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

Spin correlations in the electron-doped high-transition-temperature superconductor Nd{2-x}Ce{x}CuO{4+/-delta}

High-transition-temperature (high-Tc) superconductivity develops near antiferromagnetic phases, and it is possible that magnetic excitations contribute to the superconducting pairing mechanism. To assess the role of antiferromagnetism, it is essential to understand the doping and temperature dependence of the two-dimensional antiferromagnetic spin correlations. The phase diagram is asymmetric with respect to electron and hole doping, and for the comparatively less-studied electron-doped materials, the antiferromagnetic phase extends much further with doping [1, 2] and appears to overlap with the superconducting phase. The archetypical electron-doped compound Nd{2-x}Ce{x}CuO{4\pm\delta} (NCCO) shows bulk superconductivity above x \approx 0.13 [3, 4], while evidence for antiferromagnetic order has been found up to x \approx 0.17 [2, 5, 6]. Here we report inelastic magnetic neutron-scattering measurements that point to the distinct possibility that genuine long-range antiferromagnetism and superconductivity do not coexist. The data reveal a magnetic quantum critical point where superconductivity first appears, consistent with an exotic quantum phase transition between the two phases [7]. We also demonstrate that the pseudogap phenomenon in the electron-doped materials, which is associated with pronounced charge anomalies [8-11], arises from a build-up of spin correlations, in agreement with recent theoretical proposals [12, 13].Comment: 5 pages, 4 figure

Gauge (non-)invariant Green functions of Dirac fermions coupled to gauge fields

We develop a unified approach to both infrared and ultraviolet asymptotics of the fermion Green functions in the condensed matter systems that allow for an effective description in the framework of the Quantum Electrodynamics. By applying a path integral representation to the previously suggested form of the physical electron propagator we demonstrate that in the massless case this gauge invariant function features a "stronger-than-a-pole" branch-cut singularity instead of the conjectured Luttinger-like behavior. The obtained results alert one to the possibility that construction of physically relevant amplitudes in the effective gauge theories might prove more complex than previously thought

Linear-T resistivity and change in Fermi surface at the pseudogap critical point of a high-Tc superconductor

A fundamental question of high-temperature superconductors is the nature of the pseudogap phase which lies between the Mott insulator at zero doping and the Fermi liquid at high doping p. Here we report on the behaviour of charge carriers near the zero-temperature onset of that phase, namely at the critical doping p* where the pseudogap temperature T* goes to zero, accessed by investigating a material in which superconductivity can be fully suppressed by a steady magnetic field. Just below p*, the normal-state resistivity and Hall coefficient of La1.6-xNd0.4SrxCuO4 are found to rise simultaneously as the temperature drops below T*, revealing a change in the Fermi surface with a large associated drop in conductivity. At p*, the resistivity shows a linear temperature dependence as T goes to zero, a typical signature of a quantum critical point. These findings impose new constraints on the mechanisms responsible for inelastic scattering and Fermi surface transformation in theories of the pseudogap phase.Comment: 24 pages, 6 figures. Published in Nature Physics. Online at http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys1109.htm

Point contact spectroscopy of the electron-doped cuprate superconductor Pr{2-x}Ce{x}CuO4: The dependence of conductance-voltage spectra on cerium doping, barrier strength and magnetic field

We present conductance-voltage (G-V) data for point contact junctions between a normal metal and the electron doped cuprate superconductor Pr{2-x}Ce{x}CuO4 (PCCO). We observe a zero bias conductance peak (ZBCP) for the under-doped composition of this cuprate (x=0.13) which is consistent with d-wave pairing symmetry. For optimally-doped (x=0.15) and over-doped (x=0.17) PCCO, we find that the G-V characteristics indicate the presence of an order parameter without nodes. We investigate this further by obtaining point contact spectroscopy data for different barrier strengths and as a function of magnetic field.Comment: 13 pages, 9 figure

Observation of Andreev reflection in the c-axis transport of Bi_2Sr_2CaCu_2O_{8+x} single crystals near T_c and search for the preformed-pair state

We observed an enhancement of the $c$-axis differential conductance around the zero-bias in Au$/$Bi$_2$Sr$_2$CaCu$_2$O$_{8+x}$ (Bi2212) junctions near the superconducting transition temperature $T_c$. We attribute the conductance enhancement to the Andreev reflection between the surface Cu-O bilayer with suppressed superconductivity and the neighboring superconducting inner bilayer. The continuous evolution from depression to an enhancement of the zero-bias differential conductance, as the temperature approaches $T_c$ from below, points to weakening of the barrier strength of the non-superconducting layer between adjacent Cu-O bilayers. We observed that the conductance enhancement persisted up to a few degrees above $T_c$ in junctions prepared on slightly overdoped Bi2212 crystals. However, no conductance enhancement was observed above $T_c$ in underdoped crystals, although recently proposed theoretical consideration suggests an even wider temperature range of enhanced zero-bias conductance. This seems to provide negative perspective to the existence of the phase-incoherent preformed pairs in the pseudogap state.Comment: 17 pages including 4 figure

The Localization Transition of the Two-Dimensional Lorentz Model

We investigate the dynamics of a single tracer particle performing Brownian motion in a two-dimensional course of randomly distributed hard obstacles. At a certain critical obstacle density, the motion of the tracer becomes anomalous over many decades in time, which is rationalized in terms of an underlying percolation transition of the void space. In the vicinity of this critical density the dynamics follows the anomalous one up to a crossover time scale where the motion becomes either diffusive or localized. We analyze the scaling behavior of the time-dependent diffusion coefficient D(t) including corrections to scaling. Away from the critical density, D(t) exhibits universal hydrodynamic long-time tails both in the diffusive as well as in the localized phase.Comment: 13 pages, 7 figures

In-plane Tunneling Spectrum into a [110]-Oriented High-TcT_c Superconductor in the Pseudogap Regime

Both the differential tunneling conductance and the surface local density of states (LDOS) of a [110]-oriented high-temperature superconductor in the pseudogap (PG) regime are studied theoretically. As a competing candidate for the mechanism of PG state, the charge-density wave (CDW), spin-density wave (SDW), $d$-density wave (DDW), and d-wave superconducting (DSC) orderings show distinct features in the tunneling conductance. For the CDW, SDW, and DSC orderings, the tunneling conductance approaches the surface LDOS as the barrier potential is increased. For the DDW ordering, we show for the first time that there exist midgap states at the [110] surface, manifesting themselves as a sharp zero-energy peak in the LDOS, as in the case of DSC ordering. However, due to the particle-hole pair nature of the DDW state, these states do not carry current, and consequently the one-to-one correspondence between the tunneling conductance and the surface LDOS is absent.Comment: 5 pages, 4 figures embedded in the tex

How much information is needed to infer reticulate evolutionary histories?

Phylogenetic networks are a generalization of evolutionary trees and are an important tool for analyzing reticulate evolutionary histories. Recently, there has been great interest in developing new methods to construct rooted phylogenetic networks, that is, networks whose internal vertices correspond to hypothetical ancestors, whose leaves correspond to sampled taxa, and in which vertices with more than one parent correspond to taxa formed by reticulate evolutionary events such as recombination or hybridization. Several methods for constructing evolutionary trees use the strategy of building up a tree from simpler building blocks (such as triplets or clusters), and so it is natural to look for ways to construct networks from smaller networks. In this article, we shall demonstrate a fundamental issue with this approach. Namely, we show that even if we are given all of the subnetworks induced on all proper subsets of the leaves of some rooted phylogenetic network, we still do not have all of the information required to completely determine that network. This implies that even if all of the building blocks for some reticulate evolutionary history were to be taken as the input for any given network building method, the method might still output an incorrect history. We also discuss some potential consequences of this result for constructing phylogenetic networks

Locating a Tree in a Phylogenetic Network in Quadratic Time

International audienceA fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in the number of taxa