Size-Change Abstraction and Max-Plus Automata

Max-plus automata (over ℕ ∪ − ∞) are finite devices that map input words to non-negative integers or − ∞. In this paper we present (a) an algorithm allowing to compute the asymptotic behaviour of max-plus automata, and (b) an application of this technique to the evaluation of the computational time complexity of programs

Interactive Termination Proofs Using Termination Cores

Abstract. Recent advances in termination analysis have yielded new methods and tools that are highly automatic. However, when they fail, even experts have difficulty understanding why and determining how to proceed. In this paper, we address the issue of building termination analysis engines that are both highly automatic and easy to use in an interactive setting. We consider the problem in the context of ACL2, which has a first-order, functional programming language. We introduce the notion of a termination core, a simplification of the program under consideration which consists of a single loop that the termination engine cannot handle. We show how to extend the Size Change Termination (SCT) algorithm so that it generates termination cores when it fails to prove termination, with no increase to its complexity. We show how to integrate this into the Calling Context Graph (CCG) termination analysis, a powerful SCT-based automatic termination analysis that is part of the ACL2 Sedan. We also present several new, convenient ways of allowing users to interface with the CCG analysis, in order to guide it to a termination proof.

HIV-1 gp41 and TCRα Trans-Membrane Domains Share a Motif Exploited by the HIV Virus to Modulate T-Cell Proliferation

Viruses have evolved several strategies to modify cellular processes and evade the immune response in order to successfully infect, replicate, and persist in the host. By utilizing in-silico testing of a transmembrane sequence library derived from virus protein sequences, we have pin-pointed a nine amino-acid motif shared by a group of different viruses; this motif resembles the transmembrane domain of the α-subunit of the T-cell receptor (TCRα). The most striking similarity was found within the immunodeficiency virus (SIV and HIV) glycoprotein 41 TMD (gp41 TMD). Previous studies have shown that stable interactions between TCRα and CD3 are localized to this nine amino acid motif within TCRα, and a peptide derived from it (TCRα TMD, GLRILLLKV) interfered and intervened in the TCR function when added exogenously. We now report that the gp41 TMD peptide co-localizes with CD3 within the TCR complex and inhibits T cell proliferation in vitro. However, the inhibitory mechanism of gp41 TMD differs from that of the TCRα TMD and also from the other two known immunosuppressive regions within gp41

Depression and anxiety in patients with rheumatoid arthritis: prevalence rates based on a comparison of the Depression, Anxiety and Stress Scale (DASS) and the hospital, Anxiety and Depression Scale (HADS)

<p>Abstract</p> <p>Background</p> <p>While it is recognised that depression is prevalent in Rheumatoid Arthritis (RA), recent studies have also highlighted significant levels of anxiety in RA patients. This study compared two commonly used scales, the Depression Anxiety and Stress Scale (DASS) and the Hospital Anxiety and Depression Scale (HADS), in relation to their measurement range and cut points to consider the relative prevalence of both constructs, and if prevalence rates may be due to scale-specific case definition.</p> <p>Methods</p> <p>Patients meeting the criteria for RA were recruited in Leeds, UK and Sydney, Australia and asked to complete a survey that included both scales. The data was analysed using the Rasch measurement model.</p> <p>Results</p> <p>A total of 169 RA patients were assessed, with a repeat subsample, resulting in 323 cases for analysis. Both scales met Rasch model expectations. Using the 'possible+probable' cut point from the HADS, 58.3% had neither anxiety nor depression; 13.5% had anxiety only; 6.4% depression only and 21.8% had both 'possible+probable' anxiety and depression. Cut points for depression were comparable across the two scales while a lower cut point for anxiety in the DASS was required to equate prevalence.</p> <p>Conclusions</p> <p>This study provides further support for high prevalence of depression and anxiety in RA. It also shows that while these two scales provide a good indication of possible depression and anxiety, the estimates of prevalence so derived could vary, particularly for anxiety. These findings are discussed in terms of comparisons across studies and selection of scales for clinical use.</p

Generating Correct-by-Construction Distributed Implementations from Formal Maude Designs

Developing a reliable distributed system meeting desired performance requirements is a hard and very labor-intensive task. Formal specification of a system design and formal analysis can yield provably correct designs as well as reliable performance predictions. But there is still a formality gap between verified designs and distributed implementations. We present a correct-by-construction automatic transformation mapping a formal specification of a system design M in Maude to a distributed implementation D(M) with the same safety and liveness properties as M. Two case studies applying this transformation to state-of-the art distributed transaction systems show that high-quality implementations with acceptable performance and meeting performance predictions can be obtained in this way. To the best of our knowledge, this is the first time that formal models of distributed systems analyzed within the same formal framework for both logical and performance properties are automatically transformed into correct-by-construction implementations for which similar performance trends can be shown.Ope

Termination Analysis with Calling Context Graphs

Abstract. We introduce calling context graphs and various static and theorem proving based analyses that together provide a powerful method for proving termination of programs written in feature-rich, first order, functional programming languages. In contrast to previous work, our method is highly automated and handles any source of looping behavior in such languages, including recursive definitions, mutual recursion, the use of recursive data structures, etc. We have implemented our method for the ACL2 programming language and evaluated the result using the ACL2 regression suite, which consists of numerous libraries with a total of over 10,000 function definitions. Our method was able to automatically detect termination of over 98 % of these functions.