Verifying Monadic Second-Order Properties of Graph Programs

The core challenge in a Hoare- or Dijkstra-style proof system for graph programs is in defining a weakest liberal precondition construction with respect to a rule and a postcondition. Previous work addressing this has focused on assertion languages for first-order properties, which are unable to express important global properties of graphs such as acyclicity, connectedness, or existence of paths. In this paper, we extend the nested graph conditions of Habel, Pennemann, and Rensink to make them equivalently expressive to monadic second-order logic on graphs. We present a weakest liberal precondition construction for these assertions, and demonstrate its use in verifying non-local correctness specifications of graph programs in the sense of Habel et al.Comment: Extended version of a paper to appear at ICGT 201

Optimising fusion detection through sequential DNA and RNA molecular profiling of non-small cell lung cancer

OBJECTIVES: There is an increasing number of driver fusions in NSCLC which are amenable to targeted therapy. Panel testing for fusions is increasingly appropriate but can be costly and requires adequate good quality biopsy material. In light of the typical mutual exclusivity of driver events in NSCLC, the objective of this study was to trial a novel testing pathway, supported by industrial collaboration, in which only patients negative for driver mutations on DNA-NGS were submitted for fusion panel analysis. MATERIALS AND METHODS: Over 18 months, all patients from a single centre with non-squamous NSCLC were submitted for DNA-NGS, plus ALK and ROS1 immunohistochemistry +/− FISH. Those which were negative for a driver mutation were then recalled for RNA panel testing. RESULTS: 307 samples were referred for DNA-NGS mutation analysis, of which, 10% of cases were unsuitable for or failed DNA-NGS analysis. Driver mutations were detected in 61% (167/275) of all those successfully tested. Of those without a driver mutation and with some remaining tissue available, 28% had insufficient tissue/extracted RNA or failed RNA-NGS. Of those successfully tested, 24% (17/72) had a fusion gene detected involving either ALK, ROS, MET, RET, FGFR or EGFR. Overall, 66% (184/277) of patients had a driver event detected through the combination of DNA and RNA panels. CONCLUSION: Sequential DNA and RNA based molecular profiling increased the efficacy of detecting fusion driven NSCLCs. Continued optimisation of tissue procurement, handling and the diagnostic pathways for gene fusion analysis is necessary to reduce analysis failure rates and improve detection rate for treatment with the next generation of small molecule inhibitors

Targeted next generation sequencing of pancreatic solid pseudopapillary neoplasms show mutations in Wnt signaling pathway genes.

Solid pseudopapillary neoplasms of the pancreas are rare neoplasms that have been shown to harbor recurrent somatic pathogenic variants in the beta-catenin gene, CTNNB1. Here, we used targeted next generation sequencing to analyze these tumors for other associated mutations. Six cases of solid pseudopapillary neoplasms were studied. DNA extracted from formalin-fixed paraffin embedded tissue blocks was analyzed using the Ion Torrent platform, with the 50-gene Ampliseq Cancer Hotspot Panel v2 (CHPv2), with further variant validation performed by Sanger sequencing. Four tumors (67%) were confirmed to harbor mutations within CTNNB1, two with c.109T > G p.(Ser37Ala) and two with c.94G > A p.(Asp32Asn). One case showed a frameshift deletion in the Adenomatous Polyposis Coli gene, APC c.3964delG p.(Glu1322Lysfs*93) with a variant allele frequency of 42.6%. Sanger sequencing on non-tumoral tissue confirmed the variant was somatic. The patient with the APC mutation developed metastasis and died. In addition to the four cases harboring CTNNB1 variants, we found a case characterized by poor outcome, showing a rare frameshift deletion in the APC gene. Since the APC product interacts with beta-catenin, APC variants may, in addition to CTNNB1, contribute to the pathogenesis of solid pseudopapillary neoplasms via the Wnt signaling pathway

On verifying ATL transformations using 'off-the-shelf' SMT solvers

International audienceMDE is a software development process where models constitute pivotal elements of the software to be built. If models are well-specified, transformations can be employed for various purposes, e.g., to produce final code. However, transformations are only meaningful when they are 'correct': they must produce valid models from valid input models. A valid model has conformance to its meta-model and fulfils its constraints, usually written in OCL. In this paper, we propose a novel methodology to perform automatic, unbounded verification of ATL transformations. Its main component is a novel first-order semantics for ATL transformations, based on the interpretation of the corresponding rules and their execution semantics as first-order predicates. Although, our semantics is not complete, it does cover a significant subset of the ATL language. Using this semantics, transformation correctness can be automatically verified with respect to non-trivial OCL pre- and postconditions by using SMT solvers, e.g. Z3 and Yices

Impacts of the 2014-2015 Holuhraun eruption on the UK atmosphere

Volcanic emissions, specifically from Iceland, pose a pan-European risk and are on the UK National Risk Register due to potential impacts on aviation, public health, agriculture, the environment and the economy, both from effusive and explosive activity. During the 2014-2015 fissure eruption at Holuhraun in Iceland, the UK atmosphere was significantly perturbed. This study focuses one major incursion in September 2014, affecting the surface concentrations of both aerosols and gases across the UK, with sites in Scotland experiencing the highest sulfur dioxide (SO2) concentrations. The perturbation event observed was confirmed to originate from the fissure eruption using satellite data from GOME2B and the chemical transport model, EMEP4UK, which was used to establish the spatial distribution of the plume over the UK during the event of interest. At the two UK European Monitoring and Evaluation Program (EMEP) supersite observatories (Auchencorth Moss, SE Scotland and Harwell, SE England) significant alterations in sulfate (SO42-) content of PM10 and PM2.5 during this event, concurrently with evidence of an increase in ultrafine aerosol, most likely due to nucleation and growth of aerosol within the plume, were observed. At Auchencorth Moss, higher hydrochloric acid (HCl) concentrations during the September event (max = 1.21 µg m-3, c.f annual average 0.12 µg m-3 35 in 2013), were assessed to be due to acid displacement of chloride (Cl-) from sea salt (NaCl) to form HCl gas rather than due to primary emissions of HCl from Holuhraun. The gas and aerosol partioning at Auchencorth moss of inorganic species by thermodynamic modelling, confirmed the observed partioning of HCl. Using the data from the chemical thermodynamic model, ISORROPIA-II, there is evidence that the background aerosol, which is typically basic at this site, became acidic with an estimated pH of 3.8 during the peak of the event. Volcano plume episodes were periodically observed by the majority of the UK air quality monitoring networks during the first 4 months of the eruption (August – December 2014), at both hourly and monthly resolution. In the low resolution networks, which provide monthly SO2 averages, concentrations were found to be significantly elevated at remote “clean” sites in NE Scotland and SW England, with record high SO2 concentrations for some sites in September 2014. For sites which are regularly influenced by anthropogenic emissions, taking into account the underlying trends, the eruption led to statistically unremarkable SO2 concentrations (return probabilities >0.1, ~10 months). However for a few sites, SO2 concentrations were clearly much higher than has been previously observed (return probability 3000 months). The Holuhraun Icelandic eruption has resulted in a unique study providing direct evidence of atmospheric chemistry perturbation of both gases and aerosols in the UK background atmosphere. The measurements can be used to both challenge and verify existing atmospheric chemistry of volcano plumes, especially those originating from effusive eruptions, which have been under-explored, due to limited observations available in the literature. If all European data sets were collated this would allow improved model verification and risk assessments for future volcanic eruptions of this type

Length of carotid stenosis predicts peri-procedural stroke or death and restenosis in patients randomized to endovascular treatment or endarterectomy.

BACKGROUND: The anatomy of carotid stenosis may influence the outcome of endovascular treatment or carotid endarterectomy. Whether anatomy favors one treatment over the other in terms of safety or efficacy has not been investigated in randomized trials. METHODS: In 414 patients with mostly symptomatic carotid stenosis randomized to endovascular treatment (angioplasty or stenting; n = 213) or carotid endarterectomy (n = 211) in the Carotid and Vertebral Artery Transluminal Angioplasty Study (CAVATAS), the degree and length of stenosis and plaque surface irregularity were assessed on baseline intraarterial angiography. Outcome measures were stroke or death occurring between randomization and 30 days after treatment, and ipsilateral stroke and restenosis ≥50% during follow-up. RESULTS: Carotid stenosis longer than 0.65 times the common carotid artery diameter was associated with increased risk of peri-procedural stroke or death after both endovascular treatment [odds ratio 2.79 (1.17-6.65), P = 0.02] and carotid endarterectomy [2.43 (1.03-5.73), P = 0.04], and with increased long-term risk of restenosis in endovascular treatment [hazard ratio 1.68 (1.12-2.53), P = 0.01]. The excess in restenosis after endovascular treatment compared with carotid endarterectomy was significantly greater in patients with long stenosis than with short stenosis at baseline (interaction P = 0.003). Results remained significant after multivariate adjustment. No associations were found for degree of stenosis and plaque surface. CONCLUSIONS: Increasing stenosis length is an independent risk factor for peri-procedural stroke or death in endovascular treatment and carotid endarterectomy, without favoring one treatment over the other. However, the excess restenosis rate after endovascular treatment compared with carotid endarterectomy increases with longer stenosis at baseline. Stenosis length merits further investigation in carotid revascularisation trials

Prevalence of Melanocortin-4 Receptor Deficiency in Europeans and Their Age-Dependent Penetrance in Multigenerational Pedigrees

OBJECTIVE— Melanocortin-4 receptor (MC4R) deficiency is the most frequent genetic cause of obesity. However, there is uncertainty regarding the degree of penetrance of this condition, and the putative impact of the environment on the development of obesity in MC4R mutation carriers is unknown

Polish 2010 growth references for school-aged children and adolescents

Growth references are useful in monitoring a child's growth, which is an essential part of child care. The aim of this paper was to provide updated growth references for Polish school-aged children and adolescents and show the prevalence of overweight and obesity among them. Growth references for height, weight, and body mass index (BMI) were constructed with the lambda, mu, sigma (LMS) method using data from a recent, large, population-representative sample of school-aged children and adolescents in Poland (n = 17,573). The prevalence of overweight and obesity according to the International Obesity Taskforce definition was determined with the use of LMSGrowth software. Updated growth references for Polish school-aged children and adolescents were compared with Polish growth references from the 1980s, the Warsaw 1996–1999 reference, German, and 2000 CDC references. A positive secular trend in height was observed in children and adolescents from 7 to 15 years of age. A significant shift of the upper tail of the BMI distribution occurred, especially in Polish boys at younger ages. The prevalence of overweight or obesity was 18.7% and 14.1% in school-aged boys and girls, respectively. The presented height, weight, and BMI references are based on a current, nationally representative sample of Polish children and adolescents without known disorders affecting growth. Changes in the body size of children and adolescents over the last three decades suggest an influence of the changing economical situation on anthropometric indices