codes and in combination with spatial parallelisation

Block Jacobi relaxation for plane wave discontinuous Galerkin methods

In recent years plane wave approximation methods have become popular for the solution of Helmholtz problems, where instead of standard polynomial basis functions plane waves are used on each element to approximate the solution. One possibility to enforce inter-element continuity conditions for these basis functions is to use the plane wave discontinuous Galerkin Method (PWDG). In this paper we investigate block Jacobi relaxation methods for the PWDG. We show that for a certain choice of flux parameters in the PWDG block Jacobi is identical to a Schwarz method with standard impedance boundary conditions. This result motivates a simple algebraic decomposition method whose numerical performance is demonstrated for various wavenumbers. For high-frequency problem it is important to choose optimized transmission conditions between subdomains, and a first result of how to modify fluxes to incorporate optimized transmission conditions is presented

Fast interior point solution of quadratic programming problems arising from PDE-constrained optimization

Interior point methods provide an attractive class of approaches for solving linear, quadratic and nonlinear programming problems, due to their excellent efficiency and wide applicability. In this paper, we consider PDE-constrained optimization problems with bound constraints on the state and control variables, and their representation on the discrete level as quadratic programming problems. To tackle complex problems and achieve high accuracy in the solution, one is required to solve matrix systems of huge scale resulting from Newton iteration, and hence fast and robust methods for these systems are required. We present preconditioned iterative techniques for solving a number of these problems using Krylov subspace methods, considering in what circumstances one may predict rapid convergence of the solvers in theory, as well as the solutions observed from practical computations

Modeling and discretization of flow in porous media with thin, full-tensor permeability inclusions

When modeling fluid flow in fractured reservoirs, it is common to represent the fractures as lower-dimensional inclusions embedded in the host medium. Existing discretizations of flow in porous media with thin inclusions assume that the principal directions of the inclusion permeability tensor are aligned with the inclusion orientation. While this modeling assumption works well with tensile fractures, it may fail in the context of faults, where the damage zone surrounding the main slip surface may introduce anisotropy that is not aligned with the main fault orientation. In this article, we introduce a generalized dimensional reduced model which preserves full-tensor permeability effects also in the out-of-plane direction of the inclusion. The governing equations of flow for the lower-dimensional objects are obtained through vertical averaging. We present a framework for discretization of the resulting mixed-dimensional problem, aimed at easy adaptation of existing simulation tools. We give numerical examples that show the failure of existing formulations when applied to anisotropic faulted porous media, and go on to show the convergence of our method in both two-dimensional and three-dimensional.publishedVersio

The effect of pond dyes on oviposition and survival in wild UK Culex mosquitoes

British Culex pipiens complex [Culex pipiens sensu lato) mosquito distribution, abundance, and potential for disease transmission are intimately linked to their environment. Pond and lake dyes that block light to restrict algal photosynthesis are a relatively new product assumed to be an environmentally friendly since they are based on food dyes. Their use in urban garden ponds raises questions linked to mosquito oviposition, since coloured water can be an attractant. Culex (mostly pipiens) is commonly found in UK gardens and is a potential vector of viruses including the West Nile Virus (WNV). Any factors that significantly change the distribution and population of Cx pipiens could impact future risks of disease transmission. A gravid trap was used to catch female Cx pipiens mosquitoes for use in oviposition choice tests in laboratory and semi-field conditions. Two types of pond dye, blue and shadow (which looks slightly red), were tested for their impact on oviposition and survival of wild caught Cx pipiens. There were no significant differences in the number of egg batches laid when gravid mosquitoes were given a choice between either blue dye and clear water or shadow dye and clear water indicating that these dyes are not attractants. Larvae hatched from egg batches laid by wild-caught gravid females were used to measure survival to adulthood with or without dye, , in a habitat controlled to prevent further colonisation. The experiment was run twice, once in the summer and again in the autumn, whereas the dyes had no impact on emergence in the summer, there were highly significant reductions in emergence of adults in both dye treated habitats in the autumn. Containers with or without shadow dye were placed outside to colonise naturally and were sampled weekly for larvae and pupae over a 6 month period through summer and autumn. There was a significant negative effect of shadow dye on pupal abundance in a three week period over the summer, but otherwise there was no effect. It is likely that population abundance and food was a more powerful factor for mosquito survival than the dye

Mental Health Diagnoses and Utilization of VA Non-Mental Health Medical Services Among Returning Iraq and Afghanistan Veterans

Over 35% of returned Iraq and Afghanistan veterans in VA care have received mental health diagnoses; the most prevalent is post-traumatic stress disorder (PTSD). Little is known about these patients’ use of non-mental health medical services and the impact of mental disorders on utilization. To compare utilization across three groups of Iraq and Afghanistan veterans: those without mental disorders, those with mental disorders other than PTSD, and those with PTSD. National, descriptive study of 249,440 veterans newly utilizing VA healthcare between October 7, 2001 and March 31, 2007, followed until March 31, 2008. We used ICD9-CM diagnostic codes to classify mental health status. We compared utilization of outpatient non-mental health services, primary care, medical subspecialty, ancillary services, laboratory tests/diagnostic procedures, emergency services, and hospitalizations during veterans’ first year in VA care. Results were adjusted for demographics and military service and VA facility characteristics. Veterans with mental disorders had 42–146% greater utilization than those without mental disorders, depending on the service category (all P < 0.001). Those with PTSD had the highest utilization in all categories: 71–170% greater utilization than those without mental disorders (all P < 0.001). In adjusted analyses, compared with veterans without mental disorders, those with mental disorders other than PTSD had 55% higher utilization of all non-mental health outpatient services; those with PTSD had 91% higher utilization. Female sex and lower rank were also independently associated with greater utilization. Veterans with mental health diagnoses, particularly PTSD, utilize significantly more VA non-mental health medical services. As more veterans return home, we must ensure resources are allocated to meet their outpatient, inpatient, and emergency needs

Heterogeneity of O6-alkylguanine DNA-alkyltransferase expression in human breast tumours

An important determinant of cellular resistance to chemotherapeutic O6-alkylating agents, which comprise methylating and chloroethylating agents, is the ability of cells to repair alkylation damage at the O6-position of guanine in DNA. This is achieved by a specific DNA repair enzyme O6-alkylguanine DNA-alkyltransferase. In this study O6-alkylguanine DNA-alkyltransferase expression was measured in human breast tumours using both biochemical and immunohistochemical techniques. O6-alkylguanine DNA-alkyltransferase activity was then compared with known clinical prognostic indices to assess the potential role of O6-alkylguanine DNA-alkyltransferase in predicting the behaviour of this common malignancy. The application of both biochemical and immunohistochemical techniques was feasible and practical. Most breast tumours expressed high levels of O6-alkylguanine DNA-alkyltransferase. Immunohistochemical analysis showed marked variation in expression not only between individuals but also within individual tumours, and in the same patient, between metastases and between primary tumour and metastatic site. O6-alkylguanine DNA-alkyltransferase activity in tissue extracts significantly correlated not only with immunohistochemical staining intensity determined by subjective quantitation, but also with measures of protein levels using a computerised image analysis system including mean grey (P<0.001), percentage of cells positive for O6-alkylguanine DNA-alkyltransferase (P<0.001), and integrated optical density (P<0.001). O6-alkylguanine DNA-alkyltransferase expression did not correlate with any of the established clinical prognostic indicators for current treatment regimens. However, immunohistochemical offers a rapid and convenient method for assessing potential utility of O6-alkylating agents or O6-alkylguanine DNA-alkyltransferase inactivating agents in future studies of breast cancer treatment