Causal graphical models in systems genetics: A unified framework for joint inference of causal network and genetic architecture for correlated phenotypes

Causal inference approaches in systems genetics exploit quantitative trait loci (QTL) genotypes to infer causal relationships among phenotypes. The genetic architecture of each phenotype may be complex, and poorly estimated genetic architectures may compromise the inference of causal relationships among phenotypes. Existing methods assume QTLs are known or inferred without regard to the phenotype network structure. In this paper we develop a QTL-driven phenotype network method (QTLnet) to jointly infer a causal phenotype network and associated genetic architecture for sets of correlated phenotypes. Randomization of alleles during meiosis and the unidirectional influence of genotype on phenotype allow the inference of QTLs causal to phenotypes. Causal relationships among phenotypes can be inferred using these QTL nodes, enabling us to distinguish among phenotype networks that would otherwise be distribution equivalent. We jointly model phenotypes and QTLs using homogeneous conditional Gaussian regression models, and we derive a graphical criterion for distribution equivalence. We validate the QTLnet approach in a simulation study. Finally, we illustrate with simulated data and a real example how QTLnet can be used to infer both direct and indirect effects of QTLs and phenotypes that co-map to a genomic region.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS288 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Local status and power in area-based health improvement partnerships

This is the authors' PDF version of an article published in Health© 2014. The definitive version is available at http://hea.sagepub.comArea-based initiatives (ABIs) have formed an important part of public policy towards more socio-economically deprived areas in many countries. Co-ordinating service provision within and across sectors has been a common feature of these initiatives. Despite sustained policy interest in ABIs, little empirical work has explored relations between ABI providers and partnership development within this context remains under-theorised. This paper addresses both of these gaps by exploring partnerships as a social and developmental process, drawing on concepts from figurational sociology to explain how provider relations develop within an ABI. Qualitative methods were used to explore, prospectively, the development of an ABI targeted at a town in the north west of England. A central finding was that, although effective delivery of ABIs is premised on a high level of coordination between service providers, the pattern of interdependencies between providers limits the frequency and effectiveness of cooperation. In particular, the interdependency of ABI providers with others in their organisation (what is termed here ‘organisational pull’) constrained the ways in which they worked with providers outside of their own organisations. ‘Local’ status, which could be earned over time, enabled some providers to exert greater control over the way in which provider relations developed during the course of the initiative. These findings demonstrate how historically constituted social networks, within which all providers are embedded, shape partnership development. The theoretical insight developed here suggests a need for more realistic expectations among policy makers about how and to what extent provider partnerships can be managed. Keywords: partnership, collaboration, community services, area-based initiatives, organisational pull, figurational sociologyNational Health Service (NHS

Succinct Dictionary Matching With No Slowdown

The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in a any text T all occurrences of strings belonging to S. The classical solution for this problem is the Aho-Corasick automaton which finds all occ occurrences in a text T in time O(|T| + occ) using a data structure that occupies O(m log m) bits of space where m <= n + 1 is the number of states in the automaton. In this paper we show that the Aho-Corasick automaton can be represented in just m(log sigma + O(1)) + O(d log(n/d)) bits of space while still maintaining the ability to answer to queries in O(|T| + occ) time. To the best of our knowledge, the currently fastest succinct data structure for the dictionary matching problem uses space O(n log sigma) while answering queries in O(|T|log log n + occ) time. In this paper we also show how the space occupancy can be reduced to m(H0 + O(1)) + O(d log(n/d)) where H0 is the empirical entropy of the characters appearing in the trie representation of the set S, provided that sigma < m^epsilon for any constant 0 < epsilon < 1. The query time remains unchanged.Comment: Corrected typos and other minor error

Liquid-vapor interface of a polydisperse fluid

We report a Grand Canonical Monte Carlo simulation study of the liquid-vapor interface of a model fluid exhibiting polydispersity in terms of the particle size $\sigma$. The bulk density distribution, $\rho^0(\sigma)$, of the system is controlled by the imposed chemical potential distribution $\mu(\sigma)$. We choose the latter such that $\rho^0(\sigma)$ assumes a Schulz form with associated degree of polydispersity $\approx 14$. By introducing a smooth attractive wall, a planar liquid-vapor interface is formed for bulk state points within the region of liquid-vapor coexistence. Owing to fractionation, the pure liquid phase is enriched in large particles, with respect to the coexisting vapor. We investigate how the spatial non-uniformity of the density near the liquid-vapor interface affects the evolution of the local distribution of particle sizes between the limiting pure phase forms. We find (as previously predicted by density functional theory, Bellier-Castella {\em et al}, Phys. Rev. {\bf E65}, 021503 (2002)) a segregation of smaller particles to the interface. The magnitude of this effect is quantified for various $\sigma$ via measurements of the relative adsorption. Additionally, we consider the utility of various estimators for the interfacial width and highlight the difficulties of isolating the intrinsic contribution of polydispersity to this width.Comment: 9 pages, 10 Fig

Flows on Graphs with Random Capacities

We investigate flows on graphs whose links have random capacities. For binary trees we derive the probability distribution for the maximal flow from the root to a leaf, and show that for infinite trees it vanishes beyond a certain threshold that depends on the distribution of capacities. We then examine the maximal total flux from the root to the leaves. Our methods generalize to simple graphs with loops, e.g., to hierarchical lattices and to complete graphs.Comment: 8 pages, 6 figure

SN 2013df, a double-peaked IIb supernova from a compact progenitor and an extended H envelope

Optical observations of the type IIb SN 2013df from a few days to about 250 days after explosion are presented. These observations are complemented with UV photometry taken by \textit{SWIFT} up to 60 days post-explosion. The double-peak optical light curve is similar to those of SNe 1993J and 2011fu although with different decline and rise rates. From the modelling of the bolometric light curve, we have estimated that the total mass of synthesised $^{56}$Ni in the explosion is $\sim0.1$ M$_{\odot}$, while the ejecta mass is $0.8-1.4$ M$_{\odot}$ and the explosion energy $0.4-1.2 \times 10^{51}$erg. In addition, we have estimated a lower limit to the progenitor radius ranging from $64-169$ $R_{\odot}$. The spectral evolution indicates that SN 2013df had a hydrogen envelope similar to SN 1993J ($\sim 0.2$ M$_{\odot}$). The line profiles in nebular spectra suggest that the explosion was asymmetric with the presence of clumps in the ejecta, while the [O\,{\sc i}] $\lambda$$\lambda$$6300$, $6364$ luminosities, may indicate that the progenitor of SN 2013df was a relatively low mass star ( $\sim 12-13$ M$_{\odot}$).Comment: 18 pages, 11 figures, 9 tables, accepted for publication in MNRA

Reed-Muller codes for random erasures and errors

This paper studies the parameters for which Reed-Muller (RM) codes over $GF(2)$ can correct random erasures and random errors with high probability, and in particular when can they achieve capacity for these two classical channels. Necessarily, the paper also studies properties of evaluations of multi-variate $GF(2)$ polynomials on random sets of inputs. For erasures, we prove that RM codes achieve capacity both for very high rate and very low rate regimes. For errors, we prove that RM codes achieve capacity for very low rate regimes, and for very high rates, we show that they can uniquely decode at about square root of the number of errors at capacity. The proofs of these four results are based on different techniques, which we find interesting in their own right. In particular, we study the following questions about $E(m,r)$, the matrix whose rows are truth tables of all monomials of degree $\leq r$ in $m$ variables. What is the most (resp. least) number of random columns in $E(m,r)$ that define a submatrix having full column rank (resp. full row rank) with high probability? We obtain tight bounds for very small (resp. very large) degrees $r$, which we use to show that RM codes achieve capacity for erasures in these regimes. Our decoding from random errors follows from the following novel reduction. For every linear code $C$ of sufficiently high rate we construct a new code $C'$, also of very high rate, such that for every subset $S$ of coordinates, if $C$ can recover from erasures in $S$, then $C'$ can recover from errors in $S$. Specializing this to RM codes and using our results for erasures imply our result on unique decoding of RM codes at high rate. Finally, two of our capacity achieving results require tight bounds on the weight distribution of RM codes. We obtain such bounds extending the recent \cite{KLP} bounds from constant degree to linear degree polynomials

Emotions, Violence and Social Belonging: an Eliasian Analysis of Sports Spectatorship

This paper examines the development of different forms of spectator violence in terms of the socio-temporal structure of situational dynamics at Gaelic football matches in Ireland. The nature of violent encounters has shifted from a collective form based on local solidarity and a reciprocal code of honour, through a transitional collective form based on deferred emotional satisfaction and group pride, towards increasing individualization of spectator violence. This occurs due to the shifting objects of emotional involvement. As the functional specialization of the various roles in the game is partially accepted by spectators, the referee becomes the target of anger. Violence becomes more individualized as ‘mutually expected self-restraint’ proceeds within the context of relative state pacification beyond the field of play and the formation of a less volatile habitus. We use Elias’s figurational perspective on violence over the micro-interactional approach of Randall Collins, but support Collins’ emphasis on state legitimacy