ABC: software for interactive browsing of genomic multiple sequence alignment data

BACKGROUND: Alignment and comparison of related genome sequences is a powerful method to identify regions likely to contain functional elements. Such analyses are data intensive, requiring the inclusion of genomic multiple sequence alignments, sequence annotations, and scores describing regional attributes of columns in the alignment. Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task. RESULTS: The Application for Browsing Constraints (ABC) is interactive Java software for intuitive and efficient exploration of multiple sequence alignments and data typically associated with alignments. It is used to move quickly from a summary view of the entire alignment via arbitrary levels of resolution to individual alignment columns. It allows for the simultaneous display of quantitative data, (e.g., sequence similarity or evolutionary rates) and annotation data (e.g. the locations of genes, repeats, and constrained elements). It can be used to facilitate basic comparative sequence tasks, such as export of data in plain-text formats, visualization of phylogenetic trees, and generation of alignment summary graphics. CONCLUSIONS: The ABC is a lightweight, stand-alone, and flexible graphical user interface for browsing genomic multiple sequence alignments of specific loci, up to hundreds of kilobases or a few megabases in length. It is coded in Java for cross-platform use and the program and source code are freely available under the General Public License. Documentation and a sample data set are also available

Leveraging material efficiency as an energy and climate instrument for heavy industries in the EU

Material efficiency is indispensable to reaching agreed targets for industry's energy and carbon emissions. Yet, in the EU, the energy- and emissions-saving potentials of this strategy continue to be framed as secondary outcomes of resource-related policies. Understanding why material efficiency has been overlooked as an energy/climate solution is a prerequisite for proposing ways of changing its framing, but existing studies have failed to do so. This paper fills this gap by triangulating interviews, policy documents and three policy theories: namely, historical and rational choice institutionalism, and multiple streams framework. Factors discouraging material efficiency as an energy and climate strategy include: difficulties in reframing the prevailing rationale to pursue it; the inadequacy of monitored indicators; the lack of high-level political buy-in from DG Energy and Clima; the ETS policy lock-in; uncoordinated policy management across Directorates; the lack of a designated industry lobby. Policy solutions are proposed. Before 2030, these are limited to minor amendments, e.g. guidance on embodied energy calculations or industry standards. Post-2030, more radical interventions are possible, such as introducing new fiscal drivers, re-designing the ETS emissions cap or benchmarks for allowances. This evidence suggests that the transition to a low-carbon industry will require Member State- and industry-level action.Emerson Electric co

Coulomb Explosion Dynamics of Chlorocarbonylsulfenyl Chloride

The Coulomb explosion dynamics following strong field ionization of chlorocarbonylsulfenyl chloride was studied using multimass coincidence detection and covariance imaging analysis, supported by density functional theory calculations. These results show evidence of multiple dissociation channels from various charge states. Double ionization to low-lying electronic states leads to a dominant C-S cleavage channel, while higher states can alternatively correlate to the loss of Cl+. Triple ionization leads to a double dissociation channel, the observation of which is confirmed via three-body covariance analysis, while further ionization leads primarily to atomic or diatomic fragments whose relative momenta depend strongly on the starting structure of the molecule

From Rotating Atomic Rings to Quantum Hall States

Considerable efforts are currently devoted to the preparation of ultracold neutral atoms in the emblematic strongly correlated quantum Hall regime. The routes followed so far essentially rely on thermodynamics, i.e. imposing the proper Hamiltonian and cooling the system towards its ground state. In rapidly rotating 2D harmonic traps the role of the transverse magnetic field is played by the angular velocity. For particle numbers significantly larger than unity, the required angular momentum is very large and it can be obtained only for spinning frequencies extremely near to the deconfinement limit; consequently, the required control on experimental parameters turns out to be far too stringent. Here we propose to follow instead a dynamic path starting from the gas confined in a rotating ring. The large moment of inertia of the fluid facilitates the access to states with a large angular momentum, corresponding to a giant vortex. The initial ring-shaped trapping potential is then adiabatically transformed into a harmonic confinement, which brings the interacting atomic gas in the desired quantum Hall regime. We provide clear numerical evidence that for a relatively broad range of initial angular frequencies, the giant vortex state is adiabatically connected to the bosonic $\nu=1/2$ Laughlin state, and we discuss the scaling to many particles.Comment: 9 pages, 5 figure

A smart and responsive crystalline porous organic cage membrane with switchable pore apertures for graded molecular sieving

Membranes with high selectivity offer an attractive route to molecular separations, where technologies such as distillation and chromatography are energy intensive. However, it remains challenging to fine tune the structure and porosity in membranes, particularly to separate molecules of similar size. Here, we report a process for producing composite membranes that comprise crystalline porous organic cage films fabricated by interfacial synthesis on a polyacrylonitrile support. These membranes exhibit ultrafast solvent permeance and high rejection of organic dyes with molecular weights over 600 g mol-1. The crystalline cage film is dynamic, and its pore aperture can be switched in methanol to generate larger pores that provide increased methanol permeance and higher molecular weight cut-offs (1,400 g mol-1). By varying the water/methanol ratio, the film can be switched between two phases that have different selectivities, such that a single, 'smart' crystalline membrane can perform graded molecular sieving. We exemplify this by separating three organic dyes in a single-stage, single-membrane process

A solution-processable dissymmetric porous organic cage

A dissymmetric, soluble, porous organic cage from a low-cost racemic precursor.</p

Species Doublers as Super Multiplets in Lattice Supersymmetry: Exact Supersymmetry with Interactions for D=1 N=2

We propose a new lattice superfield formalism in momentum representation which accommodates species doublers of the lattice fermions and their bosonic counterparts as super multiplets. We explicitly show that one dimensional N=2 model with interactions has exact Lie algebraic supersymmetry on the lattice for all super charges. In coordinate representation the finite difference operator is made to satisfy Leibnitz rule by introducing a non local product, the ``star'' product, and the exact lattice supersymmetry is realized. The standard momentum conservation is replaced on the lattice by the conservation of the sine of the momentum, which plays a crucial role in the formulation. Half lattice spacing structure is essential for the one dimensional model and the lattice supersymmetry transformation can be identified as a half lattice spacing translation combined with alternating sign structure. Invariance under finite translations and locality in the continuum limit are explicitly investigated and shown to be recovered. Supersymmetric Ward identities are shown to be satisfied at one loop level. Lie algebraic lattice supersymmetry algebra of this model suggests a close connection with Hopf algebraic exactness of the link approach formulation of lattice supersymmetry.Comment: 34 pages, 2 figure

Transplantation in HIV⁺ patients

Twenty-five whole-organ recipients treated from 1981 through September 1988 were HIV carriers. Eleven were infected before transplantation, although this was not known until later in 8 recipients. The other 14 were infected perioperatively. Ten of the 25 recipients were infants or children. The organs transplanted were the liver (n = 15), and the heart or kidney (n = 5, each). After a mean follow-up of 2.75 years (range, 0.7- 6.6 years), 13 recipients are alive. Survival is 7/15, 2/ 5, and 4/5 of the liver, heart, and kidney recipients, respectively. The best results were in the pediatric group (70% survival) in which only 1 of 10 patients died of AIDS. In contrast, AIDS caused the death of 5 of 15 adult recipients and was the leading cause of death. Transplantation plus immunosuppression appeared to shorten the AIDS-free time in HIV+ patients as compared to nontransplant hemophiliac and transfusion control groups. Accrual of HIV+ transplant recipients has slowed markedly since the systematic screening of donors, recipients, and blood products was begun in 1985. © 1990 by Williams & Wilkins

Vortex nucleation as a case study of symmetry breaking in quantum systems

Mean-field methods are a very powerful tool for investigating weakly interacting many-body systems in many branches of physics. In particular, they describe with excellent accuracy trapped Bose-Einstein condensates. A generic, but difficult question concerns the relation between the symmetry properties of the true many-body state and its mean-field approximation. Here, we address this question by considering, theoretically, vortex nucleation in a rotating Bose-Einstein condensate. A slow sweep of the rotation frequency changes the state of the system from being at rest to the one containing one vortex. Within the mean-field framework, the jump in symmetry occurs through a turbulent phase around a certain critical frequency. The exact many-body ground state at the critical frequency exhibits strong correlations and entanglement. We believe that this constitutes a paradigm example of symmetry breaking in - or change of the order parameter of - quantum many-body systems in the course of adiabatic evolution.Comment: Minor change

Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials