Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

Inferring Latent Structure From Mixed Real and Categorical Relational Data

We consider analysis of relational data (a matrix), in which the rows correspond to subjects (e.g., people) and the columns correspond to attributes. The elements of the matrix may be a mix of real and categorical. Each subject and attribute is characterized by a latent binary feature vector, and an inferred matrix maps each row-column pair of binary feature vectors to an observed matrix element. The latent binary features of the rows are modeled via a multivariate Gaussian distribution with low-rank covariance matrix, and the Gaussian random variables are mapped to latent binary features via a probit link. The same type construction is applied jointly to the columns. The model infers latent, low-dimensional binary features associated with each row and each column, as well correlation structure between all rows and between all columns

Visuospatial bootstrapping: spatialized displays enhance digit and nonword sequence learning

Visuospatial bootstrapping describes the observation that performance on a verbal memory task is enhanced by presenting the to‐be‐remembered material in a format with additional embedded spatial information. Thus far, it has only been reported in short‐term memory tasks. Here, we report two experiments assessing the impact of spatial information on the learning of sequences in long‐term memory. Experiment 1 used digits presented within a familiar numeric keypad as stimuli compared against single digits presented in one location. Experiment 2 used novel nonwords, which were either presented in an unchanging arrangement permitting the building‐up of location knowledge or in a constantly changing arrangement. Both experiments demonstrated strong evidence that reliable spatial information facilitated sequence learning, particularly in later sequence positions. It is concluded that the incidental availability of spatialized information during study can facilitate learning of sequences of digits and nonwords. Furthermore, the spatial information can be learned during the task itself and does not need to be preexistent in long‐term knowledge

New limits for neutrinoless tau decays

Neutrinoless 3-prong tau lepton decays into a charged lepton and either two charged particles or one neutral meson have been searched for using 4.79fb^(-1) of data collected with the CLEO II detector at Cornell Electron Storage Ring. This analysis represents an update of a previous study and the addition of six decay channels. In all channels the numbers of events found are compatible with background estimates and branching fraction upper limits are set for 28 different decay modes. These limits are either more stringent than those set previously or represent the first attempt to find these decays

Volume contraction at the Jahn-Teller transition of LaMnO3_3

We have studied the volume collapse of LaMnO$_3$ at the Jahn- Teller (JT) transition temperature T$_{JT}$=750 K which has recently been found in high temperature powder x- ray and neutron diffraction experiments. We construct a model Hamiltonian involving the pseudospin of Mn$^{3+}$ e$_g$ states, the staggered JT distortion and the volume strain coordinate. We show that the anharmonic coupling between these primary and secondary order parameters leads to the first order JT phase transition associated with a comparatively large reduction of the unit cell volume of $\Delta$V/V$\simeq$ 10$^{-2}$. We explain the temperature dependence of JT distortions and volume strain and discuss the volume change as function of the anharmonic coupling constant. A continuous change to a second order transition as function of model parameters is obtained. This behaviour is also observed under Ba doping.Comment: 5 pages, 4 figure

genoPlotR: comparative gene and genome visualization in R

Summary: The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools. Complementing existing software for comparison and exploration of genomics data, genoPlotR automatically creates publication-grade linear maps of gene and genomes, in a highly automatic, flexible and reproducible way

Exact Maximal Height Distribution of Fluctuating Interfaces

We present an exact solution for the distribution P(h_m,L) of the maximal height h_m (measured with respect to the average spatial height) in the steady state of a fluctuating Edwards-Wilkinson interface in a one dimensional system of size L with both periodic and free boundary conditions. For the periodic case, we show that P(h_m,L)=L^{-1/2}f(h_m L^{-1/2}) for all L where the function f(x) is the Airy distribution function that describes the probability density of the area under a Brownian excursion over a unit interval. For the free boundary case, the same scaling holds but the scaling function is different from that of the periodic case. Numerical simulations are in excellent agreement with our analytical results. Our results provide an exactly solvable case for the distribution of extremum of a set of strongly correlated random variables.Comment: 4 pages revtex (two-column), 1 .eps figure include

Properties of Active Galaxies Deduced from H I Observations

We completed a new survey for H I emission for a large, well-defined sample of 154 nearby (z < 0.1) galaxies with type 1 AGNs. We make use of the extensive database presented in a companion paper to perform a comprehensive appraisal of the cold gas content in active galaxies and to seek new strategies to investigate the global properties of the host galaxies and their relationship to their central black holes (BHs). We show that the BH mass obeys a strong, roughly linear relation with the host galaxy's dynamical mass. BH mass follows a looser, though still highly significant, correlation with the maximum rotation velocity of the galaxy, as expected from the known scaling between rotation velocity and central velocity dispersion. Neither of these H I-based correlations is as tight as the more familiar relations between BH mass and bulge luminosity or velocity dispersion, but they offer the advantage of being insensitive to the glare of the nucleus and therefore are promising new tools for probing the host galaxies of both nearby and distant AGNs. We present evidence for substantial ongoing BH growth in the most actively accreting AGNs. In these nearby systems, BH growth appears to be delayed with respect to the assembly of the host galaxy but otherwise has left no detectable perturbation to its mass-to-light ratio or its global gas content. The host galaxies of type 1 AGNs, including those luminous enough to qualify as quasars, are generally gas-rich systems, possessing a cold interstellar medium reservoir at least as abundant as that in inactive galaxies of the same morphological type. This calls into question current implementations of AGN feedback in models of galaxy formation that predict strong cold gas depletion in unobscured AGNs. (Abridged)Comment: To appear in ApJ; 14 page