From Event-B models to Dafny code contracts

International audienceThe constructive approach to software correctness aims at formal modelling and verification of the structure and behaviour of a system in different levels of abstraction. In contrast, the analytical approach to software verification focuses on code level correctness and its verification. Therefore it would seem that the constructive and analytical approaches should complement each other well. To demonstrate this idea we present a case for linking two existing verification methods, Event-B (constructive) and Dafny (analytical). This approach combines the power of Event-B abstraction and its stepwise refinement with the verification capabilities of Dafny. We presented a small case study to demonstrate this approach and outline of the rules for transforming Event-B events to Dafny contracts. Finally, a tool for automatic generation of Dafny contracts from Event-B formal models is presented

Metabolic insights into infochemicals induced colony formation and flocculation in scenedesmus subspicatus unraveled by quantitative proteomics

Microalgae can respond to natural cues from crustacean grazers, such as Daphnia, by forming colonies and aggregations called flocs. Combining microalgal biology, physiological ecology, and quantitative proteomics, we identified how infochemicals from Daphnia trigger physiological and cellular level changes in the microalga Scenedesmus subspicatus, underpinning colony formation and flocculation. We discovered that flocculation occurs at an energy-demanding ‘alarm’ phase, with an important role proposed in cysteine synthesis. Flocculation appeared to be initially stimulated by the production of an extracellular matrix where polysaccharides and fatty acids were present, and later sustained at an ‘acclimation’ stage through mitogen-activated protein kinase (MAPK) signaling cascades. Colony formation required investment into fatty acid metabolism, likely linked to separation of membranes during cell division. Higher energy demands were required at the alarm phase, which subsequently decreased at the acclimation stage, thus suggesting a trade-off between colony formation and flocculation. From an ecological and evolutionary perspective, our findings represent an improved understanding of the effect of infochemicals on microalgae-grazers interactions, and how they can therefore potentially impact on the structure of aquatic communities. Moreover, the mechanisms revealed are of interest in algal biotechnology, for exploitation in low-cost, sustainable microalgal biomass harvesting

Electromagnetic Decays of Heavy Baryons

The electromagnetic decays of the ground state baryon multiplets with one heavy quark are calculated using Heavy Hadron Chiral Perturbation Theory. The M1 and E2 amplitudes for S^{*}--> S gamma, S^{*} --> T gamma and S --> T gamma are separately computed. All M1 transitions are calculated up to O(1/Lambda_chi^2). The E2 amplitudes contribute at the same order for S^{*}--> S gamma, while for S^{*} --> T gamma they first appear at O(1/(m_Q \Lambda_\chi^2)) and for S --> T gamma are completely negligible. The renormalization of the chiral loops is discussed and relations among different decay amplitudes are derived. We find that chiral loops involving electromagnetic interactions of the light pseudoscalar mesons provide a sizable enhancement of these decay widths. Furthermore, we obtain an absolute prediction for the widths of Xi^{0'(*)}_c--> Xi^{0}_c gamma and Xi^{-'(*)}_b--> Xi^{-}_b gamma. Our results are compared to other estimates existing in the literature.Comment: 17 pages, 3 figures, submitted to Phys. Rev.

Challenging Perceptions of Disability through Performance Poetry Methods: The "Seen but Seldom Heard" Project.

This paper considers performance poetry as a method to explore lived experiences of disability. We discuss how poetic inquiry used within a participatory arts-based research framework can enable young people to collectively question society’s attitudes and actions towards disability. Poetry will be considered as a means to develop a more accessible and effective arena in which young people with direct experience of disability can be empowered to develop new skills that enable them to tell their own stories. Discussion of how this can challenge audiences to critically reflect upon their own perceptions of disability will also be developed

Enhanced T-odd P-odd Electromagnetic Moments in Reflection Asymmetric Nuclei

Collective P- and T- odd moments produced by parity and time invariance violating forces in reflection asymmetric nuclei are considered. The enhanced collective Schiff, electric dipole and octupole moments appear due to the mixing of rotational levels of opposite parity. These moments can exceed single-particle moments by more than two orders of magnitude. The enhancement is due to the collective nature of the intrinsic moments and the small energy separation between members of parity doublets. In turn these nuclear moments induce enhanced T- and P- odd effects in atoms and molecules. First a simple estimate is given and then a detailed theoretical treatment of the collective T-, P- odd electric moments in reflection asymmetric, odd-mass nuclei is presented and various corrections evaluated. Calculations are performed for octupole deformed long-lived odd-mass isotopes of Rn, Fr, Ra, Ac and Pa and the corresponding atoms. Experiments with such atoms may improve substantially the limits on time reversal violation.Comment: 28 pages, Revte

Effects of rapid prey evolution on predator-prey cycles

We study the qualitative properties of population cycles in a predator-prey system where genetic variability allows contemporary rapid evolution of the prey. Previous numerical studies have found that prey evolution in response to changing predation risk can have major quantitative and qualitative effects on predator-prey cycles, including: (i) large increases in cycle period, (ii) changes in phase relations (so that predator and prey are cycling exactly out of phase, rather than the classical quarter-period phase lag), and (iii) "cryptic" cycles in which total prey density remains nearly constant while predator density and prey traits cycle. Here we focus on a chemostat model motivated by our experimental system [Fussmann et al. 2000,Yoshida et al. 2003] with algae (prey) and rotifers (predators), in which the prey exhibit rapid evolution in their level of defense against predation. We show that the effects of rapid prey evolution are robust and general, and furthermore that they occur in a specific but biologically relevant region of parameter space: when traits that greatly reduce predation risk are relatively cheap (in terms of reductions in other fitness components), when there is coexistence between the two prey types and the predator, and when the interaction between predators and undefended prey alone would produce cycles. Because defense has been shown to be inexpensive, even cost-free, in a number of systems [Andersson and Levin 1999, Gagneux et al. 2006,Yoshida et al. 2004], our discoveries may well be reproduced in other model systems, and in nature. Finally, some of our key results are extended to a general model in which functional forms for the predation rate and prey birth rate are not specified.Comment: 35 pages, 8 figure

Colloquium: Mechanical formalisms for tissue dynamics

The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes being expressed. This information suggests that ourunderstanding of the respective contributions of gene expression and mechanics, and of their crucialentanglement, will soon leap forward. Biomechanics increasingly benefits from models, which assistthe design and interpretation of experiments, point out the main ingredients and assumptions, andultimately lead to predictions. The newly accessible local information thus calls for a reflectionon how to select suitable classes of mechanical models. We review both mechanical ingredientssuggested by the current knowledge of tissue behaviour, and modelling methods that can helpgenerate a rheological diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and tissue scale ("inter-cell") contributions. We recall the mathematical framework developpedfor continuum materials and explain how to transform a constitutive equation into a set of partialdifferential equations amenable to numerical resolution. We show that when plastic behaviour isrelevant, the dissipation function formalism appears appropriate to generate constitutive equations;its variational nature facilitates numerical implementation, and we discuss adaptations needed in thecase of large deformations. The present article gathers theoretical methods that can readily enhancethe significance of the data to be extracted from recent or future high throughput biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few corrections to the published version, all in Appendix D.2 devoted to large deformation

The ‘Self-Regulated Learning Opportunities Questionnaire': a diagnostic instrument for teacher educators' professional development

Many recent studies have stressed the importance of students’ self-regulated learning (SRL) skills for successful learning. Although primary teacher educators are aware of the importance of SRL for their students, they often find it difficult to implement SRL opportunities in their teaching. To support teacher professional development, an SRL model was described in a previous theoretical study. In the present article, this SRL model is elaborated towards the ‘SRL Opportunities Questionnaire’ (SRLOQ) that can be applied by primary teacher educators as a diagnostic instrument for classroom settings. A four-phase research design is applied consisting of scale development, score validation, further validation of the SRLOQ in primary teacher education, and a confirmatory factor analysis. Finally, a single case study is described that illustrates the usefulness of the SRLOQ in classroom practice

MMN and Differential Waveform

A mismatch negativity response (MMN) and a new differential waveform were derived in an effort to evaluate a neural refractory or recovery effect in adult listeners. The MMN was elicited using oddball test runs in which the standard and deviant stimuli differed in frequency. To derive the differential waveform, the same standard and deviant stimuli were presented alone. MMN responses were obtained by subtracting the averaged responses to standards from the deviants. The differential waveforms were obtained by subtracting the averaged responses to standards presented alone from deviants presented alone. Scalp topography for the MMN and differential waveforms were similar. A significant (p < .05) positive and negative correlation was found between the earlier and later components of the bimodal MMN and the N1 and P2 component of the differential waveform, respectively. Further, N1 and P2 of the differential waveform were significant (p < .05) predictor variables of early and late peak amplitudes of the MMN. These results suggest that refractory effects may overlay/modify the morphology of the MMN waveform

Feasibility study of large-scale deployment of colour-ringing on black-legged kittiwake populations to improve the realism of demographic models assessing the population impacts of offshore wind farms

• Renewable energy developments, including offshore wind farms have been identified as a key component in international efforts to mitigate climate change and its impact on biodiversity. This has led to an increasing number of offshore wind farms around the UK, however, these can have negative impacts on seabird populations. • Population Viability Analysis (PVA) is frequently used to quantify these potential negative effects on seabird populations and is a vital part of the consenting process. However, a lack of empirical data on many aspects of seabird demography means that there can be considerable uncertainty in these assessments. • Black-legged Kittiwake Rissa tridactyla populations are thought to be particularly sensitive to additional mortality caused by collision with offshore wind turbines and are often highlighted as a feature of Special Protection Areas (SPAs). Offshore wind farms, therefore, have been identified as potentially causing an adverse effect on site integrity at some SPAs. • Despite being a relatively well-studied species, there is still much uncertainty in our knowledge of Kittiwake demographic rates and meta-population dynamics, which impedes our ability to accurately assess the way populations might respond to additional wind farm-induced mortality. • The Offshore Wind Strategic Monitoring and Research Forum (OWSMRF) identified a large-scale colour-ringing programme of Kittiwake colonies across the UK as one potential approach for improving empirical estimates of Kittiwake demographic rates. • Therefore, the main aim of this project was to determine the extent to which colour-ringing can be used to obtain reliable baseline estimates of key demographic rates in Kittiwake populations to improve the realism of demographic models assessing the population impacts of offshore wind farms, and thereby reduce uncertainty around these predicted impacts