Effective Sample Size: Quick Estimation of the Effect of Related Samples in Genetic Case-Control Association Analyses

Correlated samples have been frequently avoided in case-control
genetic association
 studies in part because the methods for handling them are either not
easily implemented or not widely known. We
advocate one method for case-control association analysis of correlated
samples -- the effective sample size method -- as a simple and
accessible approach that does not require specialized computer programs.
The effective sample size method captures the variance inflation
of allele frequency estimation exactly, and can be used to modify the
chi-square test statistic, p-value, and 95% confidence interval of
odds-ratio simply by replacing the apparent number of allele counts with the
effective ones. For genotype frequency estimation, although a single
effective sample size is unable to completely characterize the variance inflation,
an averaged one can satisfactorily approximate the simulated result.
The effective sample size method is applied to the rheumatoid arthritis
siblings data collected from the North American Rheumatoid Arthritis Consortium (NARAC)
to establish a significant association with the interferon-induced
helicasel gene (IFIH1) previously being identified as a type 1 diabetes
susceptibility locus. Connections between the effective sample size
method and other methods, such as generalized estimation equation,
variance of eigenvalues for correlation matrices, and genomic controls,
are also discussed.
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Comprehensive Nuclear-Test-Ban Treaty – a peace-keeping initiative with scientific impact

Any major shaking of the Earth can be recorded on a seismograph regardless of the nature of the source. Earthquakes and large explosions generate waves with similar frequency content. This fact has been used for decades to construct systems to monitor detonations of underground nuclear explosions. The quality of the monitoring system has increased significantly in recent years, and we demonstrate here that the data are useful in Danish earthquake research

Seismology: neotectonics and structure of the Baltic Shield

Recent Danish seismological projects involving neotectonic investigations and structural studies have determined the edge of the Baltic Shield underlying Denmark. The most active earthquake zones in Denmark are located in northwestern Jylland and adjoining offshore areas, and in the region around Kattegat, Øresund and north-east Sjælland (Fig. 1). This pattern was originally recognised by Lehmann (1956) and has been confirmed by several later studies, e.g. Gregersen et al. (1998). Recent, more detailed investigations have documented that changes in the pattern of earthquake activity have occurred within a short time span. The most pronounced example of change – possibly related to exploitation of hydrocarbons – is an activity recorded in the Central Graben area of the North Sea that was first documented by Gregersen et al. (1998). The south-western margin of the Precambrian Baltic Shield separates areas of different earthquake activity (Fig. 1; Gregersen et al. 1991). Although lithospheric stresses are more or less uniform in northern Europe, there are pronounced differences in the behaviour of the lithosphere across Denmark. The north-eastern area underlain by the Baltic Shield experiences brittle failure as recorded by common earthquakes, whereas earthquakes are virtually absent in the region southwest of the shield (Fig. 1). The margin of the Baltic Shield as defined by earthquake activity is not identical with that distinguished structurally in sedimentary studies (EUGENO-S Working Group 1988; Vejbæk & Britze 1994), in crustal studies (Abramovitz & Thybo 2000), or by recent studies of the structure of the subcrustal lithosphere (Gregersen et al. 2002; Shomali et al. 2002). The physical edge of the Baltic Shield cannot be uniquely determined on the basis of seismological studies. The earthquakes recorded, although of low magnitude, do give information about the released stresses. The earthquakes seem to be a response to a dominant NW–SE compression, also apparent elsewhere in Scandinavia and northern Europe (Slunga et al. 1984; Slunga 1989; Gregersen 1992; Müller et al. 1992). These stresses are part of the large-scale stress systems associated with continued plate motion pattern (Gregersen & Basham 1989; Zoback et al. 1989). In contrast to present low-magnitude earthquakes, postglacial sediments in northern Scandinavia have preserved features interpreted as caused by earthquakes of magnitudes around 7; these major, c. 9000 years old earthquakes are believed to be related to the post-glacial uplift of Scandinavia (e.g. Arvidsson et al. 1991; Gregersen 2002). Earthquakes are always related to fault activity, but attempts to link recent earthquakes occurring in and around Denmark to geologically known faults have only been partly successful (Gregersen et al. 1996). The most significant fault zone in Denmark, the Sorgenfrei–Tornquist Zone, is only locally active. Recent geodetic and seismic investigations demonstrate that the two sides of the Sorgenfrei–Tornquist Zone are characterised by different patterns of deformation, but the zone itself is not defined by a present-day seismicity trend crossing the central parts of Denmark (Fig. 1)

A numerical analysis of finite Debye-length effects in induced-charge electro-osmosis

For a microchamber filled with a binary electrolyte and containing a flat un-biased center electrode at one wall, we employ three numerical models to study the strength of the resulting induced-charge electro-osmotic (ICEO) flow rolls: (i) a full nonlinear continuum model resolving the double layer, (ii) a linear slip-velocity model not resolving the double layer and without tangential charge transport inside this layer, and (iii) a nonlinear slip-velocity model extending the linear model by including the tangential charge transport inside the double layer. We show that compared to the full model, the slip-velocity models significantly overestimate the ICEO flow. This provides a partial explanation of the quantitative discrepancy between observed and calculated ICEO velocities reported in the literature. The discrepancy increases significantly for increasing Debye length relative to the electrode size, i.e. for nanofluidic systems. However, even for electrode dimensions in the micrometer range, the discrepancies in velocity due to the finite Debye length can be more than 10% for an electrode of zero height and more than 100% for electrode heights comparable to the Debye length.Comment: 11 pages, Revtex, 7 eps figure

OpenMI: the essential concepts and their implications for legacy software

International audienceInformation & Communication Technology (ICT) tools such as computational models are very helpful in designing river basin management plans (rbmp-s). However, in the scientific world there is consensus that a single integrated modelling system to support e.g. the implementation of the Water Framework Directive cannot be developed and that integrated systems need to be very much tailored to the local situation. As a consequence there is an urgent need to increase the flexibility of modelling systems, such that dedicated model systems can be developed from available building blocks. The HarmonIT project aims at precisely that. Its objective is to develop and implement a standard interface for modelling components and other relevant tools: The Open Modelling Interface (OpenMI) standard. The OpenMI standard has been completed and documented. It relies entirely on the "pull" principle, where data are pulled by one model from the previous model in the chain. This paper gives an overview of the OpenMI standard, explains the foremost concepts and the rational behind it

Does Infall End Before the Class I Stage?

We have observed HCO+ J=3-2 toward 16 Class I sources and 18 Class 0 sources, many of which were selected from Mardones et al. (1997). Eight sources have profiles significantly skewed to the blue relative to optically thin lines. We suggest six sources as new infall candidates. We find an equal "blue excess" among Class 0 and Class I sources after combining this sample with that of Gregersen et al. (1997). We used a Monte Carlo code to simulate the temporal evolution of line profiles of optically thick lines of HCO+, CS and H2CO in a collapsing cloud and found that HCO+ had the strongest asymmetry at late times. If a blue-peaked line profile implies infall, then the dividing line between the two classes does not trace the end of the infall stage.Comment: 21 pages, 8 figures, accepted by ApJ for April 20, 2000, added acknowledgmen

Sumatra-jordskælvet - de geofysiske konsekvenser

Sumatra-jordskælvet udløste en næsten ubegribelig menneskelig katastrofe i landene omkring Det Indiske Ocean med tæt på 300.000 omkomne. Langt de fleste blev ofre for den tsunami, som jordskælvet satte i gang. Jordskælvet er også opsigtsvækkende rent videnskabeligt på grund af sin voldsomhed og de naturvidenskabelige fænomener der fulgte med; den enorme brudzone, de store forskydninger, tsunamien og de kraftige rystelser, som satte hele jordkloden i svingninger

Better abstractions for timed automata

We consider the reachability problem for timed automata. A standard solution to this problem involves computing a search tree whose nodes are abstractions of zones. These abstractions preserve underlying simulation relations on the state space of the automaton. For both effectiveness and efficiency reasons, they are parametrized by the maximal lower and upper bounds (LU-bounds) occurring in the guards of the automaton. We consider the aLU abstraction defined by Behrmann et al. Since this abstraction can potentially yield non-convex sets, it has not been used in implementations. We prove that aLU abstraction is the biggest abstraction with respect to LU-bounds that is sound and complete for reachability. We also provide an efficient technique to use the aLU abstraction to solve the reachability problem.Comment: Extended version of LICS 2012 paper (conference paper till v6). in Information and Computation, available online 27 July 201