Using Answer Set Programming in the Development of Verified Software

Software forms a key component of many modern safety and security critical systems. One approach to achieving the required levels of assurance is to prove that the software is free from bugs and meets its specification. If a proof cannot be constructed it is important to identify the root cause as it may be a flaw in the specification or a bug. Novice users often find this process frustrating and discouraging, and it can be time-consuming for experienced users. The paper describes a commercial application based on Answer Set Programming called Riposte. It generates simple counter-examples for false and unprovable verification conditions (VCs). These help users to understand why problematic VC are false and makes the development of verified software easier and faster

A modular physics methodology for games

Currently, games with rich environments allowing a wide range of possible interactions and supporting a large number of physical simulations make use of a large number of scripts and bespoke physical simulations, adapted to fit the needs of the game. This thesis proposes a methodology that can be used to tie together various different physical simulations, both off-the-shelf and bespoke, such as rigid body physics, electrical and magnetic simulations to give something greater than the sum of the individual parts. We present a notation for designing the overall physical simulation and a means for the different parts to interact. Experiments using an implementation of the methodology containing electricity, rigid body simulation, magnetics (including electro-magnetics), buoyancy and sound show that it is possible to model everyday objects such an electric motor or a doorbell. These object work ‘as expected’, without the need for special scripts and new, originally unexpected, interactions are possible without further modification of the experiment setup.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Functional Requirements-Based Automated Testing for Avionics

We propose and demonstrate a method for the reduction of testing effort in safety-critical software development using DO-178 guidance. We achieve this through the application of Bounded Model Checking (BMC) to formal low-level requirements, in order to generate tests automatically that are good enough to replace existing labor-intensive test writing procedures while maintaining independence from implementation artefacts. Given that existing manual processes are often empirical and subjective, we begin by formally defining a metric, which extends recognized best practice from code coverage analysis strategies to generate tests that adequately cover the requirements. We then formulate the automated test generation procedure and apply its prototype in case studies with industrial partners. In review, the method developed here is demonstrated to significantly reduce the human effort for the qualification of software products under DO-178 guidance

Complement activating antibodies to myelin oligodendrocyte glycoprotein in neuromyelitis optica and related disorders

<p>Abstract</p> <p>Background</p> <p>Serum autoantibodies against the water channel aquaporin-4 (AQP4) are important diagnostic biomarkers and pathogenic factors for neuromyelitis optica (NMO). However, AQP4-IgG are absent in 5-40% of all NMO patients and the target of the autoimmune response in these patients is unknown. Since recent studies indicate that autoimmune responses to myelin oligodendrocyte glycoprotein (MOG) can induce an NMO-like disease in experimental animal models, we speculate that MOG might be an autoantigen in AQP4-IgG seronegative NMO. Although high-titer autoantibodies to human native MOG were mainly detected in a subgroup of pediatric acute disseminated encephalomyelitis (ADEM) and multiple sclerosis (MS) patients, their role in NMO and High-risk NMO (HR-NMO; recurrent optic neuritis-rON or longitudinally extensive transverse myelitis-LETM) remains unresolved.</p> <p>Results</p> <p>We analyzed patients with definite NMO (n = 45), HR-NMO (n = 53), ADEM (n = 33), clinically isolated syndromes presenting with myelitis or optic neuritis (CIS, n = 32), MS (n = 71) and controls (n = 101; 24 other neurological diseases-OND, 27 systemic lupus erythematosus-SLE and 50 healthy subjects) for serum IgG to MOG and AQP4. Furthermore, we investigated whether these antibodies can mediate complement dependent cytotoxicity (CDC). AQP4-IgG was found in patients with NMO (n = 43, 96%), HR-NMO (n = 32, 60%) and in one CIS patient (3%), but was absent in ADEM, MS and controls. High-titer MOG-IgG was found in patients with ADEM (n = 14, 42%), NMO (n = 3, 7%), HR-NMO (n = 7, 13%, 5 rON and 2 LETM), CIS (n = 2, 6%), MS (n = 2, 3%) and controls (n = 3, 3%, two SLE and one OND). Two of the three MOG-IgG positive NMO patients and all seven MOG-IgG positive HR-NMO patients were negative for AQP4-IgG. Thus, MOG-IgG were found in both AQP4-IgG seronegative NMO patients and seven of 21 (33%) AQP4-IgG negative HR-NMO patients. Antibodies to MOG and AQP4 were predominantly of the IgG1 subtype, and were able to mediate CDC at high-titer levels.</p> <p>Conclusions</p> <p>We could show for the first time that a subset of AQP4-IgG seronegative patients with NMO and HR-NMO exhibit a MOG-IgG mediated immune response, whereas MOG is not a target antigen in cases with an AQP4-directed humoral immune response.</p

NMDAR antibody ΔMFI at different serum dilutions in NMDAR antibody positive and negative sera.

<p>NMDAR antibody positive (n = 9) and negative (n = 12) serum samples have been determined by CBA. (A) Serum dilutions of 1:100 and 1:20 are shown. Respective cut-off ΔMFI values are indicated by dashed horizontal lines. The table shows cut-off ΔMFI and numbers of samples tested positive for NMDAR antibodies by the FACS assay at different serum dilutions. (B) Correlation of ΔMFI obtained by using 1:100 and 1:20 dilution in the re-evaluation group of NMDAR positive samples in the CBA. Respective cut-off values are indicated by dashed lines. The one false negative sample at both dilutions is shown in red. For a better graphical presentation, ΔMFI values below 1,000 were set to 1,000. Correlation of exact ΔMFI values were calculated using non-parametric Spearman correlation. Correlation coefficient (R) and the p-value are shown in the graph. Here, the cut-off at the 1:100 dilution differs from the original cut-off (20,700), since a different batch of cells was used for analysis of this subsample. ¹ Data were analyzed using ROC analysis. CBA = cell-based assay. CTRL = control sample. ΔMFI = delta median fluorescence intensity. NMDAR-E = <i>N</i>-methyl-D-aspartate receptor encephalitis. ROC = receiver operating characteristic.</p

NMDAR IgG antibody titers and ΔMFI values in the discovery group.

<p>(A) Using the CBA serum NMDAR IgG antibodies were exclusively detected in serum samples of patients with NMDAR encephalitis, but not in neurological and healthy controls. (B) In the FACS assay serum NMDAR IgG ΔMFI levels were higher in patients with NMDAR encephalitis than in neurological and healthy controls, but one serum positive for NMDAR antibodies was missed with this method (shown in red). The cut-off ΔMFI value of 20,700 is indicated by a dashed horizontal line. Antibody titers and ΔMFI values were compared using a non-parametric test (Kruskal Wallis test) and overall p-values are shown in the graphs. Medians are indicated by horizontal bars. CBA = cell-based assay. ΔMFI = delta median fluorescence intensity. FACS = fluorescence activated cell sorting. HC = healthy controls. NC = neurological controls. NMDAR-E = <i>N</i>-methyl-D-aspartate receptor encephalitis.</p

Immunofluorescence CBA with HEK293A cells transiently overexpressing functional NMDAR tagged with green fluorescent proteins.

<p>Staining pattern with NMDAR antibody positive (A-C) and negative (D) serum. HEK293A cells were transiently transfected to overexpress EmGFP-tagged NR1, NR2A and GFP-tagged NR2B, incubated with diluted human serum and NMDAR antibodies were visualized by a Cy3-conjugated secondary antibody and counter-stained with DAPI to detect dead cells (left column: green fluorescence/EmGFP+GFP; middle column: red fluorescence/Cy3; right column: overlay of EmGFP/GFP, Cy3 and DAPI (A+D)). (B)+(C) Images show colocalization of NMDAR and serum NMDAR antibodies at high magnification (scale bars: 10 μm). (B) NMDAR antibodies bound to surface of cells. (C) Bound NMDAR antibodies internalized by the cells. CBA = cell-based assay. DAPI = 4’,6-diamidino-2-phenylindole. (Em)GFP = (emerald) green fluorescent protein. NMDAR = <i>N</i>-methyl-D-aspartate receptor.</p

NMDAR IgG antibody titers and ΔMFI values in the validation group.

<p>(A) With the CBA all sera of NMDAR encephalitis patients were positive for NMDAR IgG antibodies, but none of the neurological controls. (B) Using the FACS assay serum NMDAR IgG ΔMFI levels were higher in patients with NMDAR encephalitis than in neurological controls, but again two sera positive for NMDAR antibodies were missed with this method (shown in red). The cut-off ΔMFI value of 20,700 as determined in the discovery group is indicated by a dashed horizontal line. Antibody titers and ΔMFI values were compared using a non-parametric test (Mann-Whitney <i>U</i> test) and overall p-values are shown in the graphs. Medians are indicated by horizontal bars. CBA = cell-based assay. ΔMFI = delta median fluorescence intensity. FACS = fluorescence activated cell sorting. NC = neurological controls. NMDAR-E = <i>N</i>-methyl-D-aspartate receptor encephalitis.</p

Demographic data of patients and controls.

<p>CBA = cell-based assay. FACS = fluorescence activated cell sorting. HC = healthy controls. NC = neurological controls. NMDAR-E = <i>N</i>-methyl-D-aspartate receptor encephalitis.</p><p>¹ Data are shown as median (range), p-value: groups were compared using</p><p>² Chi-Square test and</p><p>³ Kruskal-Wallis test,</p><p>⁴ Fisher’s exact test and</p><p>⁵ Mann-Whitney <i>U</i> test.</p><p>Demographic data of patients and controls.</p

Comparison of Diagnostic Accuracy of Microscopy and Flow Cytometry in Evaluating <i>N</i>-Methyl-D-Aspartate Receptor Antibodies in Serum Using a Live Cell-Based Assay

<div><p><i>N</i>-methyl-D-aspartate receptor (NMDAR) encephalitis is an autoimmune neurological disease, diagnosed by a specific autoantibody against NMDAR. Antibody testing using commercially available cell-based assays (CBA) or immunohistochemistry on rat brain tissue has proven high specificity and sensitivity. Here we compare an immunofluorescence live CBA to a flow cytometry (FACS) based assay to detect NMDAR antibodies by their binding to the surface of HEK293A cells functionally expressing NMDAR. Both assays were first established using a discovery group of 76 individuals and then validated in a group of 32 patients in a blinded manner. In the CBA, 23 of 23 patients with NMDAR encephalitis were positive for NMDAR antibodies and 0 of 85 controls (32 healthy controls and 53 patients with other neurological diseases), resulting in a sensitivity and specificity of 100% (95% confidence intervals (CI) 85.1–100.0 and 95.7–100.0, respectively). The FACS based assay detected NMDAR antibodies in 20 of 23 patients and in 0 of 85 controls. Therefore, with an equally high specificity (95% CI 95.7–100.0) the sensitivity of the FACS based assay was 87% (95% CI 66.4–97.2). Comparing antibody titers from CBA with delta median fluorescence intensities from FACS showed a high concordance (kappa = 0.943, p<0.0001) and correlation (r = 0.697, p<0.0001). In conclusion, evaluation of the FACS based assay revealed a lower sensitivity and high inter-assay variation, making the CBA a more reliable detection method.</p></div