The Regularizing Capacity of Metabolic Networks

Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from steady states. This leads to the interesting question, how metabolic networks avoid complex dynamics and maintain a steady-state behavior. Here, we expose metabolic network topologies to binary dynamics generated by simple local rules. We find that the networks' response is highly specific: Complex dynamics are systematically reduced on metabolic networks compared to randomized networks with identical degree sequences. Already small topological modifications substantially enhance the capacity of a network to host complex dynamic behavior and thus reduce its regularizing potential. This exceptionally pronounced regularization of dynamics encoded in the topology may explain, why steady-state behavior is ubiquitous in metabolism.Comment: 6 pages, 4 figure

Direct calculation of the hard-sphere crystal/melt interfacial free energy

We present a direct calculation by molecular-dynamics computer simulation of the crystal/melt interfacial free energy, $\gamma$, for a system of hard spheres of diameter $\sigma$. The calculation is performed by thermodynamic integration along a reversible path defined by cleaving, using specially constructed movable hard-sphere walls, separate bulk crystal and fluid systems, which are then merged to form an interface. We find the interfacial free energy to be slightly anisotropic with $\gamma$ = 0.62$\pm 0.01$, 0.64$\pm 0.01$ and 0.58$\pm 0.01 k_BT/\sigma^2$ for the (100), (110) and (111) fcc crystal/fluid interfaces, respectively. These values are consistent with earlier density functional calculations and recent experiments measuring the crystal nucleation rates from colloidal fluids of polystyrene spheres that have been interpreted [Marr and Gast, Langmuir {\bf 10}, 1348 (1994)] to give an estimate of $\gamma$ for the hard-sphere system of $0.55 \pm 0.02 k_BT/\sigma^2$, slightly lower than the directly determined value reported here.Comment: 4 pages, 4 figures, submitted to Physical Review Letter

Troubles with Bayesianism: An introduction to the psychological immune system

A Bayesian mind is, at its core, a rational mind. Bayesianism is thus well-suited to predict and explain mental processes that best exemplify our ability to be rational. However, evidence from belief acquisition and change appears to show that we do not acquire and update information in a Bayesian way. Instead, the principles of belief acquisition and updating seem grounded in maintaining a psychological immune system rather than in approximating a Bayesian processor

Healthy Human T-Cell Responses to Aspergillus fumigatus Antigens

Aspergillus fumigatus is associated with both invasive and allergic pulmonary diseases, in different hosts. The organism is inhaled as a spore, which, if not cleared from the airway, germinates into hyphal morphotypes that are responsible for tissue invasion and resultant inflammation. Hyphae secrete multiple products that function as antigens, evoking both a protective (T(H)1-T(H)17) and destructive allergic (T(H)2) immunity. How Aspergillus allergens (Asp f proteins) participate in the development of allergic sensitization is unknown.To determine whether Asp f proteins are strictly associated with T(H)2 responses, or represent soluble hyphal products recognized by healthy hosts, human T cell responses to crude and recombinant products were characterized by ELISPOT. While responses (number of spots producing IFN-gamma, IL-4 or IL-17) to crude hyphal antigen preparations were weak, responses to recombinant Asp f proteins were higher. Recombinant allergens stimulated cells to produce IFN-gamma more so than IL-4 or IL-17. Volunteers exhibited a diverse CD4+ and CD8+ T cell antigen recognition profile, with prominent CD4 T(H)1-responses to Asp f3 (a putative peroxismal membrane protein), Asp f9/16 (cell wall glucanase), Asp f11 (cyclophilin type peptidyl-prolyl isomerase) and Asp f22 (enolase). Strong IFN-gamma responses were reproduced in most subjects tested over 6 month intervals.Products secreted after conidial germination into hyphae are differentially recognized by protective T cells in healthy, non-atopic individuals. Defining the specificity of the human T cell repertoire, and identifying factors that govern early responses may allow for development of novel diagnostics and therapeutics for both invasive and allergic Aspergillus diseases

Neurofeedback: principles, appraisal and outstanding issues

Neurofeedback is a form of brain training in which subjects are fed back information about some measure of their brain activity which they are instructed to modify in a way thought to be functionally advantageous. Over the last twenty years, NF has been used to treat various neurological and psychiatric conditions, and to improve cognitive function in various contexts. However, despite its growing popularity, each of the main steps in NF comes with its own set of often covert assumptions. Here we critically examine some conceptual and methodological issues associated with the way general objectives and neural targets of NF are defined, and review the neural mechanisms through which NF may act, and the way its efficacy is gauged. The NF process is characterised in terms of functional dynamics, and possible ways in which it may be controlled are discussed. Finally, it is proposed that improving NF will require better understanding of various fundamental aspects of brain dynamics and a more precise definition of functional brain activity and brain-behaviour relationships.Comment: 12 page

Chemoenzymatic Labeling of Proteins for Imaging in Bacterial Cells

Reliable methods to determine the subcellular localization of bacterial proteins are needed for the study of prokaryotic cell biology. We describe here a simple and general technique for imaging of bacterial proteins in situ by fluorescence microscopy. The method uses the eukaryotic enzyme N-myristoyltransferase to modify the N-terminus of the protein of interest with an azido fatty acid. Subsequent strain-promoted azide–alkyne cycloaddition allows conjugation of dyes and imaging of tagged proteins by confocal fluorescence microscopy. We demonstrate the method by labeling the chemotaxis proteins Tar and CheA and the cell division proteins FtsZ and FtsA in Escherichia coli. We observe distinct spatial patterns for each of these proteins in both fixed and live cells. The method should prove broadly useful for protein imaging in bacteria

Kinematic Age Estimates for 4 Compact Symmetric Objects from the Pearson-Readhead Survey

Based on multi-epoch observations at 15 and 43 GHz with the Very Long Baseline Array (VLBA) we detect significant angular expansions between the two hot spots of 4 Compact Symmetric Objects (CSOs). From these relative motions we derive kinematic ages of between 300 and 1200 years for the radio emission. These ages lend support to the idea that CSOs are produced in a recent phase of activity. These observations also allow us to study the evolution of the hot spots dynamically in individual sources. In all 4 sources the hot spots are separating along the source axis, but in 1031+567 the tip of one hot spot appears to be moving almost orthogonally to the source axis. Jet components, seen in 3 of the 4 sources observed, are found to be moving relativistically outward from the central engines towards the more slowly moving hot spots.Comment: in press at ApJ for v. 541 Oct. 1, 2000, 23 page LaTeX document includes 6 postscript figure

Separation and identification of dominant mechanisms in double photoionization

Double photoionization by a single photon is often discussed in terms of two contributing mechanisms, {\it knock-out} (two-step-one) and {\it shake-off} with the latter being a pure quantum effect. It is shown that a quasi-classical description of knock-out and a simple quantum calculation of shake-off provides a clear separation of the mechanisms and facilitates their calculation considerably. The relevance of each mechanism at different photon energies is quantified for helium. Photoionization ratios, integral and singly differential cross sections obtained by us are in excellent agreement with benchmark experimental data and recent theoretical results.Comment: 4 pages, 5 figure

SB9: The Ninth Catalogue of Spectroscopic Binary Orbits

The Ninth Catalogue of Spectroscopic Binary Orbits (http://sb9.astro.ulb.ac.be) continues the series of compilations of spectroscopic orbits carried out over the past 35 years by Batten and collaborators. As of 2004 May 1st, the new Catalogue holds orbits for 2,386 systems. Some essential differences between this catalogue and its predecessors are outlined and three straightforward applications are presented: (1) Completeness assessment: period distribution of SB1s and SB2s; (2) Shortest periods across the H-R diagram; (3) Period-eccentricity relation.Comment: Accepte for publication in A&A, 6 pages, 6 figure

Treatment Outcomes for DIP Clients in Liverpool (July 11 - June 12)

The main objective of the Drug Interventions Programme (DIP) is to identify and engage with drug users in the criminal justice system in order to channel them into appropriate treatment services. In line with research evidence it is assumed that if this treatment is effective it will result in reduced drug use and therefore reduced offending. This report aims to investigate outcomes for DIP clients resident in Liverpool who were referred to treatment between 1st July 2011 and 31st December 2011 as part of their DIP care plan and who had a corresponding treatment journey recorded on the National Drug Treatment Monitoring System (NDTMS) (including data from the Treatment Outcomes Profile) between 1st July 2011 and 30th June 2012