Chemical structure matching using correlation matrix memories

This paper describes the application of the Relaxation By Elimination (RBE) method to matching the 3D structure of molecules in chemical databases within the frame work of binary correlation matrix memories. The paper illustrates that, when combined with distributed representations, the method maps well onto these networks, allowing high performance implementation in parallel systems. It outlines the motivation, the neural architecture, the RBE method and presents some results of matching small molecules against a database of 100,000 models

Regions of the T cell receptor alpha and beta chains that are responsible for interactions with CD3.

The T cell antigen receptor consists of the Ti alpha/beta heterodimer which recognizes antigen, and the associated CD3 chains, thought to be involved in signal transduction. To understand the nature of the interaction between Ti and CD3, chimeric molecules which included the COOH-terminal segments of Ti alpha or beta linked to the extracellular segment of CD8, were transfected into a mutant T cell deficient in Ti beta chain expression and cell surface CD3. Both chimeric chains were required to express the chimeric Ti and to restore CD3 surface expression. CD8/Ti and CD3 cointernalized and coimmunoprecipitated. Stimulation of the chimeric receptor induced transmembrane signaling events and cell activation. These results demonstrate that the Ti alpha and beta COOH termini containing the transmembrane domains are sufficient for structural and functional coupling of Ti to CD3

Dust Transport in Protostellar Disks Through Turbulence and Settling

We apply ionization balance and MHD calculations to investigate whether magnetic activity moderated by recombination on dust can account for the mass accretion rates and the mid-infrared spectra and variability of protostellar disks. The MHD calculations use the stratified shearing-box approach and include grain settling and the feedback from the changing dust abundance on the resistivity of the gas. The two-decade spread in accretion rates among T Tauri stars is too large to result solely from variety in the grain size and stellar X-ray luminosity, but can be produced by varying these together with the disk magnetic flux. The diversity in the silicate bands can come from the coupling of grain settling to the distribution of the magneto-rotational turbulence, through three effects: (1) Recombination on grains yields a magnetically inactive dead zone extending above two scale heights, while turbulence in the magnetically active disk atmosphere overshoots the dead zone boundary by only about one scale height. (2) Grains deep in the dead zone oscillate vertically in waves driven by the turbulent layer above, but on average settle at the laminar rates, so the interior of the dead zone is a particle sink and the disk atmosphere becomes dust-depleted. (3) With sufficient depletion, the dead zone is thinner and mixing dredges grains off the midplane. The MHD results also show that the magnetic activity intermittently lifts clouds of dust into the atmosphere. The photosphere height changes by up to one-third over a few orbits, while the extinction along lines of sight grazing the disk surface varies by factors of two over times down to 0.1 orbit. We suggest that the changing shadows cast by the dust clouds on the outer disk are a cause of the daily to monthly mid-infrared variability in some young stars. (Abridged.)Comment: ApJ in pres

Cost benefit analysis vs. referenda

We consider a planner who chooses between two possible public policies and ask whether a referendum or a cost benefit analysis leads to higher welfare. We find that a referendum leads to higher welfare than a cost benefit analyses in "common value" environments. Cost benefit analysis is better in "private value" environments.Cost benefit analysis, elections, referenda, project evaluation

Scattering of elastic waves in heterogeneous media with local isotropy

The scattering of elastic waves in heterogeneous media is discussed. Explicit expressions are derived for the attenuation of longitudinal and transverse elastic waves in terms of the statistics of the density and Lame´ parameter fluctuations. The derivation is based upon diagrammatic methods with the problem posed in terms of the Dyson equation. The Dyson equation is solved for the mean field response. The results are given here in a straightforward manner, in which the attenuations reduce to simple integrals on the unit circle. The medium is assumed statistically homogeneous and statistically isotropic. This model, with assumed local isotropic properties, is expected to apply to many materials

Why fencers should bounce: a new method of movement to engage the stretch-shortening cycle

While teaching a heel first contact style of footwork in fencing (also referred to as toe contribution avoidance) is in keeping with long standing traditions, it is not conducive to today’s modern style of fast paced and explosive fencing. Equally, fencers towards the elite-end seem to be gradually adopting a more spring-based style, as their body progressively and organically transitions to “ball of the foot” based footwork, in order for them to fence competitively in the manner they have intuitively associated with success. Therefore, if from a young age fencers are taught to make full use of the stretch shortening cycle (SSC) via “bouncing” or simply by initiating movement via the ball of the foot, this will expedite the learning process. It will demonstrate to them how the SSC can be used to move at greater speed, cover greater distances when advancing, retreating and lunging, and conserve the much-needed energy required to compete over day long competitions. This paper details the mechanistic underpinnings of the SSC and its application to the modern day fencer

Xenon isotopes in nanodiamonds and other presolar grains

pdf freely available cb 18/07/0

The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes