A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Terahertz epsilon-near-zero graded-index lens

An epsilon-near-zero graded-index converging lens with planar faces is proposed and analyzed. Each perfectly-electric conducting (PEC) waveguide comprising the lens operates slightly above its cut-off frequency and has the same length but different cross-sectional dimensions. This allows controlling individually the propagation constant and the normalized characteristic impedance of each waveguide for the desired phase front at the lens output while Fresnel reflection losses are minimized. A complete theoretical analysis based on the waveguide theory and Fermat’s principle is provided. This is complemented with numerical simulation results of two-dimensional and three-dimensional lenses, made of PEC and aluminum, respectively, and working in the terahertz regime, which show good agreement with the analytical work.Effort sponsored by Spanish Government under contracts Consolider “Engineering Metamaterials” CSD2008-00066 and TEC2011-28664-C02-01. P.R.-U. is sponsored by the Government of Navarra under funding program “Formación de tecnólogos” 055/01/11. M.N.- C. is supported by the Imperial College Junior Research Fellowship. M. B. acknowledges funding by the Spanish Government under the research contract program Ramon y Cajal RYC-2011-08221. N.E. acknowledges the support from the US Office of Naval Research (ONR) Multidisciplinary University Research Initiatives (MURI) grant number N00014-10-1- 0942

Reliable scaling of position weight matrices for binding strength comparisons between transcription factors

Background: Scoring DNA sequences against PositionWeight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between a specific transcription factor and the DNA, these scores are not directly comparable between different transcription factors. Other methods, including p-value associated approaches (Touzet H, Varré J-S. Efficient and accurate p-value computation for position weight matrices. Algorithms Mol Biol. 2007;2(1510.1186):1748–7188), provide more rigorous ways to identify potential binding sites, but their results are difficult to interpret in terms of binding energy, which is essential for the modeling of transcription factor binding dynamics and enhancer activities. Results: Here, we provide two different ways to find the scaling parameter λ that allows us to infer binding energy from a PWM score. The first approach uses a PWM and background genomic sequence as input to estimate λ for a specific transcription factor, which we applied to show that λ distributions for different transcription factor families correspond with their DNA binding properties. Our second method can reliably convert λ between different PWMs of the same transcription factor, which allows us to directly compare PWMs that were generated by different approaches. Conclusion: These two approaches provide computationally efficient ways to scale PWM scores and estimate the strength of transcription factor binding sites in quantitative studies of binding dynamics. Their results are consistent with each other and previous reports in most of cases.Chinese Scholarship Council (CSC) ScholarshipMarshall ScholarshipDGICT, Madrid TIN2013-41990-RRoyal Society of Londo

Galaxy-Induced Transformation of Dark Matter Halos

We use N-body/gasdynamical LambdaCDM cosmological simulations to examine the effect of the assembly of a central galaxy on the shape and mass profile of its dark halo. Two series of simulations are compared; one that follows only the evolution of the dark matter component and a second one where a baryonic component is added. These simulations include radiative cooling but neglect star formation and feedback, leading most baryons to collect at the halo center in a disk which is too small and too massive when compared with typical spiral. This unrealistic model allows us, nevertheless, to gauge the maximum effect that galaxies may have in transforming their dark halos. We find that the shape of the halo becomes more axisymmetric: halos are transformed from triaxial into essentially oblate systems, with well-aligned isopotential contours of roughly constant flattening (c/a ~ 0.85). Halos always contract as a result of galaxy assembly, but the effect is substantially less pronounced than predicted by the "adiabatic contraction" hypothesis. The reduced contraction helps to reconcile LambdaCDM halos with constraints on the dark matter content inside the solar circle and should alleviate the long-standing difficulty of matching simultaneously the scaling properties of galaxy disks and the luminosity function. The halo contraction is also less pronounced than found in earlier simulations, a disagreement that suggests that halo contraction is not solely a function of the initial and final distribution of baryons. Not only how much baryonic mass has been deposited at the center of a halo matters, but also the mode of its deposition. It might prove impossible to predict the halo response without a detailed understanding of a galaxy's assembly history. (Abriged)Comment: 11 pages and 9 figure

Phages in the human body

Bacteriophages, viruses that infect bacteria, have re-emerged as powerful regulators of bacterial populations in natural ecosystems. Phages invade the human body, just as they do other natural environments, to such an extent that they are the most numerous group in the human virome. This was only revealed in recent metagenomic studies, despite the fact that the presence of phages in the human body was reported decades ago. The influence of the presence of phages in humans has yet to be evaluated; but as in marine environments, a clear role in the regulation of bacterial populations could be envisaged, that might have an impact on human health. Moreover, phages are excellent vehicles of genetic transfer, and they contribute to the evolution of bacterial cells in the human body by spreading and acquiring DNA horizontally. The abundance of phages in the human body does not pass unnoticed and the immune system reacts to them, although it is not clear to what extent. Finally, the presence of phages in human samples, which most of the time is not considered, can influence and bias microbiological and molecular results; and, in view of the evidences, some studies suggest that more attention needs to be paid to their interference

Adaptive Shape Servoing of Elastic Rods using Parameterized Regression Features and Auto-Tuning Motion Controls

In this paper, we present a new vision-based method to control the shape of elastic rods with robot manipulators. Our new method computes parameterized regression features from online sensor measurements that enable to automatically quantify the object's configuration and establish an explicit shape servo-loop. To automatically deform the rod into a desired shape, our adaptive controller iteratively estimates the differential transformation between the robot's motion and the relative shape changes; This valuable capability allows to effectively manipulate objects with unknown mechanical models. An auto-tuning algorithm is introduced to adjust the robot's shaping motion in real-time based on optimal performance criteria. To validate the proposed theory, we present a detailed numerical and experimental study with vision-guided robotic manipulators.Comment: 13 pages, 22 figures, 2 table

The joint evolution of baryons and dark matter haloes

We have studied the dark matter (DM) distribution in a approx 10^12 h^-1 M_sun mass halo extracted from a simulation consistent with the concordance cosmology, where the physics regulating the transformation of gas into stars was allowed to change producing galaxies with different morphologies. The presence of baryons produces the concentration of the DM halo with respect to its corresponding dissipationless run, but we found that this response does not only depend on the amount of baryons gathered in the central region but also on the way they have been assembled. DM and baryons affect each other in a complex way so the formation history of a galaxy plays an important role on its final total mass distribution. Supernova (SN) feedback regulates the star formation and triggers galactic outflows not only in the central galaxy but also in its satellites. Our results suggest that, as the effects of SN feedback get stronger, satellites get less massive and can even be more easily disrupted by dynamical friction, transferring less angular momentum. We found indications that this angular momentum could be acquired not only by the outer part of the DM halo but also by the inner ones and by the stellar component in the central galaxy. The latter effect produces stellar migration which contributes to change the inner potential well, probably working against further DM contraction. As a consequence of the action of these processes, when the halo hosts a galaxy with an important disc structure formed by smooth gas accretion, it is more concentrated than when it hosts a spheroidal system which experienced more massive mergers and interactions. (abridged)Comment: 16 pages, 16 figures, accepted to MNRA

Constraining Dark Energy From Splitting Angle Statistic of Strong Gravitational Lenses

Utilizing the CLASS statistical sample, we investigate the constraint of the splitting angle statistic of strong gravitational lenses(SGL) on the equation-of-state parameter $w=p/\rho$ of the dark energy in the flat cold dark matter cosmology. Through the comoving number density of dark halos described by Press-Schechter theory, dark energy affects the efficiency with which dark-matter concentrations produce strong lensing signals. The constraints on both constant $w$ and time-varying $w(z)=w_0+w_az/(1+z)$ from the SGL splitting angle statistic are consistently obtained by adopting a two model combined mechanism of dark halo density profile matched at the mass scale $M_c$. Our main observations are: (a) the resulting model parameter $M_c$ is found to be $M_c \sim 1.4$ for both constant $w$ and time-varying $w(z)$, which is larger than $M_c \sim 1$ obtained in literatures; (b) the fitting results for the constant $w$ are found to be $w =-0.89^{+0.49}_{-0.26}$ and $w =-0.94^{+0.57}_{-0.16}$ for the source redshift distributions of the Gaussian models $g(z_s)$ and $g^c(z_s)$ respectively, which are consistent with the $\Lambda \rm CDM$ at 95% C.L; (c) the time-varying $w(z)$ is found to be for $\sigma_8 = 0.74$: $(M_c; w_0, w_a)=(1.36; -0.92, -1.31)$ and $(M_c; w_0, w_a)=(1.38; -0.89, -1.21)$ for $g(z_s)$ and $g^c(z_s)$ respectively.Comment: 30 pages, 10 figures, references added, improved version to be published in Ap