Intelligence in Scientific Computing

Combining numerical techniques with ideas from symbolic computation and with methods incorporating knowledge of science and mathematics leads to a new category of intelligent computational tools for scientists and engineers. These tools autonomously prepare simulation experiments from high-level specifications of physical models. For computationally intensive experiments, they automatically design special-purpose numerical engines optimized to perform the necessary computations. They actively monitor numerical and physical experiments. They interpret experimental data and formulate numerical results in qualitative terms. They enable their human users to control computational experiments in terms of high-level behavioral descriptions.

Compiling Scientific Code Using Partial Evaluation

Scientists are faced with a dilemma: either they can write abstract programs that express their understanding of a problem, but which do not execute efficiently; or they can write programs that computers can execute efficiently, but which are difficult to write and difficult to understand. We have developed a compiler that uses partial evaluation and scheduling techniques to provide a solution to this dilemma.

Partial Evaluation for Scientific Computing: The Supercomputer Toolkit Experience

We describe the key role played by partial evaluation in the Supercomputer Toolkit, a parallel computing system for scientific applications that effectively exploits the vast amount of parallelism exposed by partial evaluation. The Supercomputer Toolkit parallel processor and its associated partial evaluation-based compiler have been used extensively by scientists at M.I.T., and have made possible recent results in astrophysics showing that the motion of the planets in our solar system is chaotically unstable.

Demokratyzacja kultury współczesnej

Wydział Historyczny: Instytut Etnologii i Antropologii Kulturowej

Discourses Commemorative of Professor Tayler Lewis and Professor Isaac W. Jackson

Discourses

An examination of the construction of meanings for obesity in Ireland

Obesity has been defined as a consequence of energy imbalance, where energy intake exceeds energy expenditure and results in a build-up of adipose tissue. However, this scientific definition masks the complicated social meanings associated with the condition. This research investigated the construction of meaning around obesity at various levels of inquiry to inform how obesity is portrayed and understood in Ireland. A multi-paradigmatic approach was adopted, drawing on theory and methods from psychology and sociology and an analytical framework combining the Common Sense Model and framing theory was employed. In order to examine the exo-level meanings of obesity, content analysis was performed on two media data sets (n=479, n=346) and a thematic analysis was also performed on the multiple newspaper sample (n=346). At the micro-level, obesity discourses were investigated via the thematic analysis of comments sampled from an online message board. Finally, an online survey assessed individual-level beliefs and understandings of obesity. The media analysis revealed that individual blame for obesity was pervasive and the behavioural frame was dominant. A significant increase in attention to obesity over time was observed, manifestations of weight stigma were common, and there was an emotive discourse of blame directed towards the parents of obese children. The micro-level analysis provided insight into the weight-based stigma in society and a clear set of negative ‘default’ judgements accompanied the obese label. The survey analysis confirmed that the behavioural frame was the dominant means of understanding obesity. One of the strengths of this thesis is the link created between framing and the Common Sense Model in the development of an analytical framework for application in the examination of health/illness representations. This approach helped to ascertain the extent of the pervasive biomedical and individual blame discourse on obesity, which establishes the basis for the stigmatisation of obese persons.

Broadening public input into science policy decision making: can the democratic model for science communication influence scientific, innovation and technological trajectories?

This PhD thesis investigates the potential use of science communication models to engage a broader swathe of actors in decision making in relation to scientific and technological innovation in order to address possible democratic deficits in science and technology policy-making. A four-pronged research approach has been employed to examine different representations of the public(s) and different modes of engagement. The first case study investigates whether patient-groups could represent an alternative needs-driven approach to biomedical and health sciences R & D. This is followed by enquiry into the potential for Science Shops to represent a bottom-up approach to promote research and development of local relevance. The barriers and opportunities for the involvement of scientific researchers in science communication are next investigated via a national survey which is comparable to a similar survey conducted in the UK. The final case study investigates to what extent opposition or support regarding nanotechnology (as an emerging technology) is reflected amongst the YouTube user community and the findings are considered in the context of how support or opposition to new or emerging technologies can be addressed using conflict resolution based approaches to manage potential conflict trajectories. The research indicates that the majority of communication exercises of relevance to science policy and planning take the form of a one-way flow of information with little or no facility for public feedback. This thesis proposes that a more bottom-up approach to research and technology would help broaden acceptability and accountability for decisions made relating to new or existing technological trajectories. This approach could be better integrated with and complementary to government, institutional, e.g. university, and research funding agencies activities and help ensure that public needs and issues are better addressed directly by the research community. Such approaches could also facilitate empowerment of societal stakeholders regarding scientific literacy and agenda-setting. One-way information relays could be adapted to facilitate feedback from representative groups e.g. Non-governmental organisations or Civil Society Organisations (such as patient groups) in order to enhance the functioning and socio-economic relevance of knowledge-based societies to the betterment of human livelihoods.

WriteSim TCExam--an open source text simulation environment for training novice researchers in scientific writing.

BACKGROUND: The ability to write clearly and effectively is of central importance to the scientific enterprise. Encouraged by the success of simulation environments in other biomedical sciences, we developed WriteSim TCExam, an open-source, Web-based, textual simulation environment for teaching effective writing techniques to novice researchers. We shortlisted and modified an existing open source application - TCExam to serve as a textual simulation environment. After testing usability internally in our team, we conducted formal field usability studies with novice researchers. These were followed by formal surveys with researchers fitting the role of administrators and users (novice researchers) RESULTS: The development process was guided by feedback from usability tests within our research team. Online surveys and formal studies, involving members of the Research on Research group and selected novice researchers, show that the application is user-friendly. Additionally it has been used to train 25 novice researchers in scientific writing to date and has generated encouraging results. CONCLUSION: WriteSim TCExam is the first Web-based, open-source textual simulation environment designed to complement traditional scientific writing instruction. While initial reviews by students and educators have been positive, a formal study is needed to measure its benefits in comparison to standard instructional methods.

Scientific writing: a randomized controlled trial comparing standard and on-line instruction.

BACKGROUND: Writing plays a central role in the communication of scientific ideas and is therefore a key aspect in researcher education, ultimately determining the success and long-term sustainability of their careers. Despite the growing popularity of e-learning, we are not aware of any existing study comparing on-line vs. traditional classroom-based methods for teaching scientific writing. METHODS: Forty eight participants from a medical, nursing and physiotherapy background from US and Brazil were randomly assigned to two groups (n = 24 per group): An on-line writing workshop group (on-line group), in which participants used virtual communication, google docs and standard writing templates, and a standard writing guidance training (standard group) where participants received standard instruction without the aid of virtual communication and writing templates. Two outcomes, manuscript quality was assessed using the scores obtained in Six subgroup analysis scale as the primary outcome measure, and satisfaction scores with Likert scale were evaluated. To control for observer variability, inter-observer reliability was assessed using Fleiss's kappa. A post-hoc analysis comparing rates of communication between mentors and participants was performed. Nonparametric tests were used to assess intervention efficacy. RESULTS: Excellent inter-observer reliability among three reviewers was found, with an Intraclass Correlation Coefficient (ICC) agreement = 0.931882 and ICC consistency = 0.932485. On-line group had better overall manuscript quality (p = 0.0017, SSQSavg score 75.3 +/- 14.21, ranging from 37 to 94) compared to the standard group (47.27 +/- 14.64, ranging from 20 to 72). Participant satisfaction was higher in the on-line group (4.3 +/- 0.73) compared to the standard group (3.09 +/- 1.11) (p = 0.001). The standard group also had fewer communication events compared to the on-line group (0.91 +/- 0.81 vs. 2.05 +/- 1.23; p = 0.0219). CONCLUSION: Our protocol for on-line scientific writing instruction is better than standard face-to-face instruction in terms of writing quality and student satisfaction. Future studies should evaluate the protocol efficacy in larger longitudinal cohorts involving participants from different languages.

Developments among International Scientific and Health Bodies on Dual-Use Issue

Presentation at the Controlling Dangerous Pathogens Project Regional Workshop on Dual-Use Research, Teresopolis, Brazil

Current scenario of scientific publications related to weeds in Argentina : comparison with some countries of America

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Current scenario of scientific publications related to weeds in Argentina : comparison with some countries of America

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The semi-automatic parallelisation of scientific application codes using a computer aided parallelisation toolkit

The shared-memory programming model can be an effective way to achieve parallelism on shared memory parallel computers. Historically however, the lack of a programming standard using directives and the limited scalability have affected its take-up. Recent advances in hardware and software technologies have resulted in improvements to both the performance of parallel programs with compiler directives and the issue of portability with the introduction of OpenMP. In this study, the Computer Aided Parallelisation Toolkit has been extended to automatically generate OpenMP-based parallel programs with nominal user assistance. We categorize the different loop types and show how efficient directives can be placed using the toolkit's in-depth interprocedural analysis. Examples are taken from the NAS parallel benchmarks and a number of real-world application codes. This demonstrates the great potential of using the toolkit to quickly parallelise serial programs as well as the good performance achievable on up to 300 processors for hybrid message passing-directive parallelisations.