H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

International audienceSoil microbial communities are continuously exposed to H2 diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2 can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2 exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2 exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2 oxidation activity in soil changed drastically upon elevated H2 exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2 exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2 exposure, suggesting that H2 affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities

Flame propagation in random media

We introduce a phase-field model to describe the dynamics of a self-sustaining propagating combustion front within a medium of randomly distributed reactants. Numerical simulations of this model show that a flame front exists for reactant concentration $c > c^* > 0$, while its vanishing at $c^*$ is consistent with mean-field percolation theory. For $c > c^*$, we find that the interface associated with the diffuse combustion zone exhibits kinetic roughening characteristic of the Kardar-Parisi-Zhang equation.Comment: 4, LR541

Symplectic integrators with adaptive time steps

In recent decades, there have been many attempts to construct symplectic integrators with variable time steps, with rather disappointing results. In this paper we identify the causes for this lack of performance, and find that they fall into two categories. In the first, the time step is considered a function of time alone, \Delta=\Delta(t). In this case, backwards error analysis shows that while the algorithms remain symplectic, parametric instabilities arise because of resonance between oscillations of \Delta(t) and the orbital motion. In the second category the time step is a function of phase space variables \Delta=\Delta(q,p). In this case, the system of equations to be solved is analyzed by introducing a new time variable \tau with dt=\Delta(q,p) d\tau. The transformed equations are no longer in Hamiltonian form, and thus are not guaranteed to be stable even when integrated using a method which is symplectic for constant \Delta. We analyze two methods for integrating the transformed equations which do, however, preserve the structure of the original equations. The first is an extended phase space method, which has been successfully used in previous studies of adaptive time step symplectic integrators. The second, novel, method is based on a non-canonical mixed-variable generating function. Numerical trials for both of these methods show good results, without parametric instabilities or spurious growth or damping. It is then shown how to adapt the time step to an error estimate found by backward error analysis, in order to optimize the time-stepping scheme. Numerical results are obtained using this formulation and compared with other time-stepping schemes for the extended phase space symplectic method.Comment: 23 pages, 9 figures, submitted to Plasma Phys. Control. Fusio

Scaling, Propagation, and Kinetic Roughening of Flame Fronts in Random Media

We introduce a model of two coupled reaction-diffusion equations to describe the dynamics and propagation of flame fronts in random media. The model incorporates heat diffusion, its dissipation, and its production through coupling to the background reactant density. We first show analytically and numerically that there is a finite critical value of the background density, below which the front associated with the temperature field stops propagating. The critical exponents associated with this transition are shown to be consistent with mean field theory of percolation. Second, we study the kinetic roughening associated with a moving planar flame front above the critical density. By numerically calculating the time dependent width and equal time height correlation function of the front, we demonstrate that the roughening process belongs to the universality class of the Kardar-Parisi-Zhang interface equation. Finally, we show how this interface equation can be analytically derived from our model in the limit of almost uniform background density.Comment: Standard LaTeX, no figures, 29 pages; (to appear in J. Stat. Phys. vol.81, 1995). Complete file available at http://www.physics.helsinki.fi/tft/tft.html or anonymous ftp at ftp://rock.helsinki.fi/pub/preprints/tft

The Impact of EU Norms and Policies on Consumer Protection Enforcement in Serbia

Pursuant to its 2008 Stabilization and Association Agreement governing the process of EU integration, Serbia is obliged to align its consumer protection standards (including those related to enforcement) with those of the EU. This article considers the overall approach to enforcement of consumer law in Serbia, focussing in particular on the extent to which EU enforcement principles have been successfully exported to Serbia and whether the goals of EU consumer policy have been achieved. It argues that the incorporation of EU norms has brought fundamental changes to Serbian enforcement mechanisms at a formal level, such as in relation to mediation processes as well as the introduction of injunctions for the protection of collective consumer interests. In practice, however, the impact of this incorporation is quite limited. A number of factors that restrict the practical effectiveness of the mediation processes and injunctions required by EU law are explored in the article, including weak sanctions, excessive reliance on poorly resourced consumer organizations, absence of a business culture of compliance or a sophisticated and determined consumer protection enforcement culture sufficiently grounded in expertise, as well as an overarching political, legislative, and institutional instability. These factors also undermine the general aim of EU policy to achieve effective consumer protection enforcement in the Serbian context

Targeted T1 Magnetic Resonance Imaging Contrast Enhancement with Extraordinarily Small CoFe2O4 Nanoparticles

Extraordinarily small (2.4 nm) cobalt ferrite nanoparticles (ESCIoNs) were synthesized by a one-pot thermal decomposition approach to study their potential as magnetic resonance imaging (MRI) contrast agents. Fine size control was achieved using oleylamine alone, and annular dark-field scanning transmission electron microscopy revealed highly crystalline cubic spinel particles with atomic resolution. Ligand exchange with dimercaptosuccinic acid rendered the particles stable in physiological conditions with a hydrodynamic diameter of 12 nm. The particles displayed superparamagnetic properties and a low r2/r1 ratio suitable for a T1 contrast agent. The particles were functionalized with bile acid, which improved biocompatibility by significant reduction of reactive oxygen species generation and is a first step toward liver-targeted T1 MRI. Our study demonstrates the potential of ESCIoNs as T1 MRI contrast agents

Catalogue of BRITE-Constellation targets I. Fields 1 to 14 (November 2013 - April 2016)

The BRIght Target Explorer (BRITE) mission collects photometric time series in two passbands aiming to investigate stellar structure and evolution. Since their launches in the years 2013 and 2014, the constellation of five BRITE nano-satellites has observed a total of more than 700 individual bright stars in 64 fields. Some targets have been observed multiple times. Thus, the total time base of the data sets acquired for those stars can be as long as nine years. Our aim is to provide a complete description of ready-to-use BRITE data, to show the scientific potential of the BRITE-Constellation data by identifying the most interesting targets, and to demonstrate and encourage how scientists can use these data in their research. We apply a decorrelation process to the automatically reduced BRITE-Constellation data to correct for instrumental effects. We perform a statistical analysis of the light curves obtained for the 300 stars observed in the first 14 fields during the first ~2.5 years of the mission. We also perform cross-identification with the International Variable Star Index. We present the data obtained by the BRITE-Constellation mission in the first 14 fields it observed from November 2013 to April 2016. We also describe the properties of the data for these fields and the 300 stars observed in them. Using these data, we detected variability in 64% of the presented sample of stars. Sixty-four stars or 21.3% of the sample have not yet been identified as variable in the literature and their data have not been analysed in detail. They can therefore provide valuable scientific material for further research. All data are made publicly available through the BRITE Public Data Archive and the Canadian Astronomy Data Centre.Comment: accepted by Astronomy & Astrophysics, 13 pages main text, 22 pages of appendi

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin