115,927 research outputs found
A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances
Spaced seeds have been recently shown to not only detect more alignments, but
also to give a more accurate measure of phylogenetic distances (Boden et al.,
2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower
misclassification rate when used with Support Vector Machines (SVMs) (On-odera
and Shibuya, 2013), We confirm by independent experiments these two results,
and propose in this article to use a coverage criterion (Benson and Mak, 2008,
Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both
cases in order to design better seed patterns. We show first how this coverage
criterion can be directly measured by a full automaton-based approach. We then
illustrate how this criterion performs when compared with two other criteria
frequently used, namely the single-hit and multiple-hit criteria, through
correlation coefficients with the correct classification/the true distance. At
the end, for alignment-free distances, we propose an extension by adopting the
coverage criterion, show how it performs, and indicate how it can be
efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017
Distributions associated with general runs and patterns in hidden Markov models
This paper gives a method for computing distributions associated with
patterns in the state sequence of a hidden Markov model, conditional on
observing all or part of the observation sequence. Probabilities are computed
for very general classes of patterns (competing patterns and generalized later
patterns), and thus, the theory includes as special cases results for a large
class of problems that have wide application. The unobserved state sequence is
assumed to be Markovian with a general order of dependence. An auxiliary Markov
chain is associated with the state sequence and is used to simplify the
computations. Two examples are given to illustrate the use of the methodology.
Whereas the first application is more to illustrate the basic steps in applying
the theory, the second is a more detailed application to DNA sequences, and
shows that the methods can be adapted to include restrictions related to
biological knowledge.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS125 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Voyager electronic parts radiation program, volume 1
The Voyager spacecraft is subject to radiation from external natural space, from radioisotope thermoelectric generators and heater units, and from the internal environment where penetrating electrons generate surface ionization effects in semiconductor devices. Methods for radiation hardening and tests for radiation sensitivity are described. Results of characterization testing and sample screening of over 200 semiconductor devices in a radiation environment are summarized
Selecting fast folding proteins by their rate of convergence
We propose a general method for predicting potentially good folders from a
given number of amino acid sequences. Our approach is based on the calculation
of the rate of convergence of each amino acid chain towards the native
structure using only the very initial parts of the dynamical trajectories. It
does not require any preliminary knowledge of the native state and can be
applied to different kinds of models, including atomistic descriptions. We
tested the method within both the lattice and off-lattice model frameworks and
obtained several so far unknown good folders. The unbiased algorithm also
allows to determine the optimal folding temperature and takes at least 3--4
orders of magnitude less time steps than those needed to compute folding times
Cryogenic seal remains leaktight during thermal displacement
Cryogenic seals protect the surfaces of a plastic member in a low-pressure system subjected to extreme temperature changes. The outer seal is an aluminum expansion ring bonded to the lens outer surface and the inner seal consists of a resin-filled aluminum U-ring bonded to the inner surface
Voyager electronic parts radiation program. Volume 2: Test requirements and procedures
Documents are presented outlining the conditions and requirements of the test program. The Appendixes are as follows: appendix A -- Electron Simulation Radiation Test Specification for Voyager Electronic Parts and Devices, appendix B -- Electronic Piece-Part Testing Program for Voyager, appendix C -- Test Procedure for Radiation Screening of Voyager Piece Parts, appendix D -- Boeing In Situ Test Fixture, and appendix E -- Irradiate - Anneal (IRAN) Screening Documents
Leaky vessels as a potential source of stromal acidification in tumours
Malignant tumours are characterised by higher rates of acid production and a lower extracellular pH than normal tissues. Previous mathematical modelling has indicated that the tumour-derived production of acid leads to a gradient of low pH in the interior of the tumour extending to a normal pH in the peritumoural tissue. This paper uses mathematical modelling to examine the potential of leaky vessels as an additional source of stromal acidification in tumours. We explore whether and to what extent increasing vascular permeability in vessels can lead to the breakdown of the acid gradient from the core of the tumour to the normal tissue, and a progressive acidification of the peritumoural stroma. We compare our mathematical simulations to experimental results found in vivo with a tumour implanted in the mammary fat pad of a mouse in a window chamber construct. We find that leaky vasculature can cause a net acidification of the normal tissue away from the tumour boundary, though not a progressive acidification over time as seen in the experiments. Only through progressively increasing the leakiness can the model qualitatively reproduce the experimental results. Furthermore, the extent of the acidification predicted by the mathematical model is less than as seen in the window chamber, indicating that although vessel leakiness might be acting as a source of acid, it is not the only factor contributing to this phenomenon. Nevertheless, tumour destruction of vasculature could result in enhanced stromal acidification and invasion, hence current therapies aimed at buffering tumour pH should also examine the possibility of preventing vessel disruption
Helical Magnetic Fields from Inflation
We analyze the generation of seed magnetic fields during de Sitter inflation
considering a non-invariant conformal term in the electromagnetic Lagrangian of
the form , where
is a pseudoscalar function of a non-trivial background field .
In particular, we consider a toy model, that could be realized owing to the
coupling between the photon and either a (tachyonic) massive pseudoscalar field
and a massless pseudoscalar field non-minimally coupled to gravity, where
follows a simple power-law behavior during
inflation, while it is negligibly small subsequently. Here, is a positive
dimensionless constant, the wavenumber, the conformal time, and
a real positive number. We find that only when and astrophysically interesting fields can be produced as
excitation of the vacuum, and that they are maximally helical.Comment: 17 pages, 1 figure, subsection IIc and references added; accepted for
publication in IJMP
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