Mining State-Based Models from Proof Corpora

Interactive theorem provers have been used extensively to reason about various software/hardware systems and mathematical theorems. The key challenge when using an interactive prover is finding a suitable sequence of proof steps that will lead to a successful proof requires a significant amount of human intervention. This paper presents an automated technique that takes as input examples of successful proofs and infers an Extended Finite State Machine as output. This can in turn be used to generate proofs of new conjectures. Our preliminary experiments show that the inferred models are generally accurate (contain few false-positive sequences) and that representing existing proofs in such a way can be very useful when guiding new ones.Comment: To Appear at Conferences on Intelligent Computer Mathematics 201

Property-Based Testing - The ProTest Project

The ProTest project is an FP7 STREP on property based testing. The purpose of the project is to develop software engineering approaches to improve reliability of service-oriented networks; support fault-finding and diagnosis based on specified properties of the system. And to do so we will build automated tools that will generate and run tests, monitor execution at run-time, and log events for analysis. The Erlang / Open Telecom Platform has been chosen as our initial implementation vehicle due to its robustness and reliability within the telecoms sector. It is noted for its success in the ATM telecoms switches by Ericsson, one of the project partners, as well as for multiple other uses such as in facebook, yahoo etc. In this paper we provide an overview of the project goals, as well as detailing initial progress in developing property based testing techniques and tools for the concurrent functional programming language Erlang

Cardiac autonomic regulation and repolarization during acute experimental hypoglycemia in Type 2 diabetes

Hypoglycemia is associated with increased cardiovascular mortality in trials of intensive therapy in type 2 diabetes (T2DM). We previously observed an increase in arrhythmias during spontaneous prolonged hypoglycemia in T2DM patients. Our aim was to examine changes in cardiac autonomic function and repolarization during sustained experimental hypoglycemia. Twelve adults with T2DM and eleven age, BMI-matched nondiabetic controls underwent paired hyperinsulinemic clamps separated by 4 weeks. Glucose was maintained at euglycemia (6.0mmol/L) or hypoglycemia (2.5mmol/L) for one hour. Heart rate, blood pressure, heart rate variability were assessed every thirty minutes and corrected QT (QTc) and T wave morphology every 60 minutes. Heart rate initially increased in T2DM participants but then fell towards baseline despite maintained hypoglycemia at 1 hour, accompanied by reactivation of vagal tone. In nondiabetic participants, vagal tone remained depressed during sustained hypoglycemia. Diabetic participants exhibited greater heterogeneity of repolarization during hypoglycemia as demonstrated by T wave symmetry and Principal Component Analysis (PCA) ratio compared with the nondiabetic group. Epinephrine levels during hypoglycemia were similar between groups. Cardiac autonomic regulation during hypoglycemia appears time-dependent. T2DM individuals demonstrate greater repolarization abnormalities for a given hypoglycemic stimulus despite comparable sympathoadrenal responses. These mechanisms could contribute to arrhythmias during clinical hypoglycemic episodes

Digital-twin-based testing for cyber–physical systems: a systematic literature review

Context: Cyber–physical systems present a challenge to testers, bringing complexity and scale to safety-critical and collaborative environments. Digital twins enhance these systems through data-driven and simulation based models coupled to physical systems to provide visualisation, predict future states and communication. Due to the coupling between digital and physical worlds, digital twins provide a new perspective into cyber–physical system testing. Objective: The objectives of this study are to summarise the existing literature on digital-twin-based testing. We aim to uncover emerging areas of adoptions, the testing techniques used in these areas and identify future research areas. Method: We conducted a systematic literature review which answered the following research questions: What cyber–physical systems are digital twins currently being used to test? How are test oracles defined for cyber–physical systems? What is the distribution of white-box, black-box and grey-box modelling techniques used for digital twins in the context of testing? How are test cases defined and how does this affect test inputs? Results: We uncovered 26 relevant studies from 480 produced by searching with a curated search query. These studies showed an adoption of digital-twin-based testing following the introduction of digital twins in industry as well as the increasing accessibility of the technology. The oracles used in testing are the digital twin themselves and therefore rely on both system specification and data derivation. Cyber–physical systems are tested through passive testing techniques, as opposed to either active testing through test cases or predictive testing using digital twin prediction. Conclusions: This review uncovers the existing areas in which digital twins are used to test cyber–physical systems as well as outlining future research areas in the field. We outline how the infancy of digital twins has affected their wide variety of definitions, emerging specialised testing and modelling techniques as well as the current lack of predictive ability

Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Proteins need to interconvert between many conformations in order to function, many of which are formed transiently, and sparsely populated. Particularly when the lifetimes of these states approach the millisecond timescale, identifying the relevant structures and the mechanism by which they interconvert remains a tremendous challenge. Here we introduce a novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore these ‘excited’ conformational states. Applying this to the highly dynamic protein CypA, a protein involved in immune response and associated with HIV infection, we identify five principally populated conformational states and the atomistic mechanism by which they interconvert. A rational design strategy predicted that the mutant D66A should stabilise the minor conformations and substantially alter the dynamics, whereas the similar mutant H70A should leave the landscape broadly unchanged. These predictions are confirmed using CPMG and R1ρ solution state NMR measurements. By efficiently exploring functionally relevant, but sparsely populated conformations with millisecond lifetimes in silico, our aMD/MSM method has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery

Structural and kinetic characterisation of Trypanosoma congolense pyruvate kinase

Trypanosoma are blood-borne parasites and are the causative agents of neglected tropical diseases (NTDs) affecting both humans and animals. These parasites mainly rely on glycolysis for their energy production within the mammalian host, which is why trypanosomal glycolytic enzymes have been pursued as interesting targets for the development of trypanocidal drugs. The structure-function relationships of pyruvate kinases (PYKs) from trypanosomatids (Trypanosoma and Leishmania) have been well-studied within this context. In this paper, we describe the structural and enzymatic characterization of PYK from T. congolense (TcoPYK), the main causative agent of Animal African Trypanosomosis (AAT), by employing a combination of enzymatic assays, thermal unfolding studies and X-ray crystallography

Satisfaction with the Use of Different Technologies for Insulin Delivery and Glucose Monitoring Among Adults with Long-Standing Type 1 Diabetes and Problematic Hypoglycemia: 2-Year Follow-Up in the HypoCOMPaSS Randomized Clinical Trial

Background In the HypoCOMPaSS trial, adults with long-standing type 1 diabetes and problematic hypoglycaemia were randomised to compare insulin pump (CSII) vs multiple daily injections (MDI) and real-time continuous glucose monitoring (RT-CGM) vs conventional self-monitoring (SMBG). Our aim was to investigate participants\u27 satisfaction with these technologies at 6-month RCT endpoint and at 2-year follow-up. Methods Participants completed the Insulin Treatment Satisfaction Questionnaire (ITSQ) subscales \u27device delivery\u27 and \u27hypoglycaemia control\u27; and Glucose Monitoring Experience Questionnaire (GME-Q), assessing \u27convenience\u27, \u27effectiveness\u27, \u27intrusiveness\u27 and \u27total satisfaction\u27. We assessed change over time and between group differences by insulin and monitoring modalities. Results Participants (N=96) were: 64% women, aged 49\ub112 years, diabetes duration 29\ub112 years. At 6 months, participants reported improvements compared to baseline (all p<0.001) in satisfaction with insulin \u27delivery device\u27 (r=0.39) and \u27hypoglycaemia control\u27 (r=0.52), and trends towards significance in perceived \u27effectiveness\u27 (r=0.42) and \u27intrusiveness\u27 (r=0.27) of monitoring device (but not \u27convenience\u27, p=0.139). All improvements were sustained at 2 years. At 6 months, the only difference between arms was that greater satisfaction with insulin \u27delivery device\u27 was reported in the CSII group compared to MDI (p<0.001, r=0.40). No between-group differences were observed at 2 years. Conclusions Overall, significant improvements in participant satisfaction with diabetes technologies were observed over the 6-month RCT, in all domains except \u27convenience\u27, maintained at 2 years. While HypoCOMPaSS demonstrated non-inferiority of SMBG versus CGM, and MDI versus CSII in terms of biomedical outcomes, detailed assessments confirm participants\u27 satisfaction with delivery device was greater in those allocated to CSII than MDI

M2 pyruvate kinase provides a mechanism for nutrient sensing and regulation of cell proliferation

We show that the M2 isoform of pyruvate kinase (M2PYK) exists in equilibrium between monomers and tetramers regulated by allosteric binding of naturally occurring small-molecule metabolites. Phenylalanine stabilizes an inactive T-state tetrameric conformer and inhibits M2PYK with an IC(50) value of 0.24 mM, whereas thyroid hormone (triiodo-l-thyronine, T3) stabilizes an inactive monomeric form of M2PYK with an IC(50) of 78 nM. The allosteric activator fructose-1,6-bisphosphate [F16BP, AC(50) (concentration that gives 50% activation) of 7 μM] shifts the equilibrium to the tetrameric active R-state, which has a similar activity to that of the constitutively fully active isoform M1PYK. Proliferation assays using HCT-116 cells showed that addition of inhibitors phenylalanine and T3 both increased cell proliferation, whereas addition of the activator F16BP reduced proliferation. F16BP abrogates the inhibitory effect of both phenylalanine and T3, highlighting a dominant role of M2PYK allosteric activation in the regulation of cancer proliferation. X-ray structures show constitutively fully active M1PYK and F16BP-bound M2PYK in an R-state conformation with a lysine at the dimer-interface acting as a peg in a hole, locking the active tetramer conformation. Binding of phenylalanine in an allosteric pocket induces a 13° rotation of the protomers, destroying the peg-in-hole R-state interface. This distinct T-state tetramer is stabilized by flipped out Trp/Arg side chains that stack across the dimer interface. X-ray structures and biophysical binding data of M2PYK complexes explain how, at a molecular level, fluctuations in concentrations of amino acids, thyroid hormone, and glucose metabolites switch M2PYK on and off to provide the cell with a nutrient sensing and growth signaling mechanism

The AIQ Meta-Testbed: Pragmatically Bridging Academic AI Testing and Industrial Q Needs

AI solutions seem to appear in any and all application domains. As AI becomes more pervasive, the importance of quality assurance increases. Unfortunately, there is no consensus on what artificial intelligence means and interpretations range from simple statistical analysis to sentient humanoid robots. On top of that, quality is a notoriously hard concept to pinpoint. What does this mean for AI quality? In this paper, we share our working definition and a pragmatic approach to address the corresponding quality assurance with a focus on testing. Finally, we present our ongoing work on establishing the AIQ Meta-Testbed.Comment: Accepted for publication in the Proc. of the Software Quality Days 2021, Vienna, Austri