Unstructured Randomness, Small Gaps and Localization

We study the Hamiltonian associated with the quantum adiabatic algorithm with a random cost function. Because the cost function lacks structure we can prove results about the ground state. We find the ground state energy as the number of bits goes to infinity, show that the minimum gap goes to zero exponentially quickly, and we see a localization transition. We prove that there are no levels approaching the ground state near the end of the evolution. We do not know which features of this model are shared by a quantum adiabatic algorithm applied to random instances of satisfiability since despite being random they do have bit structure

Genomic characterisation of an endometrial pathogenic <i>Escherichia coli</i> strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity

&lt;b&gt;Background&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Strains of &lt;i&gt;Escherichia coli&lt;/i&gt; cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylogenetic relationship exists that distinguishes most &lt;i&gt;E. Coli&lt;/i&gt; causing intestinal disease from those that cause extra-intestinal disease, however, isolates within a recently described subclass of Extra-Intestinal Pathogenic &lt;i&gt;E. Coli&lt;/i&gt; (ExPEC), termed endometrial pathogenic &lt;i&gt;E. Coli&lt;/i&gt;, tend to be phylogenetically distant from the vast majority of characterised ExPECs, and more closely related to human intestinal pathogens. In this work, we investigate the genetic basis for ExPEC infection in the prototypic endometrial pathogenic &lt;i&gt;E. Coli&lt;/i&gt; strain MS499.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt;&lt;p&gt;&lt;/p&gt; By investigating the genome of MS499 in comparison with a range of other E. coli sequences, we have discovered that this bacterium has acquired substantial lengths of DNA which encode factors more usually associated with ExPECs and less frequently found in the phylogroup relatives of MS499. Many of these acquired factors, including several iron acquisition systems and a virulence plasmid similar to that found in several ExPECs such as APEC O1 and the neonatal meningitis &lt;i&gt;E. Coli&lt;/i&gt; S88, play characterised roles in a variety of typical ExPEC infections and appear to have been acquired recently by the evolutionary lineage leading to MS499.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Taking advantage of the phylogenetic relationship we describe between MS499 and several other closely related &lt;i&gt;E. Coli&lt;/i&gt; isolates from across the globe, we propose a step-wise evolution of a novel clade of sequence type 453 ExPECs within phylogroup B1, involving the recruitment of ExPEC virulence factors into the genome of an ancestrally non-extraintestinal &lt;i&gt;E. Coli&lt;/i&gt;, which has repurposed this lineage with the capacity to cause extraintestinal disease. These data reveal the genetic components which may be involved in this phenotype switching, and argue that horizontal gene exchange may be a key factor in the emergence of novel lineages of ExPECs.&lt;p&gt;&lt;/p&gt

Topological Excitations and their Contribution to Quantum Criticality in 2+1 D Antiferromagnets

It has been proposed that there are new degrees of freedom intrinsic to quantum critical points that contribute to quantum critical physics. We study 2+1 D antiferromagnets in order to explore possible new quantum critical physics arising from nontrivial topological effects. We show that skyrmion excitations are stable at criticality and have nonzero probability at arbitrarily low temperatures. To include quantum critical skyrmion effects, we find a class of exact solutions composed of skyrmion and antiskyrmion superpositions, which we call topolons. We include the topolons in the partition function and renormalize by integrating out small size topolons and short wavelength spin waves. We obtain a correlation length critical exponent nu=0.9297 and anomalous dimension eta=0.3381.Comment: 20 page

Novel single nucleotide polymorphism-based assay for genotyping Mycobacterium avium subsp. paratuberculosis

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates

Improving Perception to Make Distant Connections Closer

One of the challenges for perceptually grounded accounts of high-level cognition is to explain how people make connections and draw inferences between situations that superficially have little in common. Evidence suggests that people draw these connections even without having explicit, verbalizable knowledge of their bases. Instead, the connections are based on sub-symbolic representations that are grounded in perception, action, and space. One reason why people are able to spontaneously see relations between situations that initially appear to be unrelated is that their eventual perceptions are not restricted to initial appearances. Training and strategic deployment allow our perceptual processes to deliver outputs that would have otherwise required abstract or formal reasoning. Even without people having any privileged access to the internal operations of perceptual modules, these modules can be systematically altered so as to better serve our high-level reasoning needs. Moreover, perceptually based processes can be altered in a number of ways to closely approximate formally sanctioned computations. To be concrete about mechanisms of perceptual change, we present 21 illustrations of ways in which we alter, adjust, and augment our perceptual systems with the intention of having them better satisfy our needs

Democratic Transitions

Przeworski et al. (2000) challenge the key hypothesis in modernization theory: political regimes do not transition to democracy as per capita incomes rise, they argue. Rather, democratic transitions occur randomly, but once there, countries with higher levels of GDP per capita remain democratic. We retest the modernization hypothesis using new data, new techniques, and a three-way rather than dichotomous classification of regimes. Contrary to Przeworski et al. (2000) we find that the modernization hypothesis stands up well. We also find that partial democracies emerge as among the most important and least understood regime types.African and African American StudiesGovernmen

A Quantum Monte Carlo Method at Fixed Energy

In this paper we explore new ways to study the zero temperature limit of quantum statistical mechanics using Quantum Monte Carlo simulations. We develop a Quantum Monte Carlo method in which one fixes the ground state energy as a parameter. The Hamiltonians we consider are of the form $H=H_{0}+\lambda V$ with ground state energy E. For fixed $H_{0}$ and V, one can view E as a function of $\lambda$ whereas we view $\lambda$ as a function of E. We fix E and define a path integral Quantum Monte Carlo method in which a path makes no reference to the times (discrete or continuous) at which transitions occur between states. For fixed E we can determine $\lambda(E)$ and other ground state properties of H

Quantum Adiabatic Algorithms, Small Gaps, and Different Paths

We construct a set of instances of 3SAT which are not solved efficiently using the simplest quantum adiabatic algorithm. These instances are obtained by picking random clauses all consistent with two disparate planted solutions and then penalizing one of them with a single additional clause. We argue that by randomly modifying the beginning Hamiltonian, one obtains (with substantial probability) an adiabatic path that removes this difficulty. This suggests that the quantum adiabatic algorithm should in general be run on each instance with many different random paths leading to the problem Hamiltonian. We do not know whether this trick will help for a random instance of 3SAT (as opposed to an instance from the particular set we consider), especially if the instance has an exponential number of disparate assignments that violate few clauses. We use a continuous imaginary time Quantum Monte Carlo algorithm in a novel way to numerically investigate the ground state as well as the first excited state of our system. Our arguments are supplemented by Quantum Monte Carlo data from simulations with up to 150 spins.Comment: The original version considered a unique satisfying assignment and one problematic low lying state. The revision argues that the algorithm with path change will succeed when there are polynomially many low lying state