367 research outputs found
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm
In this work, we consider the Combinatorial RNA Design problem, a minimal
instance of the RNA design problem which aims at finding a sequence that admits
a given target as its unique base pair maximizing structure. We provide
complete characterizations for the structures that can be designed using
restricted alphabets. Under a classic four-letter alphabet, we provide a
complete characterization of designable structures without unpaired bases. When
unpaired bases are allowed, we provide partial characterizations for classes of
designable/undesignable structures, and show that the class of designable
structures is closed under the stutter operation. Membership of a given
structure to any of the classes can be tested in linear time and, for positive
instances, a solution can be found in linear time. Finally, we consider a
structure-approximating version of the problem that allows to extend bands
(helices) and, assuming that the input structure avoids two motifs, we provide
a linear-time algorithm that produces a designable structure with at most twice
more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun
2015, Ischia Island, Italy. LNCS, 201
Development of High Ic Long REBCO Tapes with High Production Rate by PLD Method
AbstractWe have been developing long REBa2Cu3O7-δ coated conductors with high performance by the combination of the IBAD and the PLD methods. To realize the low production cost for REBa2Cu3O7-δ coated conductors, growth conditions were optimized for long tape fabrication in the “in-plume PLD method”. As a result, the Ic performance was confirmed with a high production rate under the high oxygen gas pressure and high laser energy density of > 800 mTorr and > 3J/cm2, respectively. We successfully fabricated a 35 m long GdBa2Cu3O7-δ coated conductor with high Ic value of 619 A/cm-w by the production rate of 30 m/h
Rational solutions of the discrete time Toda lattice and the alternate discrete Painleve II equation
The Yablonskii-Vorob'ev polynomials , which are defined by a second
order bilinear differential-difference equation, provide rational solutions of
the Toda lattice. They are also polynomial tau-functions for the rational
solutions of the second Painlev\'{e} equation (). Here we define
two-variable polynomials on a lattice with spacing , by
considering rational solutions of the discrete time Toda lattice as introduced
by Suris. These polynomials are shown to have many properties that are
analogous to those of the Yablonskii-Vorob'ev polynomials, to which they reduce
when . They also provide rational solutions for a particular
discretisation of , namely the so called {\it alternate discrete}
, and this connection leads to an expression in terms of the Umemura
polynomials for the third Painlev\'{e} equation (). It is shown that
B\"{a}cklund transformation for the alternate discrete Painlev\'{e} equation is
a symplectic map, and the shift in time is also symplectic. Finally we present
a Lax pair for the alternate discrete , which recovers Jimbo and Miwa's
Lax pair for in the continuum limit .Comment: 23 pages, IOP style. Title changed, and connection with Umemura
polynomials adde
Creating drag and lift curves from soccer trajectories
Trajectory analysis is an alternative to using wind tunnels to measure a soccer
balls aerodynamic properties. It has advantages over wind tunnel testing such as being
more representative of game play. However, previous work has not presented a method that
produces complete, speed -dependent drag and lift coefficients. Four high-speed cameras in
stereo-calibrated pairs were used to measure the spatial co-ordinates for 29 separate soccer
trajectories. Those trajectories span a range of launch speeds from 9.3 m/s to 29.9 m/s. That
range encompasses low-speed laminar flow of air over a soccer ball, through the drag crises
where air flow is both laminar and turbulent, and up to high-speed turbulent air flow. Results
from trajectory analysis were combined to give speed-dependent drag and lift coefficient
curves for the entire range of speeds found in the 29 trajectories. Average root mean square
error between measured and modelled trajectory was 0.028 m horizontally and 0.034 m
vertically. The drag and lift crises can be observed in the plots of drag and lift coefficients
respectively
Occurrence and impact of delayed cerebral ischemia after coiling and after clipping in the International Subarachnoid Aneurysm Trial (ISAT)
Delayed cerebral ischemia (DCI) is an important cause of poor outcome after aneurysmal subarachnoid hemorrhage (SAH). We studied differences in incidence and impact of DCI as defined clinically after coiling and after clipping in the International Subarachnoid Aneurysm Trial. We calculated odds ratios (OR) for DCI for clipping versus coiling with logistic regression analysis. With coiled patients without DCI as the reference group, we calculated ORs for poor outcome at 2 months and 1 year for coiled patients with DCI and for clipped patients without, and with DCI. With these ORs, we calculated relative excess risk due to Interaction (RERI). Clipping increased the risk of DCI compared to coiling in the 2,143 patients OR 1.24, 95% confidence interval (95% CI 1.01–1.51). Coiled patients with DCI, clipped patients without DCI, and clipped patients with DCI all had higher risks of poor outcome than coiled patients without DCI. Clipping and DCI showed no interaction for poor outcome at 2 months: RERI 0.12 (95% CI −1.16 to 1.40) or 1 year: RERI −0.48 (95% CI −1.69 to 0.74). Only for patients treated within 4 days, coiling and DCI was associated with a poorer outcome at 1 year than clipping and DCI (RERI −2.02, 95% CI −3.97 to −0.08). DCI was more common after clipping than after coiling in SAH patients in ISAT. Impact of DCI on poor outcome did not differ between clipped and coiled patients, except for patients treated within 4 days, in whom DCI resulted more often in poor outcome after coiling than after clipping
Subtropical mode water variability in a climatologically forced model in the northwestern Pacific Ocean
Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 42 (2012): 126–140, doi:10.1175/2011JPO4513.1.A climatologically forced high-resolution model is used to examine variability of subtropical mode water (STMW) in the northwestern Pacific Ocean. Despite the use of annually repeating atmospheric forcing, significant interannual to decadal variability is evident in the volume, temperature, and age of STMW formed in the region. This long time-scale variability is intrinsic to the ocean. The formation and characteristics of STMW are comparable to those observed in nature. STMW is found to be cooler, denser, and shallower in the east than in the west, but time variations in these properties are generally correlated across the full water mass. Formation is found to occur south of the Kuroshio Extension, and after formation STMW is advected westward, as shown by the transport streamfunction. The ideal age and chlorofluorocarbon tracers are used to analyze the life cycle of STMW. Over the full model run, the average age of STMW is found to be 4.1 yr, but there is strong geographical variation in this, from an average age of 3.0 yr in the east to 4.9 yr in the west. This is further evidence that STMW is formed in the east and travels to the west. This is qualitatively confirmed through simulated dye experiments known as transit-time distributions. Changes in STMW formation are correlated with a large meander in the path of the Kuroshio south of Japan. In the model, the large meander inhibits STMW formation just south of Japan, but the export of water with low potential vorticity leads to formation of STMW in the east and an overall increase in volume. This is correlated with an increase in the outcrop area of STMW. Mixed layer depth, on the other hand, is found to be uncorrelated with the volume of STMW.E.M.D. acknowledges support of the
Doherty Foundation and National Science Foundation
(OCE-0849808). S.R.J was sponsored by the National
Science Foundation (OCE-0849808). Participation of
S.P. and F.B. was supported by the National Science
Foundation by its sponsorship of the National Center for
Atmospheric Research.2012-07-0
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast
<p>Abstract</p> <p>Background</p> <p>Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA) discovery.</p> <p>Results</p> <p>We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared <it>S. cerevisiae </it>genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp) sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%). By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences.</p> <p>Conclusion</p> <p>The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.</p
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