56 research outputs found
Null-plane Quantum Universal -matrix
A non-linear map is applied onto the (non-standard) null-plane deformation of
(3+1) Poincar\'e algebra giving rise to a simpler form of this triangular
quantization. A universal -matrix for the null plane quantum algebra is then
obtained from a universal -matrix corresponding to a Hopf subalgebra.
Finally, the associated Poincar\'e Poisson--Lie group is quantized by using the
FRT approach.Comment: 8 pages, LaTe
Two Amino Acid Changes at the N-Terminus of Transmissible Gastroenteritis Coronavirus Spike Protein Result in the Loss of Enteric Tropism
AbstractTo study the molecular basis of TGEV tropism, a collection of recombinants between the PUR46-MAD strain of transmissible gastroenteritis coronavirus (TGEV) infecting the enteric and respiratory tracts and the PTV strain, which only infects the respiratory tract, was generated. The recombinant isolation frequency was about 10−9recombinants per nucleotide and was 3.7-fold higher at the 5′-end of the S gene than in other areas of the genome. Thirty recombinants were plaque purified and characterized phenotypically and genetically. All recombinant viruses had a single crossover and had inherited the 5′- and 3′-halves of their genome from the enteric and respiratory parents, respectively. Recombinant viruses were classified into three groups, named 1 to 3, according to the location of the crossover. Group 1 recombinants had the crossover in the S gene, while in Groups 2 and 3 the crossovers were located in ORF1b and ORF1a, respectively. The tropism of the recombinants was studied. Recombinants of Group 1 had enteric and respiratory tropism, while Group 2 recombinants infected the respiratory, but not the enteric, tract. Viruses of both groups differed by two nucleotide changes at positions 214 and 655. Both changes may be in principle responsible for the loss of enteric tropism but only the change in nucleotide 655 was specifically found in the respiratory isolates and most likely this single nucleotide change, which leads to a substitution in amino acid 219 of the S protein, was responsible for the loss of enteric tropism in the closely related PUR-46 isolates. The available data indicate that in order to infect enteric tract cells with TGEV, two different domains of the S protein, mapping between amino acids 522 and 744 and around amino acid 219, respectively, are involved. The first domain binds to porcine aminopeptidase N, the cellular receptor for TGEV. In the other domain maps a second factor of undefined nature but which may be the binding site for a coreceptor essential for the enteric tropism of TGEV
The Percolation Signature of the Spin Glass Transition
Magnetic ordering at low temperature for Ising ferromagnets manifests itself
within the associated Fortuin-Kasteleyn (FK) random cluster representation as
the occurrence of a single positive density percolating network. In this paper
we investigate the percolation signature for Ising spin glass ordering -- both
in short-range (EA) and infinite-range (SK) models -- within a two-replica FK
representation and also within the different Chayes-Machta-Redner two-replica
graphical representation. Based on numerical studies of the EA model in
three dimensions and on rigorous results for the SK model, we conclude that the
spin glass transition corresponds to the appearance of {\it two} percolating
clusters of {\it unequal} densities.Comment: 13 pages, 6 figure
Improving the Accuracy of a Two-Stage Algorithm in Evolutionary Product Unit Neural Networks for Classification by Means of Feature Selection
This paper introduces a methodology that improves the accuracy
of a two-stage algorithm in evolutionary product unit neural networks
for classification tasks by means of feature selection. A couple
of filters have been taken into consideration to try out the proposal.
The experimentation has been carried out on seven data sets from the
UCI repository that report test mean accuracy error rates about twenty
percent or above with reference classifiers such as C4.5 or 1-NN. The
study includes an overall empirical comparison between the models obtained
with and without feature selection. Also several classifiers have
been tested in order to illustrate the performance of the different filters
considered. The results have been contrasted with nonparametric statistical
tests and show that our proposal significantly improves the test
accuracy of the previous models for the considered data sets. Moreover,
the current proposal is much more efficient than a previous methodology
developed by us; lastly, the reduction percentage in the number of inputs
is above a fifty five, on average.MICYT TIN2007-68084-C02-02MICYT TIN2008-06681-C06-03Junta de Andalucía P08-TIC-374
Crossover and self-averaging in the two-dimensional site-diluted Ising model
Using the newly proposed probability-changing cluster (PCC) Monte Carlo
algorithm, we simulate the two-dimensional (2D) site-diluted Ising model. Since
we can tune the critical point of each random sample automatically with the PCC
algorithm, we succeed in studying the sample-dependent and the sample
average of physical quantities at each systematically. Using the
finite-size scaling (FSS) analysis for , we discuss the importance of
corrections to FSS both in the strong-dilution and weak-dilution regions. The
critical phenomena of the 2D site-diluted Ising model are shown to be
controlled by the pure fixed point. The crossover from the percolation fixed
point to the pure Ising fixed point with the system size is explicitly
demonstrated by the study of the Binder parameter. We also study the
distribution of critical temperature . Its variance shows the power-law
dependence, , and the estimate of the exponent is consistent
with the prediction of Aharony and Harris [Phys. Rev. Lett. {\bf 77}, 3700
(1996)]. Calculating the relative variance of critical magnetization at the
sample-dependent , we show that the 2D site-diluted Ising model
exhibits weak self-averaging.Comment: 6 pages including 6 eps figures, RevTeX, to appear in Phys. Rev.
Jacobi-Lie systems: Fundamentals and low-dimensional classification
A Lie system is a system of differential equations describing the integral
curves of a -dependent vector field taking values in a finite-dimensional
real Lie algebra of vector fields, a Vessiot-Guldberg Lie algebra. We define
and analyze Lie systems possessing a Vessiot-Guldberg Lie algebra of
Hamiltonian vector fields relative to a Jacobi manifold, the hereafter called
Jacobi-Lie systems. We classify Jacobi-Lie systems on and
. Our results shall be illustrated through examples of physical
and mathematical interest.Comment: 15 pages. Examples, references and comments added. Based on the
contribution presented at "The 10th AIMS Conference on Dynamical Systems,
Differential Equations and Applications", July 07-11, 2014, Madrid, Spain. To
appear in the Proceedings of the 10th AIMS Conferenc
Breast cancer PAM50 signature: Correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series
Background: Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular. Results: The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80. Conclusions: In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method
Interstellar MHD Turbulence and Star Formation
This chapter reviews the nature of turbulence in the Galactic interstellar
medium (ISM) and its connections to the star formation (SF) process. The ISM is
turbulent, magnetized, self-gravitating, and is subject to heating and cooling
processes that control its thermodynamic behavior. The turbulence in the warm
and hot ionized components of the ISM appears to be trans- or subsonic, and
thus to behave nearly incompressibly. However, the neutral warm and cold
components are highly compressible, as a consequence of both thermal
instability in the atomic gas and of moderately-to-strongly supersonic motions
in the roughly isothermal cold atomic and molecular components. Within this
context, we discuss: i) the production and statistical distribution of
turbulent density fluctuations in both isothermal and polytropic media; ii) the
nature of the clumps produced by thermal instability, noting that, contrary to
classical ideas, they in general accrete mass from their environment; iii) the
density-magnetic field correlation (or lack thereof) in turbulent density
fluctuations, as a consequence of the superposition of the different wave modes
in the turbulent flow; iv) the evolution of the mass-to-magnetic flux ratio
(MFR) in density fluctuations as they are built up by dynamic compressions; v)
the formation of cold, dense clouds aided by thermal instability; vi) the
expectation that star-forming molecular clouds are likely to be undergoing
global gravitational contraction, rather than being near equilibrium, and vii)
the regulation of the star formation rate (SFR) in such gravitationally
contracting clouds by stellar feedback which, rather than keeping the clouds
from collapsing, evaporates and diperses them while they collapse.Comment: 43 pages. Invited chapter for the book "Magnetic Fields in Diffuse
Media", edited by Elisabete de Gouveia dal Pino and Alex Lazarian. Revised as
per referee's recommendation
Finite-size scaling above the upper critical dimension in Ising models with long-range interactions
The correlation length plays a pivotal role in finite-size scaling and
hyperscaling at continuous phase transitions. Below the upper critical
dimension, where the correlation length is proportional to the system length,
both finite-size scaling and hyperscaling take conventional forms. Above the
upper critical dimension these forms break down and a new scaling scenario
appears. Here we investigate this scaling behaviour in one-dimensional Ising
ferromagnets with long-range interactions. We show that the correlation length
scales as a non-trivial power of the linear system size and investigate the
scaling forms. For interactions of sufficiently long range, the disparity
between the correlation length and the system length can be made arbitrarily
large, while maintaining the new scaling scenarios. We also investigate the
behavior of the correlation function above the upper critical dimension and the
modifications imposed by the new scaling scenario onto the associated Fisher
relation.Comment: 16 pages, 5 figure
Scaling and universality in the phase diagram of the 2D Blume-Capel model
We review the pertinent features of the phase diagram of the zero-field
Blume-Capel model, focusing on the aspects of transition order, finite-size
scaling and universality. In particular, we employ a range of Monte Carlo
simulation methods to study the 2D spin-1 Blume-Capel model on the square
lattice to investigate the behavior in the vicinity of the first-order and
second-order regimes of the ferromagnet-paramagnet phase boundary,
respectively. To achieve high-precision results, we utilize a combination of
(i) a parallel version of the multicanonical algorithm and (ii) a hybrid
updating scheme combining Metropolis and generalized Wolff cluster moves. These
techniques are combined to study for the first time the correlation length of
the model, using its scaling in the regime of second-order transitions to
illustrate universality through the observed identity of the limiting value of
with the exactly known result for the Ising universality class.Comment: 16 pages, 7 figures, 1 table, submitted to Eur. Phys. J. Special
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