Productive and efficient computational science through domain-specific abstractions

In an ideal world, scientific applications are computationally efficient, maintainable and composable and allow scientists to work very productively. We argue that these goals are achievable for a specific application field by choosing suitable domain-specific abstractions that encapsulate domain knowledge with a high degree of expressiveness. This thesis demonstrates the design and composition of domain-specific abstractions by abstracting the stages a scientist goes through in formulating a problem of numerically solving a partial differential equation. Domain knowledge is used to transform this problem into a different, lower level representation and decompose it into parts which can be solved using existing tools. A system for the portable solution of partial differential equations using the finite element method on unstructured meshes is formulated, in which contributions from different scientific communities are composed to solve sophisticated problems. The concrete implementations of these domain-specific abstractions are Firedrake and PyOP2. Firedrake allows scientists to describe variational forms and discretisations for linear and non-linear finite element problems symbolically, in a notation very close to their mathematical models. PyOP2 abstracts the performance-portable parallel execution of local computations over the mesh on a range of hardware architectures, targeting multi-core CPUs, GPUs and accelerators. Thereby, a separation of concerns is achieved, in which Firedrake encapsulates domain knowledge about the finite element method separately from its efficient parallel execution in PyOP2, which in turn is completely agnostic to the higher abstraction layer. As a consequence of the composability of those abstractions, optimised implementations for different hardware architectures can be automatically generated without any changes to a single high-level source. Performance matches or exceeds what is realistically attainable by hand-written code. Firedrake and PyOP2 are combined to form a tool chain that is demonstrated to be competitive with or faster than available alternatives on a wide range of different finite element problems.Open Acces

The use of proteolytic enzymes (chymoral) in sporting injuries

SAMJ 45(6): 181-18

HORIZONTAL FLOW LOOP DESIGN FOR THE STUDY OF DRILL STRING ROTATION EFFECTS ON CUTTINGS TRANSPORT

Exploration and Production companies are continually focusing more time, energy and resources into Extended Reach Drilling in order to maximize reservoir production while minimizing both environmental impact and development costs. These long laterals (2:1 Measured Depth: True Vertical Depth) are often more difficult to drill and can be severely impacted by inadequate drilling practices. Cuttings transport efficiency is a critical parameter of Extended Reach Drilling operations, and poor wellbore cleaning can lead to excessive torque, drag, and several other serious downhole problems. Although many studies have been performed that identify the importance of drill string rotation on cuttings movement, there is still much to be learned about the correlation between rotation and hole cleaning. This increase in transport cuttings efficiency is more pronounced in larger diameter holes, where often sudden increases in transport efficiency occur when drill string rotation nears both 120 and 180 RPM. This document presents a design of a flow loop capable of emulating downhole flow conditions and high RPM drill string rotation in a large diameter wellbore, which would allow for the study and better understanding of this phenomenon. This design will also be the first that allows drill string interchangeability and adjustment of drill string centerline within the casing, further increasing research capabilities. A comprehensive computational fluid dynamics (CFD) model has also been designed. This model will be used alongside the flow loop and will be refined and validated by future flow loop experiments. This flow loop and CFD model can be used to develop working correlations and provide real world predictive models. A strong comprehension of these step changes in cuttings removal rates could allow for the development of new technology or drilling practices that could replicate this effect, increasing transport efficiency dramatically. With the ever-increasing importance of successful Extended Reach Campaigns, companies are relying heavily on technological and operational breakthroughs to push the envelope of Extended Reach

Postmortem changes in meat quality and myofibrillar protein degradation in turkey breast muscle

The purpose of this research was to evaluate the effect of elevated carcass temperature in combination with rapidly declining pH or with postrigor muscle on turkey breast meat quality. Two groups of twelve turkey carcasses with similar ultimate pH values were selected based on 15 min postmortem (PM) breast muscle pH (rapid-glycolyzing (RG), pH 6.0). One side of each carcass was held near 40°C and immersion chilling was delayed until 110 min PM (DC), while the other side was chilled at 20 min PM (IC). Raw breast meat quality was assessed using measurements of colour and protein extractability, while quality characteristics of cooked product were assessed using cook yield and torsion gelometry. The extractability and degradation of 10 specific proteins was monitored using SDS-PAGE and Western blotting. Additionally, holding postrigor turkey breast meat at 40°C was evaluated as a model for mimicking changes due to rapid PM glycolysis. Sarcoplasmic and myofibrillar protein extractability was reduced for breast samples from RG and DC carcasses as well as for postrigor meat held at 40°C (P < 0.05). All colour values ('L*a*b*') increased for DC ground breast meat. Strain at fracture for breast meat gels was lower for RG samples. Both stress and strain at fracture and cook yield were reduced for DC breast meat gels. The reduction in meat quality measurements was additive for RG samples that were delay-chilled. Densitometry of Western blot analyses revealed that the extractability of glycogen phosphorylase, creatine kinase, and M-protein was reduced for RG or DC samples. Increased myosin degradation was observed for samples from either RG or DC carcasses with up to 20% of myosin degraded in RG/DC samples. Nebulin degradation was also more extensive in RG samples than for controls. Heating postrigor breast increased myosin degradation, however, differences in the banding pattern of myosin fragments compared to samples from RG carcasses were observed. These results provide conclusive evidence that rapid PM glycolysis and delayed chilling have detrimental effects on turkey breast meat quality. The association of postmortem protein degradation with meat of reduced quality merits further investigations into the relationship between postmortem proteolytic activity and meat quality

Role and Identity for Europe in Space Security

This article is reprinted here with permission from the authors. See “Executive Summary” in Wolfgang Rathgeber and Nina- Louisa Remuss, Space Security: A Formative Role and Principled Identity for Europe (European Space Policy Institute Report 16, January 2009). Modern societies have become heavily dependent on space and its applications. As a consequence, the issue of security in space is increasingly being recognized as critical for humankind. This development is reinforced by events like the Chinese anti-satellite (ASAT) test in January 2007. Various alternatives to support the peaceful uses of space, to promote international cooperation, and to prevent an arms race in outer space are under discussion. These attempts occasionally lack support by space actors that emphasize the right to act freely when national security concerns are at stake. Possible routes forward include legally binding treaties, confidence building measures, and soft law, such as codes of conduct or rules of the road

Report of the first external review of the Systemwide Program on Participatory Research and Gender Analysis (PRGA)

Providing compelling empirical evidence of the impacts of participatory research has been a major goal of the PRGA Program since its initiation. The number of our published Impact Assessment documents over the past 5 years supports the conclusion that the Program has well reached that goal. We are pleased to note that the EPMR report recognizes the high quality of our “conventional” economic ex post impact assessment work, but we had expected an acknowledgment of an equal importance of process-oriented documentation of impacts, associated with the incorporation of participatory research (PR) and gender analysis (GA) in research processes. To accomplish this major Program goal of substantial body of empirical evidence has required first convincing researchers to see value in assessing the impact of a participatory research approach, and forming a network of people interested in working together to accomplish this goal. Furthermore, reaching this goal has required developing frameworks for assessing the impacts of the PR methods as compared to the impacts of technologies alone, developing and testing some specific tools and methodologies for such assessment, conducting case studies, organizing workshops and international meetings to build the impact assessment capacity in the CG system and to promote mutual leaning among the impact assessment practitioners and maintaining the network amongst them, and providing support and backstopping to the centers conducting impact studies of participatory research

The three co's to jointly model commodity markets: co-production, co-consumption, co-trading

In this study, we develop a framework, based on a global vector autoregression (GVAR) model, to unite two perspectives on commodity markets, the commodity-specific, single-market-centered approach, investigating the micro- and macroeconomic drivers of commodity prices, and the market perspective, which observes joint movements of commodity prices on exchanges. Thereby, the GVAR model disentangles single market from inter-market effects, while simultaneously accounting for the impact of macroeconomic factors. We apply the framework to the six industrial metals markets, reflecting their interdependencies via their co-production, co-consumption, or co-trading relation. In particular, the numerous significant spillover effects in the cross-commodity dimension underline the importance of jointly modeling commodity markets. While the strong co-movement between industrial metal prices is represented exceptionally well by our framework, the microeconomic supply and demand attributes of the commodities have significant impact, within and across markets, even on price variables, highlighting their relevance in modern commodity market models. Moreover, we detect global shocks, e.g., an increase in global demand, affect each commodity market to a similar extent