Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

BACKGROUND: Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. RESULTS: Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. CONCLUSIONS: We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.This research was funded by GlaxoSmithKline, the Centre for Environment, Fisheries and Aquaculture Science and the Biotechnology and Biological Sciences Research Council under an industrial CASE studentship. The funder Centre for Environment, Fisheries and Aquaculture Science provided support in the form of salaries, research materials and facilities for authors DVJ and CBA, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funder GlaxoSmithKline provided support in the form of salaries for author JR, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final version. It was first published by PLOS at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133492

There Is No Such Thing As A “Legal Name”

The phrase “legal name” appears everywhere. And wherever it appears, it seems to come with an assumption that it picks out one, clear such name for each person. So, do “legal” names as the phrase is commonly understood really exist? As far as federal and most state law is concerned, it turns out the answer is a clear no. This article seeks to highlight the legal, moral, and philosophical wrongness of the notion that people have one uniquely identifying legal name. To do that, we survey the status of names in various legal domains, highlighting that legal consensus tends to be that there is no one “correct legal name” for individuals (if anything, people often have many “legal” names). We argue this common notion that every person has a single, clearly defined “legal” name is a kind of collective delusion we all seem to share (emerging somewhere in the late twentieth century), but is not grounded in legal or social reality. To address this harmful delusion, we present a series of ready-to-cite conclusions about the current state of the law and introduce a normative framework for how institutions and individuals ought to choose between people’s various legal names. Engaging with legal theory, feminist philosophy, and philosophy of language, we discuss the social function of names and argue that names enable people to communicate important social information about themselves—which can include their gender, religion, and familial relations. Thus, we conclude by arguing that individuals and legal institutions have a normative responsibility to respect peoples’ preferred legal names, thereby allowing them to authentically represent these facets of their social identities

Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments

Three recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar to Ferroplasma acidiphilum Y-T by 16S rRNA gene sequencing. All four Ferroplasma isolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate "Ferroplasma acidarmanus" Fer1(T) required much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42degreesC and the pH optima were 1.0 to 1.7, and "F. acidarmanus" Fer1(T) was capable of growing at pH 0. The optimum yeast extract concentration for "F. acidarmanus" Fer1(T) was higher than that for the other three isolates. Phenotypic results suggested that isolate "F. acidarmanus" Fer1(T) is of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and Y-T group as a single species. "F. acidarmanus" Fer1(T) groups separately, and we propose the new species "F. acidarmanus" Fer1(T) sp. nov

Corticosterone Regulates Both Naturally Occurring and Cocaine‐Induced Dopamine Signaling by Selectively Decreasing Dopamine Uptake

Stressful and aversive events promote maladaptive reward‐seeking behaviors such as drug addiction by acting, in part, on the mesolimbic dopamine system. Using animal models, data from our laboratory and others show that stress and cocaine can interact to produce a synergistic effect on reward circuitry. This effect is also observed when the stress hormone corticosterone is administered directly into the nucleus accumbens (NAc), indicating that glucocorticoids act locally in dopamine terminal regions to enhance cocaine\u27s effects on dopamine signaling. However, prior studies in behaving animals have not provided mechanistic insight. Using fast‐scan cyclic voltammetry, we examined the effect of systemic corticosterone on spontaneous dopamine release events (transients) in the NAc core and shell in behaving rats. A physiologically relevant systemic injection of corticosterone (2 mg/kg i.p.) induced an increase in dopamine transient amplitude and duration (both voltammetric measures sensitive to decreases in dopamine clearance), but had no effect on the frequency of transient release events. This effect was compounded by cocaine (2.5 mg/kg i.p.). However, a second experiment indicated that the same injection of corticosterone had no detectable effect on the dopaminergic encoding of a palatable natural reward (saccharin). Taken together, these results suggest that corticosterone interferes with naturally occurring dopamine uptake locally, and this effect is a critical determinant of dopamine concentration specifically in situations in which the dopamine transporter is pharmacologically blocked by cocaine

Galleria mellonella as an infection model to investigate virulence of Vibrio parahaemolyticus

This is the final version. Available from Taylor & Francis via the DOI in this recordNon-toxigenic V. parahaemolyticus isolates (tdh-/trh-/T3SS2-) have recently been isolated from patients with gastroenteritis. In this study we report that the larvae of the wax moth (Galleria mellonella) are susceptible to infection by toxigenic or non-toxigenic clinical isolates of V. parahaemolyticus. In comparison larvae inoculated with environmental isolates of V. parahaemolyticus did not succumb to disease. Whole genome sequencing of clinical non-toxigenic isolates revealed the presence of a gene encoding a nudix hydrolase, identified as mutT. A V. parahaemolyticus mutT mutant was unable to kill G. mellonella at 24 h post inoculation, indicating a role of this gene in virulence. Our findings show that G. mellonella is a valuable model for investigating screening of possible virulence genes of V. parahaemolyticus and can provide new insights into mechanisms of virulence of atypical non-toxigenic V. parahaemolyticus. These findings will allow improved genetic tests for the identification of pathogenic V. parahaemolyticus to be developed and will have a significant impact for the scientific community.This work was partly supported by Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT097835MF) Medical Research Council Clinical Infrastructure Funding (MR/M008924/1) and Biotechnology and Biological Sciences Research Council (BBSRC) funding (BB/N016513/1)

Do Hadronic Charge Exchange Reactions Measure Electroweak L = 1 Strength?

An eikonal model has been used to assess the relationship between calculated strengths for first forbidden beta decay and calculated cross sections for (p,n) charge exchange reactions. It is found that these are proportional for strong transitions, suggesting that hadronic charge exchange reactions may be useful in determining the spin-dipole matrix elements for astrophysically interesting leptonic transitions.Comment: 14 pages, 5 figures, Submitted to Physical Review

Trolling in asynchronous computer-mediated communication: From user discussions to academic definitions

Whilst computer-mediated communication (CMC) can benefit users by providing quick and easy communication between those separated by time and space, it can also provide varying degrees of anonymity that may encourage a sense of impunity and freedom from being held accountable for inappropriate online behaviour. As such, CMC is a fertile ground for studying impoliteness, whether it occurs in response to perceived threat (flaming), or as an end in its own right (trolling). Currently, first and secondorder definitions of terms such as im/politeness (Brown and Levinson 1987; Bousfield 2008; Culpeper 2008; Terkourafi 2008), in-civility (Lakoff 2005), rudeness (Beebe 1995, Kienpointner 1997, 2008), and etiquette (Coulmas 1992), are subject to much discussion and debate, yet the CMC phenomenon of trolling is not adequately captured by any of these terms. Following Bousfield (in press), Culpeper (2010) and others, this paper suggests that a definition of trolling should be informed first and foremost by user discussions. Taking examples from a 172-million-word, asynchronous CMC corpus, four interrelated conditions of aggression, deception, disruption, and success are discussed. Finally, a working definition of trolling is presented

Migratory and winter activity of bats in Yellowstone National Park

A substantial body of work exists describing timing of migration and hibernation among bats in eastern North America, but less is known about these events among bats inhabiting the Rocky Mountain region. Yellowstone National Park is a geothermally influenced landscape comprised of diverse habitats, creating the opportunity for unique behaviors to develop among local bat populations. We identified the timing of migration for the local bat community and determined if bats overwinter in Yellowstone. To accomplish this, we radiotracked 7 little brown myotis (Myotis lucifugus), 5 western long-eared myotis (M. evotis), 4 big brown bats (Eptesicus fuscus), 4 silver-haired bats (Lasionycteris noctivagans), and 1 western small-footed myotis (M. ciliolabrum) from August to September 2010 and September to October 2011. We also used acoustic detectors to record bat activity from November through April 2011–2014 and sampled abundance of nocturnal insects using black-light traps from 2011 to 2012. Although availability of insects declined rapidly during August and afterward, several bat species remained active throughout autumn and winter. Bat activity was recorded during all months, even during periods of extreme cold. Radiotagged big brown bats, little brown myotis, and western small-footed myotis remained active in the study area throughout October, after the 1st snowfall of the season. While data for activity patterns in late autumn and winter prevented an estimation of the onset of hibernation, spring emergence occurred in April despite persistence of winter conditions. These data provide insights into the migration and hibernation strategies of bat populations in the Rocky Mountains and highlight gaps in our understanding of seasonal changes in these species

Evaluation of the protection against norovirus afforded by E. coli monitoring of shellfish production areas under EU regulations

EC Regulation 854/2004 requires the classification of bivalve mollusc harvesting areas according to the faecal pollution status of sites. It has been reported that determination of Escherichia coli in bivalve shellfish is a poor predictor of norovirus (NoV) contamination in individual samples. We explore the correlation of shellfish E. coli data with norovirus presence using data from studies across 88 UK sites (1,184 paired samples). We investigate whether current E. coli legislative standards could be refined to reduce NoV infection risk. A significant relationship between E. coli and NoV was found in the winter months (October to February) using data from sites with at least 10 data pairs (51 sites). We found that the ratio of arithmetic means (log10 E. coli to log10 NoV) at these sites ranged from 0.6 to 1.4. The lower ratios (towards 0.6) might typically indicate situations where the contribution from UV disinfected sewage discharges was more significant. Conversely, higher ratios (towards 1.4) might indicate a prevalence of animal sources of pollution; however, this relationship did not always hold true and so further work is required to fully elucidate the factors of relevance. Reducing the current class B maximum (allowed in 10% of samples) from 46,000 E. coli per 100 g (corresponding NoV value of 75750±103) to 18,000 E. coli per 100 g (corresponding NoV value of 29365±69) reduces maximum levels of NoV by a factor of 2.6 to 1; reducing the upper class B limit to 100% compliance with 4,600 E. coli per 100 g (corresponding NoV value of 7403±39) reduces maximum levels of NoV by a factor of 10.2 to 1. We found using the UK filtered winter dataset that a maximum of 200 NoV corresponded to a maximum of 128±7 E. coli per 100 g. A maximum of 1,000 NoV corresponded to a maximum of 631±14 E. coli per 100 g

New record in the Hawaiian Islands of Orasema minutissima (Hymenoptera: Eucharitidae), an ant-parasitic wasp and a potential biocontrol agent against the Little Fire Ant, Wasmannia auropunctata (Hymenoptera: Formicidae)

Orasema minutissima Howard (Hymenoptera: Eucharitidae) is recorded fromthe Hawaiian Islands for the first time. It has been established on the island of Hawai?isince at least 2019. The wasp is a parasitoid of the immature stages of Pheidole andWasmannia (Formicidae: Myrmicinae), both of which are significant pests on several ofthe Hawaiian Islands. Already found in substantial numbers, the wasp is a potential biological control agent for Wasmannia auropunctata, the Little Fire Ant.Fil: Heraty, John Michael. University of California; Estados UnidosFil: Rogers, Valle D.. University of California; Estados UnidosFil: Johnson, M. Tracy. Institute of Pacific Islands Forestry; Estados UnidosFil: Perreira, Williams D.. No especifíca;Fil: Baker, Austin J.. University of California; Estados UnidosFil: Bitume, Ellyn. Institute of Pacific Islands Forestry; Estados UnidosFil: Murray, Elizabeth. Washington State University; Estados UnidosFil: Varone, Laura. Fundación para el Estudio de Especies Invasivas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin