The interpretive approach to religious education : challenging Thompson's interpretation

In a recent book chapter, Matthew Thompson makes some criticisms of my work, including the interpretive approach to religious education and the research and activity of Warwick Religions and Education Research Unit. Against the background of a discussion of religious education in the public sphere, my response challenges Thompson’s account, commenting on his own position in relation to dialogical approaches to religious education. The article rehearses my long held view that the ideal form of religious education in fully state funded schools of a liberal democracy should be ‘secular’ but not ‘secularist’; there should be no implication of an axiomatic secular humanist interpretation of religions

Quantum-enhanced atomic gyroscope with tunable precision

We model a gyroscope that exploits quantum effects in an atomic Bose–Einstein condensate to gain a tunable enhancement in precision. Current inertial navigation systems rely on the Sagnac effect using unentangled photons in fibre-optic systems and there are proposals for improving how the precision scales with the number of particles by using entanglement. Here we exploit a different route based on sharp resonances associated with quantum phase transitions. By adjusting the interaction between the particles and/or the shape of their trapping potential we are able to tune the width of the resonance and hence the precision of the measurement. Here we show how we can use this method to increase the overall sensitivity of a gyroscope by adjusting the system parameters as the measurement proceeds and our knowledge of the rotation improves. We illustrate this with an example where the precision is enhanced by a factor of more than 20 over the case without tuning, after 100 repetitions. Metrology schemes with tunable precision based on quantum phase transitions could offer an important complementary method to other quantum-enhanced measurement and sensing schemes

Practical quantum metrology with large precision gains in the low photon number regime

Quantum metrology exploits quantum correlations to make precise measurements with limited particle numbers. By utilizing inter- and intra- mode correlations in an optical interferometer, we find a state that combines entanglement and squeezing to give a 7-fold enhancement in the quantum Fisher information (QFI) - a metric related to the precision - over the shot noise limit, for low photon numbers. Motivated by practicality we then look at the squeezed cat-state, which has recently been made experimentally, and shows further precision gains over the shot noise limit and a 3-fold improvement in the QFI over the optimal Gaussian state. We present a conceptually simple measurement scheme that saturates the QFI, and we demonstrate a robustness to loss for small photon numbers. The squeezed cat-state can therefore give a significant precision enhancement in optical quantum metrology in practical and realistic conditions

Revision history aware repositories of computational models of biological systems

<p>Abstract</p> <p>Background</p> <p>Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model.</p> <p>One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file.</p> <p>The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs) for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems.</p> <p>Results</p> <p>We have extended the Physiome Model Repository software to be fully revision history aware, by building it on top of Mercurial, an existing DVCS. We have demonstrated the utility of this approach, when used in conjunction with the model composition facilities in CellML, to build and understand more complex models. We have also demonstrated the ability of the repository software to present version history to casual users over the web, and to highlight specific versions which are likely to be useful to users.</p> <p>Conclusions</p> <p>Providing facilities for maintaining and using revision history information is an important part of building a useful repository of computational models, as this information is useful both for understanding the source of and justification for parts of a model, and to facilitate automated processes such as merges. The availability of fully revision history aware repositories, and associated tools, will therefore be of significant benefit to the community.</p

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

CellML metadata standards, associated tools and repositories

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website

Interactions of Shiga-like toxin with human peripheral blood monocytes

The cytotoxic effect of Shiga-like toxin (Stx; produced by certain Escherichia coli strains) plays a central role in typical hemolytic uremic syndrome (HUS). It damages the renal endothelium by inhibiting the cellular protein synthesis. Also, the monocyte has a specific receptor for Stx but is not sensitive for the cytotoxic effect. In this work, monocytes were studied as a potential transporter for Stx to the renal endothelium. Coincubation of isolated human monocytes loaded with Stx and target cells (vero cells and human umbilical vascular endothelial cells) were performed. Transfer was determined by measuring the protein synthesis of target cells and by flow cytometry. Furthermore, the effect of a temperature shift on loaded monocytes was investigated. Stx-loaded monocytes reduced the protein synthesis of target cells. After adding an antibody against Stx, incomplete recovery occurred. Also, adding only the supernatant of coincubation was followed by protein synthesis inhibition. Stx detached from its receptor on the monocyte after a change in temperature, and no release was detected without this temperature shift. Although the monocyte plays an important role in the pathogenesis of HUS, it has no role in the transfer of Stx