The EM Algorithm in Genetics, Genomics and Public Health

The popularity of the EM algorithm owes much to the 1977 paper by Dempster, Laird and Rubin. That paper gave the algorithm its name, identified the general form and some key properties of the algorithm and established its broad applicability in scientific research. This review gives a nontechnical introduction to the algorithm for a general scientific audience, and presents a few examples characteristic of its application.Comment: Published in at http://dx.doi.org/10.1214/08-STS270 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Role of Family-Based Designs in Genome-Wide Association Studies

Genome-Wide Association Studies (GWAS) offer an exciting and promising new research avenue for finding genes for complex diseases. Traditional case-control and cohort studies offer many advantages for such designs. Family-based association designs have long been attractive for their robustness properties, but robustness can mean a loss of power. In this paper we discuss some of the special features of family designs and their relevance in the era of GWAS.Comment: Published in at http://dx.doi.org/10.1214/08-STS280 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Energy-based Structure Prediction for d(Al70Co20Ni10)

We use energy minimization principles to predict the structure of a decagonal quasicrystal - d(AlCoNi) - in the Cobalt-rich phase. Monte Carlo methods are then used to explore configurations while relaxation and molecular dynamics are used to obtain a more realistic structure once a low energy configuration has been found. We find five-fold symmetric decagons 12.8 A in diameter as the characteristic formation of this composition, along with smaller pseudo-five-fold symmetric clusters filling the spaces between the decagons. We use our method to make comparisons with a recent experimental approximant structure model from Sugiyama et al (2002).Comment: 10pp, 2 figure

Implication of the B -> rho rho data on the B -> pi pi puzzle

We point out that the B -> rho rho data have seriously constrained the possibility of resolving the B -> pi pi puzzle from the large observed B^0 -> pi^0 pi^0 branching ratio in the available theoretical approaches. The next-to-leading-order (NLO) contributions from the vertex corrections, the quark loops, and the magnetic penguin evaluated in the perturbative QCD (PQCD) approach have saturated the experimental upper bound of the B^0 -> rho^0 rho^0 branching ratio, and do not help. The NLO PQCD predictions for the B^0 -> rho^\mp rho^\pm and B^\pm -> rho^\pm rho^0 branching ratios are consistent with the data. The inclusion of the NLO jet function from the soft-collinear effective theory into the QCD-improved factorization approach, though enhancing the B^0 -> pi^0 pi^0 branching ratio sufficiently, overshoots the bound of the B^0 -> rho^0 rho^0 branching ratio, and deteriorates the predictions for the B^\pm -> pi^0 K^\pm and B^0 -> pi^\mp K^\pm direct CP asymmetries.Comment: 15 pages, 1 figure, REVTeX4; title changed, version to appear in Phys. Rev.

The Structure of the Cold Neutral ISM on 10-100 Astronomical Unit Scales

We have used the Very Long Baseline Array (VLBA) and the Very Large Array (VLA) to image Galactic neutral hydrogen in absorption towards four compact extragalactic radio sources with 10 milliarcsecond resolution. Previous VLBA data by Faison et al (1998) have shown the existence of prominent structures in the direction of the extragalactic source 3C~138 with scale sizes of 10-20 AU with changes in HI optical depth in excess of 0.8 $\pm$ 0.1. In this paper we confirm the small scale \hi optical depth variations toward 3C~147 suggested earlier at a level up to 20 % $\pm$ 5% . The sources 3C~119, 2352+495 and 0831+557 show no significant change in \hi optical depth across the sources with one sigma limits of 30%, 50%, and 100%. Of the seven sources recently investigated with the VLBA and VLA, only 3C~138 and 3C~147 show statistically significant variations in HI opacities. Deshpande (2000) have attempted to explain the observed small-scale structure as an extension of the observed power spectrum of structure on parsec size scales. The predictions of Deshpande (2000) are consistent with the VLBA HI data observed in the directions of a number of sources, including 3C~147, but are not consistent with our previous observations of the HI opacity structure toward 3C~138

fgui: A Method for Automatically Creating Graphical User Interfaces for Command-Line R Packages

The fgui R package is designed for developers of R packages, to help rapidly, and sometimes fully automatically, create a graphical user interface for a command line R package. The interface is built upon the Tcl/Tk graphical interface included in R. The package further facilitates the developer by loading in the help files from the command line functions to provide context sensitive help to the user with no additional effort from the developer. Passing a function as the argument to the routines in the fgui package creates a graphical interface for the function, and further options are available to tweak this interface for those who want more flexibility.

Quantum Computer Using Coupled Quantum Dot Molecules

We propose a method for implementation of a quantum computer using artificial molecules. The artificial molecule consists of two coupled quantum dots stacked along z direction and one single electron. One-qubit and two-qubit gates are constructed by one molecule and two coupled molecules, respectively.The ground state and the first excited state of the molecule are used to encode the |0> and |1> states of a qubit. The qubit is manipulated by a resonant electromagnetic wave that is applied directly to the qubit through a microstrip line. The coupling between two qubits in a quantum controlled NOT gate is switched on (off) by floating (grounding) the metal film electrodes. We study the operations of the gates by using a box-shaped quantum dot model and numerically solving a time-dependent Schridinger equation, and demonstrate that the quantum gates can perform the quantum computation. The operating speed of the gates is about one operation per 4ps. The reading operation of the output of the quantum computer can be performed by detecting the polarization of the qubits.Comment: 18 pages, 7 figures, submitted to Jpn. J. Appl. Phys, please send your e-mail to Nan-Jian Wu <[email protected]