Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

AbstractSimulation of in vivo cellular processes with the reaction–diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel efficiency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems

Is the meiofauna a good indicator for climate change and anthropogenic impacts?

Our planet is changing, and one of the most pressing challenges facing the scientific community revolves around understanding how ecological communities respond to global changes. From coastal to deep-sea ecosystems, ecologists are exploring new areas of research to find model organisms that help predict the future of life on our planet. Among the different categories of organisms, meiofauna offer several advantages for the study of marine benthic ecosystems. This paper reviews the advances in the study of meiofauna with regard to climate change and anthropogenic impacts. Four taxonomic groups are valuable for predicting global changes: foraminifers (especially calcareous forms), nematodes, copepods and ostracods. Environmental variables are fundamental in the interpretation of meiofaunal patterns and multistressor experiments are more informative than single stressor ones, revealing complex ecological and biological interactions. Global change has a general negative effect on meiofauna, with important consequences on benthic food webs. However, some meiofaunal species can be favoured by the extreme conditions induced by global change, as they can exhibit remarkable physiological adaptations. This review highlights the need to incorporate studies on taxonomy, genetics and function of meiofaunal taxa into global change impact research

Us knows us in the UK: On director networks and CEO compensation

We analyze the relation between CEO compensation and networks of executive and non-executive directors for all listed UK companies over the period 1996-2007. We examine whether networks are built for reasons of information gathering or for the accumulation of managerial influence. Both indirect networks (enabling directors to collect information) and direct networks (leading to more managerial influence) enable the CEO to obtain higher compensation. Direct networks can harm the efficiency of the remuneration contracting in the sense that the performance sensitivity of compensation is then lower. We find that in companies with strong networks and hence busy boards the directors' monitoring effectiveness is reduced which leads to higher and less performance-sensitive CEO compensation. Our results suggest that it is important to have the 'right' type of network: some networks enable a firm to access valuable information whereas others can lead to strong managerial influence that may come at the detriment of the firm and its shareholders. We confirm that there are marked conflicts of interest when a CEO increases his influence by being a member of board committees (such as the remuneration committee) as we observe that his or her compensation is then significantly higher. We also find that hiring remuneration consultants with sizeable client networks also leads to higher CEO compensation especially for larger firms. © 2011 Elsevier B.V

Creating a Local Geographic Influenza-like Illness Activity Report

Description of the development of an auto-generated color coded map showing an academic medical centers current seven day moving average influenza-like illness rate by zip code

Annual Cycles of Gonadal Development of Six Common Gorgonians from Biscayne National Park, Florida, Usa

Gonadal development was examined in six common gorgonian species using histological sections prepared from branch segments collected monthly between 1978 and 1981 from patch reefs in Biscayne National Park (25°21′N; 80°10′W), Florida. Species studied accounted for more than 50% of the octocorals encountered in transect surveys of sampled reefs between 1977 and 1981. Small, precursor eggs were present year round in all species. Five species exhibited seasonal reproduction; all six species appeared to be dioecious. Male and female colonies were equally represented in the sampled branches of Plexaura flexuosa, P. homomalla, and Muricea atlantica, which spawned during summer or early autumn each year. In Gorgonia ventalina, Muriceopsis flavida and Pseudopterogorgia americana, female colonies outnumbered male colonies by as much as 2:1. Muriceopsis flavida and P. americana spawned each autumn or early winter, while Gorgonia ventalina exhibited year-round reproductive potential. The unique archival data set utilized in this study provides invaluable historical data against which future studies can be compared

Preoperative Identification of Perforating Vessels to the Skin by Color Duplex Imaging.

Recent improvements in high-frequency linear array transducers with color duplex imaging permit the precise identification and estimation of the caliber of minute perforating vessels to the skin as small as 0.5 mm. An obvious corollary role would be the accurate preoperative delineation of the vascular anatomy of a skin flap, which could be essential to ensure its viability. This technology was then applied to map the blood supply to skin flaps in eight patients, which was subsequently verified at the time of their actual surgical dissection. Because anomalies of the skin circulation are not uncommon, this extended capability for color duplex imaging can facilitate a more optimal design of skin flaps to better ensure their chance for survival by the inclusion of appropriate nutritive blood vessels

The Impact of Weather on Influenza-like Illness Rates in Chicago

Description of a statistical model to account for weather variation in influenza-like illness surveillance.

A Syndrome Definition Validation Approach for Ebola Virus Disease

Describes the development and validation of an Ebola virus disease syndrome definition within the GUARDIAN (Geographic Utilization of Artificial Intelligence in Real-Time for Disease Identification and Alert Notification) surveillance system