Identifying short motifs by means of extreme value analysis

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: (a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.Comment: 6 pages, 5 figure

Simple model for quantum general relativity from loop quantum gravity

New progress in loop gravity has lead to a simple model of `general-covariant quantum field theory'. I sum up the definition of the model in self-contained form, in terms accessible to those outside the subfield. I emphasize its formulation as a generalized topological quantum field theory with an infinite number of degrees of freedom, and its relation to lattice theory. I list the indications supporting the conjecture that the model is related to general relativity and UV finite.Comment: 8 pages, 3 figure

Competing with stationary prediction strategies

In this paper we introduce the class of stationary prediction strategies and construct a prediction algorithm that asymptotically performs as well as the best continuous stationary strategy. We make mild compactness assumptions but no stochastic assumptions about the environment. In particular, no assumption of stationarity is made about the environment, and the stationarity of the considered strategies only means that they do not depend explicitly on time; we argue that it is natural to consider only stationary strategies even for highly non-stationary environments.Comment: 20 page

The Collaborative Development of New CFD Methods Adapted for Tilt Rotor Aircraft in the HiPerTilt Project

No abstract available

Low energy onset of nuclear shadowing in photoabsorption

The early onset of nuclear shadowing in photoabsorption at low photon energies has recently been interpreted as a possible signature of a decrease of the rho meson mass in nuclei. We show that one can understand this early onset within simple Glauber theory if one takes the negative real part of the rho N scattering amplitudes into account, corresponding to a higher effective mass of the rho meson in nuclear medium.Comment: REVTEX, 9 pages, including 4 eps figure

Evidence for spin liquid ground state in SrDy2_2O4_4 frustrated magnet probed by muSR

Muon spin relaxation ($\mu$SR) measurements were carried out on SrDy$_2$O$_4$, a frustrated magnet featuring short range magnetic correlations at low temperatures. Zero-field muon spin depolarization measurements demonstrate that fast magnetic fluctuations are present from $T=300$ K down to 20 mK. The coexistence of short range magnetic correlations and fluctuations at $T=20$ mK indicates that SrDy$_2$O$_4$ features a spin liquid ground state. Large longitudinal fields affect weakly the muon spin depolarization, also suggesting the presence of fast fluctuations. For a longitudinal field of $\mu_0H=2$ T, a non-relaxing asymmetry contribution appears below $T=6$ K, indicating considerable slowing down of the magnetic fluctuations as field-induced magnetically-ordered phases are approached.Comment: 6 pages, 4 figures, to be published as a proceeding of HFM2016 in Journal of Physics: Conference Series (JPCS

Probing 3-D matter distribution at z~2 with QSO multiple lines of sight

We investigate the 3-D matter distribution at z~2 with high resolution (R ~ 40000) spectra of QSO pairs and groups obtained with the UVES spectrograph at ESO VLT. Our sample is unique for the number density of objects and the variety of separations, between 0.5 and 7 proper Mpc. We compute the real space cross-correlation function of the Lyman-alpha forest transmitted fluxes. There is a significant clustering signal up to ~2 proper Mpc, which is still present when absorption lines with high column density (log N > 13.8) are excluded.Comment: Poster paper presented at the IAU Colloquium #199 on "Probing Galaxies through Quasar Absorption Lines" held in Shanghai, China from March 14th to 18th, 200

Tomography of the intergalactic medium with Ly-alpha forests in close QSO pairs

We study the three-dimensional distribution of non virialised matter at z~2 using high resolution spectra of QSO pairs and simulated spectra drawn from cosmological hydrodynamical simulations. We have collected the largest sample of QSO pairs ever observed with UVES at the ESO-VLT, with angular separations between ~1 and 14 arcmin. The observed correlation functions of the transmitted flux in the HI Lyman alpha forest along and transverse to the lines of sight are in good agreement implying that the distortions in redshift space due to peculiar velocities are small. The clustering signal is significant up to velocity separations of ~200 km/s, or about 3 h^{-1} comoving Mpc. The regions at lower overdensity (rho/ < 6.5) are still clustered but on smaller scales (Delta v < 100 km/s). The observed and simulated correlation functions are compatible at the 3 sigma level. A better concordance is obtained when only the low overdensity regions are selected for the analysis or when the effective optical depth of the simulated spectra is increased artificially, suggesting a deficiency of strong lines in the simulated spectra. We found that also a lower value of the power-law index of the temperature-density relation for the Lyman alpha forest gas improves the agreement between observed and simulated results. If confirmed, this would be consistent with other observations favouring a late HeII reionization epoch (at z~3). We remark the detection of a significant clustering signal in the cross correlation coefficient at a transverse velocity separation Delta v_{\perp} ~500 km/s whose origin needs further investigation.Comment: Accepted for publication in MNRAS, revised version matching the accepted on

Leading strategies in competitive on-line prediction

We start from a simple asymptotic result for the problem of on-line regression with the quadratic loss function: the class of continuous limited-memory prediction strategies admits a "leading prediction strategy", which not only asymptotically performs at least as well as any continuous limited-memory strategy but also satisfies the property that the excess loss of any continuous limited-memory strategy is determined by how closely it imitates the leading strategy. More specifically, for any class of prediction strategies constituting a reproducing kernel Hilbert space we construct a leading strategy, in the sense that the loss of any prediction strategy whose norm is not too large is determined by how closely it imitates the leading strategy. This result is extended to the loss functions given by Bregman divergences and by strictly proper scoring rules.Comment: 20 pages; a conference version is to appear in the ALT'2006 proceeding