Learning from the Success of MPI

The Message Passing Interface (MPI) has been extremely successful as a portable way to program high-performance parallel computers. This success has occurred in spite of the view of many that message passing is difficult and that other approaches, including automatic parallelization and directive-based parallelism, are easier to use. This paper argues that MPI has succeeded because it addresses all of the important issues in providing a parallel programming model.Comment: 12 pages, 1 figur

Patient-derived mutations within the N-terminal domains of p85α impact PTEN or Rab5 binding and regulation

The p85α protein regulates flux through the PI3K/PTEN signaling pathway, and also controls receptor trafficking via regulation of Rab-family GTPases. In this report, we determined the impact of several cancer patient-derived p85α mutations located within the N-terminal domains of p85α previously shown to bind PTEN and Rab5, and regulate their respective functions. One p85α mutation, L30F, significantly reduced the steady state binding to PTEN, yet enhanced the stimulation of PTEN lipid phosphatase activity. Three other p85α mutations (E137K, K288Q, E297K) also altered the regulation of PTEN catalytic activity. In contrast, many p85α mutations reduced the binding to Rab5 (L30F, I69L, I82F, I177N, E217K), and several impacted the GAP activity of p85α towards Rab5 (E137K, I177N, E217K, E297K). We determined the crystal structure of several of these p85α BH domain mutants (E137K, E217K, R262T E297K) for bovine p85α BH and found that the mutations did not alter the overall domain structure. Thus, several p85α mutations found in human cancers may deregulate PTEN and/or Rab5 regulated pathways to contribute to oncogenesis. We also engineered several experimental mutations within the p85α BH domain and identified L191 and V263 as important for both binding and regulation of Rab5 activit

Electronic structure of the Magnesium hydride molecular ion

In this paper, using a standard quantum chemistry approach based on pseudopotentials for atomic core representation, Gaussian basis sets, and effective core polarization potentials, we investigate the electronic properties of the MgH$^+$ ion. We first determine potential energy curves for several states using different basis sets and discuss their predicted accuracy by comparing our values of the well depths and position with other available results. We then calculate permanent and transition dipole moments for several transitions. Finally for the first time, we calculate the static dipole polarizability of MgH$^+$ as function of the interatomic distance. This study represents the first step towards the modeling of collisions between trapped cold Mg$^+$ ions and H$_2$ molecules.Comment: submitted to J. Phys. B, special issue on Cold trapped ion

Time and Origin of Cichlid Colonization of the Lower Congo Rapids

Most freshwater diversity is arguably located in networks of rivers and streams, but, in contrast to lacustrine systems riverine radiations, are largely understudied. The extensive rapids of the lower Congo River is one of the few river stretches inhabited by a locally endemic cichlid species flock as well as several species pairs, for which we provide evidence that they have radiated in situ. We use more that 2,000 AFLP markers as well as multilocus sequence datasets to reconstruct their origin, phylogenetic history, as well as the timing of colonization and speciation of two Lower Congo cichlid genera, Steatocranus and Nanochromis. Based on a representative taxon sampling and well resolved phylogenetic hypotheses we demonstrate that a high level of riverine diversity originated in the lower Congo within about 5 mya, which is concordant with age estimates for the hydrological origin of the modern lower Congo River. A spatial genetic structure is present in all widely distributed lineages corresponding to a trisection of the lower Congo River into major biogeographic areas, each with locally endemic species assemblages. With the present study, we provide a phylogenetic framework for a complex system that may serve as a link between African riverine cichlid diversity and the megadiverse cichlid radiations of the East African lakes. Beyond this we give for the first time a biologically estimated age for the origin of the lower Congo River rapids, one of the most extreme freshwater habitats on earth

Additional Key Words and Phrases: Fortran.

RAL-TR-1998-060 Co-Array Fortran, formerly known as F, is a small extension of Fortran 95 for parallel processing. A Co-Array Fortran program is interpreted as if it were replicated a number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is termed an image. The array syntax of Fortran 95 is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of any access to data that is spread across images. References without square brackets are to local data, so code that can run independently is uncluttered. Only where there are square brackets, or where there is a procedure call and the procedure contains square brackets, is communication between images involved. There are intrinsic procedures to synchronize images, return the number of images, and return the index of the current image. We introduce the extension; give examples to illustrate how clear, powerful, and flexible it can be; and provide a technical definition. Categories and subject descriptors: D.3 [PROGRAMMING LANGUAGES]