SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

Jet quenching in a strongly coupled anisotropic plasma

The jet quenching parameter of an anisotropic plasma depends on the relative orientation between the anisotropic direction, the direction of motion of the parton, and the direction along which the momentum broadening is measured. We calculate the jet quenching parameter of an anisotropic, strongly coupled N=4 plasma by means of its gravity dual. We present the results for arbitrary orientations and arbitrary values of the anisotropy. The anisotropic value can be larger or smaller than the isotropic one, and this depends on whether the comparison is made at equal temperatures or at equal entropy densities. We compare our results to analogous calculations for the real-world quark-gluon plasma and find agreement in some cases and disagreement in others.Comment: 22 pages, 10 figures; v2: minor changes, added reference. Extends arXiv:1202.369

Thermal architecture for the QUBIC cryogenic receiver

QUBIC, the QU Bolometric Interferometer for Cosmology, is a novel forthcoming instrument to measure the B-mode polarization anisotropy of the Cosmic Microwave Background. The detection of the B-mode signal will be extremely challenging; QUBIC has been designed to address this with a novel approach, namely bolometric interferometry. The receiver cryostat is exceptionally large and cools complex optical and detector stages to 40 K, 4 K, 1 K and 350 mK using two pulse tube coolers, a novel 4He sorption cooler and a double-stage 3He/4He sorption cooler. We discuss the thermal and mechanical design of the cryostat, modelling and thermal analysis, and laboratory cryogenic testing.Fil: May, A. J.. University of Manchester; Reino UnidoFil: Chapron, C.. Astroparticule et Cosmologie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Coppi, G.. University of Manchester; Reino UnidoFil: D’Alessandro, G.. Università di Roma; ItaliaFil: de Bernardis, P.. Università di Roma; ItaliaFil: Masi, S.. Università di Roma; ItaliaFil: Melhuish, S.. University of Manchester; Reino UnidoFil: Piat, M.. Astroparticule et Cosmologie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Piccirillo, L.. University of Manchester; Reino UnidoFil: Schillaci, A.. Università di Roma; ItaliaFil: Thermeau, J. P.. Astroparticule et Cosmologie; Francia. Centre National de la Recherche Scientifique; FranciaFil: Bonaparte, J.. Comisión Nacional de Energía Atómica; ArgentinaFil: Di Donato, Andrés Leonardo. Comisión Nacional de Energía Atómica; ArgentinaFil: Fasciszewski Zeballos, Alejandro Miguel. Comisión Nacional de Energía Atómica; ArgentinaFil: Gamboa Lerena, Martín Miguel. Universidad Nacional de La Plata. Facultad de Ciencias Astronómicas y Geofísicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Garcia, Beatriz Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Tecnología en Detección y Astropartículas. Comisión Nacional de Energía Atómica. Instituto de Tecnología en Detección y Astropartículas. Universidad Nacional de San Martín. Instituto de Tecnología en Detección y Astropartículas; ArgentinaFil: Etchegoyen, Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Tecnología en Detección y Astropartículas. Comisión Nacional de Energía Atómica. Instituto de Tecnología en Detección y Astropartículas. Universidad Nacional de San Martín. Instituto de Tecnología en Detección y Astropartículas; ArgentinaFil: Gomez Berisso, Mariano. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: González, M.. Comisión Nacional de Energía Atómica; ArgentinaFil: Harari, Diego Dario. Comisión Nacional de Energía Atómica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Kristukat, C.. Universidad Nacional de San Martín; ArgentinaFil: Medina, Maria Clementina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Ringegni, P.. Universidad Nacional de la Plata. Facultad de Ingeniería. Uidet Grupo de Ensayos Mecanicos Aplicados.; ArgentinaFil: Romero, Gustavo Esteban. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Argentino de Radioastronomía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Argentino de Radioastronomía; ArgentinaFil: Suarez, C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Tecnología en Detección y Astropartículas. Comisión Nacional de Energía Atómica. Instituto de Tecnología en Detección y Astropartículas. Universidad Nacional de San Martín. Instituto de Tecnología en Detección y Astropartículas; ArgentinaFil: Mundo, Luis Mariano. Universidad Nacional de la Plata. Facultad de Ingeniería. Uidet Grupo de Ensayos Mecanicos Aplicados.; ArgentinaFil: Watson, B.. University of Manchester; Reino UnidoFil: Wicek, F.. Laboratoire de l’Accélérateur Linéaire; FranciaFil: Zannoni, M.. Università degli Studi di Milano; ItaliaFil: Zullo, A.. Istituto Nazionale Di Fisica Nucleare; ItaliaMillimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy IXEstados UnidosSociety of Photographic Instrumentation Engineer

MAP1B Regulates Axonal Development by Modulating Rho-GTPase Rac1 Activity

This article shows a novel function for the MAP1B protein, related to the control of actin dynamics through interaction with Tiam1

A Variable Ionized Disk Wind in the Black Hole Candidate EXO 1846–031

After 34 yr, the black hole candidate EXO 1846–031 went into outburst again in 2019. We investigate its spectral properties in the hard intermediate and the soft states with NuSTAR and Insight-HXMT. A reflection component has been detected in the two spectral states but possibly originating from different illumination spectra: in the intermediate state, the illuminating source is attributed to a hard coronal component, which has been commonly observed in other X-ray binaries, whereas in the soft state, the reflection is probably produced by disk self-irradiation. Both cases support EXO 1846–031 as a low-inclination system of ~40°. An absorption line is clearly detected at ~7.2 keV in the hard intermediate state, corresponding to a highly ionized disk wind (log} ξ > 6.1) with a velocity of up to 0.06c. Meanwhile, quasi-simultaneous radio emissions have been detected before and after the X-rays, implying the coexistence of disk winds and jets in this system. If only the high-flux segment of the NuSTAR observation is considered, the observed wind appears to be magnetically driven. The absorption line disappeared in the soft state and a narrow emission line appeared at ~6.7 keV on top of the reflection component, which may be evidence for disk winds, but data with higher spectral resolution are required to examine this

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London