Lagrangian temperature, velocity and local heat flux measurement in Rayleigh-Benard convection

We have developed a small, neutrally buoyant, wireless temperature sensor. Using a camera for optical tracking, we obtain simultaneous measurements of position and temperature of the sensor as it is carried along by the flow in Rayleigh-B\'enard convection, at $Ra \sim 10^{10}$. We report on statistics of temperature, velocity, and heat transport in turbulent thermal convection. The motion of the sensor particle exhibits dynamics close to that of Lagrangian tracers in hydrodynamic turbulence. We also quantify heat transport in plumes, revealing self-similarity and extreme variations from plume to plume.Comment: 4 page

Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci

<p>Abstract</p> <p>Background</p> <p>The soil fungus <it>Rhizoctonia solani </it>anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of <it>R. solani </it>AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of <it>R. solani </it>AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of <it>R. solani </it>AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of <it>R. solani </it>AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89).</p> <p>Results</p> <p>Populations of <it>R. solani </it>AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of <it>R. solani </it>AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of <it>R. solani </it>AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Φ_{<it>ST </it>}= 0.257, significant at P < 0.05) but not for locus pP42F (Φ_{<it>ST </it>}= 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of <it>R. solani </it>AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of <it>R. solani </it>AG-3.</p> <p>Conclusion</p> <p>The two sisters populations of the basidiomycete fungus <it>R. solani </it>AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.</p

Characterizing flows with an instrumented particle measuring Lagrangian accelerations

We present in this article a novel Lagrangian measurement technique: an instrumented particle which continuously transmits the force/acceleration acting on it as it is advected in a flow. We develop signal processing methods to extract information on the flow from the acceleration signal transmitted by the particle. Notably, we are able to characterize the force acting on the particle and to identify the presence of a permanent large-scale vortex structure. Our technique provides a fast, robust and efficient tool to characterize flows, and it is particularly suited to obtain Lagrangian statistics along long trajectories or in cases where optical measurement techniques are not or hardly applicable.Comment: submitted to New Journal of Physic

Monte Carlo study of the Widom-Rowlinson fluid using cluster methods

The Widom-Rowlinson model of a fluid mixture is studied using a new cluster algorithm that is a generalization of the invaded cluster algorithm previously applied to Potts models. Our estimate of the critical exponents for the two-component fluid are consistent with the Ising universality class in two and three dimensions. We also present results for the three-component fluid.Comment: 13 pages RevTex and 2 Postscript figure

Statistical Analyses Support Power Law Distributions Found in Neuronal Avalanches

The size distribution of neuronal avalanches in cortical networks has been reported to follow a power law distribution with exponent close to −1.5, which is a reflection of long-range spatial correlations in spontaneous neuronal activity. However, identifying power law scaling in empirical data can be difficult and sometimes controversial. In the present study, we tested the power law hypothesis for neuronal avalanches by using more stringent statistical analyses. In particular, we performed the following steps: (i) analysis of finite-size scaling to identify scale-free dynamics in neuronal avalanches, (ii) model parameter estimation to determine the specific exponent of the power law, and (iii) comparison of the power law to alternative model distributions. Consistent with critical state dynamics, avalanche size distributions exhibited robust scaling behavior in which the maximum avalanche size was limited only by the spatial extent of sampling (“finite size” effect). This scale-free dynamics suggests the power law as a model for the distribution of avalanche sizes. Using both the Kolmogorov-Smirnov statistic and a maximum likelihood approach, we found the slope to be close to −1.5, which is in line with previous reports. Finally, the power law model for neuronal avalanches was compared to the exponential and to various heavy-tail distributions based on the Kolmogorov-Smirnov distance and by using a log-likelihood ratio test. Both the power law distribution without and with exponential cut-off provided significantly better fits to the cluster size distributions in neuronal avalanches than the exponential, the lognormal and the gamma distribution. In summary, our findings strongly support the power law scaling in neuronal avalanches, providing further evidence for critical state dynamics in superficial layers of cortex

Non-targeting siRNA induces NPGPx expression to cooperate with exoribonuclease XRN2 for releasing the stress

Short interfering RNAs (siRNAs) target specific mRNAs for their degradation mediated by RNA-induced silencing complex (RISC). Persistent activation of siRNA-RISC frequently leads to non-targeting toxicity. However, how cells mediate this stress remains elusive. In this communication, we found that the presence of non-targeting siRNA selectively induced the expression of an endoplasmic reticulum (ER)-resident protein, non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx), but not other ER-stress proteins including GRP78, Calnexin and XBP1. Cells suffering from constant non-targeting siRNA stress grew slower and prolonged G1 phase, while NPGPx-depleted cells accumulated mature non-targeting siRNA and underwent apoptosis. Upon the stress, NPGPx covalently bound to exoribonuclease XRN2, facilitating XRN2 to remove accumulated non-targeting siRNA. These results suggest that NPGPx serves as a novel responder to non-targeting siRNA-induced stress in facilitating XRN2 to release the non-targeting siRNA accumulation

Frustrated hierarchical synchronization and emergent complexity in the human connectome network

The spontaneous emergence of coherent behavior through synchronization plays a key role in neural function, and its anomalies often lie at the basis of pathologies. Here we employ a parsimonious (mesoscopic) approach to study analytically and computationally the synchronization (Kuramoto) dynamics on the actual human-brain connectome network. We elucidate the existence of a so-far-uncovered intermediate phase, placed between the standard synchronous and asynchronous phases, i.e. between order and disorder. This novel phase stems from the hierarchical modular organization of the connectome. Where one would expect a hierarchical synchronization process, we show that the interplay between structural bottlenecks and quenched intrinsic frequency heterogeneities at many different scales, gives rise to frustrated synchronization, metastability, and chimera-like states, resulting in a very rich and complex phenomenology. We uncover the origin of the dynamic freezing behind these features by using spectral graph theory and discuss how the emerging complex synchronization patterns relate to the need for the brain to access –in a robust though flexible way– a large variety of functional attractors and dynamical repertoires without ad hoc fine-tuning to a critical pointWe acknowledge financial support from J. de Andalucía, grant P09-FQM-4682 and we thank O. Sporns for providing us access to the human connectome data

Critical synchronization dynamics of the Kuramoto model on connectome and small world graphs

The hypothesis, that cortical dynamics operates near criticality also suggests, that it exhibits universal critical exponents which marks the Kuramoto equation, a fundamental model for synchronization, as a prime candidate for an underlying universal model. Here, we determined the synchronization behavior of this model by solving it numerically on a large, weighted human connectome network, containing 804092 nodes, in an assumed homeostatic state. Since this graph has a topological dimension $d < 4$, a real synchronization phase transition is not possible in the thermodynamic limit, still we could locate a transition between partially synchronized and desynchronized states. At this crossover point we observe power-law--tailed synchronization durations, with $\tau_t \simeq 1.2(1)$, away from experimental values for the brain. For comparison, on a large two-dimensional lattice, having additional random, long-range links, we obtain a mean-field value: $\tau_t \simeq 1.6(1)$. However, below the transition of the connectome we found global coupling control-parameter dependent exponents $1 < \tau_t \le 2$, overlapping with the range of human brain experiments. We also studied the effects of random flipping of a small portion of link weights, mimicking a network with inhibitory interactions, and found similar results. The control-parameter dependent exponent suggests extended dynamical criticality below the transition point.Comment: 12 pages, 9 figures + Supplemenraty material pdf 2 pages 4 figs, 1 table, accepted version in Scientific Report

Inhibition of HIV virus by neutralizing Vhh attached to dual functional liposomes encapsulating dapivirine

Although highly active antiretroviral therapy (HAART) has greatly improved the life expectancy of HIV/AIDS patients, the treatment is not curative. It is a global challenge which fosters an urgent need to develop an effective drug or neutralizing antibody delivery approach for the prevention and treatment of this disease. Due to the low density of envelope spikes with restricted mobility present on the surface of HIV virus, which limit the antibody potency and allow virus mutation and escape from the immune system, it is important for a neutralizing antibody to form bivalent or multivalent bonds with the virus. Liposome constructs could fulfil this need due to the flexible mobility of the membrane with its attached antibodies and the capacity for drug encapsulation. In this study, we evaluated the neutralization activity of a range of liposome formulations in different sizes coated with anti-gp120 llama antibody fragments (Vhhs) conjugated via either non-covalent metal chelation or a covalent linkage. The non-covalent construct demonstrated identical binding affinity to HIV-1 envelope glycoprotein gp120 and neutralizing ability for HIV virus as free Vhh. Although covalently linked Vhh showed significant binding affinity to gp120, it unexpectedly had a lower neutralization potency. This may be due to the comparability in size of the viral and liposome particles restricting the number which can be bound to the liposome surface so involving only a fraction of the antibodies, whereas non-covalently attached antibodies dissociate from the surface after acting with gp120 and free the remainder to bind further viruses. Covalently conjugated Vhh might also trigger the cellular uptake of a liposome-virion complex. To explore the possible ability of the antibody-coated liposomes to have a further function, we encapsulated the hydrophobic antiviral drug dapivirine into both of the non-covalently and covalently conjugated liposome formulations, both of which revealed high efficacy in reducing viral replication in vitro. Thus, dual function liposomes may lead to a novel strategy for the prophylaxis of HIV/AIDS by combining the neutralizing activity of Vhh with antiviral effects of high drug concentrations