Mapping and Characterizing Subtidal Oyster Reefs Using Acoustic Techniques, Underwater Videography and Quadrat Counts

Populations of the eastern oyster Crassostrea virginica have been in long-term decline in most areas. A major hindrance to effective oyster management has been lack of a methodology for accurately and economically obtaining data on their distribution and abundance patterns. Here, we describe early results from studies aimed at development of a mapping and monitoring protocol involving acoustic techniques, underwater videography, and destructive sampling (excavated quadrats). Two subtidal reefs in Great Bay, New Hampshire, were mapped with side-scan sonar and with videography by systematically imaging multiple sampling cells in a grid covering the same areas. A single deployment was made in each cell, and a 5-10-s recording was made of a 0.25-m2 area; the location of each image was determined using a differential global position system. A still image was produced for each of the cells and all (n = 40 or 44) were combined into a single photomontage overlaid onto a geo-referenced base map for each reef using Arc View geographic information system. Quadrat (0.25 m2 ) samples were excavated from 9 or 10 of the imaged areas on each reef, and all live oysters were counted and measured. Intercomparisons of the acoustic, video, and quadrat data suggest: (1) acoustic techniques and systematic videography can readily delimit the boundaries of oyster reefs; (2) systematic videography can yield quantitative data on shell densities and information on reef structure; and (3) some combination of acoustics, systematic videography, and destructive sampling can provide spatially detailed information on oyster reef characteristics

Directed Explicit Model Checking with HSF-SPIN

We present the explicit state model checker HSF-SPIN which is based on the model checker SPIN and its Promela modeling language. HSF-SPIN incorporates directed search algorithms for checking safety and a large class of LTL-specified liveness properties. We start off from the A* algorithm and define heuristics to accelerate the search into the direction of a specified failure situation. Next we propose an improved nested depth-first search algorithm that exploits the structure of Promela Never-Claims. As a result of both improvements, counterexamples will be shorter and the explored part of the state space will be smaller than with classical approaches, allowing to analyze larger state spaces. We evaluate the impact of the new heuristics and algorithms on a set of protocol models, some of which are real-world industrial protocols

Twisted algebra R-matrices and S-matrices for bn(1)b_n^{(1)} affine Toda solitons and their bound states

We construct new $U_q(a^{(2)}_{2n-1})$ and $U_q(e^{(2)}_6)$ invariant $R$-matrices and comment on the general construction of $R$-matrices for twisted algebras. We use the former to construct $S$-matrices for $b^{(1)}_n$ affine Toda solitons and their bound states, identifying the lowest breathers with the $b^{(1)}_n$ particles.Comment: Latex, 24 pages. Various misprints corrected. New section added clarifying relationship between R-matrices and S-matrice

Nonextensive aspects of self-organized scale-free gas-like networks

We explore the possibility to interpret as a 'gas' the dynamical self-organized scale-free network recently introduced by Kim et al (2005). The role of 'momentum' of individual nodes is played by the degree of the node, the 'configuration space' (metric defining distance between nodes) being determined by the dynamically evolving adjacency matrix. In a constant-size network process, 'inelastic' interactions occur between pairs of nodes, which are realized by the merger of a pair of two nodes into one. The resulting node possesses the union of all links of the previously separate nodes. We consider chemostat conditions, i.e., for each merger there will be a newly created node which is then linked to the existing network randomly. We also introduce an interaction 'potential' (node-merging probability) which decays with distance d_ij as 1/d_ij^alpha; alpha >= 0). We numerically exhibit that this system exhibits nonextensive statistics in the degree distribution, and calculate how the entropic index q depends on alpha. The particular cases alpha=0 and alpha to infinity recover the two models introduced by Kim et al.Comment: 7 pages, 5 figure

Healthiness from Duality

Healthiness is a good old question in program logics that dates back to Dijkstra. It asks for an intrinsic characterization of those predicate transformers which arise as the (backward) interpretation of a certain class of programs. There are several results known for healthiness conditions: for deterministic programs, nondeterministic ones, probabilistic ones, etc. Building upon our previous works on so-called state-and-effect triangles, we contribute a unified categorical framework for investigating healthiness conditions. We find the framework to be centered around a dual adjunction induced by a dualizing object, together with our notion of relative Eilenberg-Moore algebra playing fundamental roles too. The latter notion seems interesting in its own right in the context of monads, Lawvere theories and enriched categories.Comment: 13 pages, Extended version with appendices of a paper accepted to LICS 201

Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli

The lytic transglycosylase MltA from Escherichia coli with its membrane anchor and signal sequence deleted has been purified to homogeneity by means of cation-exchange chromatography. The enzyme was crystallized using the hanging-drop vapour-diffusion method. The crystals belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a=b=103.70, c=109.84 Angstrom and one molecule per asymmetric unit. Crystals diffract to 2.2 Angstrom resolution on a synchrotron-radiation source

Re-entrant melting and freezing in a model system of charged colloids

We studied the phase behavior of charged and sterically stabilized colloids using confocal microscopy in a less polar solvent (dielectric constant 5.4). Upon increasing the colloid volume fraction we found a transition from a fluid to a body centered cubic crystal at 0.0415+/-0.0005, followed by re-entrant melting at 0.1165+/-0.0015. A second crystal of different symmetry, random hexagonal close-packed, was formed at a volume fraction around 0.5, similar to that of hard spheres. We attribute the intriguing phase behavior to particle interactions that depend strongly on volume fraction, mainly due to changes in the colloid charge. In this low polarity system the colloids acquire charge through ion adsorption. The low ionic strength leads to fewer ions per colloid at elevated volume fractions and consequently a density-dependent colloid charge.Comment: 25 pages, 5 figures 1 tabl

Phase behaviour of charged colloidal sphere dispersions with added polymer chains

We study the stability of mixtures of highly screened repulsive charged spheres and non-adsorbing ideal polymer chains in a common solvent using free volume theory. The effective interaction between charged colloids in an aqueous salt solution is described by a screened-Coulomb pair potential, which supplements the pure hard-sphere interaction. The ideal polymer chains are treated as spheres that are excluded from the colloids by a hard-core interaction, whereas the interaction between two ideal chains is set to zero. In addition, we investigate the phase behaviour of charged colloid-polymer mixtures in computer simulations, using the two-body (Asakura-Oosawa pair potential) approximation to the effective one-component Hamiltonian of the charged colloids. Both our results obtained from simulations and from free volume theory show similar trends. We find that the screened-Coulomb repulsion counteracts the effect of the effective polymer-mediated attraction. For mixtures of small polymers and relatively large charged colloidal spheres, the fluid-crystal transition shifts to significantly larger polymer concentrations with increasing range of the screened-Coulomb repulsion. For relatively large polymers, the effect of the screened-Coulomb repulsion is weaker. The resulting fluid-fluid binodal is only slightly shifted towards larger polymer concentrations upon increasing the range of the screened-Coulomb repulsion. In conclusion, our results show that the miscibility of dispersions containing charged colloids and neutral non-adsorbing polymers increases, upon increasing the range of the screened-Coulomb repulsion, or upon lowering the salt concentration, especially when the polymers are small compared to the colloids.Comment: 25 pages,13 figures, accepted for publication on J.Phys.:Condens. Matte