Eliminating artefacts in polarimetric images using deep learning

Polarization measurements done using Imaging Polarimeters such as the Robotic Polarimeter are very sensitive to the presence of artefacts in images. Artefacts can range from internal reflections in a telescope to satellite trails that could contaminate an area of interest in the image. With the advent of wide-field polarimetry surveys, it is imperative to develop methods that automatically flag artefacts in images. In this paper, we implement a Convolutional Neural Network to identify the most dominant artefacts in the images. We find that our model can successfully classify sources with 98 per cent true positive and 97 per cent true negative rates. Such models, combined with transfer learning, will give us a running start in artefact elimination for near-future surveys like WALOP

Eliminating artefacts in polarimetric images using deep learning

Polarization measurements done using Imaging Polarimeters such as the Robotic Polarimeter are very sensitive to the presence of artefacts in images. Artefacts can range from internal reflections in a telescope to satellite trails that could contaminate an area of interest in the image. With the advent of wide-field polarimetry surveys, it is imperative to develop methods that automatically flag artefacts in images. In this paper, we implement a Convolutional Neural Network to identify the most dominant artefacts in the images. We find that our model can successfully classify sources with 98 per cent true positive and 97 per cent true negative rates. Such models, combined with transfer learning, will give us a running start in artefact elimination for near-future surveys like WALOP

Comparative Genomic Analysis of Vibrio diabolicus and Six Taxonomic Synonyms: A First Look at the Distribution and Diversity of the Expanded Species

Vibrio is a diverse genus of Gammaproteobacteria autochthonous to marine environments worldwide. Vibrio diabolicus and V. antiquarius were originally isolated from deep-sea hydrothermal fields in the East Pacific Rise. These species are closely related to members of the Harveyi clade (e.g., V. alginolyticus and V. parahaemolyticus) that are commonly isolated from coastal systems. This study reports the discovery and draft genome sequence of a novel isolate (Vibrio sp. 939) cultured from Pacific oysters (Crassostrea gigas). Questions surrounding the identity of Vibrio sp. 939 motivated a genome-scale taxonomic analysis of the Harveyi clade. A 49-genome phylogeny based on 1,109 conserved coding sequences and a comparison of average nucleotide identity (ANI) values revealed a clear case of synonymy between Vibrio sp. 939, V. diabolicus Art-Gut C1 and CNCM I-1629, V. antiquarius EX25 and four V. alginolyticus strains (E0666, FF273, TS13, and V2). This discovery expands the V. diabolicus species and makes available six additional genomes for comparative genomic analyses. The distribution of the expanded species is thought to be global given the range of isolation sources (horse mackerel, seawater, sediment, dentex, oyster, artemia and polycheate) and origins (China, India, Greece, United States, East Pacific Rise, and Chile). A subsequent comparative genomic analysis of this new eight-genome subclade revealed a high degree of individual genome plasticity and a large repertoire of genes related to virulence and defense. These findings represent a significant revision to the understanding of V. diabolicus and V. antiquarius as both have long been regarded as distinct species. This first look at the expanded V. diabolicus subclade suggests that the distribution and diversity of this species mirrors that of other Harveyi clade species, which are notable for their ubiquity and diversity

River basin development and management

In Molden, David (Ed.). Water for food, water for life: a Comprehensive Assessment of Water Management in Agriculture. London, UK: Earthscan; Colombo, Sri Lanka: International Water Management Institute (IWMI)

Comparative Evolutionary Analysis of the Major Structural Subunit of Vibrio vulnificus Type IV Pili

Type IV pili contribute to virulence in Vibrio vulnificus, the bacterium responsible for the majority of fatal seafood-related infections. Here, we performed within- and between-species evolutionary analysis of the gene that encodes the major structural subunit of the pilus, pilA, by comparing it with pilD and gyrB, the genes encoding the type IV prepilin peptidase and β subunit of DNA gyrase, respectively. Although the diversity in pilD and gyrB is similar to each other and likely to have accumulated after speciation of V. vulnificus, pilA is several times more diverse at both nonsynonymous and synonymous levels. Also, in contrast to pilD and gyrB, there are virtually unrestricted and highly localized horizontal movements of pilA alleles between the major phylogenetic groups of V. vulnificus. The frequent movement of pilA involves homologous recombination of the entire gene with no evidence for intragenic recombination between the alleles. We propose that pilA allelic diversity and horizontal movement is maintained in the population by both diversifying and frequency-dependent selection most likely to escape shellfish innate immunity defense or lytic phages. Other possibilities leading to such selection dynamics of V. vulnificus pilA could involve adaptation to diverse host populations or within-host compartments, or natural DNA uptake and transformation. We show that the history of nucleotide diversification in pilA predates V. vulnificus speciation and this diversification started at or before the time of the last common ancestor for V. vulnificus, Vibrio parahaemolyticus, and Vibrio cholerae. At the same time, it appears that within the various pilA groups of V. vulnificus, there is no positive selection for structural mutations and consequently no evidence for source–sink selection. In contrast, pilD has accumulated a number of apparently adaptive mutations in the regions encoding the membrane-spanning portions of the prepilin peptidase, possibly affecting fimbrial expression and/or function, and is being subjected to source–sink selection dynamics

Results of the Pairwise Homoplasy Index (φ_w)^a and Sawyer’s Run Test^b for homologous recombination performed on individual loci included in the MLST scheme (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A).

a<p>mean Pairwise Homoplasy Index, see reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055726#pone.0055726-Bruen1" target="_blank">[48]</a>.</p>b<p>sum of squared lengths of condensed fragments (SSCF) and sum of squared lengths of uncondensed fragments (SSUF), see reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055726#pone.0055726-Sawyer1" target="_blank">[49]</a>.</p>*<p>significance declared at P<0.05.</p

Summary of loci statistics included in the MLST scheme (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A) such as fragment length, number of alleles and polymorphic sites, nucleotide diversity (π), rates of nonsynonymous (<i>d</i>_N) and synonymous (<i>d</i>_S) mutations, and tests of selection (<i>d</i>_N/<i>d</i>_S).

a<p>Rate of nonsynonymous (<i>d</i>_N) and synonymous (<i>d</i>_S) substitutions where <i>d</i>_N/<i>d</i>_S<1 indicates that the loci is subject to purifying selection.</p

NeighborNet analysis.

<p>SplitsTree v4 NeigborNet analysis of 77 <i>V. parahaemolyticus</i> isolates based on 7 concatenated housekeeping loci (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A) representing a total 3,682 nucleotides. Sequence typing (ST) designations for MLST analysis and phylogenetic clades (1–12) included for reference. Regions of the network showing extensive reticulation (e.g., clades 8 and 10), consistent with higher rates of recombination, contrast with the less reticulated nature of clade 12. Highlights in blue distinguish groups of isolates sharing ST and clade designations and function to facilitate comparison with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055726#pone-0055726-g002" target="_blank">Figure 2</a>.</p

REP-PCR patterns and representative dendrogram.

<p>The electrophoresis banding patterns of 167 <i>V. parahaemolyticus</i> isolates assayed by REP-PCR is shown. BioNumerics analysis of patterns revealed 39 unique REP-PCR groups comprised of N isolates. The corresponding BioNumerics dendrogram illustrates the genetic relatedness between REP-PCR groups, which we grouped into three major clusters (I, II, III). Groups 27, 28 and 3 comprise cluster I while groups 11, 29 and 34 comprise cluster III and all remaining groups comprise cluster II. Electrophoresis banding patterns shown with scale indicating fragment size in base pairs (bp).</p