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 $-\frac14 I(\phi) F_{\mu \nu} \widetilde{F}^{\mu \nu}$, where $I(\phi)$ is a pseudoscalar function of a non-trivial background field $\phi$. 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 $I$ follows a simple power-law behavior $I(k,\eta) = g/(-k\eta)^{\beta}$ during inflation, while it is negligibly small subsequently. Here, $g$ is a positive dimensionless constant, $k$ the wavenumber, $\eta$ the conformal time, and $\beta$ a real positive number. We find that only when $\beta = 1$ and $0.1 \lesssim g \lesssim 2$ 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