SVIM: Structural Variant Identification using Mapped Long Reads

Motivation: Structural variants are defined as genomic variants larger than 50bp. They have been shown to affect more bases in any given genome than SNPs or small indels. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities. Results: We present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from PacBio and Nanopore sequencing machines. Availability and implementation: The source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index. Supplementary information: Supplementary data are available at Bioinformatics online

Quantum Flux and Reverse Engineering of Quantum Wavefunctions

An interpretation of the probability flux is given, based on a derivation of its eigenstates and relating them to coherent state projections on a quantum wavefunction. An extended definition of the flux operator is obtained using coherent states. We present a "processed Husimi" representation, which makes decisions using many Husimi projections at each location. The processed Husimi representation reverse engineers or deconstructs the wavefunction, yielding the underlying classical ray structure. Our approach makes possible interpreting the dynamics of systems where the probability flux is uniformly zero or strongly misleading. The new technique is demonstrated by the calculation of particle flow maps of the classical dynamics underlying a quantum wavefunction.Comment: Accepted to EP

On the efficient computation of recurrence relations

A new parallel algorithm for the solution of a general linear recurrence is described. Its relation to the work of Kogge and Stone is discussed

Spectral analysis of 636 white dwarf - M star binaries from the Sloan Digital Sky Survey

We present a catalog of 857 white dwarf (WD)-M binaries from the sixth data release (DR6) of the Sloan Digital Sky Survey (SDSS), most of which were previously identified. For 636 of them, we complete a spectral analysis and derive the basic parameters of their stellar constituents and their distances from Earth. We attempt to measure fundamental parameters of these systems by completing spectral analyses. We use a Chi^2 minimization technique to decompose each combined spectrum and derive independent parameter estimates for its components. Forty-one of the stellar duets in our spectroscopic sample are optically resolved in their respective SDSS images. For these systems, we also derive a minimum true spatial separation and a lower limit to their orbital periods, typically which are some 10^4 yr. Spectra of 167 stellar duets show significant hydrogen emission and in most cases no additional He i or He ii features. We also find that 20 of the 636 WDs are fitted to be DOs, with 16 measured to have T_eff around 40,000 K. Furthermore, we identify 70 very low-mass objects, which are secondaries of masses smaller than about 0.1 solar masses, to be candidate substellar companions. Although various selection effects may play a role, the fraction 6.4 % of WD-M star binaries with orbital separations of around 500 AU is a criterion for evolutionary models of stellar binary systems. Active M dwarfs are likely present in 155 Balmer-emitting systems, corresponding to a fraction of 24.4 %. The excess of cool DOs is most likely due to additional WDs in the DB-DO T_eff range, for which no detailed fitting was completed. The trend of the M stars being closer to Earth than the WD component is probably due to an underestimation of the theoretical M star radii.Comment: accepted by A&A October 3, 2008, 15 pages, 16 figures, 3 tables; v2, minor grammatical changes, essential changes in Sect. 5.

Towards a holographic realization of the quarkyonic phase

Large-N_c QCD matter at intermediate baryon density and low temperatures has been conjectured to be in the so-called quarkyonic phase, i.e., to have a quark Fermi surface and on top of it a confined spectrum of excitations. It has been suggested that the presence of the quark Fermi surface leads to a homogeneous phase with restored chiral symmetry, which is unstable towards creating condensates breaking both the chiral and translational symmetry. Motivated by these exotic features, we investigate properties of cold baryonic matter in the single flavor Sakai-Sugimoto model searching for a holographic realization of the quarkyonic phase. We use a simplified mean-field description and focus on the regime of parametrically large baryon densities, of the order of the square of the 't Hooft coupling, as they turn out to lead to new physical effects similar to the ones occurring in the quarkyonic phase. One effect, the appearance of a particular marginally stable mode breaking translational invariance and linked with the presence of the Chern-Simons term in the flavor brane Lagrangian, is known to occur in the deconfined phase of the Sakai-Sugimoto model, but turns out to be absent here. The other, completely new phenomenon that we, preliminarily, study using strong simplifying assumptions are density-enhanced interactions of the flavor brane gauge field with holographically represented baryons. These seem to significantly affect the spectrum of vector and axial mesons and might lead to approximate chiral symmetry restoration in the lowest part of the spectrum, where the mesons start to qualitatively behave like collective excitations of the dense baryonic medium. We discuss the relevance of these effects for holographic searches of the quarkyonic phase and conclude with a discussion of various subtleties involved in constructing a mean-field holographic description of a dense baryonic medium.Comment: 31 pages, 16 figures; v2: inset plot in Fig. 10 removed, coloring in Fig. 13 fixed, typos fixed, matches published versio

Space probe/satellite ejection apparatus for spacecraft

An ejection apparatus for spinning and propelling objects for ejection from a spacecraft at a desired velocity and rotational speed is discussed. The apparatus includes a launch cradle on which the space object to be ejected rests. The cradle is rotatably supported by a central hub secured to the upper end of the pneumatic cylinder piston shaft. Release mechanisms consisting of a retractable pin and locking lug is utilized to hold the cradle and object to be ejected. The release mechanism has a fixed barrier member which holds the retractable pin in engagement with the locking lug until release by upward movement of the launch cradle beyond the barrier height

Synthesis of atactic and stereoregular vinylaromatic polymers and a study of their reactions with alkali metals Final report

Synthesis and characteristics of atactic and stereoregular vinylaromatic polymers and their reactions with alkali metal

Polyakov Loops and Magnetic Screening from Monopoles in SU(2) Lattice Gauge Theory

We present results from magnetic monopoles in $SU(2)$ lattice gauge theory at finite temperature. The lattices are $16^{3}\times N_{t}$, for $N_{t}=4,6,8,12$, at $\beta=2.5115$. Quantities discussed are: the spacial string tension, Polyakov loops, and the screening of timelike and spacelike magnetic currents.Comment: 5 pages, four Postscript figures, Late

Technology transfer - A selected bibliography

Selected bibliography on technology transfe

Modelling the quark propagator

The quark propagator is at the core of lattice hadron spectrum calculations as well as studies in other nonperturbative schemes. We investigate the quark propagator with an improved staggered action (Asqtad) and an improved gluon action, which provides good quality data down to small quark masses. This is used to construct ans\"{a}tze suitable for model hadron calculations as well as adding to our intuitive understanding of QCD.Comment: Lattice2002(spectrum