Coronaviruses Detected in Brazilian Wild Birds Reveal Close Evolutionary Relationships with Beta- and Deltacoronaviruses Isolated From Mammals

This study showed that the most of the coronaviruses (CoVs) detected in Brazilian wild birds clustered with the mouse hepatitis virus A59 strain, belonging to the BetaCoV group. Furthermore, CoV detected in two different bird species, Amazona vinacea and Brotogeris tirica, clustered with a CoV isolated from Sparrow (SpaCoV HKU17) belonging to a monophyletic group related with the CoVs isolated from swines (PorCoV HKU15), both belonging to the DeltaCoV genus, previously unreported in South America. Considering the risk of inter-species host switching and further adaptation to new hosts, detection in bird species of CoVs closely related to mammal CoVs should warn for the potential emergence of new threatening viruses.Fundação de Amparo à Pesquisa do Estado de São Paulo (Grants 2013/03922-6 and 2011/50919-5

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique

3D imaging and flow characterization of the pore space of carbonate core samples

Carbonate rocks are inherently heterogeneous having been laid down in a range of depositional environments and having undergone significant diagenesis. They are particularly difficult to characterise as the pore sizes can vary over orders of magnitudes and connectivity of pores of different scales can impact greatly on flow properties. For example, separate vuggy porosity in an underlying matrix pore system can increase the porosity, but not the permeability and lead to large residual oil saturations due to trapping in vugs. A touching vug network can have a dramatic effect on permeability and lead to higher recoveries. In this paper we image a range of carbonate core material; from model carbonate cores to core material from outcrops and reservoirs via 3D via micro-CT. Image-based calculations of porosity, MICP and permeability on 3D images of the carbonate systems are directly compared to experimental data from the same or sister core material and give good agreement. The carbonate systems studied include samples with well connected macroporous systems and other where the macroporosity is poorly connected. Simulation of permeability on these systems and direct analysis of local flow properties within the system allows one to directly illustrate the important role of the connectivity of macropores on flow properties. Pore network models generated from the images illustrate the varied topology obtained in different carbonate samples and show a dramatic difference when compared to clastic samples. Many carbonate samples can include a significant proportion of microporosity (pores of 2 microns or less in extent) which are not directly accessible via current micro-CT capabilities. We discuss how one can map the structure and the topology of microporous regions crucial in studies of flow, production and recovery in carbonates. A hybrid numerical scheme is developed to measure the contribution of microporosity to the overall core permeability. Overall these results show the important role of identifying the connectivity of the pore sizes in dictating the single phase flow properties. Implications to two phase relative permeability and recovery are briefly discussed

Improvements in Spelling after QEEG-based Neurofeedback in Dyslexia: A Randomized Controlled Treatment Study

Phonological theories of dyslexia assume a specific deficit in representation, storage and recall of phonemes. Various brain imaging techniques, including qEEG, point to the importance of a range of areas, predominantly the left hemispheric temporal areas. This study attempted to reduce reading and spelling deficits in children who are dyslexic by means of neurofeedback training based on neurophysiological differences between the participants and gender and age matched controls. Nineteen children were randomized into an experimental group receiving qEEG based neurofeedback (n = 10) and a control group (n = 9). Both groups also received remedial teaching. The experimental group improved considerably in spelling (Cohen’s d = 3). No improvement was found in reading. An indepth study of the changes in the qEEG power and coherence protocols evidenced no fronto-central changes, which is in line with the absence of reading improvements. A significant increase of alpha coherence was found, which may be an indication that attentional processes account for the improvement in spelling. Consideration of subtypes of dyslexia may refine the results of future studies

Prevalence Of Newcastle Disease Virus In Broiler Chickens (gallus Gallus) In Brazil.

This study was carried out during 2002/2003, aiming to determine the prevalence of virulent Newcastle disease virus strains (NDV) in Brazilian commercial poultry farms. Clinical samples were obtained from the Southeastern, Southern and Central-Western regions, which comprise the main area of the Brazilian poultry production. Serum samples and tracheal and cloacal swabs of 23,745 broiler chickens from 1,583 flocks, including both vaccinated chickens and those with no vaccination information, were tested for NDV using a diagnostic ELISA kit. The seropositivity was 39.1%, and the isolation percentage by flock varied from 1.0 to 7.6%, and by region from 6.5 to 58.4%. Higher isolation rates (74.3-83.3%) were obtained after three passages in embryonated chicken eggs. All isolates preliminarily identified as NDV were characterized as nonpathogenic strains, as their Intracerebral Pathogenicity Index (ICPI) was below 0.7. Based on results of this study, Brazil can claim a virulent NDV-free status for commercial flocks.41349-5

A Survey For Maintenance Of Virulent Newcastle Disease Virus-free Area In Poultry Production In Brazil.

In 2003, Brazil was recognized as a pathogenic Newcastle Disease Virus (NDV) strain-free country for commercial poultry. This research was conducted in Brazil between December 2003 and March 2005 to verify the maintenance of this virulent NDV-free status. Serum samples from 5,455 flocks for commercial poultry farms were collected, comprising 81,825 broiler chickens. The farms were located in nine states of the country, grouped in three geographic regions. Serological evidence of NDV infection was detected in 28.8% of the surveyed farms. However, all fifteen viruses isolated and identified as Newcastle Disease Virus (NDV) were characterized as nonpathogenic strains, based on the Intracerebral Pathogenicity Index. These results showed that Brazil preserves the virulent NDV-free status for commercial flocks.41368-7

Understanding extreme sea levels for broad-scale coastal impact and adaptation analysis

One of the main consequences of mean sea level rise (SLR) on human settlements is an increase in flood risk due to an increase in the intensity and frequency of extreme sea levels (ESL). While substantial research efforts are directed towards quantifying projections and uncertainties of future global and regional SLR, corresponding uncertainties in contemporary ESL have not been assessed and projections are limited. Here we quantify, for the first time at global scale, the uncertainties in present-day ESL estimates, which have by default been ignored in broad-scale sea-level rise impact assessments to date. ESL uncertainties exceed those from global SLR projections and, assuming that we meet the Paris agreement goals, the projected SLR itself by the end of the century in many regions. Both uncertainties in SLR projections and ESL estimates need to be understood and combined to fully assess potential impacts and adaptation needs

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte

A strategy for the rapid identification of fungal metabolites and the discovery of the antiviral activity of pyrenocine a and harzianopyridon

The isolation and identification of bioactive metabolites from complex extracts obtained from microbial growth media is a time consuming, costly, and labor-intensive task. A strategy to rapidly identify secondary metabolites isolated from extracts obtained from the culture media of marine-derived and endophytic fungal strains is described. Identification was achieved by HPLC-UV-MS and 1H NMR analyses in combination with data obtained from the Dictionary of Natural Products. Among the compounds identified, (-)-naphthoquinoneimine, citreorosein, emodin, pyrenocine A and harzianopyridone displayed moderate to potent antiviral activity. (-)-Naphthoquinoneimine was isolated as the enantiomer of its previously reported dextrorotatory congener, while 6,7-dihydroxy-2,2-dimethyl-4-chromanone is herein reported for the first time as a natural product396720731CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPBEX 4498-14-32010/50190-2; 2013/50228-8; 2011/08064-2; 2008/00331-9; 2013/23153-