gap: Genetic Analysis Package

A preliminary attempt at collecting tools and utilities for genetic data as an R package called gap is described. Genomewide association is then described as a specific example, linking the work of Risch and Merikangas (1996), Long and Langley (1997) for family-based and population-based studies, and the counterpart for case-cohort design established by Cai and Zeng (2004). Analysis of staged design as outlined by Skol et al. (2006) and associate methods are discussed. The package is flexible, customizable, and should prove useful to researchers especially in its application to genomewide association studies.

Ehrenfest scheme for complex thermodynamic systems in full phase space

For a thermodynamic system with multiple pairs of intensive/extensive variables and the thermodynamical coefficients attain finite or infinite values on the phase boundary, we obtain the two classes of Ehrenfest equations in the full phase space, and find that the rank of the matrix for these equations can tell us the dimensions of the phase boundary. We also apply this treatment to the RN-AdS black hole.Comment: 9 page

Revisiting the holographic dark energy in a non-flat universe: alternative model and cosmological parameter constraints

We propose an alternative model for the holographic dark energy in a non-flat universe. This new model differs from the previous one in that the IR length cutoff $L$ is taken to be exactly the event horizon size in a non-flat universe, which is more natural and theoretically/conceptually concordant with the model of holographic dark energy in a flat universe. We constrain the model using the recent observational data including the type Ia supernova data from SNLS3, the baryon acoustic oscillation data from 6dF, SDSS-DR7, BOSS-DR11, and WiggleZ, the cosmic microwave background data from Planck, and the Hubble constant measurement from HST. In particular, since some previous studies have shown that the color-luminosity parameter $\beta$ of supernovae is likely to vary during the cosmic evolution, we also consider such a case that $\beta$ in SNLS3 is time-varying in our data fitting. Compared to the constant $\beta$ case, the time-varying $\beta$ case reduces the value of $\chi^2$ by about 35 and results in that $\beta$ deviates from a constant at about 5$\sigma$ level, well consistent with the previous studies. For the parameter $c$ of the holographic dark energy, the constant $\beta$ fit gives $c=0.65\pm 0.05$ and the time-varying $\beta$ fit yields $c=0.72\pm 0.06$. In addition, an open universe is favored (at about 2$\sigma$) for the model by the current data.Comment: 8 pages, 4 figure

Context Modeling for Ranking and Tagging Bursty Features in Text Streams

Bursty features in text streams are very useful in many text mining applications. Most existing studies detect bursty features based purely on term frequency changes without taking into account the semantic contexts of terms, and as a result the detected bursty features may not always be interesting or easy to interpret. In this paper we propose to model the contexts of bursty features using a language modeling approach. We then propose a novel topic diversity-based metric using the context models to find newsworthy bursty features. We also propose to use the context models to automatically assign meaningful tags to bursty features. Using a large corpus of a stream of news articles, we quantitatively show that the proposed context language models for bursty features can effectively help rank bursty features based on their newsworthiness and to assign meaningful tags to annotate bursty features. ? 2010 ACM.EI