The conduction pathway of potassium channels is water free under physiological conditions.

Ion conduction through potassium channels is a fundamental process of life. On the basis of crystallographic data, it was originally proposed that potassium ions and water molecules are transported through the selectivity filter in an alternating arrangement, suggesting a "water-mediated" knock-on mechanism. Later on, this view was challenged by results from molecular dynamics simulations that revealed a "direct" knock-on mechanism where ions are in direct contact. Using solid-state nuclear magnetic resonance techniques tailored to characterize the interaction between water molecules and the ion channel, we show here that the selectivity filter of a potassium channel is free of water under physiological conditions. Our results are fully consistent with the direct knock-on mechanism of ion conduction but contradict the previously proposed water-mediated knock-on mechanism

When images work faster than words: The integration of content-based image retrieval with the Northumbria Watermark Archive

Information on the manufacture, history, provenance, identification, care and conservation of paper-based artwork/objects is disparate and not always readily available. The Northumbria Watermark Archive will incorporate such material into a database, which will be made freely available on the Internet providing an invaluable resource for conservation, research and education. The efficiency of a database is highly dependant on its search mechanism. Text based mechanisms are frequently ineffective when a range of descriptive terminologies might be used i.e. when describing images or translating from foreign languages. In such cases a Content Based Image Retrieval (CBIR) system can be more effective. Watermarks provide paper with unique visual identification characteristics and have been used to provide a point of entry to the archive that is more efficient and effective than a text based search mechanism. The research carried out has the potential to be applied to any numerically large collection of images with distinctive features of colour, shape or texture i.e. coins, architectural features, picture frame profiles, hallmarks, Japanese artists stamps etc. Although the establishment of an electronic archive incorporating a CBIR system can undoubtedly improve access to large collections of images and related data, the development is rarely trouble free. This paper discusses some of the issues that must be considered i.e. collaboration between disciplines; project management; copying and digitising objects; content based image retrieval; the Northumbria Watermark Archive; the use of standardised terminology within a database as well as copyright issues

State space c-reductions for concurrent systems in rewriting logic

We present c-reductions, a state space reduction technique. The rough idea is to exploit some equivalence relation on states (possibly capturing system regularities) that preserves behavioral properties, and explore the induced quotient system. This is done by means of a canonizer function, which maps each state into a (non necessarily unique) canonical representative of its equivalence class. The approach exploits the expressiveness of rewriting logic and its realization in Maude to enjoy several advantages over similar approaches: exibility and simplicity in the definition of the reductions (supporting not only traditional symmetry reductions, but also name reuse and name abstraction); reasoning support for checking and proving correctness of the reductions; and automatization of the reduction infrastructure via Maude's meta-programming features. The approach has been validated over a set of representative case studies, exhibiting comparable results with respect to other tools

An Analysis of the Representations of the Mapping Class Group of a Multi-Geon Three-Manifold

It is well known that the inequivalent unitary irreducible representations (UIR's) of the mapping class group $G$ of a 3-manifold give rise to ``theta sectors'' in theories of quantum gravity with fixed spatial topology. In this paper, we study several families of UIR's of $G$ and attempt to understand the physical implications of the resulting quantum sectors. The mapping class group of a three-manifold which is the connected sum of $\R^3$ with a finite number of identical irreducible primes is a semi-direct product group. Following Mackey's theory of induced representations, we provide an analysis of the structure of the general finite dimensional UIR of such a group. In the picture of quantized primes as particles (topological geons), this general group-theoretic analysis enables one to draw several interesting qualitative conclusions about the geons' behavior in different quantum sectors, without requiring an explicit knowledge of the UIR's corresponding to the individual primes.Comment: 52 pages, harvmac, 2 postscript figures, epsf required. Added an appendix proving the semi-direct product structure of the MCG, corrected an error in the characterization of the slide subgroup, reworded extensively. All our analysis and conclusions remain as befor

Properties of 3-manifolds for relativists

In canonical quantum gravity certain topological properties of 3-manifolds are of interest. This article gives an account of those properties which have so far received sufficient attention, especially those concerning the diffeomorphism groups of 3-manifolds. We give a summary of these properties and list some old and new results concerning them. The appendix contains a discussion of the group of large diffeomorphisms of the $l$-handle 3-manifold.Comment: 20 pages. Plain-TeX, no figures, 1 Table (A4 format

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics.

BackgroundTo accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos.ResultsUsing automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms.ConclusionOur work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis

Pseudomonas aeruginosa biofilm formation and slime excretion on antibiotic-loaded bone cement

Background Infection is an infrequent but serious complication of prosthetic joint surgery. These infections will usually not clear until the implant is removed and re-implantation has a high failure rate, especially when Pseudomonas aeruginosa is involved. Material and methods We examined Pseudomonas aeruginosa biofilm formation on plain and gentamicin-loaded bone cement with confocal scanning laser microscopy (CSLM). Two different stains were applied in order to visualize and quantify the distribution of bacterial cells and extracellular polymeric substances (slime) from the bone cement surface to the top of the biofilm. Staining with LIVE/DEAD viability stain differentiated between live and dead bacteria within the biofilm, and slime production was evaluated after staining with Calcofluor white. Results CSLM showed that the biofilm was a nonuniform structure of variable thickness, with differences in local bacterial cell and slime densities. Incorporation of gentamicin in bone cement resulted in a 44% reduction in bacterial viability, while the slime density increased significantly. In addition, conventional plate counting showed the development of small-colony variants on gentamicin-loaded bone cement with a decreased sensitivity for gentamicin (MIC: 8 mg/L), as compared with normal-sized colonies taken from plain and gentamicin-loaded bone cement (MIC: 3 mg/L). The enhanced slime production on antibiotic-loaded bone cement, together with the formation of small-colony variants, resulted in decreased susceptibility to antibiotics-probably concomitant with the onset of persistent and relapsing infections. Interpretation In the clinical situation, our findings help to explain the frequent re-implantation failure of joint replacements infected with P. aeruginosa when the procedure has been performed using antibiotic-loaded bone cement

Borderline Aggregation Kinetics in ``Dry'' and ``Wet'' Environments

We investigate the kinetics of constant-kernel aggregation which is augmented by either: (a) evaporation of monomers from finite-mass clusters, or (b) continuous cluster growth -- \ie, condensation. The rate equations for these two processes are analyzed using both exact and asymptotic methods. In aggregation-evaporation, if the evaporation is mass conserving, \ie, the monomers which evaporate remain in the system and continue to be reactive, the competition between evaporation and aggregation leads to several asymptotic outcomes. For weak evaporation, the kinetics is similar to that of aggregation with no evaporation, while equilibrium is quickly reached in the opposite case. At a critical evaporation rate, the cluster mass distribution decays as $k^{-5/2}$, where $k$ is the mass, while the typical cluster mass grows with time as $t^{2/3}$. In aggregation-condensation, we consider the process with a growth rate for clusters of mass $k$, $L_k$, which is: (i) independent of $k$, (ii) proportional to $k$, and (iii) proportional to $k^\mu$, with $0<\mu<1$. In the first case, the mass distribution attains a conventional scaling form, but with the typical cluster mass growing as $t\ln t$. When $L_k\propto k$, the typical mass grows exponentially in time, while the mass distribution again scales. In the intermediate case of $L_k\propto k^\mu$, scaling generally applies, with the typical mass growing as $t^{1/(1-\mu)}$. We also give an exact solution for the linear growth model, $L_k\propto k$, in one dimension.Comment: plain TeX, 17 pages, no figures, macro file prepende

Cyclic Statistics In Three Dimensions

While 2-dimensional quantum systems are known to exhibit non-permutation, braid group statistics, it is widely expected that quantum statistics in 3-dimensions is solely determined by representations of the permutation group. This expectation is false for certain 3-dimensional systems, as was shown by the authors of ref. [1,2,3]. In this work we demonstrate the existence of ``cyclic'', or $Z_n$, {\it non-permutation group} statistics for a system of n > 2 identical, unknotted rings embedded in $R^3$. We make crucial use of a theorem due to Goldsmith in conjunction with the so called Fuchs-Rabinovitch relations for the automorphisms of the free product group on n elements.Comment: 13 pages, 1 figure, LaTex, minor page reformattin