CLEVER: Clique-Enumerating Variant Finder

Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. Here we present a novel internal segment size based approach, which organizes all, including also concordant reads into a read alignment graph where max-cliques represent maximal contradiction-free groups of alignments. A specifically engineered algorithm then enumerates all max-cliques and statistically evaluates them for their potential to reflect insertions or deletions (indels). For the first time in the literature, we compare a large range of state-of-the-art approaches using simulated Illumina reads from a fully annotated genome and present various relevant performance statistics. We achieve superior performance rates in particular on indels of sizes 20--100, which have been exposed as a current major challenge in the SV discovery literature and where prior insert size based approaches have limitations. In that size range, we outperform even split read aligners. We achieve good results also on real data where we make a substantial amount of correct predictions as the only tool, which complement the predictions of split-read aligners. CLEVER is open source (GPL) and available from http://clever-sv.googlecode.com.Comment: 30 pages, 8 figure

Keeping track of worm trackers

C. elegans is used extensively as a model system in the neurosciences due to its well defined nervous system. However, the seeming simplicity of this nervous system in anatomical structure and neuronal connectivity, at least compared to higher animals, underlies a rich diversity of behaviors. The usefulness of the worm in genome-wide mutagenesis or RNAi screens, where thousands of strains are assessed for phenotype, emphasizes the need for computational methods for automated parameterization of generated behaviors. In addition, behaviors can be modulated upon external cues like temperature, O2 and CO2 concentrations, mechanosensory and chemosensory inputs. Different machine vision tools have been developed to aid researchers in their efforts to inventory and characterize defined behavioral “outputs”. Here we aim at providing an overview of different worm-tracking packages or video analysis tools designed to quantify different aspects of locomotion such as the occurrence of directional changes (turns, omega bends), curvature of the sinusoidal shape (amplitude, body bend angles) and velocity (speed, backward or forward movement)

Maximal lengths of exceptional collections of line bundles

In this paper we construct infinitely many examples of toric Fano varieties with Picard number three, which do not admit full exceptional collections of line bundles. In particular, this disproves King's conjecture for toric Fano varieties. More generally, we prove that for any constant $c>\frac34$ there exist infinitely many toric Fano varieties $Y$ with Picard number three, such that the maximal length of exceptional collection of line bundles on $Y$ is strictly less than c\rk K_0(Y). To obtain varieties without exceptional collections of line bundles, it suffices to put $c=1.$ On the other hand, we prove that for any toric nef-Fano DM stack $Y$ with Picard number three, there exists a strong exceptional collection of line bundles on $Y$ of length at least \frac34 \rk K_0(Y). The constant $\frac34$ is thus maximal with this property.Comment: 27 pages, no figures; misprints and typos corrected, an arithmetic mistake in the proof of Theorem 6.2 corrected, consequently Theorem 6.3 slightly modified, new Lemma 4.4 added, description of the constructed varieties extended, references adde

Relação creche e famílias: um olhar voltado às camadas populares.

Trabalho de Conclusão do Curso de Especialização em Educação Infantil - Segunda Edição – Polo Araranguá - SC, para a obtenção do Grau de Especialista em Educação Infantil.Este estudo teve como objetivo analisar possíveis fatores que influenciam na relação creche-família, especialmente em grupos de camadas populares, onde se constatou um maior índice de distanciamento entre familiares e professores. Assim, buscou-se perceber e analisar possíveis motivos de tensões, conflitos e distanciamento das famílias empobrecidas em relação à creche. Após pesquisa bibliográfica em livros, artigos, dissertações e documentos oficiais orientadores da área, percebeu-se que os principais fatores de conflitos e distanciamento se referem a: 1) a creche ainda ser vista pelos pais como um favor do Estado e não um direito das crianças; 2) a creche ainda ter uma visão muito idealizada das famílias, assentada no modelo de família nuclear e burguesa, a qual não corresponde às condições objetivas de vida das famílias de camadas populares e 3) a existência de perspectivas muito dissonantes em relação aos modos de socialização entre creche e famílias de camadas populares. O estudo indicou a grande importância de se conhecer as famílias concretas com que se compartilha a função de complementaridade na educação das crianças e construir modos de participação em parceria com estas, compatíveis com sua realidade e culturas

Itinerant Nature of Atom-Magnetization Excitation by Tunneling Electrons

We have performed single-atom magnetization curve (SAMC) measurements and inelastic scanning tunneling spectroscopy (ISTS) on individual Fe atoms on a Cu(111) surface. The SAMCs show a broad distribution of magnetic moments with \unit[3.5]{\mu_{\rm B}} being the mean value. ISTS reveals a magnetization excitation with a lifetime of \unit[200]{fsec} which decreases by a factor of two upon application of a magnetic field of \unit[12]{T}. The experimental observations are quantitatively explained by the decay of the magnetization excitation into Stoner modes of the itinerant electron system as shown by newly developed theoretical modeling.Comment: 3 Figures, Supplement not included, updated version after revisio

Gene expression trees in lymphoid development

<p>Abstract</p> <p>Background</p> <p>The regulatory processes that govern cell proliferation and differentiation are central to developmental biology. Particularly well studied in this respect is the lymphoid system due to its importance for basic biology and for clinical applications. Gene expression measured in lymphoid cells in several distinguishable developmental stages helps in the elucidation of underlying molecular processes, which change gradually over time and lock cells in either the B cell, T cell or Natural Killer cell lineages. Large-scale analysis of these <it>gene expression trees </it>requires computational support for tasks ranging from visualization, querying, and finding clusters of similar genes, to answering detailed questions about the functional roles of individual genes.</p> <p>Results</p> <p>We present the first statistical framework designed to analyze gene expression data as it is collected in the course of lymphoid development through clusters of co-expressed genes and additional heterogeneous data. We introduce dependence trees for continuous variates, which model the inherent dependencies during the differentiation process naturally as gene expression trees. Several trees are combined in a mixture model to allow inference of potentially overlapping clusters of co-expressed genes. Additionally, we predict microRNA targets.</p> <p>Conclusion</p> <p>Computational results for several data sets from the lymphoid system demonstrate the relevance of our framework. We recover well-known biological facts and identify promising novel regulatory elements of genes and their functional assignments. The implementation of our method (licensed under the GPL) is available at <url>http://algorithmics.molgen.mpg.de/Supplements/ExpLym/</url>.</p

Increasing planet-stirring efficiency of debris disks by "projectile stirring" and "resonant stirring"

Extrasolar debris disks are detected by observing dust, which is thought to be released during planetesimal collisions. This implies that planetesimals are dynamically excited ("stirred"), such that collisions are sufficiently common and violent. The most frequently considered stirring mechanisms are self-stirring by disk self-gravity, and planet-stirring via secular interactions. However, these models face problems when considering disk mass, self-gravity, and planet eccentricity, leading to the possibility that other, unexplored mechanisms instead stir debris. We hypothesize that planet-stirring could be more efficient than the traditional secular model implies, due to two additional mechanisms. First, a planet at the inner edge of a debris disk can scatter massive bodies onto eccentric, disk-crossing orbits, which then excite debris ("projectile stirring"). Second, a planet can stir debris over a wide region via broad mean-motion resonances, both at and between nominal resonance locations ("resonant stirring"). Both mechanisms can be effective even for low-eccentricity planets, unlike secular-planet-stirring. We run N-body simulations across a broad parameter space, to determine the viability of these new stirring mechanisms. We quantify stirring levels using a bespoke program for assessing Rebound debris simulations, which we make publicly available. We find that even low-mass projectiles can stir disks, and verify this with a simple analytic criterion. We also show that resonant stirring is effective for planets above ~0.5 MJup. By proving that these mechanisms can increase planet-stirring efficiency, we demonstrate that planets could still be stirring debris disks even in cases where conventional (secular) planet-stirring is insufficient.Comment: 21 pages, 16 figures, accepted for publication in MNRA

Stability and mode analysis of solar coronal loops using thermodynamic irreversible energy principles

We study the modes and stability of non - isothermal coronal loop models with different intensity values of the equilibrium magnetic field. We use an energy principle obtained via non - equilibrium thermodynamic arguments. The principle is expressed in terms of Hermitian operators and allow to consider together the coupled system of equations: the balance of energy equation and the equation of motion. We determine modes characterized as long - wavelength disturbances that are present in inhomogeneous media. This character of the system introduces additional difficulties for the stability analysis because the inhomogeneous nature of the medium determines the structure of the disturbance, which is no longer sinusoidal. Moreover, another complication is that we obtain a continuous spectrum of stable modes in addition to the discrete one. We obtain a unique unstable mode with a characteristic time that is comparable with the characteristic life-time observed for loops. The feasibility of wave-based and flow-based models is examined.Comment: 29 pages 10 figure