Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

Development of a multistage laser frequency stabilization for an interferometric gravitational-wave detector

Laser frequency stabilization is essential for interferometric gravitational-wave detectors to attain their target sensitivity. We have designed a multistage laser frequency stabilization system which has been applied in the development of the TAMA 300 gravitational-wave detector in Japan. The control topology consisting of two cascaded loops were employed to secure high feedback gain and reliable detector operation and thus allow the best frequency stability and uninterrupted long-term observation. We achieved simultaneously a frequency stability of 5 × 10^(−5) Hz/√HZ , and a common-mode rejection ratio (which reduces the coupling of frequency noise to spurious signals in the detector) of 37 dB. The developed system enabled us to operate TAMA 300 with sufficient sensitivity and stability that it had the potential to register gravitational-wave events. The system was confirmed to be suitable for a gravitational-wave detector from the observation run of TAMA 300

Field theory models for tachyon and gauge field string dynamics

In hep-th/0008227, the unstable lump solution of \phi^3 theory was shown to have a spectrum governed by the solvable Schroedinger equation with the \ell=3 reflectionless potential and was used as a model for tachyon condensation in string theory. In this paper we study in detail an \ell\to \infty scalar field theory model whose lump solution mimics remarkably the string theory setup: the original field theory tachyon and the lump tachyon have the same mass, the spectrum of the lump consists of equally spaced infinite levels, there is no continuous spectrum, and nothing survives after tachyon condensation. We also find exact solutions for lumps with codimension \ge 2, and show that that their tensions satisfy (1/(2\pi)) (T_p/ T_{p+1})=e/(\sqrt{2\pi}) \approx 1.08. We incorporate gauge fixed couplings to a U(1) gauge field which preserve solvability and result in massless gauge fields on the lump.Comment: latex, 21 pages, 3 figures. Added references to reflectionless potentials, minor typos corrected, uniform use of (-, +, +, ..., +) signatur

Fluorescein Redirects a Ruthenium−Octaarginine Conjugate to the Nucleus

The cellular uptake and localization of a Ru−octaarginine conjugate with and without an appended fluorescein are compared. The inherent luminescence of the Ru(II) dipyridophenazine complex allows observation of its uptake without the addition of a fluorophore. Ru−octaarginine−fluorescein stains the cytosol, nuclei, and nucleoli of HeLa cells under conditions where the Ru−octaarginine conjugate without fluorescein shows only punctate cytoplasmic labeling. At higher concentrations, however, Ru−octaarginine without the fluorescein tag does exhibit cytoplasmic, nuclear, and nucleolar staining. Attaching fluorescein to Ru−octaarginine lowers the threshold concentration required for diffuse cytoplasmic labeling and nuclear entry. Hence, the localization of the fluorophore-bound peptide cannot serve as a proxy for that of the free peptide

Pentatomidae of Arkansas

A total of 30 genera and 53 species and subspecies of Pentatomidae are reported as occurring or possibly occurring in Arkansas. Fifty species and subspecies contained in 29 genera were collected or recorded from previously collected material. Based on distributional records in the literature, three additional species and one genus are listed as probably occurring in Arkansas. County and seasonal records are reported for each taxon

Systematic experimental exploration of bifurcations with non-invasive control

We present a general method for systematically investigating the dynamics and bifurcations of a physical nonlinear experiment. In particular, we show how the odd-number limitation inherent in popular non-invasive control schemes, such as (Pyragas) time-delayed or washout-filtered feedback control, can be overcome for tracking equilibria or forced periodic orbits in experiments. To demonstrate the use of our non-invasive control, we trace out experimentally the resonance surface of a periodically forced mechanical nonlinear oscillator near the onset of instability, around two saddle-node bifurcations (folds) and a cusp bifurcation.Comment: revised and extended version (8 pages, 7 figures