Formal methods to aid the evolution of software.

Paper dated January 6, 1995There is a vast collection of operational software systems which are vitally important to their users, yet are becoming increasingly difficult to maintain, enhance and keep up to date with rapidly changing requirements. For many these so called legacy systems the option of throwing the system away and re-writing it from scratch is not economically viable. Methods are therefore urgently required which enable these systems to evolve in a controlled manner. The approach described in this paper uses formal proven program transformations, which preserve or refine the semantics of a program while changing its form. These transformations are applied to restructure and simplify the legacy systems and to extract higher-level representations. By using an appropriate sequence of transformation, the extracted representation is guaranteed to be equivalent to the code. The method is based on a formal wide spectrum language, called WSL, with accompanying formal method. Over the last ten years we have developed a large catalogue of proven transformations, together with mechanically verifiable applicability conditions. These have been applied to many software development, reverse engineering and maintenance problems. In this paper, we focus on the results of using this approach in reverse engineering of medium scale, industrial software, written mostly in languages such as assembler and JOVIAL. Results from both benchmark algorithms and heavily modified, geriatric software are summarised. We conclude that formal methods have an important practical role in software evolution.Partly funded bu Alvey project SE-088, partly through a DTI/SERC and IBM UK Ltd. funded IEATP grant "From assembler to Z using formal transformations" and partly by SERC (Science and Engineering Research Council) project "A proof theory for program refinement and equivalence: extensions"

Formal methods for legacy systems.

Paper dated January 6, 1995A method is described for obtaining useful information from legacy code. The approach uses formal proven program transformations, which preserve for refine the semantics of a construct while changing its form. The applicability of a transformation in a particular syntactic context is checked before application. By using an appropriate sequence of transformations, the extracted representation is guaranteed to be equivalent to the code. In this paper, we focus on the results of using this approach in the reverse engineering of medium scale, industrial software, written mostly in languages such as assembler and JOVIAL. Results from both benchmark algorithms and heavily modified, geriatric software are summarised. It is concluded that the approach is viable, for self-contained code, and that useful design information may be extracted from legacy systems at economic cost. We conclude that formal methods have an important practical role in the reverse engineering process.Partly funded bu Alvey project SE-088, partly through a DTI/SERC and IBM UK Ltd. funded IEATP grant "From assembler to Z using formal transformations" and partly by SERC (Science and Engineering Research Council) project "A proof theory for program refinement and equivalence: extensions"

Is It Time for Synthetic Biodiversity Conservation?

Evidence indicates that, despite some critical successes, current conservation approaches are not slowing the overall rate of biodiversity loss. The field of synthetic biology, which is capable of altering natural genomes with extremely precise editing, might offer the potential to resolve some intractable conservation problems (e.g., invasive species or pathogens). However, it is our opinion that there has been insufficient engagement by the conservation community with practitioners of synthetic biology. We contend that rapid, large-scale engagement of these two communities is urgently needed to avoid unintended and deleterious ecological consequences. To this point we describe case studies where synthetic biology is currently being applied to conservation, and we highlight the benefits to conservation biologists from engaging with this emerging technology

Persistence of the immune response induced by BCG vaccination.

BACKGROUND: Although BCG vaccination is recommended in most countries of the world, little is known of the persistence of BCG-induced immune responses. As novel TB vaccines may be given to boost the immunity induced by neonatal BCG vaccination, evidence concerning the persistence of the BCG vaccine-induced response would help inform decisions about when such boosting would be most effective. METHODS: A randomised control study of UK adolescents was carried out to investigate persistence of BCG immune responses. Adolescents were tested for interferon-gamma (IFN-gamma) response to Mycobacterium tuberculosis purified protein derivative (M.tb PPD) in a whole blood assay before, 3 months, 12 months (n = 148) and 3 years (n = 19) after receiving teenage BCG vaccination or 14 years after receiving infant BCG vaccination (n = 16). RESULTS: A gradual reduction in magnitude of response was evident from 3 months to 1 year and from 1 year to 3 years following teenage vaccination, but responses 3 years after vaccination were still on average 6 times higher than before vaccination among vaccinees. Some individuals (11/86; 13%) failed to make a detectable antigen-specific response three months after vaccination, or lost the response after 1 (11/86; 13%) or 3 (3/19; 16%) years. IFN-gamma response to Ag85 was measured in a subgroup of adolescents and appeared to be better maintained with no decline from 3 to 12 months. A smaller group of adolescents were tested 14 years after receiving infant BCG vaccination and 13/16 (81%) made a detectable IFN-gamma response to M.tb PPD 14 years after infant vaccination as compared to 6/16 (38%) matched unvaccinated controls (p = 0.012); teenagers vaccinated in infancy were 19 times more likely to make an IFN-gamma response of > 500 pg/ml than unvaccinated teenagers. CONCLUSION: BCG vaccination in infancy and adolescence induces immunological memory to mycobacterial antigens that is still present and measurable for at least 14 years in the majority of vaccinees, although the magnitude of the peripheral blood response wanes from 3 months to 12 months and from 12 months to 3 years post vaccination. The data presented here suggest that because of such waning in the response there may be scope for boosting anti-tuberculous immunity in BCG vaccinated children anytime from 3 months post-vaccination. This supports the prime boost strategies being employed for some new TB vaccines currently under development

Convection forced by a descending dry layer and low-level moist convergence

This is the post-print version of the Article - Copyright @ 2009 Wiley-BlackwellA narrow line of convective showers was observed over southern England on 18 July 2005 during the Convective Storm Initiation Project (CSIP). The showers formed behind a cold front (CF), beneath two apparently descending dry layers (i.e. sloping so that they descended relative to the instruments observing them). The lowermost dry layer was associated with a tropopause fold from a depression, which formed 2 d earlier from a breaking Rossby wave, located northwest of the UK. The uppermost dry layer had fragmented from the original streamer due to rotation around the depression (This rotation was also responsible for the observations of apparent descent—ascent would otherwise be seen behind a CF). The lowermost dry layer descended over the UK and overran higher θw air beneath it, resulting in potential instability. Combined with a surface convergence line (which triggered the convection but had less impact on the convective available potential energy than the potential instability), convection was forced up to 5.5 km where the uppermost dry layer capped it. The period when convection was possible was very short, thus explaining the narrowness of the shower band. Convective Storm Initiation Project observations and model data are presented to illustrate the unique processes in this case.This work is partly funded by the Natural Environment Research Council (NERC)

Revisiting the Higgs Mass and Dark Matter in the CMSSM

Taking into account the available accelerator and astrophysical constraints, the mass of the lightest neutral Higgs boson h in the minimal supersymmetric extension of the Standard Model with universal soft supersymmetry-breaking masses (CMSSM) has been estimated to lie between 114 and ~ 130 GeV. Recent data from ATLAS and CMS hint that m_h ~ 125 GeV, though m_h ~ 119 GeV may still be a possibility. Here we study the consequences for the parameters of the CMSSM and direct dark matter detection if the Higgs hint is confirmed, focusing on the strips in the (m_1/2, m_0) planes for different tan beta and A_0 where the relic density of the lightest neutralino chi falls within the range of the cosmological cold dark matter density allowed by WMAP and other experiments. We find that if m_h ~ 125 GeV focus-point strips would be disfavoured, as would the low-tan beta stau-chi and stop -chi coannihilation strips, whereas the stau-chi coannihilation strip at large tan beta and A_0 > 0 would be favoured, together with its extension to a funnel where rapid annihilation via direct-channel H/A poles dominates. On the other hand, if m_h ~ 119 GeV more options would be open. We give parametrizations of WMAP strips with large tan beta and fixed A_0/m_0 > 0 that include portions compatible with m_h = 125 GeV, and present predictions for spin-independent elastic dark matter scattering along these strips. These are generally low for models compatible with m_h = 125 GeV, whereas the XENON100 experiment already excludes some portions of strips where m_h is smaller.Comment: 24 pages, 9 figure

Relating the CMSSM and SUGRA models with GUT scale and Super-GUT scale Supersymmetry Breaking

While the constrained minimal supersymmetric standard model (CMSSM) with universal gaugino masses, m_{1/2}, scalar masses, m_0, and A-terms, A_0, defined at some high energy scale (usually taken to be the GUT scale) is motivated by general features of supergravity models, it does not carry all of the constraints imposed by minimal supergravity (mSUGRA). In particular, the CMSSM does not impose a relation between the trilinear and bilinear soft supersymmetry breaking terms, B_0 = A_0 - m_0, nor does it impose the relation between the soft scalar masses and the gravitino mass, m_0 = m_{3/2}. As a consequence, tan(\beta) is computed given values of the other CMSSM input parameters. By considering a Giudice-Masiero (GM) extension to mSUGRA, one can introduce new parameters to the K\"ahler potential which are associated with the Higgs sector and recover many of the standard CMSSM predictions. However, depending on the value of A_0, one may have a gravitino or a neutralino dark matter candidate. We also consider the consequences of imposing the universality conditions above the GUT scale. This GM extension provides a natural UV completion for the CMSSM.Comment: 16 pages, 11 figures; added erratum correcting several equations and results in Sec.2, Sec.3 and 4 remain unaffected and conclusions unchange