Relationships between estimated autozygosity and complex traits in the UK Biobank

<div><p>Inbreeding increases the risk of certain Mendelian disorders in humans but may also reduce fitness through its effects on complex traits and diseases. Such inbreeding depression is thought to occur due to increased homozygosity at causal variants that are recessive with respect to fitness. Until recently it has been difficult to amass large enough sample sizes to investigate the effects of inbreeding depression on complex traits using genome-wide single nucleotide polymorphism (SNP) data in population-based samples. Further, it is difficult to infer causation in analyses that relate degree of inbreeding to complex traits because confounding variables (e.g., education) may influence both the likelihood for parents to outbreed and offspring trait values. The present study used runs of homozygosity in genome-wide SNP data in up to 400,000 individuals in the UK Biobank to estimate the proportion of the autosome that exists in autozygous tracts—stretches of the genome which are identical due to a shared common ancestor. After multiple testing corrections and controlling for possible sociodemographic confounders, we found significant relationships in the predicted direction between estimated autozygosity and three of the 26 traits we investigated: age at first sexual intercourse, fluid intelligence, and forced expiratory volume in 1 second. Our findings corroborate those of several published studies. These results may imply that these traits have been associated with Darwinian fitness over evolutionary time. However, some of the autozygosity-trait relationships were attenuated after controlling for background sociodemographic characteristics, suggesting that alternative explanations for these associations have not been eliminated. Care needs to be taken in the design and interpretation of ROH studies in order to glean reliable information about the genetic architecture and evolutionary history of complex traits.</p></div

Multidimensional simulations of magnetic field amplification and electron acceleration to near-energy equipartition with ions by a mildly relativistic quasi-parallel plasma collision

The energetic electromagnetic eruptions observed during the prompt phase of gamma-ray bursts are attributed to synchrotron emissions. The internal shocks moving through the ultrarelativistic jet, which is ejected by an imploding supermassive star, are the likely source of this radiation. Synchrotron emissions at the observed strength require the simultaneous presence of powerful magnetic fields and highly relativistic electrons. We explore with one and three-dimensional relativistic particle-in-cell simulations the transition layer of a shock, that evolves out of the collision of two plasma clouds at a speed 0.9c and in the presence of a quasi-parallel magnetic field. The cloud densities vary by a factor of 10. The number densities of ions and electrons in each cloud, which have the mass ratio 250, are equal. The peak Lorentz factor of the electrons is determined in the 1D simulation, as well as the orientation and the strength of the magnetic field at the boundary of the two colliding clouds. The relativistic masses of the electrons and ions close to the shock transition layer are comparable as in previous work. The 3D simulation shows rapid and strong plasma filamentation behind the transient precursor. The magnetic field component orthogonal to the initial field direction is amplified in both simulations to values that exceed those expected from the shock compression by over an order of magnitude. The forming shock is quasi-perpendicular due to this amplification. The simultaneous presence of highly relativistic electrons and strong magnetic fields will give rise to significant synchrotron emissions.Comment: 8 pages, 5 figures. This work was presented at 21st International Conference on Numerical Simulation of Plasmas (ICNSP'09). Accepted for publication IEEE Trans. on Plasma Scienc

Decidable Models of Recursive Asynchronous Concurrency

Asynchronously communicating pushdown systems (ACPS) that satisfy the empty-stack constraint (a pushdown process may receive only when its stack is empty) are a popular decidable model for recursive programs with asynchronous atomic procedure calls. We study a relaxation of the empty-stack constraint for ACPS that permits concurrency and communication actions at any stack height, called the shaped stack constraint, thus enabling a larger class of concurrent programs to be modelled. We establish a close connection between ACPS with shaped stacks and a novel extension of Petri nets: Nets with Nested Coloured Tokens (NNCTs). Tokens in NNCTs are of two types: simple and complex. Complex tokens carry an arbitrary number of coloured tokens. The rules of NNCT can synchronise complex and simple tokens, inject coloured tokens into a complex token, and eject all tokens of a specified set of colours to predefined places. We show that the coverability problem for NNCTs is Tower-complete. To our knowledge, NNCT is the first extension of Petri nets, in the class of nets with an infinite set of token types, that has primitive recursive coverability. This result implies Tower-completeness of coverability for ACPS with shaped stacks

How can semantic annotation help us to analyse the discourse of climate change in online user comments?

User comments in response to newspaper articles published online offer a unique resource for studying online discourse. The number of comments that articles often elicit poses many methodological challenges and analyses of online user comments have inevitably been cursory when limited to a manual content or thematic analysis. Corpus analysis tools can systematically identify features such as keywords in large datasets. This article reports on the semantic annotation feature of the corpus analysis tool Wmatrix which also allows us to identify key semantic domains. Building on this feature, I introduce a novel method of sampling key comments through an examination of user comment threads taken from The Guardian website on the topic of climate change