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

The Influence of Spatial Resolution on Nonlinear Force-Free Modeling

The nonlinear force-free field (NLFFF) model is often used to describe the solar coronal magnetic field, however a series of earlier studies revealed difficulties in the numerical solution of the model in application to photospheric boundary data. We investigate the sensitivity of the modeling to the spatial resolution of the boundary data, by applying multiple codes that numerically solve the NLFFF model to a sequence of vector magnetogram data at different resolutions, prepared from a single Hinode/SOT-SP scan of NOAA Active Region 10978 on 2007 December 13. We analyze the resulting energies and relative magnetic helicities, employ a Helmholtz decomposition to characterize divergence errors, and quantify changes made by the codes to the vector magnetogram boundary data in order to be compatible with the force-free model. This study shows that NLFFF modeling results depend quantitatively on the spatial resolution of the input boundary data, and that using more highly resolved boundary data yields more self-consistent results. The free energies of the resulting solutions generally trend higher with increasing resolution, while relative magnetic helicity values vary significantly between resolutions for all methods. All methods require changing the horizontal components, and for some methods also the vertical components, of the vector magnetogram boundary field in excess of nominal uncertainties in the data. The solutions produced by the various methods are significantly different at each resolution level. We continue to recommend verifying agreement between the modeled field lines and corresponding coronal loop images before any NLFFF model is used in a scientific setting.Comment: Accepted to ApJ; comments/corrections to this article are welcome via e-mail, even after publicatio

Expression of a truncated form of hHb1 hair keratin in human breast carcinomas.

Human hHb1 belongs to the type II hard keratin family and is physiologically expressed in hair shafts. In the present study, using specific 3' and 5' probes for hHb1, we established that breast carcinomas ectopically express a hHb1 5'-truncated mRNA, and that this transcript is restricted to malignant epithelial cells. Furthermore, an in vitro study indicated that it could be translated. We concluded that, in breast carcinomas, expression of truncated hHb1 is related to epithelial cell transformation. Because the hHb1 gene maps to 12q11-q13, a chromosome region known to present several breakpoints in solid tumours, we propose that the hHb1 gene might represent a target for such alterations

Nonlinear force-free and potential field models of active-region and global coronal fields during the Whole Heliospheric Interval

Between 2008/3/24 and 2008/4/2, the three active regions NOAA active regions 10987, 10988 and 10989 were observed daily by the Synoptic Optical Long-term Investigations of the Sun (SOLIS) Vector Spectro-Magnetograph (VSM) while they traversed the solar disk. We use these measurements and the nonlinear force-free magnetic field code XTRAPOL to reconstruct the coronal magnetic field for each active region and compare model field lines with images from the Solar Terrestrial RElations Observatory (STEREO) and Hinode X-ray Telescope (XRT) telescopes. Synoptic maps made from continuous, round-the-clock Global Oscillations Network Group (GONG) magnetograms provide information on the global photospheric field and potential-field source-surface models based on these maps describe the global coronal field during the Whole Heliospheric Interval (WHI) and its neighboring rotations. Features of the modeled global field, such as the coronal holes and streamer belt locations, are discussed in comparison with extreme ultra-violet and coronagraph observations from STEREO. The global field is found to be far from a minimum, dipolar state. From the nonlinear models we compute physical quantities for the active regions such as the photospheric magnetic and electric current fluxes, the free magnetic energy and the relative helicity for each region each day where observations permit. The interconnectivity of the three regions is addressed in the context of the potential-field source-surface model. Using local and global quantities derived from the models, we briefly discuss the different observed activity levels of the regions.Comment: Accepted for publication in the Solar Physics Whole Heliospheric Interval (WHI) topical issue. We had difficulty squeezing this paper into arXiv's 15 Mb limit. The full paper is available here ftp://gong2.nso.edu/dsds_user/petrie/PetrieCanouAmari.pd

String Matching and 1d Lattice Gases

We calculate the probability distributions for the number of occurrences $n$ of a given $l$ letter word in a random string of $k$ letters. Analytical expressions for the distribution are known for the asymptotic regimes (i) $k \gg r^l \gg 1$ (Gaussian) and $k,l \to \infty$ such that $k/r^l$ is finite (Compound Poisson). However, it is known that these distributions do now work well in the intermediate regime $k \gtrsim r^l \gtrsim 1$. We show that the problem of calculating the string matching probability can be cast into a determining the configurational partition function of a 1d lattice gas with interacting particles so that the matching probability becomes the grand-partition sum of the lattice gas, with the number of particles corresponding to the number of matches. We perform a virial expansion of the effective equation of state and obtain the probability distribution. Our result reproduces the behavior of the distribution in all regimes. We are also able to show analytically how the limiting distributions arise. Our analysis builds on the fact that the effective interactions between the particles consist of a relatively strong core of size $l$, the word length, followed by a weak, exponentially decaying tail. We find that the asymptotic regimes correspond to the case where the tail of the interactions can be neglected, while in the intermediate regime they need to be kept in the analysis. Our results are readily generalized to the case where the random strings are generated by more complicated stochastic processes such as a non-uniform letter probability distribution or Markov chains. We show that in these cases the tails of the effective interactions can be made even more dominant rendering thus the asymptotic approximations less accurate in such a regime.Comment: 44 pages and 8 figures. Major revision of previous version. The lattice gas analogy has been worked out in full, including virial expansion and equation of state. This constitutes the main part of the paper now. Connections with existing work is made and references should be up to date now. To be submitted for publicatio

Large amplitude oscillatory motion along a solar filament

Large amplitude oscillations of solar filaments is a phenomenon known for more than half a century. Recently, a new mode of oscillations, characterized by periodical plasma motions along the filament axis, was discovered. We analyze such an event, recorded on 23 January 2002 in Big Bear Solar Observatory H$\alpha$ filtergrams, in order to infer the triggering mechanism and the nature of the restoring force. Motion along the filament axis of a distinct buldge-like feature was traced, to quantify the kinematics of the oscillatory motion. The data were fitted by a damped sine function, to estimate the basic parameters of the oscillations. In order to identify the triggering mechanism, morphological changes in the vicinity of the filament were analyzed. The observed oscillations of the plasma along the filament was characterized by an initial displacement of 24 Mm, initial velocity amplitude of 51 km/s, period of 50 min, and damping time of 115 min. We interpret the trigger in terms of poloidal magnetic flux injection by magnetic reconnection at one of the filament legs. The restoring force is caused by the magnetic pressure gradient along the filament axis. The period of oscillations, derived from the linearized equation of motion (harmonic oscillator) can be expressed as $P=\pi\sqrt{2}L/v_{A\phi}\approx4.4L/v_{A\phi}$, where $v_{A\phi} =B_{\phi0}/\sqrt{\mu_0\rho}$ represents the Alfv\'en speed based on the equilibrium poloidal field $B_{\phi0}$. Combination of our measurements with some previous observations of the same kind of oscillations shows a good agreement with the proposed interpretation.Comment: Astron. Astrophys., 2007, in pres

Bayesian Centroid Estimation for Motif Discovery

Biological sequences may contain patterns that are signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We present a Bayesian model that is an extended version of the model adopted by the Gibbs motif sampler, and propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the maximum a posteriori estimator.Comment: 24 pages, 9 figure

Sparkling extreme-ultraviolet bright dots observed with Hi-C

Observing the Sun at high time and spatial scales is a step toward understanding the finest and fundamental scales of heating events in the solar corona. The high-resolution coronal (Hi-C) instrument has provided the highest spatial and temporal resolution images of the solar corona in the EUV wavelength range to date. Hi-C observed an active region on 2012 July 11 that exhibits several interesting features in the EUV line at 193 Å. One of them is the existence of short, small brightenings "sparkling" at the edge of the active region; we call these EUV bright dots (EBDs). Individual EBDs have a characteristic duration of 25 s with a characteristic length of 680 km. These brightenings are not fully resolved by the SDO/AIA instrument at the same wavelength; however, they can be identified with respect to the Hi-C location of the EBDs. In addition, EBDs are seen in other chromospheric/coronal channels of SDO/AIA, which suggests a temperature between 0.5 and 1.5 MK. Based on their frequency in the Hi-C time series, we define four different categories of EBDs: single peak, double peak, long duration, and bursty. Based on a potential field extrapolation from an SDO/HMI magnetogram, the EBDs appear at the footpoints of large-scale, trans-equatorial coronal loops. The Hi-C observations provide the first evidence of small-scale EUV heating events at the base of these coronal loops, which have a free magnetic energy of the order of 1026 erg. © 2014. The American Astronomical Society. All rights reserved

Site effect variability of the Roio basin in the near-source area of the L'Aquila mainshock

In the frame of the microzonation studies of the April 6th, 2009 L'Aquila earthquake near-source area, we observed local seismic amplifications in the Roio area, a plain separated from L'Aquila city center by mount Luco. Six portable, digital instruments were deployed across the plain from the 15th of April until mid-May 2009. This array recorded up to 152 aftershocks. We analysed the ground motion from these events to determine relative site amplification within the plain and on the surrounding ridges. Horizontal over Vertical spectral ratio on noise data (HVSRN) and on aftershock recordings (HVEQ)as well as standard spectral ratio (SSR) show amplifications at 1.3 Hz and 4.0 Hz on the quaternary deposits. Seismic amplifications in the frequency range between 4 and 6 Hz were also observed on a carbonate ridge of Colle di Roio located on the northwest border of the plateau. A small amplification has also been noticed close to the top of mount Luco, another rocky site. This paper details the results we have obtained and addresses their interpretation.Submitted4.1. Metodologie sismologiche per l'ingegneria sismicaJCR Journalope

On the period ratio P₁/2P₂ in the oscillations of coronal loops

<p>Aims. With strong evidence of fast and slow magnetoacoustic modes arising in the solar atmosphere there is scope for improved determinations of coronal parameters through coronal seismology. Of particular interest is the ratio P<sub>1</sub>/2P<sub>2</sub>between the period P<sub>1</sub> of the fundamental mode and the period P<sub>2</sub> of its first harmonic; in an homogeneous medium this ratio is one, but in a more complex configuration it is shifted to lower values.</p> <p>Methods. We consider analytically the effects on the different magnetohydrodynamic modes of structuring and stratification, pointing out that transverse or longitudinal structuring or gravitational stratification modifies the ratio P<sub>1</sub>/2P<sub>2</sub>.</p> <p>Results. The deviations caused by gravity and structure are studied for the fast and slow modes. Structure along the loop is found to be the dominant effect.</p> <p>Conclusions. The departure of P<sub>1</sub>/2P<sub>2</sub> from unity can be used as a seismological tool in the corona. We apply our technique to the observations by Verwichte et al. (2004), deducing the density scale height in a coronal loop.</p&gt