Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.

Olfactory and visuospatial learning and memory performance in two strains of Alzheimer's disease model mice--a longitudinal study.

Using a longitudinal study design, two strains of Alzheimer's disease (AD) model mice, one expressing ß-amyloid plaques and one expressing Tau protein-associated neurofibrillary tangles were assessed for olfactory and visuospatial learning and memory and their performance compared to that of age-matched controls. No significant difference between AD and control mice was found in the initial set of olfactory tasks performed at 6 months of age whereas both strains of AD mice performed significantly poorer than the controls in visuospatial learning at this age. Subsequent tests performed on the same individual animals at 7, 8, 9, 11, 13, 15, and 18 months of age also failed to find systematic differences in olfactory performance between AD and control mice. In contrast, the AD mice performed consistently poorer than the controls in visuospatial re-learning tests performed at these ages. With most olfactory tasks, both AD and control mice displayed a marked decrease in performance between testing at 15 and 18 months of age. These results show that the two strains of AD model mice do not display an olfactory impairment in a time course consistent with human AD, but are impaired in visuospatial capabilities. The marked age-related changes observed with the olfactory tasks in both AD and control mice suggest that the observed lack of an AD-related olfactory impairment is not due to an insensitivity of the tests employed. Rather, they suggest that the olfactory system of the two AD mouse model strains may be surprisingly robust against AD-typical neuropathologies.

Optimization of alpha-ketoamide based p38 inhibitors through modifications to the region that binds to the allosteric site.

We have optimized a novel series of potent p38 MAP kinase inhibitors based on an alpha-ketoamide scaffold through structure based design that due to their extended molecular architecture bind, in addition to the ATP site, to an allosteric pocket. In vitro ADME, in vivo PK and efficacy studies show these compounds to have drug-like characteristics and have resulted in the nomination of a development candidate which is currently in phase II clinical trials for the oral treatment of inflammatory conditions.

KR-003048, a potent, orally active inhibitor of p38 mitogen-activated protein kinase.

The tumor necrosis factor-alpha (TNF-alpha) cytokine, secreted by activated monocytes/macrophages and T lymphocytes, is implicated in several diseases, including rheumatoid arthritis, chronic obstructive pulmonary disease, inflammatory bowel disease, and osteoporosis. Monocyte/macrophage production of TNF-alpha is largely driven by p38alpha mitogen-activated protein kinase (MAP kinase), an intracellular soluble serine-threonine kinase. p38alpha MAP kinase is activated by growth factors, cellular stresses, and cytokines such as TNF-alpha and interleukin-l (IL-I). The primary contribution of p38alpha activation to excess TNF-alpha in settings of both chronic and acute inflammation has instigated efforts to find inhibitors of this enzyme as possible therapies for associated disease states. Analogue design, synthesis, and structure-activity studies led to the identification of 5-tert-butyl-N-cyclopropyl-2-methoxy-3-{2-[4-(2-morpholin-4-yl-ethoxy)-naphthalen-1-yl]-2-oxo-acetylamino}-benzamide (KR-003048) as a potent inhibitor of the p38 MAP kinase signaling pathway in vitro and in vivo. The inhibition in vitro of human p38alpha enzyme activity and lipopolysaccharide (LPS)-induced p38 activation and subsequent TNF-alpha release is described. KR-00348 was demonstrated to be a potent inhibitor of inflammatory cytokine production ex vivo in rat and human whole blood, and showed good oral bioavailability. Additionally, efficacy in mouse and rat models of acute and chronic inflammation was obtained. KR-003048 possessed therapeutic activity in acute models, demonstrating substantial inhibition of carrageenan-induced paw edema and in vivo LPS-induced TNF release at 30mg/kg p.o. Collagen-induced arthritis in mice was significantly inhibited by 10 and 30mg/kg doses of KR-003048. Evidence for disease-modifying activity in this model was indicated by histological evaluation of joints.

'Reverse' alpha-ketoamide-based p38 MAP kinase inhibitors.

We have identified a second series of potent p38 inhibitors. As with our first generation series, these compounds are based on an alpha-ketoamide scaffold. The reversal of the ketoamide order, however, introduces more chemical flexibility and in addition results in improve potencies against p38.

The design and synthesis of novel alpha-ketoamide-based p38 MAP kinase inhibitors.

We have identified a novel series of potent p38 MAP kinase inhibitors through structure-based design which due to their extended molecular architecture bind, in addition to the ATP site, to an allosteric pocket. In vitro ADME and in vivo PK studies show these compounds to have drug-like characteristics which could result in the development of an oral treatment for inflammatory conditions.