102 research outputs found
Central Powering of the Largest Lyman-alpha Nebula is Revealed by Polarized Radiation
High-redshift Lyman-alpha blobs are extended, luminous, but rare structures
that appear to be associated with the highest peaks in the matter density of
the Universe. Their energy output and morphology are similar to powerful radio
galaxies, but the source of the luminosity is unclear. Some blobs are
associated with ultraviolet or infrared bright galaxies, suggesting an extreme
starburst event or accretion onto a central black hole. Another possibility is
gas that is shock excited by supernovae. However some blobs are not associated
with galaxies, and may instead be heated by gas falling into a dark matter
halo. The polarization of the Ly-alpha emission can in principle distinguish
between these options, but a previous attempt to detect this signature returned
a null detection. Here we report on the detection of polarized Ly-alpha from
the blob LAB1. Although the central region shows no measurable polarization,
the polarized fraction (P) increases to ~20 per cent at a radius of 45 kpc,
forming an almost complete polarized ring. The detection of polarized radiation
is inconsistent with the in situ production of Ly-alpha photons, and we
conclude that they must have been produced in the galaxies hosted within the
nebula, and re-scattered by neutral hydrogen.Comment: Published in the August 18 issue of Nature. 1750 words, 3 figures,
and full Supplementary Information. Version has not undergone proofing.
Reduced and processed data products are available here:
http://obswww.unige.ch/people/matthew.hayes/LymanAlpha/LabPol
New Mechanics of Traumatic Brain Injury
The prediction and prevention of traumatic brain injury is a very important
aspect of preventive medical science. This paper proposes a new coupled
loading-rate hypothesis for the traumatic brain injury (TBI), which states that
the main cause of the TBI is an external Euclidean jolt, or SE(3)-jolt, an
impulsive loading that strikes the head in several coupled degrees-of-freedom
simultaneously. To show this, based on the previously defined covariant force
law, we formulate the coupled Newton-Euler dynamics of brain's micro-motions
within the cerebrospinal fluid and derive from it the coupled SE(3)-jolt
dynamics. The SE(3)-jolt is a cause of the TBI in two forms of brain's rapid
discontinuous deformations: translational dislocations and rotational
disclinations. Brain's dislocations and disclinations, caused by the
SE(3)-jolt, are described using the Cosserat multipolar viscoelastic continuum
brain model.
Keywords: Traumatic brain injuries, coupled loading-rate hypothesis,
Euclidean jolt, coupled Newton-Euler dynamics, brain's dislocations and
disclinationsComment: 18 pages, 1 figure, Late
Multiscale analysis of materials with anisotropic microstructure as micropolar continua
Multiscale procedures are often adopted for the continuum modeling of materials composed of a specific micro-structure. Generally, in mechanics of materials only two-scales are linked. In this work the original (fine) micro-scale description, thought as a composite material made of matrix and fibers/particles/crystals which can interact among them, and a scale-dependent continuum (coarse) macro-scale are linked via an energy equivalence criterion. In particular the multiscale strategy is proposed for deriving the constitutive relations of anisotropic composites with periodic microstructure and allows us to reduce the typically high computational cost of fully microscopic numerical analyses. At the microscopic level the material is described as a lattice system while at the macroscopic level the continuum is a micropolar continuum, whose material particles are endowed with orientation besides position. The derived constitutive relations account for shape, texture and orientation of inclusions as well as internal scale parameters, which account for size effects even in the elastic regime in the presence of geometrical and/or load singularities. Applications of this procedure concern polycrystals, wherein an important descriptor of the underlying microstructure gives the orientation of the crystal lattice of each grain, fiber reinforced composites, as well as masonry-like materials. In order to investigate the effects of micropolar constants in the presence of material non central symmetries, some numerical finite element simulations, with elements specifically formulated for micropolar media, are presented. The performed simulations, which extend several parametric analyses earlier performed [1], involve two-dimensional media, in the linear framework, subjected to compression loads distributed in a small portion of the medium
Analytical Framework for Identifying and Differentiating Recent Hitchhiking and Severe Bottleneck Effects from Multi-Locus DNA Sequence Data
Hitchhiking and severe bottleneck effects have impact on the dynamics of genetic diversity of a population by inducing homogenization at a single locus and at the genome-wide scale, respectively. As a result, identification and differentiation of the signatures of such events from DNA sequence data at a single locus is challenging. This paper develops an analytical framework for identifying and differentiating recent homogenization events at multiple neutral loci in low recombination regions. The dynamics of genetic diversity at a locus after a recent homogenization event is modeled according to the infinite-sites mutation model and the Wright-Fisher model of reproduction with constant population size. In this setting, I derive analytical expressions for the distribution, mean, and variance of the number of polymorphic sites in a random sample of DNA sequences from a locus affected by a recent homogenization event. Based on this framework, three likelihood-ratio based tests are presented for identifying and differentiating recent homogenization events at multiple loci. Lastly, I apply the framework to two data sets. First, I consider human DNA sequences from four non-coding loci on different chromosomes for inferring evolutionary history of modern human populations. The results suggest, in particular, that recent homogenization events at the loci are identifiable when the effective human population size is 50000 or greater in contrast to 10000, and the estimates of the recent homogenization events are agree with the “Out of Africa” hypothesis. Second, I use HIV DNA sequences from HIV-1-infected patients to infer the times of HIV seroconversions. The estimates are contrasted with other estimates derived as the mid-time point between the last HIV-negative and first HIV-positive screening tests. The results show that significant discrepancies can exist between the estimates
Bacterial microevolution and the Pangenome
The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history
Metrics matter in community detection
We present a critical evaluation of normalized mutual information (NMI) as an
evaluation metric for community detection. NMI exaggerates the leximin method's
performance on weak communities: Does leximin, in finding the trivial
singletons clustering, truly outperform eight other community detection
methods? Three NMI improvements from the literature are AMI, rrNMI, and cNMI.
We show equivalences under relevant random models, and for evaluating community
detection, we advise one-sided AMI under the model
(all partitions of nodes). This work seeks (1) to start a conversation on
robust measurements, and (2) to advocate evaluations which do not give "free
lunch"
The Population Genetics of dN/dS
Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples
The Ciliate Paramecium Shows Higher Motility in Non-Uniform Chemical Landscapes
We study the motility behavior of the unicellular protozoan Paramecium tetraurelia in a microfluidic device that can be prepared with a landscape of attracting or repelling chemicals. We investigate the spatial distribution of the positions of the individuals at different time points with methods from spatial statistics and Poisson random point fields. This makes quantitative the informal notion of “uniform distribution” (or lack thereof). Our device is characterized by the absence of large systematic biases due to gravitation and fluid flow. It has the potential to be applied to the study of other aquatic chemosensitive organisms as well. This may result in better diagnostic devices for environmental pollutants.University of Wisconsin--Milwaukee (SURF (Salary for Undergraduate Research Fellows) Award)National Science Foundation (U.S.) (grant DMS-016214
Effective Rheology of Bubbles Moving in a Capillary Tube
We calculate the average volumetric flux versus pressure drop of bubbles
moving in a single capillary tube with varying diameter, finding a square-root
relation from mapping the flow equations onto that of a driven overdamped
pendulum. The calculation is based on a derivation of the equation of motion of
a bubble train from considering the capillary forces and the entropy production
associated with the viscous flow. We also calculate the configurational
probability of the positions of the bubbles.Comment: 4 pages, 1 figur
The Embedding Problem for Markov Models of Nucleotide Substitution
10.1371/journal.pone.0069187PLoS ONE87-POLN
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