Sealed containers in Z

Physical means of securing information, such as sealed envelopes and scratch cards, can be used to achieve cryptographic objectives. Reasoning about this has so far been informal. We give a model of distinguishable sealed envelopes in Z, exploring design decisions and further analysis and development of such models

Assessing the clinical relevance of Fenollaria massiliensis in human infections, using MALDI-TOF MS

Within the European Network for the Rapid Identification of Anaerobes (ENRIA) project eight clinical isolates of Fenollaria massiliensis were encountered. In this study a more extensive description of this species is given and the MALDI-TOF MS database is optimized for its identification. F. massiliensis is an anaerobic Gram positive rod with the tendency to decolorize quickly. It is mostly encountered in clinical samples from the groin region. Less common and non-valid species are not represented in the MALDI-TOF MS database. Therefore, F. massiliensis can only be identified by laboratories performing 16S rDNA gene sequencing. The addition of less common and non-valid species to the database will give insight in their clinical relevance

USTOPIA REQUIREMENTS THOUGHTS ON A USER-FRIENDLY SYSTEM FOR TRANSFORMATION OF PROGRAMS IN ABSTRACTO

Transformational programming is a program development method which is usually applied using 'pen and paper'. Since this requires a lot of clerical work (copying expressions, con- sistent substitution) which is tiresome and prone to error, some form of machine support is desirable. In this paper a number of systems are described that have already been built to this aim. Some of their shortcomings and limitations are identified. Based on experience with program transformation and transformation systems, a long list of features is given that would be useful in an 'utopian' transformation system. This list is presented using an orthogonal division of the problem area. A number of problems with the realisation of some aspects of our 'utopian' system are identified, and some areas for further research are indicated

Formalising the Continuous/Discrete Modeling Step

Formally capturing the transition from a continuous model to a discrete model is investigated using model based refinement techniques. A very simple model for stopping (eg. of a train) is developed in both the continuous and discrete domains. The difference between the two is quantified using generic results from ODE theory, and these estimates can be compared with the exact solutions. Such results do not fit well into a conventional model based refinement framework; however they can be accommodated into a model based retrenchment. The retrenchment is described, and the way it can interface to refinement development on both the continuous and discrete sides is outlined. The approach is compared to what can be achieved using hybrid systems techniques.Comment: In Proceedings Refine 2011, arXiv:1106.348

Comparison of data and process refinement

When is it reasonable, or possible, to refine a one place buffer into a two place buffer? In order to answer this question we characterise refinement based on substitution in restricted contexts. We see that data refinement (specifically in Z) and process refinement give differing answers to the original question, and we compare the precise circumstances which give rise to this difference by translating programs and processes into labelled transition systems, so providing a common basis upon which to make the comparison. We also look at the closely related area of subtyping of objects. Along the way we see how all these sorts of computational construct are related as far as refinement is concerned, discover and characterise some (as far as we can tell) new sorts of refinement and, finally, point up some research avenues for the future

Building a refinement checker for Z

In previous work we have described how refinements can be checked using a temporal logic based model-checker, and how we have built a model-checker for Z by providing a translation of Z into the SAL input language. In this paper we draw these two strands of work together and discuss how we have implemented refinement checking in our Z2SAL toolset. The net effect of this work is that the SAL toolset can be used to check refinements between Z specifications supplied as input files written in the LaTeX mark-up. Two examples are used to illustrate the approach and compare it with a manual translation and refinement check.Comment: In Proceedings Refine 2011, arXiv:1106.348

High-throughput Proteomics Identifies THEMIS2 as Independent Biomarker of Treatment-free Survival in Untreated CLL

It remains challenging in chronic lymphocytic leukemia (CLL) to distinguish between patients with favorable and unfavorable time-to-first treatment (TTFT). Additionally, the downstream protein correlates of well-known molecular features of CLL are not always clear. To address this, we selected 40 CLL patients with TTFT ≤24 months and compared their B cell intracellular protein expression with 40 age- and sex-matched CLL patients with TTFT &gt;24 months using mass spectrometry. In total, 3268 proteins were quantified in the cohort. Immunoglobulin heavy-chain variable (IGHV) mutational status and trisomy 12 were most impactful on the CLL proteome. Comparing cases to controls, 5 proteins were significantly upregulated, whereas 3 proteins were significantly downregulated. Of these, only THEMIS2, a signaling protein acting downstream of the B cell receptor, was significantly associated with TTFT, independently of IGHV and TP53 mutational status (hazard ratio, 2.49 [95% confidence interval, 1.62-3.84]; P &lt; 0.001). This association was validated on the mRNA and protein level by quantitative polymerase chain reaction and ELISA, respectively. Analysis of 2 independently generated RNA sequencing and mass spectrometry datasets confirmed the association between THEMIS2 expression and clinical outcome. In conclusion, we present a comprehensive characterization of the proteome of untreated CLL and identify THEMIS2 expression as a putative biomarker of TTFT.</p

Bigraphical Refinement

We propose a mechanism for the vertical refinement of bigraphical reactive systems, based upon a mechanism for limiting observations and utilising the underlying categorical structure of bigraphs. We present a motivating example to demonstrate that the proposed notion of refinement is sensible with respect to the theory of bigraphical reactive systems; and we propose a sufficient condition for guaranteeing the existence of a safety-preserving vertical refinement. We postulate the existence of a complimentary notion of horizontal refinement for bigraphical agents, and finally we discuss the connection of this work to the general refinement of Reeves and Streader.Comment: In Proceedings Refine 2011, arXiv:1106.348

Model exploration and analysis for quantitative safety refinement in probabilistic B

The role played by counterexamples in standard system analysis is well known; but less common is a notion of counterexample in probabilistic systems refinement. In this paper we extend previous work using counterexamples to inductive invariant properties of probabilistic systems, demonstrating how they can be used to extend the technique of bounded model checking-style analysis for the refinement of quantitative safety specifications in the probabilistic B language. In particular, we show how the method can be adapted to cope with refinements incorporating probabilistic loops. Finally, we demonstrate the technique on pB models summarising a one-step refinement of a randomised algorithm for finding the minimum cut of undirected graphs, and that for the dependability analysis of a controller design.Comment: In Proceedings Refine 2011, arXiv:1106.348