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

Water

[p.4] Values at stake from the new water culture = Valors en joc des de la nova cultura de l'aigua[p.10] The role of schools in the future of water = El paper de l'àmbit escolar. el futur de l'aigua[p.13] Technocracy versus sustainability: education, ecology and management of the Baix llobregat Campus lake = Tecnocràcia vs. sostenibilitat: educació, ecologia i gestió de l'estany del Campus del Baix Llobregat[p.21] Menorca: the fresh water challenge = Menorca: el repte de l'aigua dolça[p.38] Water for people, water for life: the right to water and the role of development NGOs = Aigua per a tots, aigua per a la vida: el dret a l'aigua i el rol de les ONGD[p.43] Water you shouldn't drink...: the water crisis, sustainability and education in India = Aigua que no has de beure...: crisi dels recursos hidràulics, sostenibilitat i educació a l'Índia[p.46] Interview with Maria Rieradevall, expert in education and water = Entrevista amb Maria Rieradevall, experta en educació ambientalPeer Reviewe

Genetic and phylogenetic analysis of Vibrio parahaemolyticus reveals distinct differences in strains from the Pacific Northwest of the U.S.

Genetic and phylogenetic analyses of Vibrio parahaemolyticus (Vp) strains isolated from the U.S. Pacific Northwest demonstrate that clinical isolates are genetically distinct from the environmental isolates. Several environmental isolates are clonally related to strains that have been responsible for Vp-related illnesses world-wide (the pandemic complex) but have not been responsible for illnesses in the Pacific Northwest. While both clinical and a significant proportion of environmental isolates encode one of the putative virulence markers, the thermostable direct hemolysin (tdh), clinical isolates also encoded a second virulence marker, the tdh-related hemolysin (trh). Our findings suggest that V. parahaemolyticus isolates from the Pacific Northwest encoding trh are more likely to be pathogenic than isolates encoding tdh alone

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

Ecology of \u3ci\u3eVibrio parahaemolyticus\u3c/i\u3e and \u3ci\u3eVibrio vulnificus\u3c/i\u3e in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)

Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaetnolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST

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

The Hemorrhagic Coli Pilus (HCP) of Escherichia coli O157:H7 Is an Inducer of Proinflammatory Cytokine Secretion in Intestinal Epithelial Cells

Enterohemorrhagic Escherichia coli (EHEC) O157:H7, the causative agent of hemorrhagic colitis and the hemolytic uremic syndrome (HUS), produces long bundles of type IV pili (TFP) called hemorrhagic coli pili (HCP). HCP are capable of mediating several phenomena associated with pathogenicity: i) adherence to human and bovine epithelial cells; ii) invasion of epithelial cells; iii) hemagglutination of rabbit erythrocytes; iv) biofilm formation; v) twitching motility; and vi) specific binding to laminin and fibronectin. HCP are composed of a 19 kDa pilin subunit (HcpA) encoded by the hcpA chromosomal gene (called prepilin peptidase-dependent gene [ppdD] in E. coli K-12).In this study we investigated the potential role of HCP of E. coli O157:H7 strain EDL933 in activating the release of pro- and anti-inflammatory cytokines from a variety of host epithelial cells. We found that purified HCP and a recombinant HcpA protein induced significant release of IL-8 and TNF-alpha, from cultured polarized intestinal cells (T84 and HT-29 cells) and non-intestinal HeLa cells. Levels of proinflammatory IL-8 and TNF-alpha, but not IL-2, IL6, or IL-10 cytokines, were increased in the presence of HCP and recombinant HcpA after 6 h of incubation with >or=50 ng/ml of protein, suggesting that stimulation of IL-8 and TNF-alpha are dose and time-dependent. In addition, we also demonstrated that flagella are potent inducers of cytokine production. Furthermore, MAPK activation kinetics studies showed that EHEC induces p38 phosphorylation under HCP-producing conditions, and ERK1/2 and JNK activation was detectable after 3 h of EHEC infection. HT-29 cells were stimulated with epidermal growth factor stimulation of HT-29 cells for 30 min leading to activation of three MAPKs.The HcpA pilin monomer of the HCP produced by EHEC O157:H7 is a potent inducer of IL-8 and TNF-alpha release, an event which could play a significant role in the pathogenesis of hemorrhagic colitis caused by this pathogen

Prospects for biocontrol of Vibrio parahaemolyticus contamination in blue mussels (Mytilus edulus) – a year-long study

Vibrio parahaemolyticus is an environmental organism normally found in subtropical estuarine environments which can cause seafood-related human infections. Clinical disease is associated with diagnostic presence of tdh and/or trh virulence genes and identification of these genes in our preliminary isolates from retail shellfish prompted a year-long surveillance of isolates from a temperate estuary in the north of England. The microbial and environmental analysis of 117 samples of mussels, seawater or sediment showed the presence of V. parahaemolyticus from mussels (100%) at all time-points throughout the year including the colder months although they were only recovered from 94.9% of seawater and 92.3% of sediment samples. Throughout the surveillance, 96 isolates were subjected to specific PCR for virulence genes and none tested positive for either. The common understanding that consuming poorly cooked mussels only represents a risk of infection during summer vacations therefore is challenged. Further investigations with V. parahaemolyticus using RAPD-PCR cluster analysis showed a genetically diverse population. There was no distinct clustering for ‘environmental’ or 'clinical reference strains although a wide variability and heterogeneity agreed with other reports. Continued surveillance of isolates to allay public health risks are justified since geographical distribution and composition of V. parahaemolyticus varies with future ocean warming and the potential of environmental strains to acquire virulence genes from pathogenic isolates. The prospects for intervention by phage-mediated biocontrol to reduce or eradicate V. parahaemolyticus in mussels was also investigated. Bacteriophages isolated from enriched samples collected from the river Humber were assessed for their ability to inhibit the growth of V. parahaemolyticus strains in-vitro and in-vivo (with live mussels). V. parahaemolyticus were significantly reduced in-vitro, by an average of 1 log - 2 log units and in-vivo, significant reduction of the organisms in mussels occurred in 3 replicate experimental tank set ups with a ‘phage cocktail’ containing 12 different phages. Our perspective biocontrol study suggests that a cocktail of specific phages targeted against strains of V. parahaemolyticus provides good evidence in an experimental setting of the valuable potential of phage as a decontamination agent in natural or industrial mussel processing