Optimal kinetics for quantification of antigen-induced cytokines in human peripheral blood mononuclear cells by real-time PCR and by ELISA.

Real-time polymerase chain reaction (PCR) has recently been described as a new tool to measure and accurately quantify mRNA levels. In this study, we have applied this technique to evaluate cytokine mRNA synthesis induced by antigenic stimulation with purified protein derivative (PPD) or heparin-binding haemagglutinin (HBHA) in human peripheral blood mononuclear cells (PBMC) from Mycobacterium tuberculosis-infected individuals. Whereas PPD and HBHA optimally induced IL-2 mRNA after respectively 8 and 16 to 24 h of in vitro stimulation, longer in vitro stimulation times were necessary for optimal induction of interferon-gamma (IFN-gamma) mRNA, respectively 16 to 24 h for PPD and 24 to 96 h for HBHA. IL-13 mRNA was optimally induced by in vitro stimulation after 16-48 h for PPD and after 48 to 96 h for HBHA. Comparison of antigen-induced Th1 and Th2 cytokines appears, therefore, valuable only if both cytokine types are analysed at their optimal time point of production, which, for a given cytokine, may differ for each antigen tested. Results obtained by real-time PCR for IFN-gamma and IL-13 mRNA correlated well with those obtained by measuring the cytokine concentrations in cell culture supernatants, provided they were high enough to be detected. We conclude that real-time PCR can be successfully applied to the quantification of antigen-induced cytokine mRNA and to the evaluation of the Th1/Th2 balance, only if the kinetics of cytokine mRNA appearance are taken into account and evaluated for each cytokine measured and each antigen analysed.

A domain decomposition algorithm for viscous/inviscid coupling

In fluid mechanics, it is well accepted that the Euler equation is one of the reduced forms of the Navier-Stokes equation by truncating the viscous effect. There are other truncation techniques currently being used in order to truncate the Navier-Stokes equation to a reduced form. This paper describes one such technique, suitable for adaptive domain decomposition methods for the solution of viscous flow problems. The physical domain of a viscous flow problem is partitioned into viscous and inviscid subdomains without overlapping regions, and the technique is embedded into a finite volume method. Some numerical results are provided for a flat plate and the NACA0012 aerofoil. Issues related to distributed computing are discussed.

Evaluating the effectiveness of Z: The claims made about CICS and where we go from here

There have been few genuine success stories about industrial use of formal methods. Perhaps the best known and most celebrated is the use of Z by IBM (in collaboration with Oxford University's Programming Research Group) during the development of CICS/ESA (version 3.1). This work was rewarded with the prestigious Queen's Award for Technological Achievement in 1992 and is especially notable for two reasons: 1) because it is a commercial, rather than safety- or security-critical, system and 2) because the claims made about the effectiveness of Z are quantitative as well as qualitative. The most widely publicized claims are: less than half the normal number of customer-reported errors and a 9% savings in the total development costs of the release. This paper provides an independent assessment of the effectiveness of using Z on CICS based on the set of public domain documents. Using this evidence, we believe that the case study was important and valuable, but that the quantitative claims have not been substantiated. The intellectual arguments and rationale for formal methods are attractive, but their widespread commercial use is ultimately dependent upon more convincing quantitative demonstrations of effectiveness. Despite the pioneering efforts of IBM and PRG, there is still a need for rigorous, measurement-based case studies to assess when and how the methods are most effective. We describe how future similar case studies could be improved so that the results are more rigorous and conclusive.

Network analysis of 2-mode data

Network analysis is distinguished from traditional social science by the dyadic nature of the standard data set. Whereas in traditional social science we study monadic attributes of individuals, in network analysis we study dyadic attributes of pairs of individuals. These dyadic attributes (e.g. social relations) may be represented in matrix form by a square 1-mode matrix. In contrast, the data in traditional social science are represented as 2-mode matrices. However, network analysis is not completely divorced from traditional social science, and often has occasion to collect and analyze 2-mode matrices. Furthermore, some of the methods developed in network analysis have uses in analysing non-network data. This paper presents and discusses ways of applying and interpreting traditional network analytic techniques to 2-mode data, as well as developing new techniques. Three areas are covered in detail: displaying 2-mode data as networks, detecting clusters and measuring centrality.

Reflection is alive and well, but not what you think

More and more, Business and Management students (and those in other disciplines) are being asked to undertake written reflection upon their learning as part of assessed course-work. This paper examines this trend and explores the thinking behind it: why lecturers see reflection as valuable to students, whether they undertake reflection themselves, what theoretical underpinning they perceive as justifying and explaining their views. The results of a survey undertaken among Business and Management lecturers are reported, which appear to show that the most influential writer on the subject of reflection in learning – the one most frequently cited by the respondents – is David A. Kolb, author of the well-known Experiential Learning Theory (1984), and one of the moving forces behind experiential learning in general. His ideas have attracted a good deal of criticism, but are still current, having been suitably updated and defended, (2005). The paper critically re-examines Kolb’s Experiential Learning Theory, challenging its relevance to most of Higher Education, as characterised by Peter Jarvis in his useful table of learning situations as “formal and intended” (2004; 108). Other criticisms of Kolb’s Experiential Learning Theory are advanced that are entirely new. Returning to the survey, the papers discusses the reasons lecturers believe reflection is valuable to students and concludes that Kolb’s model, and others such as Schön’s (1987), fail to adequately explain or even identify them.

How well does the Continuous Plankton Recorder (CPR) sample zooplankton? A comparison with the Longhurst Hardy Plankton Recorder (LHPR) in the northeast Atlantic

The Continuous Plankton Recorder (CPR) survey has collected data on basin- scale zooplankton abundance in the North Atlantic since the 1930s. These data have been used in many studies to elucidate seasonal patterns and long-term change in plankton populations, as well as more recently to validate ecosystem models. There has, however, been relatively little comparison of the data from the CPR with that from other samplers. In this study we compare zooplankton abundance estimated from the CPR in the northeast Atlantic with near-surface samples collected by a Longhurst-Hardy Plankton Recorder (LHPR) at Ocean Weather Station India (59 degree N, 19 degree W) between 1971 and 1975. Comparisons were made for six common copepods in the region: Acartia clausi, Calanus finmarchicus, Euchaeta norvegica, Metridia lucens, Oithona sp. and Pleuromamma robusta. Seasonal cycles based on CPR data were similar to those recorded by the LHPR. Differences in absolute abundances were apparent, however, with the CPR underestimating abundances by a factor of between 5 and 40, with the exception of A. clausi. Active avoidance by zooplankton is thought to be responsible. This avoidance is species specific, so that care must be taken describing communities, as the CPR emphasises those species that are preferentially caught, a problem common to many plankton samplers.

How well do ecosystem indicators communicate the effects of anthropogenic eutrophication?

Anthropogenic eutrophication affects the Mediterranean, Black, North and Baltic Seas to various extents. Responses to nutrient loading and methods of monitoring relevant indicators vary regionally, hindering interpretation of ecosystem state changes and preventing a straightforward pan-European assessment of eutrophication symptoms. Here we summarize responses to nutrient enrichment in Europe's seas, comparing existing time-series of selected pelagic (phytoplankton biomass and community composition, turbidity, N:P ratio) and benthic (macro flora and faunal communities, bottom oxygen condition) indicators based on their effectiveness in assessing eutrophication effects. Our results suggest that the Black Sea and Northern Adriatic appear to be recovering from eutrophication due to economic reorganization in the Black Sea catchment and nutrient abatement measures in the case of the Northern Adriatic. The Baltic is most strongly impacted by eutrophication due to its limited exchange and the prevalence of nutrient recycling. Eutrophication in the North Sea is primarily a coastal problem, but may be exacerbated by climatic changes. Indicator interpretation is strongly dependent on sea-specific knowledge of ecosystem characteristics, and no single indicator can be employed to adequately compare eutrophication state between European seas. Communicating eutrophication-related information to policy-makers could be facilitated through the use of consistent indicator selection and monitoring methodologies across European seas. This work is discussed in the context of the European Commission's recently published Marine Strategy Directive.

Influences of the Oceans on Human Health and Well-Being

Human health and well-being are tied to the vitality of the global ocean and coastal systems on which so many live and rely. We engage with these extraordinary environments to enhance both our health and our well-being. But, we need to recognize that introducing contaminants and otherwise altering these ocean systems can harm human health and well-being in significant and substantial ways. These are complex, challenging, and critically important themes. How the human relationship to the oceans evolves in coming decades may be one of the most important connections in understanding our personal and social well-being. Yet, our understanding of this relationship is far too limited. This remarkable volume brings experts from diverse disciplines and builds a workable understanding of breadth and depth of the processes – both social and environmental – that will help us to limit future costs and enhance the benefits of sustainable marine systems. In particular, the authors have developed a shared view that the global coastal environment is under threat through intensified natural resource utilization, as well as changes to global climate and other environmental systems. All these changes contribute individually, but more importantly cumulatively, to higher risks for public health and to the global burden of disease. This pioneering book will be of value to advanced undergraduate and postgraduate students taking courses in public health, environmental, economic, and policy fields. Additionally, the treatment of these complex systems is of essential value to the policy community responsible for these questions and to the broader audience for whom these issues are more directly connected to their own health and well-being.

Remote sensing of assimilation number for marine phytoplankton

Estimating primary production at large spatial scales is key to our understanding of the global carbon cycle. Algorithms to estimate primary production are well established and have been used in many studies with success. One of the key parameters in these algorithms is the chlorophyll-normalised production rate under light saturation (referred to as the light saturation parameter or the assimilation number). It is known to depend on temperature, light history and nutrient conditions, but assigning a magnitude to it at particular space-time points is difficult. In this paper, we explore two models to estimate the assimilation number at the global scale from remotely-sensed data that combine methods to estimate the carbon-to-chlorophyll ratio and the maximum growth rate of phytoplankton. The inputs to the algorithms are the surface concentration of chlorophyll, seasurface temperature, photosynthetically-active radiation af the surface of the sea, sea surface nutrient concentration and mixed-layer depth. A large database of in situ estimates of the assimilation number is used to develop the models and provide elements of validation. The comparisons with in situ observations are promising and global maps of assimilation number are produced.

Family-level AMBI is valid for use in the north-eastern Atlantic but not for assessing the health of microtidal Australian estuaries

Analysis of benthic macroinvertebrate samples at a higher taxonomic level than species, e.g. family, potentially provides a more cost-effective protocol for environmental impact assessments and monitoring as it requires less time, funds and taxonomic expertise. Using the AMBI database, species ecological group scores are shown to be coherent within families. Faunal data from a wide range of environmental impact scenarios in the north-eastern Atlantic demonstrate that AMBI, calculated from mean values for families, exhibits a strong linear relationship with species-level AMBI, the correlation improving by using square-root transformed rather than untransformed abundances. In many regions of the world, however, the sensitivity of benthic macroinvertebrates to environmental perturbations is unknown, precluding the use of AMBI for environmental assessments. Yet the families are essentially the same as in the AMBI database. The utility of family-level AMBI is tested using data for four south-western Australian estuaries previously subjected to environmental quality assessments, but where only 17 species of the 144 taxa are included in the AMBI database. Although family-level AMBI scores reflect differences in environmental quality spatially and temporally within an estuary, they do not follow variations in environmental quality among estuaries. Indeed, south-western Australia estuaries are numerically dominated by families with high AMBI scores, probably due to the detrimental effects of natural accumulations of organic material in estuaries with long residence times. As taxonomic distinctness follows trends in environmental quality among estuaries, as well as temporally and spatially within a system, it provides an appropriate substitute for assessing the 'heath' of microtidal estuaries.