Dynamical Freezing in a Spin Glass System with Logarithmic Correlations

We consider a continuous time random walk on the two-dimensional discrete torus, whose motion is governed by the discrete Gaussian free field on the corresponding box acting as a potential. More precisely, at any vertex the walk waits an exponentially distributed time with mean given by the exponential of the field and then jumps to one of its neighbors, chosen uniformly at random. We prove that throughout the low-temperature regime and at in-equilibrium timescales, the process admits a scaling limit as a spatial K-process driven by a random trapping landscape, which is explicitly related to the limiting extremal process of the field. Alternatively, the limiting process is a supercritical Liouville Brownian motion with respect to the continuum Gaussian free field on the box. This demonstrates rigorously and for the first time, as far as we know, a dynamical freezing in a spin glass system with logarithmically correlated energy levels.Comment: Final version available at Electron. J. Proba

A bound for orderings of Reidemeister moves

We provide an upper bound on the number of ordered Reidemeister moves required to pass between two diagrams of the same link. This bound is in terms of the number of unordered Reidemeister moves required.Comment: 11 pages, 15 figures; fixed minor typographical erro

“Body bags ready”: Print media coverage of avian influenza in Australia

In 2006 the avian influenza A (H5N1) virus received considerable media coverage in Australia, as it did in many other countries. It is often argued that the media sensationalizes health crises, and experts cautioned about the risk of panic as a result of fear of avian influenza. The purpose of the present study was to systematically analyze Australian print media coverage of avian influenza in 2006 and to examine whether this coverage served the purpose of informing, rather than alarming, the general public. For the period January 1, 2006 to December 31, 2006, 20 Australian newspaper titles were monitored for coverage of avian influenza. The identified articles were analyzed using aspects of protection motivation theory for theoretical direction to determine whether there were any consistent themes or perspectives in the coverage. A total of 850 articles were identified for analysis. Concerning vulnerability, 46% of articles reported the incidence of human cases, with 24% noting that avian influenza was a potential threat to Australia. The most common severity theme was “deadly” with over 50% of mentions, followed by “pandemic” with 35%. Only 11% of articles referred to any form of self-protection. We found that a considerable proportion of the articles reporting on avian influenza were framed in a way that had the potential to incite fear and panic amongst the public; the intensity of media coverage reduced over time; and, of particular concern, that there was little media coverage that focused on protective or preventative issues. Whether an influenza pandemic eventuates or not, it is prudent for governments and health authorities to continually develop appropriate resources and strategies to prepare the health system and the general public to respond to current, and future, infectious disease risks

Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium

Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility. Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. Here, Neuhaus et al. show that the bacterium Thermus thermophilus produces two forms of type IV pilus, differing in structure, protein composition, and function.Peer reviewe

A Comprehensive Three-Dimensional Model of the Cochlea

The human cochlea is a remarkable device, able to discern extremely small amplitude sound pressure waves, and discriminate between very close frequencies. Simulation of the cochlea is computationally challenging due to its complex geometry, intricate construction and small physical size. We have developed, and are continuing to refine, a detailed three-dimensional computational model based on an accurate cochlear geometry obtained from physical measurements. In the model, the immersed boundary method is used to calculate the fluid-structure interactions produced in response to incoming sound waves. The model includes a detailed and realistic description of the various elastic structures present. In this paper, we describe the computational model and its performance on the latest generation of shared memory servers from Hewlett Packard. Using compiler generated threads and OpenMP directives, we have achieved a high degree of parallelism in the executable, which has made possible several large scale numerical simulation experiments that study the interesting features of the cochlear system. We show several results from these simulations, reproducing some of the basic known characteristics of cochlear mechanics.Comment: 22 pages, 5 figure

Amici Curiae Brief for Academics in Law, Medicine, Health Policy, and Clinical Genetics in Support of Neither Party

Amicus ("friend of the court") brief written by Drs. E. Richard Gold, Tania Bubela, Robert Cook-Deegan, James Evans, Julian Kinderlerer, and Dianne Nicol, in support of neither party (Supreme Court Case Docket No. 12-398

Intramolecular and Intermolecular Interactions of Protein Kinase B Define Its Activation In Vivo

Protein kinase B (PKB/Akt) is a pivotal regulator of diverse metabolic, phenotypic, and antiapoptotic cellular controls and has been shown to be a key player in cancer progression. Here, using fluorescent reporters, we shown in cells that, contrary to in vitro analyses, 3-phosphoinositide–dependent protein kinase 1 (PDK1) is complexed to its substrate, PKB. The use of Förster resonance energy transfer detected by both frequency domain and two-photon time domain fluorescence lifetime imaging microscopy has lead to novel in vivo findings. The preactivation complex of PKB and PDK1 is maintained in an inactive state through a PKB intramolecular interaction between its pleckstrin homology (PH) and kinase domains, in a “PH-in” conformer. This domain–domain interaction prevents the PKB activation loop from being phosphorylated by PDK1. The interactive regions for this intramolecular PKB interaction were predicted through molecular modeling and tested through mutagenesis, supporting the derived model. Physiologically, agonist-induced phosphorylation of PKB by PDK1 occurs coincident to plasma membrane recruitment, and we further shown here that this process is associated with a conformational change in PKB at the membrane, producing a “PH-out” conformer and enabling PDK1 access the activation loop. The active, phosphorylated, “PH-out” conformer can dissociate from the membrane and retain this conformation to phosphorylate substrates distal to the membrane. These in vivo studies provide a new model for the mechanism of activation of PKB. This study takes a crucial widely studied regulator (physiology and pathology) and addresses the fundamental question of the dynamic in vivo behaviour of PKB with a detailed molecular mechanism. This has important implications not only in extending our understanding of this oncogenic protein kinase but also in opening up distinct opportunities for therapeutic intervention