682 research outputs found
New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity
<p>Abstract</p> <p>Background</p> <p>The development of post-genomic methods has dramatically increased the amount of qualitative and quantitative data available to understand how ecological complexity is shaped. Yet, new statistical tools are needed to use these data efficiently. In support of sequence analysis, diversity indices were developed to take into account both the relative frequencies of alleles and their genetic divergence. Furthermore, a method for describing inter-population nucleotide diversity has recently been proposed and named the double principal coordinate analysis (DPCoA), but this procedure can only be used with one locus. In order to tackle the problem of measuring and describing nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis.</p> <p>Results</p> <p>This combination of methods allows i) testing and describing differences in patterns of inter-population diversity among loci, and ii) defining the best compromise among loci. These methods are illustrated by the analysis of both simulated data sets, which include ten loci evolving under a stepping stone model and a locus evolving under an alternative population structure, and a real data set focusing on the genetic structure of two nitrogen fixing bacteria, which is influenced by geographical isolation and host specialization. All programs needed to perform multiple DPCoA are freely available.</p> <p>Conclusion</p> <p>Multiple DPCoA allows the evaluation of the impact of various loci in the measurement and description of diversity. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity.</p
A perceptual hash function to store and retrieve large scale DNA sequences
This paper proposes a novel approach for storing and retrieving massive DNA
sequences.. The method is based on a perceptual hash function, commonly used to
determine the similarity between digital images, that we adapted for DNA
sequences. Perceptual hash function presented here is based on a Discrete
Cosine Transform Sign Only (DCT-SO). Each nucleotide is encoded as a fixed gray
level intensity pixel and the hash is calculated from its significant frequency
characteristics. This results to a drastic data reduction between the sequence
and the perceptual hash. Unlike cryptographic hash functions, perceptual hashes
are not affected by "avalanche effect" and thus can be compared. The similarity
distance between two hashes is estimated with the Hamming Distance, which is
used to retrieve DNA sequences. Experiments that we conducted show that our
approach is relevant for storing massive DNA sequences, and retrieving them
SAfER: Layer-Level Sensitivity Assessment for Efficient and Robust Neural Network Inference
Deep neural networks (DNNs) demonstrate outstanding performance across most
computer vision tasks. Some critical applications, such as autonomous driving
or medical imaging, also require investigation into their behavior and the
reasons behind the decisions they make. In this vein, DNN attribution consists
in studying the relationship between the predictions of a DNN and its inputs.
Attribution methods have been adapted to highlight the most relevant weights or
neurons in a DNN, allowing to more efficiently select which weights or neurons
can be pruned. However, a limitation of these approaches is that weights are
typically compared within each layer separately, while some layers might appear
as more critical than others. In this work, we propose to investigate DNN layer
importance, i.e. to estimate the sensitivity of the accuracy w.r.t.
perturbations applied at the layer level. To do so, we propose a novel dataset
to evaluate our method as well as future works. We benchmark a number of
criteria and draw conclusions regarding how to assess DNN layer importance and,
consequently, how to budgetize layers for increased DNN efficiency (with
applications for DNN pruning and quantization), as well as robustness to
hardware failure (e.g. bit swaps)
Unsupervised spectral learning of WCFG as low-rank matrix completion
We derive a spectral method for unsupervised
learning ofWeighted Context Free Grammars.
We frame WCFG induction as finding a Hankel
matrix that has low rank and is linearly
constrained to represent a function computed
by inside-outside recursions. The proposed algorithm picks the grammar that agrees with a sample and is the simplest with respect to the nuclear norm of the Hankel matrix.Peer ReviewedPreprin
Are copepods secondary hosts of Cycliophora?
Ever since the first observations in the late 1960s, Cycliophora were found exclusively living epizoically on lobsters belonging to the family Nephropidae. The complex cycliophoran life cycle, with alternation of asexual and sexual generations, takes place only in the microhabitat provided by the host mouthparts. Herein, we report the first evidence of a symbiotic relationship between cycliophorans and organisms other than nephropid lobsters, namely, the harpacticoid copepods. Two specimens of copepods associated with cycliophoran life cycle stages were collected from the segmental mouthparts of a European lobster, Homarus gammarus. One of the copepods carried two feeding stages with long stalks, which probably belong to an undescribed Symbion sp., while the other copepod was found bearing an undetermined settled stage. We discuss the implications of these novel observations for the understanding of the Cycliophora life cycle and their dispersion abilities
Direct noise computation of adaptive control applied to a cavity flow
The Large Eddy Simulation of closed-loop active flow control applied to a 3D cavity excited by a compressible airflow with a Mach number of 0.6 is presented. The control actuator is an idealized synthetic jet located at the upstream cavity edge, and the control function is supplied by a feedback LMS-type algorithm whose input is a pressure signal measured inside the cavity. The radiated sound, provided directly by the LES simulation, was shown to decrease substantially when active control was applied. A simultaneous reduction of the vertical velocity fluctuations in the shear layer was observed. The intensity of vortical structures inside the cavity was also reduced, although the general aspect of the recirculation zone was not modified. The direct noise computation technique, which supplies the pressure field by solving the fluid mechanics equations, is shown to constitute a powerful tool for studying active aeroacoustic noise control. To cite this article: O. Marsden et al., C. R. Mecanique 331 (2003). 2003 AcadĂ©mie des sciences. Published by Ăditions scientifiques et mĂ©dicales Elsevier SAS. All rights reserved
RĂ©sistance du mortier en flexion dynamique approche non parfaitement fragile
La rupture des gĂ©o-matĂ©riaux, tel le mortier, est souvent considĂ©rĂ©e comme fragile et sensible Ă la vitesse de dĂ©formation. Pour caractĂ©riser cette rupture en traction, des essais de flexion trois points Ă diffĂ©rentes vitesses de dĂ©formation sont rĂ©alisĂ©s. Nous nous intĂ©ressons particuliĂšrement Ă une gamme de vitesse peu documentĂ©e (entre 5 et 15 sâ1). DiffĂ©rentes approches sont mises en oeuvre pour dĂ©pouiller les essais afin de dĂ©terminer la contrainte de rupture ainsi que son Ă©volution en fonction de la vitesse de dĂ©formation. La prise en compte d'un comportement avec endommagement permet une nouvelle estimation de la contrainte en rupture
The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis
<p>Abstract</p> <p>Background</p> <p>Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria".</p> <p>Results</p> <p>We describe the first complete mitochondrial genome sequence of a member of the Acoela, <it>Symsagittifera roscoffensis</it>. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of <it>Xenoturbella bocki </it>as sister group to or part of the deuterostomes was also unstable.</p> <p>Conclusions</p> <p>Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.</p
A complete three-dimensional reconstruction of the myoanatomy of Loricifera:comparative morphology of an adult and a Higgins larva stage
INTRODUCTION: Loricifera is a group of small, marine animals, with undetermined phylogenetic relationships within Ecdysozoa (molting protostome animals). Despite their well-known external morphology, data on the internal anatomy of loriciferans are still incomplete. Aiming to increase the knowledge of this enigmatic phylum, we reconstruct for the first time the three-dimensional myoanatomy of loriciferans. Adult Nanaloricus sp. and the Higgins larva of Armorloricus elegans were investigated with cytochemical labeling techniques and CLSM. We discuss our findings with reference to other loriciferan species and recently established phylogenies. RESULTS: The somatic musculature of both adult and larval stages is very complex and includes several muscles arranged in three orientations: circular, transverse and longitudinal. In adult Nanaloricus sp., the introvert is characterized by a net-like muscular arrangement, which is composed of five thin circular fibers crossed by several (up to 30) thin longitudinal fibers with bifurcated anterior ends. Two sets of muscles surround the pre-pharyngeal armature: 6 buccal tube retractors arranged 3âĂâ2 in a conical shaped structure, and 8 mouth cone retractors. Additionally, a thick, circular muscle marks the neck region and a putative anal sphincter is the posteriormost myoanatomical feature. In the Higgins larva of A. elegans, two circular muscles are distinguished anteriorly in the introvert: a dorsal semicircular fiber and a thin ring muscle. The posteriormost region of the body is characterized by an anal sphincter and a triangular muscle. CONCLUSIONS: Based on the currently available knowledge, the myoanatomical bodyplan of adult loriciferans includes: (i) 8 mouth cone retractors, (ii) a pharynx bulb composed of transversal fibers arranged radially, (iii) circular muscles of the head and neck, (iv) internal muscles of the spinoscalids, (v) longitudinal muscles spanning all body regions, and (vi) transverse (circular) muscles in the abdomen. Concerning the Higgins larva, the muscle subsets assigned to its myoanatomical ground pattern are the (i) longitudinal retractors of the mouth cone, introvert, and abdomen, (ii) abdominal transverse muscles, and (iii) a pharynx bulb composed of transverse, radial fibers. In a comparison with phyla traditionally regarded as phylogenetically close, our data show that the overall myoanatomy of Loricifera is more similar to Kinorhyncha and Nematomorpha than to Priapulida. However, the head musculature of all these groups is very similar, which supports homology of their introverts and head morphology
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