203 research outputs found
Design features and results from fatigue reliability research machines
Design and performance tests for reversed bending with steady torque fatigue test machine using notched steel specimen
Online Pattern Matching for String Edit Distance with Moves
Edit distance with moves (EDM) is a string-to-string distance measure that
includes substring moves in addition to ordinal editing operations to turn one
string to the other. Although optimizing EDM is intractable, it has many
applications especially in error detections. Edit sensitive parsing (ESP) is an
efficient parsing algorithm that guarantees an upper bound of parsing
discrepancies between different appearances of the same substrings in a string.
ESP can be used for computing an approximate EDM as the L1 distance between
characteristic vectors built by node labels in parsing trees. However, ESP is
not applicable to a streaming text data where a whole text is unknown in
advance. We present an online ESP (OESP) that enables an online pattern
matching for EDM. OESP builds a parse tree for a streaming text and computes
the L1 distance between characteristic vectors in an online manner. For the
space-efficient computation of EDM, OESP directly encodes the parse tree into a
succinct representation by leveraging the idea behind recent results of a
dynamic succinct tree. We experimentally test OESP on the ability to compute
EDM in an online manner on benchmark datasets, and we show OESP's efficiency.Comment: This paper has been accepted to the 21st edition of the International
Symposium on String Processing and Information Retrieval (SPIRE2014
Inferring a DNA sequence from erroneous copies
AbstractWe suggest a novel approach for efficiently reconstructing an original DNA sequence from erroneous copies
Observation of Sommerfeld precursors on a fluid surface
We report the observation of two types of Sommerfeld precursors (or
forerunners) on the surface of a layer of mercury. When the fluid depth
increases, we observe a transition between these two precursor surface waves in
good agreement with the predictions of asymptotic analysis. At depths thin
enough compared to the capillary length, high frequency precursors propagate
ahead of the ''main signal'' and their period and amplitude, measured at a
fixed point, increase in time. For larger depths, low frequency ''precursors''
follow the main signal with decreasing period and amplitude. These behaviors
are understood in the framework of the analysis first introduced for linear
transient electromagnetic waves in a dielectric medium by Sommerfeld and
Brillouin [1].Comment: to be published in Physical Review Letter
In search of lost introns
Many fundamental questions concerning the emergence and subsequent evolution
of eukaryotic exon-intron organization are still unsettled. Genome-scale
comparative studies, which can shed light on crucial aspects of eukaryotic
evolution, require adequate computational tools.
We describe novel computational methods for studying spliceosomal intron
evolution. Our goal is to give a reliable characterization of the dynamics of
intron evolution. Our algorithmic innovations address the identification of
orthologous introns, and the likelihood-based analysis of intron data. We
discuss a compression method for the evaluation of the likelihood function,
which is noteworthy for phylogenetic likelihood problems in general. We prove
that after preprocessing time, subsequent evaluations take time almost surely in the Yule-Harding random model of -taxon
phylogenies, where is the input sequence length.
We illustrate the practicality of our methods by compiling and analyzing a
data set involving 18 eukaryotes, more than in any other study to date. The
study yields the surprising result that ancestral eukaryotes were fairly
intron-rich. For example, the bilaterian ancestor is estimated to have had more
than 90% as many introns as vertebrates do now
High proportion of genetic cases in patients with advanced cardiomyopathy including a novel homozygous Plakophilin 2-gene mutation
Dependence of paracentric inversion rate on tract length
BACKGROUND: We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths. RESULTS: We apply the method to data from Drosophila melanogaster and D. yakuba. We find that pericentric inversions occur at a much lower rate compared to paracentric inversions. The average paracentric inversion tract length is approx. 4.8 Mb with small inversions being more frequent than large inversions. If the two breakpoints defining a paracentric inversion tract are uniformly and independently distributed over chromosome arms there will be more short tract-length inversions than long; we find an even greater preponderance of short tract lengths than this would predict. Thus there appears to be a correlation between the positions of breakpoints which favors shorter tract lengths. CONCLUSION: The method developed in this paper provides the first statistical estimator for estimating the distribution of inversion tract lengths from marker data. Application of this method for a number of data sets may help elucidate the relationship between the length of an inversion and the chance that it will get accepted
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