Deriving real-time action systems with multiple time bands using algebraic reasoning

The verify-while-develop paradigm allows one to incrementally develop programs from their specifications using a series of calculations against the remaining proof obligations. This paper presents a derivation method for real-time systems with realistic constraints on their behaviour. We develop a high-level interval-based logic that provides flexibility in an implementation, yet allows algebraic reasoning over multiple granularities and sampling multiple sensors with delay. The semantics of an action system is given in terms of interval predicates and algebraic operators to unify the logics for an action system and its properties, which in turn simplifies the calculations and derivations

Completeness and Incompleteness of Synchronous Kleene Algebra

Synchronous Kleene algebra (SKA), an extension of Kleene algebra (KA), was proposed by Prisacariu as a tool for reasoning about programs that may execute synchronously, i.e., in lock-step. We provide a countermodel witnessing that the axioms of SKA are incomplete w.r.t. its language semantics, by exploiting a lack of interaction between the synchronous product operator and the Kleene star. We then propose an alternative set of axioms for SKA, based on Salomaa's axiomatisation of regular languages, and show that these provide a sound and complete characterisation w.r.t. the original language semantics.Comment: Accepted at MPC 201

Convolution as a unifying concept: Applications in separation logic, interval calculi and concurrency

The research reported here was supported in part by Australian Research Council Grant No. DP130102901 and EPSRC Grant No. EP/J003727/1

Association of Relative Age in the School Year With Diagnosis of Intellectual Disability, Attention-Deficit/Hyperactivity Disorder, and Depression

IMPORTANCE: Young relative age within the school year has previously been associated with attention-deficit/hyperactivity disorder (ADHD) diagnosis and, based on limited evidence, diagnosis of intellectual disability. No study to date has examined the association between relative age and diagnosis of depression. OBJECTIVE: To estimate the associations with intellectual disability and ADHD and investigate a potential novel association between relative age and childhood depression. DESIGN, SETTING, AND PARTICIPANTS: This population-based cohort study of 1 042 106 children aged 4 to 15 years used electronic record data collected before January 3, 2017, from more than 700 general practices contributing to the UK Clinical Practice Research Datalink. Multivariable Cox proportional hazards regression modeling was used to explore the association between relative age and the incidence of intellectual disability, ADHD, and depression before age 16 years. Data were analyzed between July 2017 and January 2019. EXPOSURES: Relative age within school year determined by month of birth and categorized into four 3-month groups. MAIN OUTCOMES AND MEASURES: Intellectual disability, ADHD, and depression. RESULTS: In the total cohort of 1 042 106 children, 532 876 were male (51.1%) and the median age at study entry was 4.0 years (interquartile range, 4.0-5.0). There was evidence that being born in the last quarter of the school year (ie, being the youngest group in a school year) was associated with diagnosis of intellectual disability (adjusted hazard ratio [aHR], 1.30; 95% CI, 1.18-1.42), ADHD (aHR, 1.36; 95% CI, 1.28-1.45), and depression (aHR, 1.31; 95% CI, 1.08-1.59) compared with being born in the first quarter. A graded association was seen with intermediate age groups at a smaller increased risk of each diagnosis compared with the oldest group, with aHRs for intellectual disability for those born in the second quarter of 1.06 (95% CI, 0.96-1.17) and for those born in the third quarter of 1.20 (95% CI, 1.09-1.32); aHRs for ADHD for those born in the second quarter of 1.15 (95% CI, 1.08-1.23) and for those born in the third quarter of 1.31 (95% CI, 1.23-1.40); and aHRs for depression for those born in the second quarter of 1.05 (95% CI, 0.85-1.29) and for those born in the third quarter of 1.13 (95% CI, 0.92-1.38). CONCLUSIONS AND RELEVANCE: In this study, relative youth status in the school year is associated with an increased risk of diagnosis of ADHD, intellectual disability, and depression in childhood. Further research into clinical and policy interventions to minimize these associations appears to be needed

A wide-spectrum language for verification of programs on weak memory models

Modern processors deploy a variety of weak memory models, which for efficiency reasons may (appear to) execute instructions in an order different to that specified by the program text. The consequences of instruction reordering can be complex and subtle, and can impact on ensuring correctness. Previous work on the semantics of weak memory models has focussed on the behaviour of assembler-level programs. In this paper we utilise that work to extract some general principles underlying instruction reordering, and apply those principles to a wide-spectrum language encompassing abstract data types as well as low-level assembler code. The goal is to support reasoning about implementations of data structures for modern processors with respect to an abstract specification. Specifically, we define an operational semantics, from which we derive some properties of program refinement, and encode the semantics in the rewriting engine Maude as a model-checking tool. The tool is used to validate the semantics against the behaviour of a set of litmus tests (small assembler programs) run on hardware, and also to model check implementations of data structures from the literature against their abstract specifications

Genetic variation in the HLA region is associated with susceptibility to herpes zoster.

Herpes zoster, commonly referred to as shingles, is caused by the varicella zoster virus (VZV). VZV initially manifests as chicken pox, most commonly in childhood, can remain asymptomatically latent in nerve tissues for many years and often re-emerges as shingles. Although reactivation may be related to immune suppression, aging and female sex, most inter-individual variability in re-emergence risk has not been explained to date. We performed a genome-wide association analyses in 22,981 participants (2280 shingles cases) from the electronic Medical Records and Genomics Network. Using Cox survival and logistic regression, we identified a genomic region in the combined and European ancestry groups that has an age of onset effect reaching genome-wide significance (P>1.0 × 10(-8)). This region tags the non-coding gene HCP5 (HLA Complex P5) in the major histocompatibility complex. This gene is an endogenous retrovirus and likely influences viral activity through regulatory functions. Variants in this genetic region are known to be associated with delay in development of AIDS in people infected by HIV. Our study provides further suggestion that this region may have a critical role in viral suppression and could potentially harbor a clinically actionable variant for the shingles vaccine

Psychosocial functioning and intelligence both partly explain socioeconomic inequalities in premature death. A population-based male cohort study

The possible contributions of psychosocial functioning and intelligence differences to socioeconomic status (SES)-related inequalities in premature death were investigated. None of the previous studies focusing on inequalities in mortality has included measures of both psychosocial functioning and intelligence.The study was based on a cohort of 49 321 men born 1949-1951 from the general community in Sweden. Data on psychosocial functioning and intelligence from military conscription at ∼18 years of age were linked with register data on education, occupational class, and income at 35-39 years of age. Psychosocial functioning was rated by psychologists as a summary measure of differences in level of activity, power of initiative, independence, and emotional stability. Intelligence was measured through a multidimensional test. Causes of death between 40 and 57 years of age were followed in registers.The estimated inequalities in all-cause mortality by education and occupational class were attenuated with 32% (95% confidence interval: 20-45%) and 41% (29-52%) after adjustments for individual psychological differences; both psychosocial functioning and intelligence contributed to account for the inequalities. The inequalities in cardiovascular and injury mortality were attenuated by as much as 51% (24-76%) and 52% (35-68%) after the same adjustments, and the inequalities in alcohol-related mortality were attenuated by up to 33% (8-59%). Less of the inequalities were accounted for when those were measured by level of income, with which intelligence had a weaker correlation. The small SES-related inequalities in cancer mortality were not attenuated by adjustment for intelligence.Differences in psychosocial functioning and intelligence might both contribute to the explanation of observed SES-related inequalities in premature death, but the magnitude of their contributions likely varies with measure of socioeconomic status and cause of death. Both psychosocial functioning and intelligence should be considered in future studies

Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays

GSTT2 promoter polymorphisms and colorectal cancer risk

BACKGROUND: Glutathione S-transferases are a group of enzymes that participate in detoxification and defense mechanisms against toxic carcinogens and other compounds. These enzymes play an important role in human carcinogenesis. In the present study, we sought to determine whether GSTT2 promoter single nucleotide polymorphisms (SNPs) are associated with colorectal cancer risk. METHODS: A total of 436 colorectal cancer patients and 568 healthy controls were genotyped for three GSTT2 promoter SNPs (-537G>A, -277T>C and -158G>A), using real-time TaqMan assay and direct sequencing. An electrophoretic mobility shift assay (EMSA) was performed to determine the effects of polymorphisms on protein binding to the GSTT2 promoter. RESULTS: The -537A allele (-537G/A or A/A) was significantly associated with colorectal cancer risk (OR = 1.373, p = 0.025), while the -158A allele (-158G/A or A/A) was involved in protection against colorectal cancer (OR = 0.539, p = 0.032). Haplotype 2 (-537A, -277T, -158G) was significantly associated with colorectal cancer risk (OR = 1.386, p = 0.021), while haplotype 4 (-537G, -277C, -158A) protected against colorectal cancer (OR = 0.539, p = 0.032). EMSA data revealed lower promoter binding activity in the -537A allele than its -537G counterpart. CONCLUSION: Our results collectively suggest that SNPs and haplotypes of the GSTT2 promoter region are associated with colorectal cancer risk in the Korean population