Object oriented programming : data preparation and visualization of FEM models

In this paper two object oriented applications are described. The former is intended to generate data associated with the finite element method (FEM) and the later is a three-dimensional visualization tool named 3DMesh. Both are based on the principles of object oriented programming, namely encapsulation, inheritance and polymorphism. To support the preparation of FEM data, a language named 3DO was developed. Its syntax is similar to a subset of the C++ programming language. 3DO is based on object construction and modification by methods that require a small number of arguments. With this tool, mesh generation, definition of properties and loads and mesh refinement can be performed with limited user effort, even when the model is complex. All the generated information can be visualized with the program 3DMesh. This application is based on the OpenGL library and uses the Microsoft Foundation Classes to simplify its integration in the MS-Windows environment. 3DMesh implements an interactive navigation technique that allows the visualization of the model interior, preserving its integrity. Model attributes and the results of the FEM analysis can also be visualized

Protocol-based verification of MPI programs

We present a methodology for the verification of Message Passing Interface (MPI) programs written in C. The aim is to statically verify programs against protocol specifications, enforcing properties such as fidelity and absence of deadlocks. We make use of a protocol language based on a dependent type system for message-passing parallel programs. % For the verification of a program against a given protocol, the protocol is first translated into a representation read by VCC, a software verifier for the~C programming language. % The program is then annotated with specific assertions that, together with a pre-established set of contracts for MPI primitives, guide the verifier to either prove or disprove the program's conformance to the protocol. We successfully verified MPI programs in a running time that is independent of the number of processes or other input parameters. This contrasts with other techniques, notably model checking and symbolic execution, that suffer from the state-explosion problem. We experimentally evaluated our approach against TASS, a state-of-the-art tool for MPI program verification.Under revie

Type-Based Verification of Message-Passing Parallel Programs

We present a type-based approach to the verification of the communication structure of parallel programs. We model parallel imperative programs where a fixed number of processes, each equipped with its local memory, communicates via a rich diversity of primitives, including point-to-point messages, broadcast, reduce, and array scatter and gather. The paper proposes a decidable dependent type system incorporating abstractions for the various communication operators, a form of primitive recursion, and collective choice. Term types may refer to values in the programming language, including integer, floating point and arrays. The paper further introduces a core programming language for imperative, message-passing, parallel programming, and shows that the language enjoys progress.Under revie

Asymptotic behavior of solutions to the σk\sigma_k-Yamabe equation near isolated singularities

$\sigma_k$-Yamabe equations are conformally invariant equations generalizing the classical Yamabe equation. In an earlier work YanYan Li proved that an admissible solution with an isolated singularity at $0\in \mathbb R^n$ to the $\sigma_k$-Yamabe equation is asymptotically radially symmetric. In this work we prove that an admissible solution with an isolated singularity at $0\in \mathbb R^n$ to the $\sigma_k$-Yamabe equation is asymptotic to a radial solution to the same equation on $\mathbb R^n \setminus \{0\}$. These results generalize earlier pioneering work in this direction on the classical Yamabe equation by Caffarelli, Gidas, and Spruck. In extending the work of Caffarelli et al, we formulate and prove a general asymptotic approximation result for solutions to certain ODEs which include the case for scalar curvature and $\sigma_k$ curvature cases. An alternative proof is also provided using analysis of the linearized operators at the radial solutions, along the lines of approach in a work by Korevaar, Mazzeo, Pacard, and Schoen.Comment: 55 page

An emerging clone, KPC-2-producing Klebsiella pneumoniae ST16, associated with high mortality rates in a CC258 endemic setting

Background Carbapenemase-producing K. pneumoniae have become a global priority, not least in low-middle income countries. Here, we report the emergence and clinical impact of a novel KPC-K. pneumoniae ST16 clone in a Clonal Complex (CC)258 endemic setting. Methods In a teaching Brazilian hospital, a retrospective cohort of adult KPC-KP bloodstream infections (BSI) cases (January 2014 to December 2016) was established to study the molecular epidemiology and its impact on outcome (30-day all-cause mortality). KPC-KP isolates were MLST-typed. Survival analysis between ST/CC groups and risk factors for fatal outcome (logistic regression) were evaluated. Representative isolates underwent whole genome sequencing (WGS), and had their virulence tested in a Galleria larvae model. Results One hundred sixty-five unique KPC-KP BSI cases were identified. CC258 was predominant (66%), followed by ST16 (12%). The overall 30-day mortality rate was 60%; in contrast, 95% of ST16 cases were fatal. Patient’s severity scores were high and baseline clinical variables were not statistically different across ST’s. In multivariate analysis, ST16 (OR 21.4; CI95% 2.3-202.8; p=0,008) and septic shock (OR 11.9; CI95% 4.2-34.1; p<0,001) were independent risk factors for fatal outcome. ST16 clone carried up to 14 resistance genes, including blaKPC-2 in an IncFIBpQIL plasmid, KL51 capsule and Yersiniabactin virulence determinants. ST16 clone was highly pathogenic in the larvae model. Conclusions Mortality rates were high in this KPC-KP BSI cohort, where CC258 is endemic. An emerging ST16 clone was associated with high mortality. Our results suggest that even in endemic settings, highly virulent clones can rapidly emerge demanding constant monitoring