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

Efluxo de Co2 do Solo em uma Área de Bosque Localizada no Campus ii da UFPA, Santarém, PA

Este trabalho tem como objetivo determinar as trocas de CO2na interface solo-atmosfera. As medidas de CO2 foram realizadas porum analisador de gás por infravermelho (IRGA) LI-COR 6262, câmarasestática de concentração, conectado a um notebook. A média do fluxode CO2 para o solo seco e úmido foram 4,3 ± 1,0 μmol CO2 m-2 s-1 e 5,2± 1,8 μmol CO2 m-2 s-1, respectivamente. Essa diferença dos fluxos podeter sido devido à precipitação na área de estudo

A repairability index for reinforced concrete members based on fracture mechanics

This paper proposes a repairability index for damage assessment in reinforced concrete structural members. The procedure discussed in this paper differs from the standard methods in two aspects: the structural and damage analyses are coupled and it is based on the concepts of fracture and continuum damage mechanics. The relationship between the repairability index and the well-known Park and Ang index is shown in some particular cases

The QUIJOTE experiment: project overview and first results

QUIJOTE (Q-U-I JOint TEnerife) is a new polarimeter aimed to characterize the polarization of the Cosmic Microwave Background and other Galactic and extragalactic signals at medium and large angular scales in the frequency range 10-40 GHz. The multi-frequency (10-20~GHz) instrument, mounted on the first QUIJOTE telescope, saw first light on November 2012 from the Teide Observatory (2400~m a.s.l). During 2014 the second telescope has been installed at this observatory. A second instrument at 30~GHz will be ready for commissioning at this telescope during summer 2015, and a third additional instrument at 40~GHz is now being developed. These instruments will have nominal sensitivities to detect the B-mode polarization due to the primordial gravitational-wave component if the tensor-to-scalar ratio is larger than r=0.05.Comment: To appear in "Highlights of Spanish Astrophysics VIII", Proceedings of the XI Scientific Meeting of the Spanish Astronomical Society, Teruel, Spain (2014

First narrow-band search for continuous gravitational waves from known pulsars in advanced detector data

Spinning neutron stars asymmetric with respect to their rotation axis are potential sources of continuous gravitational waves for ground-based interferometric detectors. In the case of known pulsars a fully coherent search, based on matched filtering, which uses the position and rotational parameters obtained from electromagnetic observations, can be carried out. Matched filtering maximizes the signalto- noise (SNR) ratio, but a large sensitivity loss is expected in case of even a very small mismatch between the assumed and the true signal parameters. For this reason, narrow-band analysis methods have been developed, allowing a fully coherent search for gravitational waves from known pulsars over a fraction of a hertz and several spin-down values. In this paper we describe a narrow-band search of 11 pulsars using data from Advanced LIGO’s first observing run. Although we have found several initial outliers, further studies show no significant evidence for the presence of a gravitational wave signal. Finally, we have placed upper limits on the signal strain amplitude lower than the spin-down limit for 5 of the 11 targets over the bands searched; in the case of J1813-1749 the spin-down limit has been beaten for the first time. For an additional 3 targets, the median upper limit across the search bands is below the spin-down limit. This is the most sensitive narrow-band search for continuous gravitational waves carried out so far

The QUIJOTE experiment: project status and first scientific results

We present the current status of the QUIJOTE (Q-U-I JOint TEnerife) experiment, a new polarimeter with the aim of characterizing the polarization of the Cosmic Microwave Background, and other galactic or extra-galactic physical processes that emit in microwaves in the frequency range 10–42 GHz, and at large angular scales (around 1 degree resolution). The experiment has been designed to reach the required sensitivity to detect a primordial gravitational wave component in the CMB, provided its tensor-to-scalar ratio is larger than r ∼ 0.05. The project consists of two telescopes and three instruments which will survey a large sky area from the Teide Observatory to provide I, Q and U maps of high sensitivity. The first QUIJOTE instrument, known as Multi-Frequency Instrument (MFI), has been surveying the northern sky in four individual frequencies between 10 and 20 GHz since November 2012, providing data with an average sensitivity of 80 µK beam−1 in Q and U in a region of 20, 000 square-degrees. The second instrument, or Thirty-GHz Instrument (TGI), is currently undergoing the commissioning phase, and the third instrument, or Forty-GHz Instrument (FGI), is in the final fabrication phase. Finally, we describe the first scientific results obtained with the MFI. Some specific regions, mainly along the Galactic plane, have been surveyed to a deeper depth, reaching sensitivities of around 40 µK beam−1. We present new upper limits on the polarization of the anomalous dust emission, resulting from these data, in the Perseus molecular complex and in the W43 molecular complex

The status of the Quijote multi-frequency instrument

The QUIJOTE-CMB project has been described in previous publications. Here we present the current status of the QUIJOTE multi-frequency instrument (MFI) with five separate polarimeters (providing 5 independent sky pixels): two which operate at 10-14 GHz, two which operate at 16-20 GHz, and a central polarimeter at 30 GHz. The optical arrangement includes 5 conical corrugated feedhorns staring into a dual reflector crossed-draconian system, which provides optimal cross-polarization properties (designed to be < -35 dB) and symmetric beams. Each horn feeds a novel cryogenic on-axis rotating polar modulator which can rotate at a speed of up to 1 Hz. The science driver for this first instrument is the characterization of the galactic emission. The polarimeters use the polar modulator to derive linear polar parameters Q, U and I and switch out various systematics. The detection system provides optimum sensitivity through 2 correlated and 2 total power channels. The system is calibrated using bright polarized celestial sources and through a secondary calibration source and antenna. The acquisition system, telescope control and housekeeping are all linked through a real-time gigabit Ethernet network. All communication, power and helium gas are passed through a central rotary joint. The time stamp is synchronized to a GPS time signal. The acquisition software is based on PLCs written in Beckhoffs TwinCat and ethercat. The user interface is written in LABVIEW. The status of the QUIJOTE MFI will be presented including pre-commissioning results and laboratory testing

The QUIJOTE-CMB experiment: studying the polarisation of the galactic and cosmological microwave emissions

The QUIJOTE (Q-U-I JOint Tenerife) CMB Experiment will operate at the Teide Observatory with the aim of characterizing the polarisation of the CMB and other processes of Galactic and extragalactic emission in the frequency range of 10-40GHz and at large and medium angular scales. The first of the two QUIJOTE telescopes and the first multi-frequency (10-30GHz) instrument are already built and have been tested in the laboratory. QUIJOTE-CMB will be a valuable complement at low frequencies for the Planck mission, and will have the required sensitivity to detect a primordial gravitational-wave component if the tensor-to-scalar ratio is larger than r = 0.05.The QUIJOTE-CMB experiment is being developed by the Instituto de Astrofisica de Canarias (IAC), the Instituto de Fisica de Cantabria (IFCA), and the Universities of Cantabria, Manchester and Cambridge. Partial financial support is provided by the Spanish Ministry of Economy and Competitiveness (MINECO) under the projects AYA2010-21766-C03 (01, 02 and 03), and also by the Consolider-Ingenio project CSD2010-00064 (EPI: Exploring the Physics of Inflation49)