Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Chemotaxonomy as a tool for interpreting the cryptic diversity of Poaceae pollen

The uniform morphology of different species of Poaceae (grass) pollen means that identification to below family level using light microscopy is extremely challenging. Poor taxonomic resolution reduces recoverable information from the grass pollen record, for example, species diversity and environmental preferences cannot be extracted. Recent research suggests Fourier Transform Infra-red Spectroscopy (FTIR) can be used to identify pollen grains based on their chemical composition. Here, we present a study of twelve species from eight subfamilies of Poaceae, selected from across the phylogeny but from a relatively constrained geographical area (tropical West Africa) to assess the feasibility of using this chemical method for identification within the Poaceae family. We assess several spectral processing methods and use K-nearest neighbour (k-nn) analyses, with a leave-one-out cross-validation, to generate identification success rates at different taxonomic levels. We demonstrate we can identify grass pollen grains to subfamily level with an 80% success rate. Our success in identifying Poaceae to subfamily level using FTIR provides an opportunity to generate high taxonomic resolution datasets in research areas such as palaeoecology, forensics, and melissopalynology quickly and at a relatively low cost

Renormalization of composite operators

The blocked composite operators are defined in the one-component Euclidean scalar field theory, and shown to generate a linear transformation of the operators, the operator mixing. This transformation allows us to introduce the parallel transport of the operators along the RG trajectory. The connection on this one-dimensional manifold governs the scale evolution of the operator mixing. It is shown that the solution of the eigenvalue problem of the connection gives the various scaling regimes and the relevant operators there. The relation to perturbative renormalization is also discussed in the framework of the $\phi^3$ theory in dimension $d=6$.Comment: 24 pages, revtex (accepted by Phys. Rev. D), changes in introduction and summar

Effect of tensor couplings in a relativistic Hartree approach for finite nuclei

The relativistic Hartree approach describing the bound states of both nucleons and anti-nucleons in finite nuclei has been extended to include tensor couplings for the $\omega$- and $\rho$-meson. After readjusting the parameters of the model to the properties of spherical nuclei, the effect of tensor-coupling terms rises the spin-orbit force by a factor of 2, while a large effective nucleon mass $m^{*}/M_{N} \approx 0.8$ sustains. The overall nucleon spectra of shell-model states are improved evidently. The predicted anti-nucleon spectra in the vacuum are deepened about 20 -- 30 MeV.Comment: 31 pages, 4 postscript figures include

Wegner-Houghton equation and derivative expansion

We study the derivative expansion for the effective action in the framework of the Exact Renormalization Group for a single component scalar theory. By truncating the expansion to the first two terms, the potential $U_k$ and the kinetic coefficient $Z_k$, our analysis suggests that a set of coupled differential equations for these two functions can be established under certain smoothness conditions for the background field and that sharp and smooth cut-off give the same result. In addition we find that, differently from the case of the potential, a further expansion is needed to obtain the differential equation for $Z_k$, according to the relative weight between the kinetic and the potential terms. As a result, two different approximations to the $Z_k$ equation are obtained. Finally a numerical analysis of the coupled equations for $U_k$ and $Z_k$ is performed at the non-gaussian fixed point in $D<4$ dimensions to determine the anomalous dimension of the field.Comment: 15 pages, 3 figure

Noncommutative massive Thirring model in three-dimensional spacetime

We evaluate the noncommutative Chern-Simons action induced by fermions interacting with an Abelian gauge field in a noncommutative massive Thirring model in (2+1)-dimensional spacetime. This calculation is performed in the Dirac and Majorana representations. We observe that in Majorana representation when $\theta$ goes to zero we do not have induced Chern-Simons term in the dimensional regularization scheme.Comment: Accepted to Phys. Rev. D; 9 pages, Revtex4, no figures, references added, minor improvements, Eq.31 correcte

The modern pollen-vegetation relationship of a tropical forest-savannah mosaic landscape, Ghana, West Africa

Transitions between forest and savannah vegetation types in fossil pollen records are often poorly understood due to over-production by taxa such as Poaceae and a lack of modern pollen-vegetation studies. Here, modern pollen assemblages from within a forest-savannah transition in West Africa are presented and compared, their characteristic taxa discussed, and implications for the fossil record considered. Fifteen artificial pollen traps were deployed for 1 year, to collect pollen rain from three vegetation plots within the forest-savannah transition in Ghana. High percentages of Poaceae and Melastomataceae/Combretaceae were recorded in all three plots. Erythrophleum suaveolens characterised the forest plot, Manilkara obovata the transition plot and Terminalia the savannah plot. The results indicate that Poaceae pollen influx rates provide the best representation of the forest-savannah gradient, and that a Poaceae abundance of >40% should be considered as indicative of savannah-type vegetation in the fossil record

South African NGOs and the public sphere: between popular movements and partnerships for development.

This article examines the widespread notion that post-apartheid democracy can be deepened and civil society strengthened by NGO activities in the sphere of public debate and participation. I focus on a number of interrelated processes which I argue may compromise NGOs' ability to expand the public sphere: first, donors' overwhelming focus on NGOs as the sole representative of civil society may contribute to a homogenous and institutionalised public sphere; second, the tendency for NGOs to be drawn into partnerships with government bodies and corporate sponsors casts doubt on their ability to open up spaces for critical public debate. By directing attention to popular movements as potentially offering a site for the production of critique, NGOs' relationships to such movements are examined. It is argued that attention must be paid to the processes of NGO-isation and reformism by which NGOs themselves come to define what civil society should be and may consequently contain counterpublic spheres

Effective Action for QED with Fermion Self-Interaction in D=2 and D=3 Dimensions

In this work we discuss the effect of the quartic fermion self-interaction of Thirring type in QED in D=2 and D=3 dimensions. This is done through the computation of the effective action up to quadratic terms in the photon field. We analyze the corresponding nonlocal photon propagators nonperturbatively in % \frac{k}{m}, where k is the photon momentum and m the fermion mass. The poles of the propagators were determined numerically by using the Mathematica software. In D=2 there is always a massless pole whereas for strong enough Thirring coupling a massive pole may appear . For D=3 there are three regions in parameters space. We may have one or two massive poles or even no pole at all. The inter-quark static potential is computed analytically in D=2. We notice that the Thirring interaction contributes with a screening term to the confining linear potential of massive QED_{2}. In D=3 the static potential must be calculated numerically. The screening nature of the massive QED$_{3}$ prevails at any distance, indicating that this is a universal feature of % D=3 electromagnetic interaction. Our results become exact for an infinite number of fermion flavors.Comment: Latex, 13 pages, 3 figure

Boundary conditions of workplace coaching outcomes

Purpose In order to address the need for greater understanding about the occupational and practice determinants of effective workplace coaching, this study examines the associations of two coaching practice factors (coaching format and external versus internal coaching provision), and coachees’ job complexity with perceived outcomes from coaching. Design/methodology/approach A survey of 161 individuals who had received workplace coaching was conducted. Participants provided data on two outcome criteria (self-reported work well-being and personal effectiveness at work). Findings Analysis indicated that external coaches and blended format coaching were most strongly associated with work well-being outcomes. Our examination of interaction effects showed that coaching provided by external coaches was more strongly associated with outcomes for individuals working in the most complex job roles. Originality/value The original contribution of our findings are in terms of the implications for coaches, managers and HR practitioners by showing how coaching can be implemented differentially and most effectively based on desired outcome criteria and features of coachees’ job situations