354 research outputs found
Lie Markov models with purine/pyrimidine symmetry
Continuous-time Markov chains are a standard tool in phylogenetic inference.
If homogeneity is assumed, the chain is formulated by specifying
time-independent rates of substitutions between states in the chain. In
applications, there are usually extra constraints on the rates, depending on
the situation. If a model is formulated in this way, it is possible to
generalise it and allow for an inhomogeneous process, with time-dependent rates
satisfying the same constraints. It is then useful to require that there exists
a homogeneous average of this inhomogeneous process within the same model. This
leads to the definition of "Lie Markov models", which are precisely the class
of models where such an average exists. These models form Lie algebras and
hence concepts from Lie group theory are central to their derivation. In this
paper, we concentrate on applications to phylogenetics and nucleotide
evolution, and derive the complete hierarchy of Lie Markov models that respect
the grouping of nucleotides into purines and pyrimidines -- that is, models
with purine/pyrimidine symmetry. We also discuss how to handle the subtleties
of applying Lie group methods, most naturally defined over the complex field,
to the stochastic case of a Markov process, where parameter values are
restricted to be real and positive. In particular, we explore the geometric
embedding of the cone of stochastic rate matrices within the ambient space of
the associated complex Lie algebra.
The whole list of Lie Markov models with purine/pyrimidine symmetry is
available at http://www.pagines.ma1.upc.edu/~jfernandez/LMNR.pdf.Comment: 32 page
FeH Absorption in the Near-Infrared Spectra of Late M and L Dwarfs
We present medium-resolution z-, J-, and H-band spectra of four late-type
dwarfs with spectral types ranging from M8 to L7.5. In an attempt to determine
the origin of numerous weak absorption features throughout their near-infrared
spectra, and motivated by the recent tentative identification of the E 4\Pi- A
^4\Pi system of FeH near 1.6 microns in umbral and cool star spectra, we have
compared the dwarf spectra to a laboratory FeH emission spectrum. We have
identified nearly 100 FeH absorption features in the z-, J-, and H-band spectra
of the dwarfs. In particular, we have identified 34 features which dominate the
appearance of the H-band spectra of the dwarfs and which appear in the
laboratory FeH spectrum. Finally, all of the features are either weaker or
absent in the spectrum of the L7.5 dwarf which is consistent with the weakening
of the known FeH bandheads in the spectra of the latest L dwarfs.Comment: accepted by Ap
Panel: COVID-19 Challenges to Project Management
COVID-19 has presented many new challenges and new opportunities for project management professionals and IT leaders. This panel will address these challenges and identify project management best practices and processes which have been effective in meeting these challenges. The panelists will share specific instances and challenges explaining how Project Cost Management, Time Management, Risk Management, Human Resources Management, and Risk Management have enabled them to manage during the pandemic and as a part of âreturn-to-workâ scenarios. Hearing from these leaders as they accomplish digital transformations for their businesses and organizations will be an opportunity to bridge the gap between research and practice and to establish a dialogue between academic leaders and IT industry leaders which will provide many new questions to come
Protonâinduced Thermonuclear Reaction Rates for A = 20â40 Nuclei
Proton-induced reaction rates on 26 stable and 29 unstable target nuclei in the mass A = 20â40 region have been evaluated and compiled. Recommended reaction rates, assuming that all interacting nuclei are in the ground state, are presented in tabular form on a temperature grid in the range T = 0.01â10.0 GK. Most reaction rates involving stable targets were normalized to a set of measured standard resonance strengths in the sd shell. For the majority of reaction rates, experimental information from transfer reaction studies has been used consistently. Our results are compared with recent statistical model (Hauser-Feshbach) calculations. Reaction rate uncertainties are presented and amount to several orders of magnitude for many of the reactions. Several of these reaction rates and/or their corresponding uncertainties deviate from results of previous compilations. In most cases, the deviations are explained by the fact that new experimental information became available recently. Examples are given for calculating reaction rates and reverse reaction rates for thermally excited nuclei from the present results. The survey of literature for this review was concluded in 2000 August
Is the general time-reversible model bad for molecular phylogenetics?
The general time reversible model (GTR) is presently the most popular model
used in phylogentic studies. However, GTR has an undesirable mathematical
property that is potentially of significant concern. It is the purpose of this
article to give examples that demonstrate why this deficit may pose a problem
for phylogenetic analysis and interpretation.Comment: 10 pages, 2 figure
A Detailed Observational Analysis of V1324 Sco, the Most Gamma-Ray Luminous Classical Nova to Date
It has recently been discovered that some, if not all, classical novae emit
GeV gamma rays during outburst, but the mechanisms involved in the production
of the gamma rays are still not well understood. We present here a
comprehensive multi-wavelength dataset---from radio to X-rays---for the most
gamma-ray luminous classical nova to-date, V1324 Sco. Using this dataset, we
show that V1324 Sco is a canonical dusty Fe-II type nova, with a maximum ejecta
velocity of 2600 km s and an ejecta mass of few
M. There is also evidence for complex shock interactions, including a
double-peaked radio light curve which shows high brightness temperatures at
early times. To explore why V1324~Sco was so gamma-ray luminous, we present a
model of the nova ejecta featuring strong internal shocks, and find that higher
gamma-ray luminosities result from higher ejecta velocities and/or mass-loss
rates. Comparison of V1324~Sco with other gamma-ray detected novae does not
show clear signatures of either, and we conclude that a larger sample of
similarly well-observed novae is needed to understand the origin and variation
of gamma rays in novae.Comment: 26 pages, 13 figure
UK science press officers, professional vision and the generation of expectations
Science press officers can play an integral role in helping promote expectations and hype about biomedical research. Using this as a starting point, this article draws on interviews with 10 UK-based science press officers, which explored how they view their role as science reporters and as generators of expectations. Using Goodwinâs notion of âprofessional visionâ, we argue that science press officers have a specific professional vision that shapes how they produce biomedical press releases, engage in promotion of biomedical research and make sense of hype. We discuss how these insights can contribute to the sociology of expectations, as well as inform responsible science communication.This project was funded by the Wellcome Trust (Wellcome Trust Biomedical Strategic Award 086034)
Inherent limits of light-level geolocation may lead to over-interpretation
In their 2015 Current Biology paper, Streby et al. [1] reported that Golden-winged Warblers (Vermivora chrysoptera), which had just migrated to their breeding location in eastern Tennessee, performed a facultative and up to â>1,500 km roundtripâ to the Gulf of Mexico to avoid a severe tornadic storm. From light-level geolocator data, wherein geographical locations are estimated via the timing of sunrise and sunset, Streby et al. [1] concluded that the warblers had evacuated their breeding area approximately 24 hours before the storm and returned about five days later. The authors presented this finding as evidence that migratory birds avoid severe storms by temporarily moving long-distances. However, the tracking method employed by Streby et al. [1] is prone to considerable error and uncertainty. Here, we argue that this interpretation of the data oversteps the limits of the used tracking technique. By calculating the expected geographical error range for the tracked birds, we demonstrate that the hypothesized movements fell well within the geolocatorsâ inherent error range for this species and that such deviations in latitude occur frequently even if individuals remain stationary
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