Summarizing a set of time series by averaging: From Steiner sequence to compact multiple alignment

AbstractSummarizing a set of sequences is an old topic that has been revived in the last decade, due to the increasing availability of sequential datasets. The definition of a consensus object is on the center of data analysis issues, since it crystallizes the underlying organization of the data.Dynamic Time Warping (DTW) is currently the most relevant similarity measure between sequences for a large panel of applications, since it makes it possible to capture temporal distortions. In this context, averaging a set of sequences is not a trivial task, since the average sequence has to be consistent with this similarity measure.The Steiner theory and several works in computational biology have pointed out the connection between multiple alignments and average sequences. Taking inspiration from these works, we introduce the notion of compact multiple alignment, which allows us to link these theories to the problem of summarizing under time warping. Having defined the link between the multiple alignment and the average sequence, the second part of this article focuses on the scan of the space of compact multiple alignments in order to provide an average sequence of a set of sequences. We propose to use a genetic algorithm based on a specific representation of the genotype inspired by genes. This representation of the genotype makes it possible to consistently paint the fitness landscape.Experiments carried out on standard datasets show that the proposed approach outperforms existing methods

Graphene-based heterojunction between two topological insulators

Quantum Hall (QH) and quantum spin Hall (QSH) phases have very different edge states and, when going from one phase to the other, the direction of one edge state must be reversed. We study this phenomena in graphene in presence of a strong perpendicular magnetic field on top of a spin-orbit (SO) induced QSH phase. We show that, below the SO gap, the QSH phase is virtually unaffected by the presence of the magnetic field. Above the SO gap, the QH phase is restored. An electrostatic gate placed on top of the system allows to create a QSH-QH junction which is characterized by the existence of a spin-polarized chiral state, propagating along the topological interface. We find that such a setup naturally provides an extremely sensitive spin-polarized current switch.Comment: 10 pages, 5 figure

New reaction rates for improved primordial D/H calculation and the cosmic evolution of deuterium

Primordial or big bang nucleosynthesis (BBN) is one of the three historical strong evidences for the big bang model. Standard BBN is now a parameter free theory, since the baryonic density of the Universe has been deduced with an unprecedented precision from observations of the anisotropies of the cosmic microwave background (CMB) radiation. There is a good agreement between the primordial abundances of 4He, D, 3He and 7Li deduced from observations and from primordial nucleosynthesis calculations. However, the 7Li calculated abundance is significantly higher than the one deduced from spectroscopic observations and remains an open problem. In addition, recent deuterium observations have drastically reduced the uncertainty on D/H, to reach a value of 1.6%. It needs to be matched by BBN predictions whose precision is now limited by thermonuclear reaction rate uncertainties. This is especially important as many attempts to reconcile Li observations with models lead to an increased D prediction. Here, we re-evaluates the D(p,g)3He, D(d,n)3He and D(d,p)3H reaction rates that govern deuterium destruction, incorporating new experimental data and carefully accounting for systematic uncertainties. Contrary to previous evaluations, we use theoretical ab initio models for the energy dependence of the S-factors. As a result, these rates increase at BBN temperatures, leading to a reduced value of D/H = (2.45$\pm0.10)\times10^{-5}$ (2$\sigma$), in agreement with observations.Comment: Submitted to Phys. Rev. D. (without the non-essential Tables IV, IX, X and XI provided here

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

International audienceBACKGROUND: Virtual screening methods are now well established as effective to identify hit and lead candidates and are fully integrated in most drug discovery programs. Ligand-based approaches make use of physico-chemical, structural and energetics properties of known active compounds to search large chemical libraries for related and novel chemotypes. While 2D-similarity search tools are known to be fast and efficient, the use of 3D-similarity search methods can be very valuable to many research projects as integration of "3D knowledge" can facilitate the identification of not only related molecules but also of chemicals possessing distant scaffolds as compared to the query and therefore be more inclined to scaffolds hopping. To date, very few methods performing this task are easily available to the scientific community. RESULTS: We introduce a new approach (LigCSRre) to the 3D ligand similarity search of drug candidates. It combines a 3D maximum common substructure search algorithm independent on atom order with a tunable description of atomic compatibilities to prune the search and increase its physico-chemical relevance. We show, on 47 experimentally validated active compounds across five protein targets having different specificities, that for single compound search, the approach is able to recover on average 52% of the co-actives in the top 1% of the ranked list which is better than gold standards of the field. Moreover, the combination of several runs on a single protein target using different query active compounds shows a remarkable improvement in enrichment. Such Results demonstrate LigCSRre as a valuable tool for ligand-based screening. CONCLUSION: LigCSRre constitutes a new efficient and generic approach to the 3D similarity screening of small compounds, whose flexible design opens the door to many enhancements. The program is freely available to the academics for non-profit research at: http://bioserv.rpbs.univ-paris-diderot.fr/LigCSRre.html

The second detection of CO at redshift larger than 4

We report the detection with the IRAM interferometer at 3mm of J=5-4 CO line in the radio quiet quasar BRI1335-0415 at redshift of z=4.41. After BR1202-0725 at z=4.69 (Ohta etal 1996, Omont etal 1996a), this is the second detection of CO at z>3. The integrated line intensity is 2.8+-0.3 Jy km s^{-1} with a linewidth of 420+-60 km s^{-1}. The dust continuum emission has also been mapped at 1.35mm. The 1.35mm flux is found to be 5.6+-1.1mJy. The ratio of the CO to 1.35mm continuum flux is slightly larger than for BR1202-0725. Contrary to the case of BR1202-0725, there is only marginal evidence of extension of the 1.35mm continuum and 3mm CO emission. In the absence of gravitational lensing, for which there is no a priori evidence, and within the uncertainties of the CO to M(H_2) conversion factors, the mass of molecular gas M(H_2) could be 10^{11} solar masses.Comment: 5 pages, 3 figures, LaTex (l-aa.sty, psfig.sty), also available at http://www.ast.cam.ac.uk/~rg

Découverte de motifs d'évolution significatifs dans les séries temporelles d'images satellites

International audienceLes séries temporelles d'images satellites (ou Satellite Image Time Series - SITS) sont d'importantes sources d'informations sur l'évolution du territoire. Étudier ces images permet de comprendre les changements sur des zones précises mais aussi de découvrir des schémas d'évolution à grande échelle. Toutefois, découvrir ces phénomènes impose de répondre à plusieurs défis qui sont liés aux caractéristiques des SITS et à leurs contraintes. Premièrement, chaque pixel d'une image satellite est décrit par plusieurs valeurs (les niveaux radiométriques sur différentes longueurs d'ondes). Deuxièmement, ces motifs d'évolution portent sur des périodes très longues et ne sont pas forcément synchrones selon les régions. Troisièmement, les régions qui ne sont pas concernées par des évolutions signiticatives sont majoritaires et leur domination rend difficile l'extraction des motifs d'évolution. Dans cet article, nous proposons une méthode qui répond à ces difficultés et nous la validons sur une série d'images satellites acquises sur une période de 20 ans

Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase

International audienceVibrational spectroscopy gives important information on the properties of ligand and metal–ligand bonds in metalloenzymes. Infrared spectroscopy is appealing for the study of metal active sites that are not amenable to Raman spectroscopy. We present a combined experimental and theoretical approach to analyze the mid- and far-IR spectra of Cu,Zn-superoxide dismutase (Cu,Zn-SOD) as a probe of the histidine ligands. This metalloenzyme provides a unique model to identify specific IR signatures of metal–histidine coordination and to study their alterations as a function of the metal (copper/zinc), the copper valence state (+I/+II), the histidine coordination mode (Nτ and Nπ) and the histidine protonation state. DFT calculations combined with normal mode descriptions from potential energy distribution calculations were performed on two slightly different cluster models. Differences in the constraints at the side chain of one histidine Cu ligand sensibly modify the geometric parameters and vibrational properties. Electrochemically induced FTIR difference spectroscopy provided mid- and far-IR fingerprint spectra of the Cu protein in aqueous media that are sensitive to the redox state of the Cu centre at the active site. Comparisons of the DFT predictions with the experimental IR modes of the histidine ligands at the Cu,Zn-SOD active site showed that useful mid-IR markers of histidine Nτ and Nπ coordination were predicted with good accuracy. The DFT analysis further demonstrated a link between the ν(C4–C5) mode frequency of His46 and the specific properties of the His46–Cu bond in Cu,Zn-SOD. A combined theoretical and experimental approach on samples in H2O and 2H2O or 15N-labelled samples identified the contributions from the histidine side chain modes in the 669–629 cm–1 region

Corrosion of E/TBCs: Chemical Interactions of Ceramic Materials with CMAS

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