MOSGA: Modular Open-Source Genome Annotator

The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies - a crucial step towards unlocking the biology of the organism of interest - has remained a complex challenge that often requires advanced bioinformatics expertise. Here we present MOSGA, a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable, and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. We provide MOSGA as a publicly free available web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga:latest. Source code can be found at https://gitlab.com/mosga/mosg

Two level anti-crossings high up in the single-particle energy spectrum of a quantum dot

We study the evolution with magnetic field of the single-particle energy levels high up in the energy spectrum of one dot as probed by the ground state of the adjacent dot in a weakly coupled vertical quantum dot molecule. We find that the observed spectrum is generally well accounted for by the calculated spectrum for a two-dimensional elliptical parabolic confining potential, except in several regions where two or more single-particle levels approach each other. We focus on two two-level crossing regions which show unexpected anti-crossing behavior and contrasting current dependences. Within a simple coherent level mixing picture, we can model the current carried through the coupled states of the probed dot provided the intrinsic variation with magnetic field of the current through the states (as if they were uncoupled) is accounted for by an appropriate interpolation scheme.Comment: 4 pages, 4 figures, accepted for publication in Physica E in MSS 13 conference proceeding

Paramagnetic colloidal ribbons in a precessing magnetic field

We investigate the dynamics of a kink in a damped parametrically driven nonlinear Klein-Gordon equation.We show by using a method of averaging that, in the high-frequency limit, the kinkmoves in an effective potential and is driven by an effective constant force. We demonstrate that the shape of the solitary wave can be controlled via the frequency and the eccentricity of the modulation. This is in accordance with the experimental results reported in a recent paper [Casic et al., Phys. Rev. Lett. 110, 168302 (2013)], where the dynamic self-assembly and propulsion of a ribbon formed from paramagnetic colloids in a time-dependent magnetic field has been studied.Ministerio de Economía y Competitividad MTM2012-36732-C03-03 (R.A.N.)Ministerio de Economía y Competitividad FIS2011-24540 (N.R.Q.)Junta de Andalucía FQM262 (R.A.N.)Junta de Andalucía FQM207 (N.R.Q.)Junta de Andalucía FQM-7276Junta de Andalucía P09-FQM-4643 (N.R.Q., R.A.N.)Alexander von Humboldt Foundation (Germany) through Research Fellowship for Experienced Researchers SPA 1146358 STP (N.R.Q.)

Impact of Baseline Magnetic Resonance Imaging on Neurologic, Functional, and Safety Outcomes in Patients With Acute Traumatic Spinal Cord Injury

Study Design: Systematic review. Objective: To perform a systematic review to evaluate the utility of magnetic resonance imaging (MRI) in patients with acute spinal cord injury (SCI). Methods: An electronic search of Medline, EMBASE, the Cochrane Collaboration Library, and Google Scholar was conducted for literature published through May 12, 2015, to answer key questions associated with the use of MRI in patients with acute SCI. Results: The literature search yielded 796 potentially relevant citations, 8 of which were included in this review. One study used MRI in a protocol to decide on early surgical decompression. The MRI-protocol group showed improved outcomes; however, the quality of evidence was deemed very low due to selection bias. Seven studies reported MRI predictors of neurologic or functional outcomes. There was moderate-quality evidence that longer intramedullary hemorrhage (2 studies) and low-quality evidence that smaller spinal canal diameter at the location of maximal spinal cord compression and the presence of cord swelling are associated with poor neurologic recovery. There was moderate-quality evidence that clinical outcomes are not predicted by SCI lesion length and the presence of cord edema. Conclusions: Certain MRI characteristics appear to be predictive of outcomes in acute SCI, including length of intramedullary hemorrhage (moderate-quality evidence), canal diameter at maximal spinal cord compression (low-quality evidence), and spinal cord swelling (low-quality evidence). Other imaging features were either inconsistently (presence of hemorrhage, maximal canal compromise, and edema length) or not associated with outcomes. The paucity of literature highlights the need for well-designed prospective studies. © 2017, © The Author(s) 2017

The place of strategic environmental assessment in the privatised electricity industry

The private sector has given relatively little attention to the emergence of strategic environmental assessment (SEA); even recently privatised utilities, where SEA might be deemed particularly appropriate, and whose activities are likely to fall within the scope of the European Union SEA Directive, have shown less interest than might be expected. However, the global trend towards the privatisation of state-owned enterprises makes the adaptation of SEA towards these industries all the more pressing. This paper addresses the place that SEA might take within the electricity sector, taking the privatised UK electricity industry as an example. Particular challenges are posed by the radical restructuring of the industry, designed to introduce competitive behaviour, making the development of comprehensive SEA processes problematic, and requiring SEA to be placed in the context of corporate environmental policy and objectives.</p

Propulsion efficiency of a dynamic self-assembled helical ribbon

We study the dynamic self-assembly and propulsion of a ribbon formed from paramagnetic colloids in a dynamic magnetic field. The sedimented ribbon assembles due to time averaged dipolar interactions between the beads. The time dependence of the dipolar interactions together with hydrodynamic interactions cause a twisted ribbon conformation. Domain walls of high twist connect domains of nearly constant orientation and negligible twist and travel through the ribbon. The particular form of the domain walls can be controlled via the frequency and the eccentricity of the modulation. The flux of twist walls—a true ribbon property absent in slender bodies—provides the thrust onto the surrounding liquid that propels this biomimetic flagellum into the opposite direction. The propulsion efficiency increases with frequency and ceases abruptly at a critical frequency where the conformation changes discontinuously to a flat standing ribbon conformation