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

Adubação e arranjo de plantas no consórcio milho e braquiária.

A otimização do manejo de milho consorciado com braquiária depende da fertilidade do solo, da densidade de plantas de braquiária e do arranjo de plantas do milho. Avaliaram-se as interações desses fatores e sua influência na produtividade de grãos e da pastagem, em experimento conduzido por duas safras, num fatorial 2x2x3+1, combinando-se duas condições de adubação do milho (para produtividade de 6 ou > 10 t ha-1 de grãos), densidade média ou alta de braquiária ( 30 plantas m-2), três arranjos de plantas de milho (A = 90 cm entre linhas, 5 plantas m-1; B = 45 cm entre linhas, 2,5 plantas m-1; e C = 45 cm entre linhas, 3 plantas m-1) e um tratamento adicional (maior adubação, sem braquiária e arranjo A do milho). A disponibilidade hídrica influenciou as respostas aos tratamentos. Em ano chuvoso, maior adubação resultou em expressivo incremento da produtividade de grãos, independentemente do arranjo de plantas de milho e da presença de braquiária. Em ano com veranico, o ganho do milho, devido à adubação, foi menor e houve efeito prejudicial da maior densidade de braquiária. A produção de matéria seca pela braquiária não apresentou relação direta com a variação na densidade de plantas

Quantitative properties of complex porous materials calculated from X-ray μCT images

A microcomputed tomography (μCT) facility and computational infrastructure developed at the Department of Applied Mathematics at the Australian National University is described. The current experimental facility is capable of acquiring 3D images made up of 20003 voxels on porous specimens up to 60 mm diameter with resolutions down to 2 μm. This allows the three-dimensional (3D) pore-space of porous specimens to be imaged over several orders of magnitude. The computational infrastructure includes the establishment of optimised and distributed memory parallel algorithms for image reconstruction, novel phase identification, 3D visualisation, structural characterisation and prediction of mechanical and transport properties directly from digitised tomographic images. To date over 300 porous specimens exhibiting a wide variety of microstructure have been imaged and analysed. In this paper, analysis of a small set of porous rock specimens with structure ranging from unconsolidated sands to complex carbonates are illustrated. Computations made directly on the digitised tomographic images have been compared to laboratory measurements. The results are in excellent agreement. Additionally, local flow, diffusive and mechanical properties can be numerically derived from solutions of the relevant physical equations on the complex geometries; an experimentally intractable problem. Structural analysis of data sets includes grain and pore partitioning of the images. Local granular partitioning yields over 70,000 grains from a single image. Conventional grain size, shape and connectivity parameters are derived. The 3D organisation of grains can help in correlating grain size, shape and orientation to resultant physical properties. Pore network models generated from 3D images yield over 100000 pores and 200000 throats; comparing the pore structure for the different specimens illustrates the varied topology and geometry observed in porous rocks. This development foreshadows a new numerical laboratory approach to the study of complex porous materials

The exceptional influence of storm ‘Xaver’ on design water levels in the German Bight

Design water levels for coastal structures are usually estimated based on extreme value statistics. Since their robustness depends heavily on the sample size of observations, regular statistical updates are needed, especially after extreme events. Here, we demonstrate the exceptional influence of such an event based on storm 'Xaver', which caused record breaking water levels for large parts of the southwestern German North Sea coastline on 6 December 2013. We show that the water level estimates for a 1 in 200 years event increased by up to 40 cm due to the update after 'Xaver', a value twice as large as the estimated regional sea level rise for the entire 20th century. However, a thorough analysis of different independent meteorological (winds and pressure) and oceanographic components (tides, surges, mean sea level (MSL) anomalies) driving the event reveals that their observed combination does not yet represent the physically possible worst case scenario. Neither tides, nor surges nor MSL anomalies were at their observational maximum, suggesting that there is a realistic risk of a storm like 'Xaver' to cause even higher extreme water levels by a few decimetres under current climate conditions. Our results question purely statistical design approaches of coastal structures, which neglect the physical boundary conditions of individual extreme events

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

Second order analysis of geometric functionals of Boolean models

This paper presents asymptotic covariance formulae and central limit theorems for geometric functionals, including volume, surface area, and all Minkowski functionals and translation invariant Minkowski tensors as prominent examples, of stationary Boolean models. Special focus is put on the anisotropic case. In the (anisotropic) example of aligned rectangles, we provide explicit analytic formulae and compare them with simulation results. We discuss which information about the grain distribution second moments add to the mean values.Comment: Chapter of the forthcoming book "Tensor Valuations and their Applications in Stochastic Geometry and Imaging" in Lecture Notes in Mathematics edited by Markus Kiderlen and Eva B. Vedel Jensen. (The second version mainly resolves minor LaTeX problems.

DNA methylation transcriptionally regulates the putative tumor cell growth suppressor ZNF677 in non-small cell lung cancers

In our study, we investigated the role of ZNF677 in non-small cell lung cancers (NSCLC). By comparing ZNF677 expression in primary tumor (TU) and in the majority of cases also of corresponding non-malignant lung tissue (NL) samples from > 1,000 NSCLC patients, we found tumor-specific downregulation of ZNF677 expression (adjusted p-values < 0.001). We identified methylation as main mechanism for ZNF677 downregulation in NSCLC cells and we observed tumor-specific ZNF677 methylation in NSCLC patients (p < 0.0001). In the majority of TUs, ZNF677 methylation was associated with loss of ZNF677 expression. Moreover, ZNF677 overexpression in NSCLC cells was associated with reduced cell proliferation and cell migration. ZNF677 was identified to regulate expression of many genes mainly involved in growth hormone regulation and interferon signalling. Finally, patients with ZNF677 methylated TUs had a shorter overall survival compared to patients with ZNF677 not methylated TUs (p = 0.013). Overall, our results demonstrate that ZNF677 is trancriptionally regulated by methylation in NSCLCs, suggest that ZNF677 has tumor cell growth suppressing properties in NSCLCs and that ZNF677 methylation might serve as prognostic parameter in these patients