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

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

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

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

Modeling Life as Cognitive Info-Computation

This article presents a naturalist approach to cognition understood as a network of info-computational, autopoietic processes in living systems. It provides a conceptual framework for the unified view of cognition as evolved from the simplest to the most complex organisms, based on new empirical and theoretical results. It addresses three fundamental questions: what cognition is, how cognition works and what cognition does at different levels of complexity of living organisms. By explicating the info-computational character of cognition, its evolution, agent-dependency and generative mechanisms we can better understand its life-sustaining and life-propagating role. The info-computational approach contributes to rethinking cognition as a process of natural computation in living beings that can be applied for cognitive computation in artificial systems.Comment: Manuscript submitted to Computability in Europe CiE 201

(1+1)-Dirac particle with position-dependent mass in complexified Lorentz scalar interactions: effectively PT-symmetric

The effect of the built-in supersymmetric quantum mechanical language on the spectrum of the (1+1)-Dirac equation, with position-dependent mass (PDM) and complexified Lorentz scalar interactions, is re-emphasized. The signature of the "quasi-parity" on the Dirac particles' spectra is also studied. A Dirac particle with PDM and complexified scalar interactions of the form S(z)=S(x-ib) (an inversely linear plus linear, leading to a PT-symmetric oscillator model), and S(x)=S_{r}(x)+iS_{i}(x) (a PT-symmetric Scarf II model) are considered. Moreover, a first-order intertwining differential operator and an $\eta$-weak-pseudo-Hermiticity generator are presented and a complexified PT-symmetric periodic-type model is used as an illustrative example.Comment: 11 pages, no figures, revise

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

Quantum Extremism: Effective Potential and Extremal Paths

The reality and convexity of the effective potential in quantum field theories has been studied extensively in the context of Euclidean space-time. It has been shown that canonical and path-integral approaches may yield different results, thus resolving the `convexity problem'. We discuss the transferral of these treatments to Minkowskian space-time, which also necessitates a careful discussion of precisely which field configurations give the dominant contributions to the path integral. In particular, we study the effective potential for the N=1 linear sigma model.Comment: 11 pages, 4 figure

Nonequilibrium Evolution of Correlation Functions: A Canonical Approach

We study nonequilibrium evolution in a self-interacting quantum field theory invariant under space translation only by using a canonical approach based on the recently developed Liouville-von Neumann formalism. The method is first used to obtain the correlation functions both in and beyond the Hartree approximation, for the quantum mechanical analog of the $\phi^{4}$ model. The technique involves representing the Hamiltonian in a Fock basis of annihilation and creation operators. By separating it into a solvable Gaussian part involving quadratic terms and a perturbation of quartic terms, it is possible to find the improved vacuum state to any desired order. The correlation functions for the field theory are then investigated in the Hartree approximation and those beyond the Hartree approximation are obtained by finding the improved vacuum state corrected up to ${\cal O}(\lambda^2)$. These correlation functions take into account next-to-leading and next-to-next-to-leading order effects in the coupling constant. We also use the Heisenberg formalism to obtain the time evolution equations for the equal-time, connected correlation functions beyond the leading order. These equations are derived by including the connected 4-point functions in the hierarchy. The resulting coupled set of equations form a part of infinite hierarchy of coupled equations relating the various connected n-point functions. The connection with other approaches based on the path integral formalism is established and the physical implications of the set of equations are discussed with particular emphasis on thermalization.Comment: Revtex, 32 pages; substantial new material dealing with non-equilibrium evolution beyond Hartree approx. based on the LvN formalism, has been adde