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

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

Mark correlations: relating physical properties to spatial distributions

Mark correlations provide a systematic approach to look at objects both distributed in space and bearing intrinsic information, for instance on physical properties. The interplay of the objects' properties (marks) with the spatial clustering is of vivid interest for many applications; are, e.g., galaxies with high luminosities more strongly clustered than dim ones? Do neighbored pores in a sandstone have similar sizes? How does the shape of impact craters on a planet depend on the geological surface properties? In this article, we give an introduction into the appropriate mathematical framework to deal with such questions, i.e. the theory of marked point processes. After having clarified the notion of segregation effects, we define universal test quantities applicable to realizations of a marked point processes. We show their power using concrete data sets in analyzing the luminosity-dependence of the galaxy clustering, the alignment of dark matter halos in gravitational $N$-body simulations, the morphology- and diameter-dependence of the Martian crater distribution and the size correlations of pores in sandstone. In order to understand our data in more detail, we discuss the Boolean depletion model, the random field model and the Cox random field model. The first model describes depletion effects in the distribution of Martian craters and pores in sandstone, whereas the last one accounts at least qualitatively for the observed luminosity-dependence of the galaxy clustering.Comment: 35 pages, 12 figures. to be published in Lecture Notes of Physics, second Wuppertal conference "Spatial statistics and statistical physics

A Brain-Computer Interface Based Attention Training Program for Treating Attention Deficit Hyperactivity Disorder

10.1371/journal.pone.0046692PLoS ONE710

Finite element modelling of the effective elastic properties of partially saturated rocks

Simulation of effective physical properties from microtomographic 3D images of porous structures allows one to relate properties of rocks directly to their microstructure. A static FEM code has been previously used to estimate effective elastic properties of fully saturated monomineralic (quartz) rock under wet and dry conditions. We use the code to calculate elastic properties under partially saturated conditions. The numerical predictions are compared to the Gassmann theory combined with Wood's formula (GW) for a mixture of pore fluids, which is exact for a monomineralic macroscopically homogeneous porous medium. Results of the numerical simulations performed for two Boolean sphere pack distributions show significant deviation from the GW limit and depend on the spatial distribution of fluids. This is shown to be a numerical artefact caused by incomplete equilibration of fluid pressure, which is primarily due to insufficient spatial resolution. To investigate the effect of pore-size and pore geometry, we perform FEM simulations for a model with regular pore geometry, where all pore channels have the same size and shape. Accuracy of these simulations increases with the total cross-section area of the channels and the size of individual channels. For the case where the total cross-section of the channels is large enough (on the same order as total porosity), there is a minimum of 4 voxels per channel diameter required for adequate fluid pressure equilibration throughout the pore space. Increasing the spatial resolution of the digital models reduces the discrepancy between the simulations and theory, but unfortunately increases the memory and CPU requirements of the simulations

Digital and experimental rock analysis of proppant injection into naturally fractured coal

Proppant-laden fluid injection has been applied to many low permeability reservoirs, such as coal seams, to enhance permeability and thus production. While there are several laboratory-scale experimental studies on proppant placement in hydraulic fractures, the possible infiltration of proppant into natural fractures and its effect on overall permeability has received little attention. We study proppant injection into a naturally fractured coal sample by a combination of experimental and digital rock technologies. The sample was imaged using a helical X-ray computed tomography (micro-CT) scanner in as-received condition. Then, proppants of different size ranges were gradually injected into the sample, using a purpose-built X-ray transparent core flooding system, and the permeability was measured at different effective stresses. Subsequently, the propped sample was re-imaged and registered to the as-received image to map the internal changes. The experimental results indicated almost no permeability change of the sample after proppant injection. While proppant collection in the outlet proved passage of the proppant through the sample, observation of the sample indicated that some of the proppants were accumulated on the inlet face of the core and created a filter leading to no permeability increment. Micro-CT images confirmed that proppants were effectively placed in the sample and kept the fractures open. Numerical computation of permeability, using the digital coal sample in which accumulated proppants at the coal surface were excluded, indicated a significant increase in the sample permeability. Such an increase resulted from the opening of the fractures, particularly in the outlet region. This demonstrated the significance of proppant size selection for coal seam hydraulic fracturing. While proppants were successfully placed in the fractures, the experiment measured the permeability of the system, including proppants accumulated on the inlet, and could not effectively map the internal changes. This, therefore, needs to be considered when an experimental program for proppant injection is executed. To accurately monitor the internal changes, application of digital rock technology is recommended for such experiments

An integrated 1D–2D hydraulic modelling approach to assess the sensitivity of a coastal region to compound flooding hazard under climate change

Coastal regions are dynamic areas that often lie at the junction of different natural hazards. Extreme events such as storm surges and high precipitation are significant sources of concern for flood management. As climatic changes and sea-level rise put further pressure on these vulnerable systems, there is a need for a better understanding of the implications of compounding hazards. Recent computational advances in hydraulic modelling offer new opportunities to support decision-making and adaptation. Our research makes use of recently released features in the HEC-RAS version 5.0 software to develop an integrated 1D–2D hydrodynamic model. Using extreme value analysis with the Peaks-Over-Threshold method to define extreme scenarios, the model was applied to the eastern coast of the UK. The sensitivity of the protected wetland known as the Broads to a combination of fluvial, tidal and coastal sources of flooding was assessed, accounting for different rates of twenty-first century sea-level rise up to the year 2100. The 1D–2D approach led to a more detailed representation of inundation in coastal urban areas, while allowing for interactions with more fluvially dominated inland areas to be captured. While flooding was primarily driven by increased sea levels, combined events exacerbated flooded area by 5–40% and average depth by 10–32%, affecting different locations depending on the scenario. The results emphasise the importance of catchment-scale strategies that account for potentially interacting sources of flooding