A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

What would you do? An investigation of stated-response data

When analysing choices or policy impacts, economists generally rely on what people actually do, rather than what they say they would do. The "stated response" approach is treated with scepticism due, for example, to concerns regarding the effect of strategic or social considerations on what people say, and a belief that people may not adequately consider such a hypothetical question. This paper evaluates an example of this approach; the direct questioning of parents as to whether they would withdraw their children from school if the Familias en Accion education subsidies were withdrawn. Our results suggest that these concerns are not entirely invalid but that the stated responses do provide important information and correlate in the expected manner with child and household characteristics. We conclude by emphasising the importance of good question design, which may allow researchers to use the "stated response" method as a complement to more typical quantitative methodologies

Channel estimation and symbol detection for block transmission using data-dependent superimposed training

We address the problem of frequency-selective channel estimation and symbol detection using superimposed training. The superimposed training consists of the sum of a known sequence and a data-dependent sequence that is unknown to the receiver. The data-dependent sequence cancels the effects of the unknown data on channel estimation. The performance of the proposed approach is shown to significantly outperform existing methods based on superimposed training (ST)

Evolved stars in the Local Group galaxies. I. AGB evolution and dust production in IC 1613

We used models of thermally-pulsing asymptotic giant branch (AGB) stars, that also describe the dust-formation process in the wind, to interpret the combination of near- and mid-infrared photometric data of the dwarf galaxy IC 1613. This is the first time that this approach is extended to an environment different from the Milky Way and the Magellanic Clouds (MCs). Our analysis, based on synthetic population techniques, shows a nice agreement between the observations and the expected distribution of stars in the colour-magnitude diagrams obtained with JHK and Spitzer bands. This allows a characterization of the individual stars in the AGB sample in terms of mass, chemical composition, and formation epoch of the progenitors. We identify the stars exhibiting the largest degree of obscuration as carbon stars evolving through the final AGB phases, descending from 1-1.25Msun objects of metallicity Z=0.001 and from 1.5-2.5Msun stars with Z=0.002. Oxygen-rich stars constitute the majority of the sample (65%), mainly low mass stars (<2Msun) that produce a negligible amount of dust (<10^{-7}Msun/yr). We predict the overall dust-production rate from IC 1613, mostly determined by carbon stars, to be 6x10^{-7}Msun/yr with an uncertainty of 30%. The capability of the current generation of models to interpret the AGB population in an environment different from the MCs opens the possibility to extend this kind of analysis to other Local Group galaxies.Comment: 14 pages, 6 figures, accepted for publication on MNRA

Wave-unlocking transition in resonantly coupled complex Ginzburg-Landau equations

We study the effect of spatial frequency-forcing on standing-wave solutions of coupled complex Ginzburg-Landau equations. The model considered describes several situations of nonlinear counterpropagating waves and also of the dynamics of polarized light waves. We show that forcing introduces spatial modulations on standing waves which remain frequency locked with a forcing-independent frequency. For forcing above a threshold the modulated standing waves unlock, bifurcating into a temporally periodic state. Below the threshold the system presents a kind of excitability.Comment: 4 pages, including 4 postscript figures. To appear in Physical Review Letters (1996). This paper and related material can be found at http://formentor.uib.es/Nonlinear