824 research outputs found
The generalized Robinson-Foulds metric
The Robinson-Foulds (RF) metric is arguably the most widely used measure of
phylogenetic tree similarity, despite its well-known shortcomings: For example,
moving a single taxon in a tree can result in a tree that has maximum distance
to the original one; but the two trees are identical if we remove the single
taxon. To this end, we propose a natural extension of the RF metric that does
not simply count identical clades but instead, also takes similar clades into
consideration. In contrast to previous approaches, our model requires the
matching between clades to respect the structure of the two trees, a property
that the classical RF metric exhibits, too. We show that computing this
generalized RF metric is, unfortunately, NP-hard. We then present a simple
Integer Linear Program for its computation, and evaluate it by an
all-against-all comparison of 100 trees from a benchmark data set. We find that
matchings that respect the tree structure differ significantly from those that
do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Vlasov-Maxwell, self-consistent electromagnetic wave emission simulations in the solar corona
1.5D Vlasov-Maxwell simulations are employed to model electromagnetic
emission generation in a fully self-consistent plasma kinetic model for the
first time in the solar physics context. The simulations mimic the plasma
emission mechanism and Larmor drift instability in a plasma thread that
connects the Sun to Earth with the spatial scales compressed appropriately. The
effects of spatial density gradients on the generation of electromagnetic
radiation are investigated. It is shown that 1.5D inhomogeneous plasma with a
uniform background magnetic field directed transverse to the density gradient
is aperiodically unstable to Larmor-drift instability. The latter results in a
novel effect of generation of electromagnetic emission at plasma frequency.
When density gradient is removed (i.e. when plasma becomes stable to
Larmor-drift instability) and a density, super-thermal, hot beam is
injected along the domain, in the direction perpendicular to the magnetic
field, plasma emission mechanism generates non-escaping Langmuir type
oscillations which in turn generate escaping electromagnetic radiation. It is
found that in the spatial location where the beam is injected, the standing
waves, oscillating at the plasma frequency, are excited. These can be used to
interpret the horizontal strips observed in some dynamical spectra. Quasilinear
theory predictions: (i) the electron free streaming and (ii) the beam long
relaxation time, in accord with the analytic expressions, are corroborated via
direct, fully-kinetic simulation. Finally, the interplay of Larmor-drift
instability and plasma emission mechanism is studied by considering
electron beam in the Larmor-drift unstable (inhomogeneous) plasma.
http://www.maths.qmul.ac.uk/~tsiklauri/movie1.mpg *
http://www.maths.qmul.ac.uk/~tsiklauri/movie2.mpg *
http://www.maths.qmul.ac.uk/~tsiklauri/movie3.mpgComment: Solar Physics (in press, the final, accepted version
ATM Mutations and Phenotypes in Ataxia-Telangiectasia Families in the British Isles: Expression of Mutant ATM and the Risk of Leukemia, Lymphoma, and Breast Cancer
SummaryWe report the spectrum of 59 ATM mutations observed in ataxia-telangiectasia (A-T) patients in the British Isles. Of 51 ATM mutations identified in families native to the British Isles, 11 were founder mutations, and 2 of these 11 conferred a milder clinical phenotype with respect to both cerebellar degeneration and cellular features. We report, in two A-T families, an ATM mutation (7271T→G) that may be associated with an increased risk of breast cancer in both homozygotes and heterozygotes (relative risk 12.7; P=.0025), although there is a less severe A-T phenotype in terms of the degree of cerebellar degeneration. This mutation (7271T→G) also allows expression of full-length ATM protein at a level comparable with that in unaffected individuals. In addition, we have studied 18 A-T patients, in 15 families, who developed leukemia, lymphoma, preleukemic T-cell proliferation, or Hodgkin lymphoma, mostly in childhood. A wide variety of ATM mutation types, including missense mutations and in-frame deletions, were seen in these patients. We also show that 25% of all A-T patients carried in-frame deletions or missense mutations, many of which were also associated with expression of mutant ATM protein
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An entomocentric view of the Janzen-Connell hypothesis
In 1987, in the first issue of Conservation Biology, Edward O. Wilson wrote about the “little things that run the world” – the importance and conservation of insects (Wilson, 1987). Readers of Insect Conservation and Diversity will no doubt be very familiar with the concept. Sadly, however, this perception is not as widely shared among the rest of the scientific community as it should be, and insects are still comparatively neglected as a prime focus of scientific investigations
Statistical Survey of Type III Radio Bursts at Long Wavelengths Observed by the Solar TErrestrial RElations Observatory (STEREO)/Waves Instruments: Radio Flux Density Variations with Frequency
We have performed a statistical study of Type III radio bursts observed
by Solar TErrestrial RElations Observatory (STEREO)/Waves between May 2007 and
February 2013. We have investigated the flux density between kHz and
MHz. Both high- and low-frequency cutoffs have been observed in of
events suggesting an important role of propagation. As already reported by
previous authors, we observed that the maximum flux density occurs at MHz on
both spacecraft. We have developed a simplified analytical model of the flux
density as a function of radial distance and compared it to the STEREO/Waves
data.Comment: published in Solar Physic
A distance for partially labeled trees
In a number of practical situations, data have structure and the relations among its component parts need to be coded with suitable data models. Trees are usually utilized for representing data for which hierarchical relations can be defined. This is the case in a number of fields like image analysis, natural language processing, protein structure, or music retrieval, to name a few. In those cases, procedures for comparing trees are very relevant. An approximate tree edit distance algorithm has been introduced for working with trees labeled only at the leaves. In this paper, it has been applied to handwritten character recognition, providing accuracies comparable to those by the most comprehensive search method, being as efficient as the fastest.This work is supported by the Spanish Ministry projects DRIMS (TIN2009-14247-C02), and Consolider Ingenio 2010 (MIPRCV, CSD2007-00018), partially supported by EU ERDF and the Pascal Network of Excellence
New Insights into White-Light Flare Emission from Radiative-Hydrodynamic Modeling of a Chromospheric Condensation
(abridged) The heating mechanism at high densities during M dwarf flares is
poorly understood. Spectra of M dwarf flares in the optical and
near-ultraviolet wavelength regimes have revealed three continuum components
during the impulsive phase: 1) an energetically dominant blackbody component
with a color temperature of T 10,000 K in the blue-optical, 2) a smaller
amount of Balmer continuum emission in the near-ultraviolet at lambda 3646
Angstroms and 3) an apparent pseudo-continuum of blended high-order Balmer
lines. These properties are not reproduced by models that employ a typical
"solar-type" flare heating level in nonthermal electrons, and therefore our
understanding of these spectra is limited to a phenomenological interpretation.
We present a new 1D radiative-hydrodynamic model of an M dwarf flare from
precipitating nonthermal electrons with a large energy flux of erg
cm s. The simulation produces bright continuum emission from a
dense, hot chromospheric condensation. For the first time, the observed color
temperature and Balmer jump ratio are produced self-consistently in a
radiative-hydrodynamic flare model. We find that a T 10,000 K
blackbody-like continuum component and a small Balmer jump ratio result from
optically thick Balmer and Paschen recombination radiation, and thus the
properties of the flux spectrum are caused by blue light escaping over a larger
physical depth range compared to red and near-ultraviolet light. To model the
near-ultraviolet pseudo-continuum previously attributed to overlapping Balmer
lines, we include the extra Balmer continuum opacity from Landau-Zener
transitions that result from merged, high order energy levels of hydrogen in a
dense, partially ionized atmosphere. This reveals a new diagnostic of ambient
charge density in the densest regions of the atmosphere that are heated during
dMe and solar flares.Comment: 50 pages, 2 tables, 13 figures. Accepted for publication in the Solar
Physics Topical Issue, "Solar and Stellar Flares". Version 2 (June 22, 2015):
updated to include comments by Guest Editor. The final publication is
available at Springer via http://dx.doi.org/10.1007/s11207-015-0708-
Asymptotically Safe Gravitons in Electroweak Precision Physics
Asymptotic safety offers a field theory based UV completion to gravity. For
low Planck scales, gravitational effects on low-energy precision observables
cannot be neglected. We compute the contribution to the rho parameter from
asymptotically safe gravitons and find that in contrast to effective theory,
constraints on models with more than three extra dimensions are significantly
weakened. The relative size of the trans-Planckian contribution increases
proportional to the number of extra dimensions.Comment: Published version; added references and additional minor changes
including appendi
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