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

Formation of cratonic lithosphere during the initiation of plate tectonics

Earth’s oldest near-surface material, the cratonic crust, is typically underlain by thick lithosphere (>200 km) of Archean age. This cratonic lithosphere likely thickened in a high-compressional-stress environment, potentially linked to the onset of crustal shortening in the Neoarchean. Mantle convection in the hotter Archean Earth would have imparted relatively low stresses on the lithosphere, whether or not plate tectonics was operating, so a high stress signal from the early Earth is paradoxical. We propose that a rapid transition from heat pipe–mode convection to the onset of plate tectonics generated the high stresses required to thicken the cratonic lithosphere. Numerical calculations are used to demonstrate that an existing buoyant and strong layer, representing depleted continental lithosphere, can thicken and stabilize during a lid-breaking event. The peak compressional stress experienced by the lithosphere is 3×–4× higher than for the stagnant-lid or mobile-lid regimes immediately before and after. It is plausible that the cratonic lithosphere has not been subjected to this high stress state since, explaining its long-term stability. The lid-breaking thickening event reproduces features observed in typical Neoarchean cratons, such as lithospheric seismological reflectors and the formation of thrust faults. Paleoarchean “pre-tectonic” structures can also survive the lid-breaking event, acting as strong rafts that are assembled during the compressive event. Together, the results indicate that the signature of a catastrophic switch from a stagnant-lid Earth to the initiation of plate tectonics has been captured and preserved in the characteristics of cratonic crust and lithosphere

IPM in Asia - A review of existing projects in the Philippines and Indonesia

peer reviewedIntegrated Pest Management means a pest management system that, in the context of the associated environment and the population dynamics of the pest species, utilizes ail suitable techniques and methods in as compatible a manner as possible and maintains the pest populations at levels below those causing economically unacceptable damage or 1055. FAO-Code- of Conduct 1984

IPM in Asia - A review of existing projects in the Philippines and Indonesia

peer reviewedIntegrated Pest Management means a pest management system that, in the context of the associated environment and the population dynamics of the pest species, utilizes ail suitable techniques and methods in as compatible a manner as possible and maintains the pest populations at levels below those causing economically unacceptable damage or 1055. FAO-Code- of Conduct 1984

On Exactness Of The Supersymmetric WKB Approximation Scheme

Exactness of the lowest order supersymmetric WKB (SWKB) quantization condition $\int^{x_2}_{x_1} \sqrt{E-\omega^2(x)} dx = n \hbar \pi$, for certain potentials, is examined, using complex integration technique. Comparison of the above scheme with a similar, but {\it exact} quantization condition, $\oint_c p(x,E) dx = 2\pi n \hbar$, originating from the quantum Hamilton-Jacobi formalism reveals that, the locations and the residues of the poles that contribute to these integrals match identically, for both of these cases. As these poles completely determine the eigenvalues in these two cases, the exactness of the SWKB for these potentials is accounted for. Three non-exact cases are also analysed; the origin of this non-exactness is shown to be due the presence of additional singularities in $\sqrt{E-\omega^2(x)}$, like branch cuts in the $x-$plane.Comment: 11 pages, latex, 1 figure available on reques

Schwinger-Dyson approach to non-equilibrium classical field theory

In this paper we discuss a Schwinger-Dyson [SD] approach for determining the time evolution of the unequal time correlation functions of a non-equilibrium classical field theory, where the classical system is described by an initial density matrix at time $t=0$. We focus on $\lambda \phi^4$ field theory in 1+1 space time dimensions where we can perform exact numerical simulations by sampling an ensemble of initial conditions specified by the initial density matrix. We discuss two approaches. The first, the bare vertex approximation [BVA], is based on ignoring vertex corrections to the SD equations in the auxiliary field formalism relevant for 1/N expansions. The second approximation is a related approximation made to the SD equations of the original formulation in terms of $\phi$ alone. We compare these SD approximations as well as a Hartree approximation with exact numerical simulations. We find that both approximations based on the SD equations yield good agreement with exact numerical simulations and cure the late time oscillation problem of the Hartree approximation. We also discuss the relationship between the quantum and classical SD equations.Comment: 36 pages, 5 figure

The Generalized PT-Symmetric Sinh-Gordon Potential Solvable within Quantum Hamilton-Jacobi Formalism

The generalized Sinh-Gordon potential is solved within quantum Hamiltonian Jacobi approach in the framework of PT symmetry. The quasi exact solutions of energy eigenvalues and eigenfunctions of the generalized Sinh-Gordon potential are found for n=0,1 states.Comment: 10 pages appear to in IJT

A Grand Canonical Ensemble Approach to the Thermodynamic Properties of the Nucleon in the Quark-Gluon Coupling Model

In this paper, we put forward a way to study the nucleon's thermodynamic properties such as its temperature, entropy and so on, without inputting any free parameters by human hand, even the nucleon's mass and radius. First we use the Lagrangian density of the quark gluon coupling fields to deduce the Dirac Equation of the quarks confined in the gluon fields. By boundary conditions we solve the wave functions and energy eigenvalues of the quarks, and thus get energy-momentum tensor, nucleon mass, and density of states. Then we utilize a hybrid grand canonical ensemble, to generate the temperature and chemical potentials of quarks, antiquarks of three flovars by the four conservation laws of the energy and the valence quark numbers, after which, all other thermodynamic properties are known. The only seemed free paremeter, the nucleon radius is finally determined by the grand potential minimal principle.Comment: 5 pages, LaTe

Dynamic Critical Behavior of the Chayes-Machta Algorithm for the Random-Cluster Model. I. Two Dimensions

We study, via Monte Carlo simulation, the dynamic critical behavior of the Chayes-Machta dynamics for the Fortuin-Kasteleyn random-cluster model, which generalizes the Swendsen-Wang dynamics for the q-state Potts ferromagnet to non-integer q \ge 1. We consider spatial dimension d=2 and 1.25 \le q \le 4 in steps of 0.25, on lattices up to 1024^2, and obtain estimates for the dynamic critical exponent z_{CM}. We present evidence that when 1 \le q \lesssim 1.95 the Ossola-Sokal conjecture z_{CM} \ge \beta/\nu is violated, though we also present plausible fits compatible with this conjecture. We show that the Li-Sokal bound z_{CM} \ge \alpha/\nu is close to being sharp over the entire range 1 \le q \le 4, but is probably non-sharp by a power. As a byproduct of our work, we also obtain evidence concerning the corrections to scaling in static observables.Comment: LaTeX2e, 75 pages including 26 Postscript figure

A Framework for Targeting Water, Sanitation and Hygiene Interventions in Pastoralist Populations in the Afar Region of Ethiopia

Globally, many populations face structural and environmental barriers to access safe water, sanitation and hygiene (WASH) services. Among these populations are many of the 200 million pastoralists whose livelihood patterns and extreme environmental settings challenge conventional WASH programming approaches. In this paper, we studied the Afar pastoralists in Ethiopia to identify WASH interventions that can mostly alleviate public health risks, within the population's structural and environmental living constraints. Surveys were carried out with 148 individuals and observational assessments made in 12 households as part of a Pastoralist Community WASH Risk Assessment. The results show that low levels of access to infrastructure are further compounded by risky behaviours related to water containment, storage and transportation. Additional behavioural risk factors were identified related to sanitation, hygiene and animal husbandry. The Pastoralist Community WASH Risk Assessment visually interprets the seriousness of the risks against the difficulty of addressing the problem. The assessment recommends interventions on household behaviours, environmental cleanliness, water storage, treatment and hand hygiene via small-scale educational interventions. The framework provides an approach for assessing risks in other marginal populations that are poorly understood and served through conventional approaches