35,197 research outputs found
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parents as to whether they would withdraw their children from school if the Familias en Accion education subsidies were withdrawn.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
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