Assessing the performance of morphologically based river typing in Scotland using a geomorphological and ecological approach

Traditionally, the interactions between geomorphic character and aquatic biodiversity have been widely acknowledged, but poorly quantified. However, the coupling of these disciplines is currently rising up legislative and political agendas, such as the European Union Water Framework Directive (EU WFD). The Directive requires Member States to classify rivers into types based on their natural morphology and geomorphic processes, and to link the biota to river types existing under natural conditions. Typing now forms the basis for evaluating environmental sensitivity to river engineering and determining reference conditions for river restoration. The Scottish Environment Protection Agency (SEPA) has adapted the Montgomery and Buffington (1997) channel typology developed in the Pacific Northwest of the USA for use in Scotland. The modified typology identifies eleven distinct channel types (e.g. bedrock, plane-bed, wandering and meandering). In this study, 43 reference condition sites in the upper River Dee catchment in the Cairngorms, Scotland were chosen to determine the geomorphic validity of the proposed typology, and assess whether channel types support a distinct macroinvertebrate community. Agglomerative Hierarchical Cluster Analysis failed to clearly identify eleven channel types based on catchment controls or on physical habitat characteristics. Four clusters were observed based on catchment drivers and six on physical habitat. Boundaries appear to be fuzzy, relating to a collective number of interacting environmental variables, geological discontinuities, and the geographic complexity of a river system. Multivariate ordinations and Analysis of Similarity indicated that macroinvertebrate communities only differed significantly between bedrock and step-pool reaches. A redundancy analysis showed differences in macroinvertebrate abundances among channel types were related to hydraulic, catchment drivers, physical habitat and physico-chemical variables. The results of the study have important implications for the use of geomorphic typologies in predicting aquatic biota.EThOS - Electronic Theses Online ServiceNatural Environment Research Council (NERC) : Scottish Environment Protection Agency (SEPA)GBUnited Kingdo

Experimental Study of Parametric Autoresonance in Faraday Waves

The excitation of large amplitude nonlinear waves is achieved via parametric autoresonance of Faraday waves. We experimentally demonstrate that phase locking to low amplitude driving can generate persistent high-amplitude growth of nonlinear waves in a dissipative system. The experiments presented are in excellent agreement with theory.Comment: 4 pages, 4 eps figures, to appear in Phys. Rev. Let

Motivated proteins: a web application for studying small three-dimensional protein motifs

<b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. <b>DESCRIPTION:</b> The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. <b>CONCLUSION:</b> Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist

The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrial-encoded RM system can function as a toxin-antitoxin selfish element and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.Peer reviewe

Variation in the carotid bifurcation geometry of young versus older adults: Implications for geometric risk of atherosclerosis

Background and Purpose - Retrospective analysis of clinical data has demonstrated major variations in carotid bifurcation geometry, in support of the notion that an individual\u27s vascular anatomy or local hemodynamics may influence the development of atherosclerosis. On the other hand, anecdotal evidence suggests that vessel geometry is more homogenous in youth, which would tend to undermine this geometric risk hypothesis. The purpose of our study was to test whether the latter is indeed the case. Methods - Cross-sectional images of the carotid bifurcations of 25 young adults (24±4 years) and a control group of 25 older subjects (63±10 years) were acquired via MRI. Robust and objective techniques were developed to automatically characterize the 3D geometry of the bifurcation and the relative dimensions of the internal, external, and common carotid arteries (ICA, ECA, and CCA, respectively). Results - Young vessels exhibited significantly less interindividual variation in the following geometric parameters: bifurcation angle (48.5±6.3° versus 63.6±15.4°); ICA angle (21.6±6.7° versus 29.2±11.3°); CCA tortuosity (0.010±0.003 versus 0.014±0.011); ICA tortuosity (0.025±0.013 versus 0.086±0.105); ECA/CCA diameter ratio (0.81±0.06 versus 0.75±0.13), ICA/CCA (0.81 ±0.06 versus 0.77±0.12) diameter ratio, and bifurcation area ratio (1.32±0.15 versus 1.19±0.35). Conclusions - The finding of more modest interindividual variations in young adults suggests that, if there is a geometric risk for atherosclerosis, its early detection may prove challenging. Taken together with the major interindividual variations seen in older vessels, it suggests a more complex interrelationship between vascular geometry, local hemodynamics, vascular aging, and atherosclerosis, the elucidation of which now calls for prospective studies. © 2005 American Heart Association, Inc

A theory of normed simulations

In existing simulation proof techniques, a single step in a lower-level specification may be simulated by an extended execution fragment in a higher-level one. As a result, it is cumbersome to mechanize these techniques using general purpose theorem provers. Moreover, it is undecidable whether a given relation is a simulation, even if tautology checking is decidable for the underlying specification logic. This paper introduces various types of normed simulations. In a normed simulation, each step in a lower-level specification can be simulated by at most one step in the higher-level one, for any related pair of states. In earlier work we demonstrated that normed simulations are quite useful as a vehicle for the formalization of refinement proofs via theorem provers. Here we show that normed simulations also have pleasant theoretical properties: (1) under some reasonable assumptions, it is decidable whether a given relation is a normed forward simulation, provided tautology checking is decidable for the underlying logic; (2) at the semantic level, normed forward and backward simulations together form a complete proof method for establishing behavior inclusion, provided that the higher-level specification has finite invisible nondeterminism.Comment: 31 pages, 10figure

The Influences of Reproductive Status and Acute Stress on the Levels of Phosphorylated Mu Opioid Receptor Immunoreactivity in Rat Hippocampus

Opioids play a critical role in hippocampally dependent behavior and plasticity. In the hippocampal formation, mu opioid receptors (MOR) are prominent in parvalbumin (PARV) containing interneurons. Previously we found that gonadal hormones modulate the trafficking of MORs in PARV interneurons. Although sex differences in response to stress are well documented, the point at which opioids, sex, and stress interact to influence hippocampal function remains elusive. Thus, we used quantitative immunocytochemistry in combination with light and electron microscopy for the phosphorylated MOR (pMOR) at the SER375 carboxy-terminal residue in male and female rats to assess these interactions. In both sexes, pMOR-immunoreactivity (ir) was prominent in axons and terminals and in a few neuronal somata and dendrites, some of which contained PARV in the mossy fiber pathway region of the dentate gyrus (DG) hilus and CA3 stratum lucidum. In unstressed rats, the levels of pMOR-ir in the DG or CA3 were not affected by sex or estrous cycle stage. However, immediately following 30 min of acute immobilization stress (AIS), males had higher levels of pMOR-ir whereas females at proestrus and estrus (high estrogen stages) had lower levels of pMOR-ir within the DG. In contrast, the number and types of neuronal profiles with pMOR-ir were not altered by AIS in either males or proestrus females. These data demonstrate that although gonadal steroids do not affect pMOR levels at resting conditions, they are differentially activated both pre and postsynaptic MORs following stress. These interactions may contribute to the reported sex differences in hippocampally dependent behaviors in stressed animals

Effective Area-Elasticity and Tension of Micro-manipulated Membranes

We evaluate the effective Hamiltonian governing, at the optically resolved scale, the elastic properties of micro-manipulated membranes. We identify floppy, entropic-tense and stretched-tense regimes, representing different behaviors of the effective area-elasticity of the membrane. The corresponding effective tension depends on the microscopic parameters (total area, bending rigidity) and on the optically visible area, which is controlled by the imposed external constraints. We successfully compare our predictions with recent data on micropipette experiments.Comment: To be published in Phys. Rev. Let

Uniqueness Typing for Resource Management in Message-Passing Concurrency

We view channels as the main form of resources in a message-passing programming paradigm. These channels need to be carefully managed in settings where resources are scarce. To study this problem, we extend the pi-calculus with primitives for channel allocation and deallocation and allow channels to be reused to communicate values of different types. Inevitably, the added expressiveness increases the possibilities for runtime errors. We define a substructural type system which combines uniqueness typing and affine typing to reject these ill-behaved programs