2,500 research outputs found
Geometric generalizations of the Tonnetz and their relation to Fourier phase space
Some recent work on generalized Tonnetze has examined the topologies resulting from Richard Cohn’s common-tone based formulation, while Tymoczko has reformulated the Tonnetz as a network of voice-leading relationships and investigated the resulting geometries. This paper adopts the original common-tone based formulation and takes a geometrical approach, showing that Tonnetze can always be realized in toroidal spaces,and that the resulting spaces always correspond to one of the possible Fourier phase spaces. We can therefore use the DFT to optimize the given Tonnetz to the space (or vice-versa). I interpret two-dimensional Tonnetze as triangulations of the 2-torus into regions associated with the representatives of a single trichord type. The natural generalization to three dimensions is therefore a triangulation of the 3-torus. This means that a three-dimensional Tonnetze is, in the general case, a network of three tetrachord-types related by shared trichordal subsets. Other Tonnetze that have been proposed with bounded or otherwise non-toroidal topologies, including Tymoczko’s voice-leading Tonnetze, can be under-stood as the embedding of the toroidal Tonnetze in other spaces, or as foldings of toroidal Tonnetze with duplicated interval types.Accepted manuscrip
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.
Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis
Simulation of a flux emergence event and comparison with observations by Hinode
We study the observational signature of flux emergence in the photosphere
using synthetic data from a 3D MHD simulation of the emergence of a twisted
flux tube. Several stages in the emergence process are considered. At every
stage we compute synthetic Stokes spectra of the two iron lines Fe I 6301.5
{\AA} and Fe I 6302.5 {\AA} and degrade the data to the spatial and spectral
resolution of Hinode's SOT/SP. Then, following observational practice, we apply
Milne-Eddington-type inversions to the synthetic spectra in order to retrieve
various atmospheric parameters and compare the results with recent Hinode
observations. During the emergence sequence, the spectral lines sample
different parts of the rising flux tube, revealing its twisted structure. The
horizontal component of the magnetic field retrieved from the simulations is
close to the observed values. The flattening of the flux tube in the
photosphere is caused by radiative cooling, which slows down the ascent of the
tube to the upper solar atmosphere. Consistent with the observations, the
rising magnetized plasma produces a blue shift of the spectral lines during a
large part of the emergence sequence.Comment: A&A Letter, 3 figure
On the Inversion-Indel Distance
Willing E, Zaccaria S, Dias Vieira Braga M, Stoye J. On the Inversion-Indel Distance. BMC Bioinformatics. 2013;14(Suppl 15: Proc. of RECOMB-CG 2013): S3.Background
The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli and Pevzner in 1995. In 2000, El-Mabrouk extended the inversion model to allow the comparison of unichromosomal genomes with unequal contents, thus insertions and deletions of DNA segments besides inversions. However, an exact algorithm was presented only for the case in which we have insertions alone and no deletion (or vice versa), while a heuristic was provided for the symmetric case, that allows both insertions and deletions and is called the inversion-indel distance. In 2005, Yancopoulos, Attie and Friedberg started a new branch of research by introducing the generic double cut and join (DCJ) operation, that can represent several genome rearrangements (including inversions). Among others, the DCJ model gave rise to two important results. First, it has been shown that the inversion distance can be computed in a simpler way with the help of the DCJ operation. Second, the DCJ operation originated the DCJ-indel distance, that allows the comparison of genomes with unequal contents, considering DCJ, insertions and deletions, and can be computed in linear time.
Results
In the present work we put these two results together to solve an open problem, showing that, when the graph that represents the relation between the two compared genomes has no bad components, the inversion-indel distance is equal to the DCJ-indel distance. We also give a lower and an upper bound for the inversion-indel distance in the presence of bad components
Magnetic field in atypical prominence structures: Bubble, tornado and eruption
Spectropolarimetric observations of prominences have been obtained with the
THEMIS telescope during four years of coordinated campaigns. Our aim is now to
understand the conditions of the cool plasma and magnetism in `atypical'
prominences, namely when the measured inclination of the magnetic field
departs, to some extent, from the predominantly horizontal field found in
`typical' prominences. What is the role of the magnetic field in these
prominence types? Are plasma dynamics more important in these cases than the
magnetic support? We focus our study on three types of `atypical' prominences
(tornadoes, bubbles and jet-like prominence eruptions) that have all been
observed by THEMIS in the He I D_3 line, from which the Stokes parameters can
be derived. The magnetic field strength, inclination and azimuth in each pixel
are obtained by using the Principal Component Analysis inversion method on a
model of single scattering in the presence of the Hanle effect. The magnetic
field in tornadoes is found to be more or less horizontal, whereas for the
eruptive prominence it is mostly vertical. We estimate a tendency towards
higher values of magnetic field strength inside the bubbles than outside in the
surrounding prominence. In all of the models in our database, only one magnetic
field orientation is considered for each pixel. While sufficient for most of
the main prominence body, this assumption appears to be oversimplified in
atypical prominence structures. We should consider these observations as the
result of superposition of multiple magnetic fields, possibly even with a
turbulent field component.Comment: 13 pages, 9 figure
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