New Travelling Wave Solutions of Two Nonlinear Physical Models by Using a Modified Tanh-Coth Method

In this work, a modified tanh – coth method is used to derive travelling wave solutions for (2 + 1)-dimensional Zakharov-Kuznetsov (ZK) equation and (3 + 1)-dimensional Burgers equation. A new variable is used to solve these equations and established new travelling wave solutions. </jats:p

Dark Matter Halo Profiles in Scale-Free Cosmologies

We explore the dependence of the central logarithmic slope of dark matter halo density profiles $\alpha$ on the spectral index $n$ of the linear matter power spectrum $P(k)$ using cosmological $N$-body simulations of scale-free models (i.e. $P(k) \propto k^n$). For each of our simulations we identify samples of well resolved haloes in dynamical equilibrium and we analyse their mass profiles. By parameterising the mass profile using a ``generalised'' Navarro, Frenk & White profile in which the central logarithmic slope $\alpha$ is allowed to vary while preserving the $r^{-3}$ asymptotic form at large radii, we obtain preferred central slopes for haloes in each of our models. There is a strong correlation between $\alpha$ and $n$, such that $\alpha$ becomes shallower as $n$ becomes steeper. However, if we normalise our mass profiles by $r_{-2}$, the radius at which the logarithmic slope of the density profile is -2, we find that these differences are no longer present. We conclude that there is no evidence for convergence to a unique central asymptotic slope, at least on the scales that we can resolve.Comment: 9 pages, 4 figures. Accepted for publication in MNRA

The Metropolis algorithm: A useful tool for epidemiologists

The Metropolis algorithm is a Markov chain Monte Carlo (MCMC) algorithm used to simulate from parameter distributions of interest, such as generalized linear model parameters. The "Metropolis step" is a keystone concept that underlies classical and modern MCMC methods and facilitates simple analysis of complex statistical models. Beyond Bayesian analysis, MCMC is useful for generating uncertainty intervals, even under the common scenario in causal inference in which the target parameter is not directly estimated by a single, fitted statistical model. We demonstrate, with a worked example, pseudo-code, and R code, the basic mechanics of the Metropolis algorithm. We use the Metropolis algorithm to estimate the odds ratio and risk difference contrasting the risk of childhood leukemia among those exposed to high versus low level magnetic fields. This approach can be used for inference from Bayesian and frequentist paradigms and, in small samples, offers advantages over large-sample methods like the bootstrap.Comment: 26 pages, 3 figure

Observed and Expected Mortality in Cohort Studies

Epidemiologists often compare the observed number of deaths in a cohort with the expected number of deaths, obtained by multiplying person-time accrued in the cohort by mortality rates for a reference population (ideally, a reference that represents the mortality rate in the cohort in the absence of exposure). However, if exposure is hazardous (or salutary), this calculation will not consistently estimate the number of deaths expected in the absence of exposure because exposure will have affected the distribution of person-time observed in the study cohort. While problems with interpretation of this standard calculation of expected counts were discussed more than 2 decades ago, these discussions had little impact on epidemiologic practice. The logic of counterfactuals may help clarify this topic as we revisit these issues. In this paper, we describe a simple way to consistently estimate the expected number of deaths in such settings, and we illustrate the approach using data from a cohort study of mortality among underground miners

A Compensatory Mutation Provides Resistance to Disparate HIV Fusion Inhibitor Peptides and Enhances Membrane Fusion

Fusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide, are peptides designed to competitively inhibit the viral fusion protein gp41. With the emergence of drug resistance, there is an increased need for effective and unique alternatives within this class of antivirals. One such alternative is a class of cyclic, cationic, antimicrobial peptides known as θ-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity. Currently, the θ-defensin analog RC-101 is being developed as a microbicide due to its specific antiviral activity, lack of toxicity to cells and tissues, and safety in animals. Understanding potential RC-101 resistance, and how resistance to other fusion inhibitors affects RC-101 susceptibility, is critical for future development. In previous studies, we identified a mutant, R5-tropic virus that had evolved partial resistance to RC-101 during in vitro selection. Here, we report that a secondary mutation in gp41 was found to restore replicative fitness, membrane fusion, and the rate of viral entry, which were compromised by an initial mutation providing partial RC-101 resistance. Interestingly, we show that RC-101 is effective against two enfuvirtide-resistant mutants, demonstrating the clinical importance of RC-101 as a unique fusion inhibitor. These findings both expand our understanding of HIV drug-resistance to diverse peptide fusion inhibitors and emphasize the significance of compensatory gp41 mutations. © 2013 Wood et al

Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data

Background: Estimates of relationships among Staphylococcus species have been hampered by poor and inconsistent resolution of phylogenies based largely on single gene analyses incorporating only a limited taxon sample. As such, the evolutionary relationships and hierarchical classification schemes among species have not been confidently established. Here, we address these points through analyses of DNA sequence data from multiple loci (16S rRNA gene, dnaJ, rpoB, and tuf gene fragments) using multiple Bayesian and maximum likelihood phylogenetic approaches that incorporate nearly all recognized Staphylococcus taxa. Results: We estimated the phylogeny of fifty-seven Staphylococcus taxa using partitioned-model Bayesian and maximum likelihood analysis, as well as Bayesian gene-tree species-tree methods. Regardless of methodology, we found broad agreement among methods that the current cluster groups require revision, although there was some disagreement among methods in resolution of higher order relationships. Based on our phylogenetic estimates, we propose a refined classification for Staphylococcus with species being classified into 15 cluster groups (based on molecular data) that adhere to six species groups (based on phenotypic properties). Conclusions: Our findings are in general agreement with gene tree-based reports of the staphylococcal phylogeny, although we identify multiple previously unreported relationships among species. Our results support the general importance of such multilocus assessments as a standard in microbial studies to more robustly infer relationships among recognized and newly discovered lineages

Hydrodynamics of cold atomic gases in the limit of weak nonlinearity, dispersion and dissipation

Dynamics of interacting cold atomic gases have recently become a focus of both experimental and theoretical studies. Often cold atom systems show hydrodynamic behavior and support the propagation of nonlinear dispersive waves. Although this propagation depends on many details of the system, a great insight can be obtained in the rather universal limit of weak nonlinearity, dispersion and dissipation (WNDD). In this limit, using a reductive perturbation method we map some of the hydrodynamic models relevant to cold atoms to well known chiral one-dimensional equations such as KdV, Burgers, KdV-Burgers, and Benjamin-Ono equations. These equations have been thoroughly studied in literature. The mapping gives us a simple way to make estimates for original hydrodynamic equations and to study the interplay between nonlinearity, dissipation and dispersion which are the hallmarks of nonlinear hydrodynamics.Comment: 18 pages, 3 figures, 1 tabl

Spirometry reference equations for central European populations from school age to old age.

Spirometry reference values are important for the interpretation of spirometry results. Reference values should be updated regularly, derived from a population as similar to the population for which they are to be used and span across all ages. Such spirometry reference equations are currently lacking for central European populations. To develop spirometry reference equations for central European populations between 8 and 90 years of age. We used data collected between January 1993 and December 2010 from a central European population. The data was modelled using "Generalized Additive Models for Location, Scale and Shape" (GAMLSS). The spirometry reference equations were derived from 118'891 individuals consisting of 60'624 (51%) females and 58'267 (49%) males. Altogether, there were 18'211 (15.3%) children under the age of 18 years. We developed spirometry reference equations for a central European population between 8 and 90 years of age that can be implemented in a wide range of clinical settings

Post-ER Stress Biogenesis of Golgi Is Governed by Giantin

Background: The Golgi apparatus undergoes disorganization in response to stress, but it is able to restore compact and perinuclear structure under recovery. This self-organization mechanism is significant for cellular homeostasis, but remains mostly elusive, as does the role of giantin, the largest Golgi matrix dimeric protein. Methods: In HeLa and different prostate cancer cells, we used the model of cellular stress induced by Brefeldin A (BFA). The conformational structure of giantin was assessed by proximity ligation assay and atomic force microscopy. The post-BFA distribution of Golgi resident enzymes was examined by 3D SIM high-resolution microscopy. Results: We detected that giantin is rather flexible than an extended coiled-coil dimer and BFA-induced Golgi disassembly was associated with giantin monomerization. A fusion of the nascent Golgi membranes after BFA washout is forced by giantin re-dimerization via disulfide bond in its luminal domain and assisted by Rab6a GTPase. GM130-GRASP65-dependent enzymes are able to reach the nascent Golgi membranes, while giantin-sensitive enzymes appeared at the Golgi after its complete recovery via direct interaction of their cytoplasmic tail with N-terminus of giantin. Conclusion: Post-stress recovery of Golgi is conducted by giantin dimer and Golgi proteins refill membranes according to their docking affiliation rather than their intra-Golgi location