4,731 research outputs found
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
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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
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<sup>+</sup> 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
A semiconductor source of triggered entangled photon pairs?
The realisation of a triggered entangled photon source will be of great
importance in quantum information, including for quantum key distribution and
quantum computation. We show here that: 1) the source reported in ``A
semiconductor source of triggered entangled photon pairs''[1. Stevenson et al.,
Nature 439, 179 (2006)]} is not entangled; 2) the entanglement indicators used
in Ref. 1 are inappropriate, relying on assumptions invalidated by their own
data; and 3) even after simulating subtraction of the significant quantity of
background noise, their source has insignificant entanglement.Comment: 5 pages in pre-print format, 1 tabl
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