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

Nucleon-Nucleon Interactions from Dispersion Relations: Coupled Partial Waves

We consider nucleon-nucleon interactions from chiral effective field theory applying the N/D method. The case of coupled partial waves is now treated, extending Ref. [1] where the uncoupled case was studied. As a result three N/D elastic-like equations have to be solved for every set of three independent partial waves coupled. As in the previous reference the input for this method is the discontinuity along the left-hand cut of the nucleon-nucleon partial wave amplitudes. It can be calculated perturbatively in chiral perturbation theory because it involves only irreducible two-nucleon intermediate states. We apply here our method to the leading order result consisting of one-pion exchange as the source for the discontinuity along the left-hand cut. The linear integral equations for the N/D method must be solved in the presence of L - 1 constraints, with L the orbital angular momentum, in order to satisfy the proper threshold behavior for L>= 2. We dedicate special attention to satisfy the requirements of unitarity in coupled channels. We also focus on the specific issue of the deuteron pole position in the 3S1-3D1 scattering. Our final amplitudes are based on dispersion relations and chiral effective field theory, being independent of any explicit regulator. They are amenable to a systematic improvement order by order in the chiral expansion.Comment: 11 pages. Extends the work of uncoupled partial waves of M. Albaladejo and J. A. Oller, Phys. Rev. C 84, 054009 (2011) to the case of coupled partial waves. This version matches the published version. Discussion about the deuteron enlarged. Some references adde

Saddle Points and Stark Ladders: Exact Calculations of Exciton Spectra in Superlattices

A new, exact method for calculating excitonic absorption in superlattices is described. It is used to obtain high resolution spectra showing the saddle point exciton feature near the top of the miniband. The evolution of this feature is followed through a series of structures with increasing miniband width. The Stark ladder of peaks produced by an axial electric field is investigated, and it is shown that for weak fields the line shapes are strongly modified by coupling to continuum states, taking the form of Fano resonances. The calculated spectra, when suitably broadened, are found to be in good agreement with experimental results.Comment: 9 pages Revtex v3.0, followed by 4 uuencoded postscript figures, SISSA-CM-94-00

Moving Mirrors and Thermodynamic Paradoxes

Quantum fields responding to "moving mirrors" have been predicted to give rise to thermodynamic paradoxes. I show that the assumption in such work that the mirror can be treated as an external field is invalid: the exotic energy-transfer effects necessary to the paradoxes are well below the scales at which the model is credible. For a first-quantized point-particle mirror, it appears that exotic energy-transfers are lost in the quantum uncertainty in the mirror's state. An accurate accounting of these energies will require a model which recognizes the mirror's finite reflectivity, and almost certainly a model which allows for the excitation of internal mirror modes, that is, a second-quantized model.Comment: 7 pages, Revtex with Latex2

Multiplexed DNA-Modified Electrodes

We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 μm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format

Strain monitoring of tapestries: results of a three-year research project

The outcomes of an interdisciplinary research project between conservators and engineers investigating the strain experienced by different areas of a tapestry are described. Two techniques were used: full-field monitoring using digital image correlation (DIC) and point measurements using optical fibre sensors. Results showed that it is possible to quantify the global strain across a discrete area of a tapestry using DIC; optical fibre and other sensors were used to validate the DIC. Strain maps created by the DIC depict areas of high and low strain and can be overlaid on images of the tapestry, creating a useful visual tool for conservators, custodians and the general public. DIC identifies areas of high strain not obvious to the naked eye. The equipment can be used in situ in a historic house. In addition the work demonstrated the close relationship between relative humidity and strain

Search for correlation effects in linear chains of trapped ions

We report a precise search for correlation effects in linear chains of 2 and 3 trapped Ca+ ions. Unexplained correlations in photon emission times within a linear chain of trapped ions have been reported, which, if genuine, cast doubt on the potential of an ion trap to realize quantum information processing. We observe quantum jumps from the metastable 3d 2D_{5/2} level for several hours, searching for correlations between the decay times of the different ions. We find no evidence for correlations: the number of quantum jumps with separations of less than 10 ms is consistent with statistics to within errors of 0.05%; the lifetime of the metastable level derived from the data is consistent with that derived from independent single-ion data at the level of the experimental errors 1%; and no rank correlations between the decay times were found with sensitivity to rank correlation coefficients at the level of |R| = 0.024.Comment: With changes to introduction. 5 pages, including 4 figures. Submitted to Europhys. Let

Plastic-crystalline solid-state electrolytes: Ionic conductivity and orientational dynamics in nitrile mixtures

Many plastic crystals, molecular solids with long-range, center-of-mass crystalline order but dynamic disorder of the molecular orientations, are known to exhibit exceptionally high ionic conductivity. This makes them promising candidates for applications as solid-state electrolytes, e.g., in batteries. Interestingly, it was found that the mixing of two different plastic-crystalline materials can considerably enhance the ionic dc conductivity, an important benchmark quantity for electrochemical applications. An example is the admixture of different nitriles to succinonitrile, the latter being one of the most prominent plastic-crystalline ionic conductors. However, until now only few such mixtures were studied. In the present work, we investigate succinonitrile mixed with malononitrile, adiponitrile, and pimelonitrile, to which 1 mol% of Li ions were added. Using differential scanning calorimetry and dielectric spectroscopy, we examine the phase behavior and the dipolar and ionic dynamics of these systems. We especially address the mixing-induced enhancement of the ionic conductivity and the coupling of the translational ionic mobility to the molecular reorientational dynamics, probably arising via a "revolving-door" mechanism.Comment: 9 pages, 7 figures; revised version as accepted for publication in J. Chem. Phy

Unitarity and the color confinement

We discuss how confinement property of QCD results in the rational unitarization scheme and how unitarity saturation leads to appearance of a hadron liquid phase at very high temperatures.Comment: 10 pages, no figire