Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions

We explore two different threading approaches on a graphics processing unit (GPU) exploiting two different characteristics of the current GPU architecture. The fat thread approach tries to minimise data access time by relying on shared memory and registers potentially sacrificing parallelism. The thin thread approach maximises parallelism and tries to hide access latencies. We apply these two approaches to the parallel stochastic simulation of chemical reaction systems using the stochastic simulation algorithm (SSA) by Gillespie (J. Phys. Chem, Vol. 81, p. 2340-2361, 1977). In these cases, the proposed thin thread approach shows comparable performance while eliminating the limitation of the reaction system’s size

STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB

Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud \ud Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2

Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

Shelf and coastal sea processes extend from the atmosphere through the water column and into the sea bed. These processes are driven by physical, chemical, and biological interactions at local scales, and they are influenced by transport and cross strong spatial gradients. The linkages between domains and many different processes are not adequately described in current model systems. Their limited integration level in part reflects lacking modularity and flexibility; this shortcoming hinders the exchange of data and model components and has historically imposed supremacy of specific physical driver models. We here present the Modular System for Shelves and Coasts (MOSSCO, http://www.mossco.de), a novel domain and process coupling system tailored---but not limited--- to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the existing coupling technology Earth System Modeling Framework and on the Framework for Aquatic Biogeochemical Models, thereby creating a unique level of modularity in both domain and process coupling; the new framework adds rich metadata, flexible scheduling, configurations that allow several tens of models to be coupled, and tested setups for coastal coupled applications. That way, MOSSCO addresses the technology needs of a growing marine coastal Earth System community that encompasses very different disciplines, numerical tools, and research questions.Comment: 30 pages, 6 figures, submitted to Geoscientific Model Development Discussion

Understanding the routes of contamination of ready-to-eat vegetables in the Middle East

publisher: Elsevier articletitle: Understanding the routes of contamination of ready-to-eat vegetables in the Middle East journaltitle: Food Control articlelink: http://dx.doi.org/10.1016/j.foodcont.2015.10.024 content_type: article copyright: Copyright © 2015 Elsevier Ltd. All rights reserved

Discharge Teaching, Readiness for Discharge, and Post-discharge Outcomes in Parents of Hospitalized Children

Purpose This study explored the sequential relationships of parent perceptions of the quality of their discharge teaching and nurse and parent perceptions of discharge readiness to post-discharge outcomes (parental post-discharge coping difficulty, readmission and emergency department visits). Design/methods In this secondary analysis of data from a longitudinal pilot study of family self-management discharge preparation, the correlational design used regression modeling with data from a convenience sample of 194 parents from two clinical units at a Midwest pediatric hospital. Data were collected on the day of discharge (Quality of Discharge Teaching Scale; Readiness for Hospital Discharge Scale), at 3 weeks post-discharge (Post-Discharge Coping Difficulty Scale), and from electronic records (readmission, ED visits). Results Parent-reported quality of discharge teaching delivery (the way nurses teach), but not the amount of content, was positively associated with parent perception (B = 0.54) and nurse assessment (B = 0.16) of discharge readiness. Parent-reported discharge readiness was negatively associated with post-discharge coping difficulty (B = − 0.52). Nurse assessment of discharge readiness was negatively associated with readmission; a one point increase in readiness (on a 10 point scale) decreased the likelihood of readmission by 52%. Conclusion There is a sequential effect of quality of discharge teaching delivery on parent discharge readiness, which is associated with parent coping difficulty and child readmission. Practice Implications Efforts to improve discharge outcomes should include strategies to build nurse teaching skills for high-quality delivery of discharge teaching. In addition, routine nurse assessment of discharge readiness can be used to identify children at risk for readmission and trigger anticipatory interventions

Measuring the Return on Investment in Research in Universities: The Value of the Human Capital Produced by these Programs

This research project assess the economic benefits to British Columbia of graduate students trained in research, and the economic and social returns of investment in research. It also looks at knowledge as a commodity, and the conditions of its production

Development of a Self‐Management Theory‐Guided Discharge Intervention for Parents of Hospitalized Children

Background Parents of hospitalized children, especially parents of children with complex and chronic health conditions, report not being adequately prepared for self‐management of their child\u27s care at home after discharge. Problem No theory‐based discharge intervention exists to guide pediatric nurses\u27 preparation of parents for discharge. Purpose To develop a theory‐based conversation guide to optimize nurses\u27 preparation of parents for discharge and self‐management of their child at home following hospitalization. Methods Two frameworks and one method influenced the development of the intervention: the Individual and Family Self‐Management Theory, Tanner\u27s Model of Clinical Judgment, and the Teach‐Back method. A team of nurse scientists, nursing leaders, nurse administrators, and clinical nurses developed and field tested the electronic version of a nine‐domain conversation guide for use in acute care pediatric hospitals. Conclusions The theory‐based intervention operationalized self‐management concepts, added components of nursing clinical judgment, and integrated the Teach‐Back method. Clinical Relevance Development of a theory‐based intervention, the translation of theoretical knowledge to clinical innovation, is an important step toward testing the effectiveness of the theory in guiding clinical practice. Clinical nurses will establish the practice relevance through future use and refinement of the intervention

Gain in Three-Dimensional Metamaterials utilizing Semiconductor Quantum Structures

We demonstrate gain in a three-dimensional metal/semiconductor metamaterial by the integration of optically active semiconductor quantum structures. The rolling-up of a metallic structure on top of strained semiconductor layers containing a quantum well allows us to achieve a three-dimensional superlattice consisting of alternating layers of lossy metallic and amplifying gain material. We show that the transmission through the superlattice can be enhanced by exciting the quantum well optically under both pulsed or continuous wave excitation. This points out that our structures can be used as a starting point for arbitrary three-dimensional metamaterials including gain