311,432 research outputs found
Energetics of Protein-DNA Interactions
Protein-DNA interactions are vital for many processes in living cells,
especially transcriptional regulation and DNA modification. To further our
understanding of these important processes on the microscopic level, it is
necessary that theoretical models describe the macromolecular interaction
energetics accurately. While several methods have been proposed, there has not
been a careful comparison of how well the different methods are able to predict
biologically important quantities such as the correct DNA binding sequence,
total binding free energy, and free energy changes caused by DNA mutation. In
addition to carrying out the comparison, we present two important theoretical
models developed initially in protein folding that have not yet been tried on
protein-DNA interactions. In the process, we find that the results of these
knowledge-based potentials show a strong dependence on the interaction distance
and the derivation method. Finally, we present a knowledge-based potential that
gives comparable or superior results to the best of the other methods,
including the molecular mechanics force field AMBER99
Shape basis interpretation for monocular deformable 3D reconstruction
© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In this paper, we propose a novel interpretable shape model to encode object non-rigidity. We first use the initial frames of a monocular video to recover a rest shape, used later to compute a dissimilarity measure based on a distance matrix measurement. Spectral analysis is then applied to this matrix to obtain a reduced shape basis, that in contrast to existing approaches, can be physically interpreted. In turn, these pre-computed shape bases are used to linearly span the deformation of a wide variety of objects. We introduce the low-rank basis into a sequential approach to recover both camera motion and non-rigid shape from the monocular video, by simply optimizing the weights of the linear combination using bundle adjustment. Since the number of parameters to optimize per frame is relatively small, specially when physical priors are considered, our approach is fast and can potentially run in real time. Validation is done in a wide variety of real-world objects, undergoing both inextensible and extensible deformations. Our approach achieves remarkable robustness to artifacts such as noisy and missing measurements and shows an improved performance to competing methods.Peer ReviewedPostprint (author's final draft
Mining Heterogeneous Multivariate Time-Series for Learning Meaningful Patterns: Application to Home Health Telecare
For the last years, time-series mining has become a challenging issue for
researchers. An important application lies in most monitoring purposes, which
require analyzing large sets of time-series for learning usual patterns. Any
deviation from this learned profile is then considered as an unexpected
situation. Moreover, complex applications may involve the temporal study of
several heterogeneous parameters. In that paper, we propose a method for mining
heterogeneous multivariate time-series for learning meaningful patterns. The
proposed approach allows for mixed time-series -- containing both pattern and
non-pattern data -- such as for imprecise matches, outliers, stretching and
global translating of patterns instances in time. We present the early results
of our approach in the context of monitoring the health status of a person at
home. The purpose is to build a behavioral profile of a person by analyzing the
time variations of several quantitative or qualitative parameters recorded
through a provision of sensors installed in the home
Distances and ages of globular clusters using Hipparcos parallaxes of local subdwarfs
We discuss the impact of Population II and Globular Cluster (GCs) stars on
the derivation of the age of the Universe, and on the study of the formation
and early evolution of galaxies, our own in particular. The long-standing
problem of the actual distance scale to Population II stars and GCs is
addressed, and a variety of different methods commonly used to derive distances
to Population II stars are briefly reviewed. Emphasis is given to the
discussion of distances and ages for GCs derived using Hipparcos parallaxes of
local subdwarfs. Results obtained by different authors are slightly different,
depending on different assumptions about metallicity scale, reddenings, and
corrections for undetected binaries. These and other uncertainties present in
the method are discussed. Finally, we outline progress expected in the near
future.Comment: Invited review article to appear in: `Post-Hipparcos Cosmic Candles',
A. Heck & F. Caputo (Eds), Kluwer Academic Publ., Dordrecht, in press. 22
pages including 3 tables and 2 postscript figures, uses Kluwer's crckapb.sty
LaTeX style file, enclose
Alignment-free Genomic Analysis via a Big Data Spark Platform
Motivation: Alignment-free distance and similarity functions (AF functions,
for short) are a well established alternative to two and multiple sequence
alignments for many genomic, metagenomic and epigenomic tasks. Due to
data-intensive applications, the computation of AF functions is a Big Data
problem, with the recent Literature indicating that the development of fast and
scalable algorithms computing AF functions is a high-priority task. Somewhat
surprisingly, despite the increasing popularity of Big Data technologies in
Computational Biology, the development of a Big Data platform for those tasks
has not been pursued, possibly due to its complexity. Results: We fill this
important gap by introducing FADE, the first extensible, efficient and scalable
Spark platform for Alignment-free genomic analysis. It supports natively
eighteen of the best performing AF functions coming out of a recent hallmark
benchmarking study. FADE development and potential impact comprises novel
aspects of interest. Namely, (a) a considerable effort of distributed
algorithms, the most tangible result being a much faster execution time of
reference methods like MASH and FSWM; (b) a software design that makes FADE
user-friendly and easily extendable by Spark non-specialists; (c) its ability
to support data- and compute-intensive tasks. About this, we provide a novel
and much needed analysis of how informative and robust AF functions are, in
terms of the statistical significance of their output. Our findings naturally
extend the ones of the highly regarded benchmarking study, since the functions
that can really be used are reduced to a handful of the eighteen included in
FADE
Bayesian analysis of ages, masses, and distances to cool stars with non-LTE spectroscopic parameters
For studies of Galactic evolution, the accurate characterization of stars in
terms of their evolutionary stage and population membership is of fundamental
importance. A standard approach relies on extracting this information from
stellar evolution models but requires the effective temperature, surface
gravity, and metallicity of a star obtained by independent means. In previous
work, we determined accurate effective temperatures and non-LTE logg and [Fe/H]
(NLTE-Opt) for a large sample of metal-poor stars, -3<[Fe/H]<-0.5, selected
from the RAVE survey. As a continuation of that work, we derive here their
masses, ages, and distances using a Bayesian scheme and GARSTEC stellar tracks.
For comparison, we also use stellar parameters determined from the widely-used
1D LTE excitation-ionization balance of Fe (LTE-Fe). We find that the latter
leads to systematically underestimated stellar ages, by 10-30%, but
overestimated masses and distances. Metal-poor giants suffer from the largest
fractional distance biases of 70%. Furthermore, we compare our results with
those released by the RAVE collaboration for the stars in common (DR3, Zwitter
et al. 2010, Seibert et al. 2011). This reveals -400 to +400 K offsets in
effective temperature, -0.5 to 1.0 dex offsets in surface gravity, and 10 to
70% in distances. The systematic trends strongly resemble the correlation we
find between the NLTE-Opt and LTE-Fe parameters, indicating that the RAVE DR3
data may be affected by the physical limitations of the 1D LTE synthetic
spectra. Our results bear on any study, where spectrophotometric distances
underlie stellar kinematics. In particular, they shed new light on the debated
controversy about the Galactic halo origin raised by the SDSS/SEGUE
observations.Comment: 13 pages and 15 figures. Accepted for publication in MNRA
Building the cosmic distance scale: from Hipparcos to Gaia
Hipparcos, the first ever experiment of global astrometry, was launched by
ESA in 1989 and its results published in 1997 (Perryman et al., Astron.
Astrophys. 323, L49, 1997; Perryman & ESA (eds), The Hipparcos and Tycho
catalogues, ESA SP-1200, 1997). A new reduction was later performed using an
improved satellite attitude reconstruction leading to an improved accuracy for
stars brighter than 9th magnitude (van Leeuwen & Fantino, Astron. Astrophys.
439, 791, 2005; van Leeuwen, Astron. Astrophys. 474, 653, 2007).
The Hipparcos Catalogue provided an extended dataset of very accurate
astrometric data (positions, trigonometric parallaxes and proper motions),
enlarging by two orders of magnitude the quantity and quality of distance
determinations and luminosity calibrations. The availability of more than 20000
stars with a trigonometric parallax known to better than 10% opened the way to
a drastic revision of our 3-D knowledge of the solar neighbourhood and to a
renewal of the calibration of many distance indicators and age estimations. The
prospects opened by Gaia, the next ESA cornerstone, planned for launch in June
2013 (Perryman et al., Astron. Astrophys. 369, 339, 2001), are still much more
dramatic: a billion objects with systematic and quasi simultaneous astrometric,
spectrophotometric and spectroscopic observations, about 150 million stars with
expected distances to better than 10%, all over the Galaxy. All stellar
distance indicators, in very large numbers, will be directly measured,
providing a direct calibration of their luminosity and making possible detailed
studies of the impacts of various effects linked to chemical element
abundances, age or cluster membership. With the help of simulations of the data
expected from Gaia, obtained from the mission simulator developed by DPAC, we
will illustrate what Gaia can provide with some selected examples.Comment: 16 pages, 16 figures, Conference "The Fundamental Cosmic Distance
scale: State of the Art and the Gaia perspective, 3-6 May 2011, INAF,
Osservatorio Astronomico di Capodimonte, Naples. Accepted for publication in
Astrophysics & Space Scienc
Evolutionary distances in the twilight zone -- a rational kernel approach
Phylogenetic tree reconstruction is traditionally based on multiple sequence
alignments (MSAs) and heavily depends on the validity of this information
bottleneck. With increasing sequence divergence, the quality of MSAs decays
quickly. Alignment-free methods, on the other hand, are based on abstract
string comparisons and avoid potential alignment problems. However, in general
they are not biologically motivated and ignore our knowledge about the
evolution of sequences. Thus, it is still a major open question how to define
an evolutionary distance metric between divergent sequences that makes use of
indel information and known substitution models without the need for a multiple
alignment. Here we propose a new evolutionary distance metric to close this
gap. It uses finite-state transducers to create a biologically motivated
similarity score which models substitutions and indels, and does not depend on
a multiple sequence alignment. The sequence similarity score is defined in
analogy to pairwise alignments and additionally has the positive semi-definite
property. We describe its derivation and show in simulation studies and
real-world examples that it is more accurate in reconstructing phylogenies than
competing methods. The result is a new and accurate way of determining
evolutionary distances in and beyond the twilight zone of sequence alignments
that is suitable for large datasets.Comment: to appear in PLoS ON
IDENTIFICATION OF COVER SONGS USING INFORMATION THEORETIC MEASURES OF SIMILARITY
13 pages, 5 figures, 4 tables. v3: Accepted version13 pages, 5 figures, 4 tables. v3: Accepted version13 pages, 5 figures, 4 tables. v3: Accepted versio
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