PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

PINPIN a-Si: H based structures for X-ray image detection using the laser scanning technique

Conventional film based X-ray imaging systems are being replaced by their digital equivalents. Different approaches are being followed by considering direct or indirect conversion, with the later technique dominating. The typical, indirect conversion, X-ray panel detector uses a phosphor for X-ray conversion coupled to a large area array of amorphous silicon based optical sensors and a couple of switching thin film transistors (TFT). The pixel information can then be readout by switching the correspondent line and column transistors, routing the signal to an external amplifier. In this work we follow an alternative approach, where the electrical switching performed by the TFT is replaced by optical scanning using a low power laser beam and a sensing/switching PINPIN structure, thus resulting in a simpler device. The optically active device is a PINPIN array, sharing both front and back electrical contacts, deposited over a glass substrate. During X-ray exposure, each sensing side photodiode collects photons generated by the scintillator screen (560 nm), charging its internal capacitance. Subsequently a laser beam (445 nm) scans the switching diodes (back side) retrieving the stored charge in a sequential way, reconstructing the image. In this paper we present recent work on the optoelectronic characterization of the PINPIN structure to be incorporated in the X-ray image sensor. The results from the optoelectronic characterization of the device and the dependence on scanning beam parameters are presented and discussed. Preliminary results of line scans are also presented. (C) 2014 Elsevier B.V. All rights reserved.

Choosing amine-based absorbents for CO2 capture

CO2 capture from gaseous effluents is one of the great challenges faced by chemical and environmental engineers, as the increase in CO2 levels in the Earth atmosphere might be responsible for dramatic climate changes. From the existing capture technologies, the only proven and mature technology is chemical absorption using aqueous amine solutions. However, bearing in mind that this process is somewhat expensive, it is important to choose the most efficient and, at the same time, the least expensive solvents. For this purpose, a pilot test facility was assembled and includes an absorption column, as well as a stripping column, a heat exchanger between the two columns, a reboiler for the stripping column, pumping systems, surge tanks and all necessary instrumentation and control systems. Some different aquous amine solutions were tested on this facility and it was found that, from a set of six tested amines, diethanol amine is the one that turned out to be the most economical choice, as it showed a higher CO2 loading capacity (0.982 mol of CO2 per mol of amine) and the lowest price per litre (25.70 ¤/L), even when compared with monoethanolamine, the benchmark solvent, exhibiting a price per litre of 30.50 ¤/L.