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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IMPROVING PROJECT MANAGEMENT FOR SUSTAINABLE DEVELOPMENT

Institutional and Behavioral Economics,

First results from a VLBA proper motion survey of H2O masers in low-mass YSOs: the Serpens core and RNO15-FIR

This article reports first results of a long-term observational program aimed to study the earliest evolution of jet/disk systems in low-mass YSOs by means of VLBI observations of the 22.2 GHz water masers. We report here data for the cluster of low-mass YSOs in the Serpens molecular core and for the single object RNO~15-FIR. Towards Serpens SMM1, the most luminous sub-mm source of the Serpens cluster, the water maser emission comes from two small (< 5 AU in size) clusters of features separated by ~25 AU, having line of sight velocities strongly red-shifted (by more than 10 km/s) with respect to the LSR velocity of the molecular cloud. The two maser clusters are oriented on the sky along a direction that is approximately perpendicular to the axis of the radio continuum jet observed with the VLA towards SMM1. The spatial and velocity distribution of the maser features lead us to favor the interpretation that the maser emission is excited by interaction of the receding lobe of the jet with dense gas in the accretion disk surrounding the YSO in SMM1. Towards RNO~15-FIR, the few detected maser features have both positions and (absolute) velocities aligned along a direction that is parallel to the axis of the molecular outflow observed on much larger angular scales. In this case the maser emission likely emerges from dense, shocked molecular clumps displaced along the axis of the jet emerging from the YSO. The protostar in Serpens SMM1 is more massive than the one in RNO~15-FIR. We discuss the case where a high mass ejection rate can generate jets sufficiently powerful to sweep away from their course the densest portions of circumstellar gas. In this case, the excitation conditions for water masers might preferably occur at the interface between the jet and the accretion disk, rather than along the jet axis.Comment: 18 pages (postscript format); 9 figures; to be published into Astronomy & Astrophysics, Main Journa

Agriculture's prominence in the INDCs

Analysis of agriculture in countries’ climate change mitigation and adaptation strategies finds: Most Parties to the UNFCCC include agriculture in their mitigation targets (80%) and adaptation strategies (64%); Non-annex 1 Parties note the need for international financial support to implement their INDCs and raise the ambition of their contributions; For countries to meet their targets, climate finance will need to address agriculture

Spitzer and HHT observations of starless cores: masses and environments

We present Spitzer observations of a sample of 12 starless cores selected to have prominent 24 micron shadows. The Spitzer images show 8 and 24 micron shadows and in some cases 70 micron shadows; these spatially resolved absorption features trace the densest regions of the cores. We have carried out a 12CO (2-1) and 13CO (2-1) mapping survey of these cores with the Heinrich Hertz Telescope (HHT). We use the shadow features to derive optical depth maps. We derive molecular masses for the cores and the surrounding environment; we find that the 24 micron shadow masses are always greater than or equal to the molecular masses derived in the same region, a discrepancy likely caused by CO freeze--out onto dust grains. We combine this sample with two additional cores that we studied previously to bring the total sample to 14 cores. Using a simple Jeans mass criterion we find that ~ 2/3 of the cores selected to have prominent 24 micron shadows are collapsing or near collapse, a result that is supported by millimeter line observations. Of this subset at least half have indications of 70 micron shadows. All cores observed to produce absorption features at 70 micron are close to collapse. We conclude that 24 micron shadows, and even more so the 70 micron ones, are useful markers of cloud cores that are approaching collapse.Comment: 41 pages, 28 figures, 5 tables; accepted by Ap

The North Sea Andrea storm and numerical simulations

A coupling of a spectral wave model with a nonlinear phase-resolving model is used to reconstruct the evolution of wave statistics during a storm crossing the North Sea on 8–9 November 2007. During this storm a rogue wave (named the Andrea wave) was recorded at the Ekofisk field. The wave has characteristics comparable to the well-known New Year wave measured by Statoil at the Draupner platform 1 January 1995. Hindcast data of the storm at the nearest grid point to the Ekofisk field are here applied as input to calculate the evolution of random realizations of the sea surface and its statistical properties. Numerical simulations are carried out using the Euler equations with a higher-order spectral method (HOSM). Results are compared with some characteristics of the Andrea wave record measured by the down-looking lasers at Ekofisk

Contemporary temperature-driven divergence in a Nordic freshwater fish under conditions commonly thought to hinder adaptation

BACKGROUND: Evaluating the limits of adaptation to temperature is important given the IPCC-predicted rise in global temperatures. The rate and scope of evolutionary adaptation can be limited by low genetic diversity, gene flow, and costs associated with adaptive change. Freshwater organisms are physically confined to lakes and rivers, and must therefore deal directly with climate variation and change. In this study, we take advantage of a system characterised by low genetic variation, small population size, gene flow and between-trait trade-offs to study how such conditions affect the ability of a freshwater fish to adapt to climate change. We test for genetically-based differences in developmental traits indicating local adaptation, by conducting a common-garden experiment using embryos and larvae from replicate pairs of sympatric grayling demes that spawn and develop in natural cold and warm water, respectively. These demes have common ancestors from a colonization event 22 generations ago. Consequently, we explore if diversification may occur under severely constraining conditions. RESULTS: We found evidence for divergence in ontogenetic rates. The divergence pattern followed adaptation predictions as cold-deme individuals displayed higher growth rates and yolk conversion efficiency than warm-deme individuals at the same temperature. The cold-deme embryos had a higher rate of muscle mass development. Most of the growth- and development differences occurred prior to hatch. The divergence was probably not caused by genetic drift as there was a strong degree of parallelism in the divergence pattern and because phenotypic differentiation (Q(ST)) was larger than estimated genetic drift levels (microsatellite F(ST)) between demes from different temperature groups. We also document that these particular grayling populations cannot develop successfully at temperatures above 12°C, whereas other European populations can, and that increasing the muscle mass development rate comes at the cost of some skeletal trait development rates. CONCLUSIONS: This study shows that genetically based phenotypic divergence can prevail even under conditions of low genetic variation and ongoing gene flow. Furthermore, population-specific maximum development temperatures along with musculoskeletal developmental trade-offs may constrain adaptation

Molecular Inventories and Chemical Evolution of Low-mass Protostellar Envelopes

This paper presents the first substantial study of the chemistry of the envelopes around a sample of 18 low-mass pre- and protostellar objects for which physical properties have previously been derived from radiative transfer modeling of their dust continuum emission. Single-dish line observations of 24 transitions of 9 molecular species (not counting isotopes) including HCO+, N2H+, CS, SO, SO2, HCN, HNC, HC3N and CN are reported. The line intensities are used to constrain the molecular abundances by comparison to Monte Carlo radiative transfer modeling of the line strengths. An empirical chemical network is constructed on the basis of correlations between the abundances of various species. For example, it is seen that the HCO+ and CO abundances are linearly correlated, both increasing with decreasing envelope mass. Species such as CS, SO and HCN show no trend with envelope mass. In particular no trend is seen between ``evolutionary stage'' of the objects and the abundances of the main sulfur- or nitrogen-containing species. Among the nitrogen-bearing species abundances of CN, HNC and HC3N are found to be closely correlated, which can be understood from considerations of the chemical network. The CS/SO abundance ratio is found to correlate with the abundances of CN and HC3N, which may reflect a dependence on the atomic carbon abundance. An anti-correlation is found between the deuteration of HCO+ and HCN, reflecting different temperature dependences for gas-phase deuteration mechanisms. The abundances are compared to other protostellar environments. In particular it is found that the abundances in the cold outer envelope of the previously studied class 0 protostar IRAS16293-2422 are in good agreement with the average abundances for the presented sample of class 0 objects.Comment: Accepted for publication in A&A. 29 pages, 23 figures. Abstract abridge