Diffusion-Induced Oscillations of Extended Defects

From a simple model for the driven motion of a planar interface under the influence of a diffusion field we derive a damped nonlinear oscillator equation for the interface position. Inside an unstable regime, where the damping term is negative, we find limit-cycle solutions, describing an oscillatory propagation of the interface. In case of a growing solidification front this offers a transparent scenario for the formation of solute bands in binary alloys, and, taking into account the Mullins-Sekerka instability, of banded structures

Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as samples from weight matrices we derive a unique probability distribution for assignments of sites into clusters. Our algorithm, 'PROCSE' (probabilistic clustering of sequences), uses Monte-Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters. The algorithm internally determines the number of clusters from the data, and assigns significance to the resulting clusters. We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from weight matrices (WMs) when these WMs are unknown. Our analysis suggests that the set of all putative sites for a single genome (e.g. E. coli) is largely inadequate for clustering. When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible. We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table

Robust on-line diagnosis tool for the early accident detection in nuclear power plants

© 2019 Any loss of coolant accident mitigation strategy is necessarily bound by the promptness of the break detection as well as the accuracy of its diagnosis. The availability of on-line monitoring tools is then crucial for enhancing safety of nuclear facilities. The requirements of robustness and short latency implied by the necessity for fast and effective actions are undermined by the challenges associated with break prediction during transients. This study presents a novel approach to tackle the challenges associated with the on-line diagnostics of loss of coolant accidents and the limitations of the current state of the art. Based on the combination of a set of artificial neural network architectures through the use of Bayesian statistics, it allows to robustly absorb different sources of uncertainty without requiring their explicit characterization in input. It provides the quantification of the output confidence bounds but also enhances of the model response accuracy. The implemented methodology allows to relax the need for model selection as well as to limit the demand for user-defined analysis parameters. A numerical case-study entailing a 220 MWe heavy-water reactor is analysed in order to test the efficiency of the developed computational tool

Generalized Dynamic Scaling for Critical Magnetic Systems

The short-time behaviour of the critical dynamics for magnetic systems is investigated with Monte Carlo methods. Without losing the generality, we consider the relaxation process for the two dimensional Ising and Potts model starting from an initial state with very high temperature and arbitrary magnetization. We confirm the generalized scaling form and observe that the critical characteristic functions of the initial magnetization for the Ising and the Potts model are quite different.Comment: 32 pages with15 eps-figure

Syndromic Diagnosis of Malaria in Rural Sierra Leone and Proposed Additions to the National Integrated Management of Childhood Illness Guidelines for Fever

Many countries in Africa, including Sierra Leone, have adopted artemisinin-based combination therapy as first-line therapy for treatment of patients with malaria. Because laboratory testing is often unavailable in rural areas, the cost-benefit and viability of this approach may depend on accurately diagnosing malaria by using clinical criteria. We assessed the accuracy of syndromic diagnosis for malaria in three peripheral health units in rural Sierra Leone and determined factors that were associated with an accurate malaria diagnosis. Of 175 children diagnosed with malaria on syndromic grounds, 143 (82%) were confirmed by the Paracheck-Pf test. In a multivariate analysis, splenomegaly (P = 0.04) was the only clinical sign significantly associated with laboratory-confirmed malaria, and sleeping under a bed net was protective (P = 0.05). Our findings show that clinical malaria is diagnosed relatively accurately in rural Sierra Leone. Incorporating bed net use and splenomegaly into the national Integrated Management of Childhood Illness guidelines for evaluation of fever may further enhance diagnostic accuracy for malaria

Dynamic structure factor of the Ising model with purely relaxational dynamics

We compute the dynamic structure factor for the Ising model with a purely relaxational dynamics (model A). We perform a perturbative calculation in the $\epsilon$ expansion, at two loops in the high-temperature phase and at one loop in the temperature magnetic-field plane, and a Monte Carlo simulation in the high-temperature phase. We find that the dynamic structure factor is very well approximated by its mean-field Gaussian form up to moderately large values of the frequency $\omega$ and momentum $k$. In the region we can investigate, $k\xi \lesssim 5$, $\omega \tau \lesssim 10$, where $\xi$ is the correlation length and $\tau$ the zero-momentum autocorrelation time, deviations are at most of a few percent.Comment: 21 pages, 3 figure

The cohesin ring concatenates sister DNA molecules

Sister chromatid cohesion, which is essential for mitosis, is mediated by a multi-subunit protein complex called cohesin whose Scc1, Smc1, and Smc3 subunits form a tripartite ring structure. It has been proposed that cohesin holds sister DNAs together by trapping them inside its ring. To test this, we used site-specific cross-linking to create chemical connections at the three interfaces between the ring’s three constituent polypeptides, thereby creating covalently closed cohesin rings. As predicted by the ring entrapment model, this procedure produces dimeric DNA/cohesin structures that are resistant to protein denaturation. We conclude that cohesin rings concatenate individual sister minichromosome DNAs

Anomalous scaling of passively advected magnetic field in the presence of strong anisotropy

Inertial-range scaling behavior of high-order (up to order N=51) structure functions of a passively advected vector field has been analyzed in the framework of the rapid-change model with strong small-scale anisotropy with the aid of the renormalization group and the operator-product expansion. It has been shown that in inertial range the leading terms of the structure functions are coordinate independent, but powerlike corrections appear with the same anomalous scaling exponents as for the passively advected scalar field. These exponents depend on anisotropy parameters in such a way that a specific hierarchy related to the degree of anisotropy is observed. Deviations from power-law behavior like oscillations or logarithmic behavior in the corrections to structure functions have not been found.Comment: 15 pages, 18 figure

Field theoretic renormalization group for a nonlinear diffusion equation

The paper is an attempt to relate two vast areas of the applicability of the renormalization group (RG): field theoretic models and partial differential equations. It is shown that the Green function of a nonlinear diffusion equation can be viewed as a correlation function in a field-theoretic model with an ultralocal term, concentrated at a spacetime point. This field theory is shown to be multiplicatively renormalizable, so that the RG equations can be derived in a standard fashion, and the RG functions (the $\beta$ function and anomalous dimensions) can be calculated within a controlled approximation. A direct calculation carried out in the two-loop approximation for the nonlinearity of the form $\phi^{\alpha}$, where $\alpha>1$ is not necessarily integer, confirms the validity and self-consistency of the approach. The explicit self-similar solution is obtained for the infrared asymptotic region, with exactly known exponents; its range of validity and relationship to previous treatments are briefly discussed.Comment: 8 pages, 2 figures, RevTe

Shedding of soluble glycoprotein 1 detected during acute Lassa virus infection in human subjects

<p>Abstract</p> <p>Background</p> <p>Lassa hemorrhagic fever (LHF) is a neglected tropical disease with significant impact on the health care system, society, and economy of Western and Central African nations where it is endemic. With a high rate of infection that may lead to morbidity and mortality, understanding how the virus interacts with the host's immune system is of great importance for generating vaccines and therapeutics. Previous work by our group identified a soluble isoform of the Lassa virus (LASV) GP1 (sGP1) <it>in vitro </it>resulting from the expression of the glycoprotein complex (GPC) gene <abbrgrp><abbr bid="B1">1</abbr><abbr bid="B2">2</abbr></abbrgrp>. Though no work has directly been done to demonstrate the function of this soluble isoform in arenaviral infections, evidence points to immunomodulatory effects against the host's immune system mediated by a secreted glycoprotein component in filoviruses, another class of hemorrhagic fever-causing viruses. A significant fraction of shed glycoprotein isoforms during viral infection and biogenesis may attenuate the host's inflammatory response, thereby enhancing viral replication and tissue damage. Such shed glycoprotein mediated effects were previously reported for Ebola virus (EBOV), a filovirus that also causes hemorrhagic fever with nearly 90% fatality rates <abbrgrp><abbr bid="B3">3</abbr><abbr bid="B4">4</abbr><abbr bid="B5">5</abbr></abbrgrp>. The identification of an analogous phenomenon <it>in vivo </it>could establish a new correlate of LHF infection leading to the development of sensitive diagnostics targeting the earliest molecular events of the disease. Additionally, the reversal of potentially untoward immunomodulatory functions mediated by sGP1 could potentiate the development of novel therapeutic intervention. To this end, we investigated the presence of sGP1 in the serum of suspected LASV patients admitted to the Kenema Government Hospital (KGH) Lassa Fever Ward (LFW), in Kenema, Sierra Leone that tested positive for viral antigen or displayed classical signs of Lassa fever.</p> <p>Results</p> <p>It is reasonable to expect that a narrow window exists for detection of sGP1 as the sole protein shed during early arenaviral biogenesis. This phenomenon was clearly distinguishable from virion-associated GP1 only prior to the emergence of <it>de novo </it>viral particles. Despite this restricted time frame, in 2/46 suspected cases in two studies performed in late 2009 and early 2010, soluble glycoprotein component shedding was identified. Differential detection of viral antigens GP1, GP2, and NP by western blot yielded five different scenarios: whole LASV virions (GP1, GP2, NP; i.e. active viremia), different combinations of these three proteins, sGP1 only, NP only, and absence of all three proteins. Four additional samples showed inconclusive evidence for sGP1 shedding due to lack of detection of GP2 and NP by western blot; however, a sensitive LASV NP antigen capture ELISA generated marginally positive signals</p> <p>Conclusions</p> <p>During a narrow window following active infection with LASV, soluble GP1 can be detected in patient sera. This phenomenon parallels other VHF infection profiles, with the actual role of a soluble viral glycoprotein component <it>in vivo </it>remaining largely speculative. The expenditure of energy and cellular resources toward secretion of a critical protein during viral biogenesis without apparent specific function requires further investigation. Future studies will be aimed at systematically identifying the role of LASV sGP1 in the infection process and outcome <it>in vitro </it>and <it>in vivo</it>.</p