Characterizing physical habitat preferences and thermal refuge occupancy of brook trout (Salvelinus fontinalis) and Atlantic salmon (Salmo salar) at high river temperatures

Anthropogenic influences, including climate change, are increasing river temperatures in northern and temperate regions and threatening the thermal habitats of native salmonids. When river temperatures exceed the tolerance levels of brook trout and Atlantic salmon, individuals exhibit behavioural thermoregulation by seeking out cold‐water refugia – often created by tributaries and groundwater discharge. Thermal infrared (TIR) imagery was used to map cold‐water anomalies along a 53 km reach of the Cains River, New Brunswick. Trout and salmon parr did not use all identified thermal anomalies as refugia during higher river temperature periods (>21°C). Most small‐bodied trout (8–30 cm) were observed in 80% of the thermal anomalies sampled. Large‐bodied trout (>35 cm) required a more specific set of physical habitat conditions for suitable refugia, that is, 100% of observed large trout used 30% of the anomalies sampled and required water depths >65 cm within or adjacent to the anomaly. Densities of trout were significantly higher within anomalies compared with areas of ambient river temperature. Salmon parr were less aligned with thermal anomalies at the observed temperatures, that is, 59% were found in 65% of the sampled anomalies; and densities were not significantly different within/ outside anomalies. Salmon parr appeared to aggregate at 27°C, and after several events over 27°C variability in aggregation behaviour was observed – some fish aggregated at 25°C, others did not. We stipulate this is due to variances of thermal fatigue. Habitat suitability curves were developed for velocity, temperature, depth, substrate, and deep water availability to characterize conditions preferred by fish during high‐temperature events. These findings are useful for managers as our climate warms, and can potentially be used as a tool to help conserve and enhance thermal refugia for brook trout and Atlantic salmon in similar systems.     

Protein design to understand peptide ligand recognition by tetratricopeptide repeat proteins

Protein design aims to understand the fundamentals of protein structure by creating novel proteins with pre-specified folds. An equally important goal is to understand protein function by creating novel proteins with pre-specified activities. Here we describe the design and characterization of a tetratricopeptide (TPR) protein, which binds to the C-terminal peptide of the eukaryotic chaperone Hsp90. The design emphasizes the importance of both direct, short-range protein-peptide interactions and of long-range electrostatic optimization. We demonstrate that the designed protein binds specifically to the desired peptide and discriminates between it and the similar C-terminal peptide of Hsp70.     

Using aspects for testing of embedded software: experiences from two industrial case studies

Aspect-oriented software testing is emerging as an important alternative to conventional procedural and object-oriented testing techniques. This paper reports experiences from two case studies where aspects were used for the testing of embedded software in the context of an industrial application. In the first study, we used code-level aspects for testing non-functional properties. The methodology we used for deriving test aspect code was based on translating high-level requirements into test objectives, which were then implemented using test aspects in AspectC++. In the second study, we used high-level visual scenario-based models for the test specification, test generation, and aspect-based test execution. To specify scenario-based tests, we used a UML2-compliant variant of live sequence charts. To automatically generate test code from the models, a modified version of the S2A Compiler, outputting AspectC++ code, was used. Finally, to examine the results of the tests, we used the Tracer, a prototype tool for model-based trace visualization and exploration. The results of the two case studies show that aspects offer benefits over conventional techniques in the context of testing embedded software; these benefits are discussed in detail. Finally, towards the end of the paper, we also discuss the lessons learned, including the technological and other barriers to the future successful use of aspects in the testing of embedded software in industry.     

Easy Algorithm Animation on the Web

The animation environment Jeliot automates visualization of algorithms over the Internet. The user can visualize algorithms of his own, not merely the selection supplied by a service provider. Jeliot is based on self-animating data types: the user selects the data objects of the source code to be visualized, and Jeliot produces the animation based on operations performed on those types. We present the design of Jeliot and the principles of its implementation. In addition, we discuss the educational applications of Jeliot.     

Self-assembled silver nanoislands formed on glass surface via out-diffusion for multiple usages in SERS applications

We demonstrate that silver nanoisland film self-assembled on the surface of silver-containing glass in the course of thermal processing in hydrogen is capable to detect 10⁻⁷ M concentration of rhodamine 6G in water using surface enhanced Raman spectroscopy (SERS) technique. The film can be multiply restored on the same glass substrate via annealing of the glass in hydrogen. We showed that the film can be self-assembled after as much as ten circles of the substrate cleaning followed by annealing. The proposed technique of the silver nanoisland film formation enables multiple usage of the same glass substrate in SERS experiments.     

Functionalized polypropylene prepared by melt free radical grafting of low volatile oxazoline and its potential in compatibilization of PP/PBT blends

This article concerns the functionalization of polypropylene (PP) with oxazoline functionality by melt free radical grafting along with a low degree of degradation of PP in a batch mixer. A low volatile oxazoline, ricinoloxazoline maleinate (OXA), was used as the monomer. The grafting yield of OXA ranged from about 0.5 phr up to 1.5 phr (grams per 100 grams of PP) when its initial concentration and that of the peroxide ranged from 1.5 to 6.0 phr and 0.1 to 0.7 phr, respectively. The corresponding conversion of OXA to grafted OXA ranged from about 15 to 50%. Addition of styrene (St) as the comonomer did not enhance the grafting yield of OXA but markedly reduced the PP degradation. Also, little homo-and/or copolymers of OXA and/or St were found in the grafting system. This agrees with our finding that OXA and St did not copolymerize easily. The potential of using an OXA modified PP (PP-g-OXA) as the compatibilizer precursor in PP/PBT blends was examined as well. The presence of PP-g-OXA reduced the particle size of the dispersed phase (PBT) along with improved cohesion between the PP and PBT phases. This is consistent with a model kinetic study, which showed that the reaction between oxazoline and carboxylic functionalities was very fast. © 1996 John Wiley & Sons, Inc.     

Rolling of manifolds without spinning

The control model of rolling of a Riemannian manifold (M; g) onto another one $ \left( {\hat{M},\hat{g}} \right) $ consists of a state space Q of relative orientations (isometric linear maps) between their tangent spaces equipped with a so-called rolling distribution $ {\mathcal D} $ _R, which models the natural constraints of no-spinning and no-slipping of the rolling motion. It turns out that the distribution $ {\mathcal D} $ _R can be built as a sub-distribution of a so-called no-spinning distribution $ {{\mathcal{D}}_{\overline{\nabla}}} $ on Q that models only the no-spinning constraint of the rolling motion. One is thus motivated to study the control problem associated to $ {{\mathcal{D}}_{\overline{\nabla}}} $ and, in particular, the geometry of $ {{\mathcal{D}}_{\overline{\nabla}}} $ -orbits. Moreover, the definition of $ {{\mathcal{D}}_{\overline{\nabla}}} $ (contrary to the definition of $ {\mathcal D} $ _R) makes sense in the general context of vector bundles equipped with linear connections. The purpose of this paper is to study the distribution $ {{\mathcal{D}}_{\overline{\nabla}}} $ determined by the product connection $ \nabla \times \hat{\nabla} $ on a tensor bundle $ {E^{*}}\otimes \hat{E}\to M\times \hat{M} $ induced by linear connections ?, $ \hat{\nabla} $ on vector bundles $ E\to M,\,\,\,\hat{E}\to \hat{M} $ . We describe completely the orbit structure of $ {{\mathcal{D}}_{\overline{\nabla}}} $ in terms of the holonomy groups of ?, $ \hat{\nabla} $ and characterize the integral manifolds of it. Moreover, we describe the general formulas for the Lie brackets of vector elds in $ {E^{*}}\otimes \hat{E} $ in terms of $ {{\mathcal{D}}_{\overline{\nabla}}} $ and the vertical tangent distribution of $ {E^{*}}\otimes \hat{E}\to M\times \hat{M} $ . In the particular case of tangent bundles $ TM\to M,\,\,\,T\hat{M}\to \hat{M} $ and Levi-Civita connections, we describe in more detail how $ {{\mathcal{D}}_{\overline{\nabla}}} $ is related to the above mentioned rolling model, where these Lie brackets formulas provide an important tool for the study of controllability of the related control system.     

New method for aroma barrier testing

A new quasi‐isostatic permeation test method has been developed for aroma barrier testing. Aroma concentrations are measured as a function of time, while the compounds diffuse from the source cell containing the model aroma solution through the tested material to the receiving cell. This method is applicable for testing various materials such as uncoated and coated paper/paperboard, and polymer films. The method utilizes automatic gas sampling from the test cells to gas chromatography. Copyright © 2007 John Wiley & Sons, Ltd.     

Prospecting hydrogen production of Escherichia coli by metabolic network modeling

Genome-scale model was applied to analyze the anaerobic metabolism of Escherichia coli. Three different methods were used to find deletions affecting fermentative hydrogen production: flux balance analysis (FBA), algorithm for blocking competing pathways (ABCP), and manual selection. Based on these methods, 81 E. coli mutants possessing one gene deletion were selected and cultivated in batch experiments. Experimental results of H₂ and biomass production were compared against the results of FBA. Several gene deletions enhancing H₂ production were found. Correctness of gene essentiality predictions of FBA for the selected genes was 78% and 77% in glucose and galactose media, respectively. 33% of the mutations that were predicted by FBA to increase H₂ production had a positive effect in experiments. Batch cultivation is a simple and straightforward experimental way to screen improvements in H₂ production. However, the ability of FBA to predict the H₂ production rate cannot be evaluated by batch experiments. Metabolic network models provide a method for gaining broader understanding of the complicated metabolic system of a cell and can aid in prospecting suitable gene deletions for enhancing H₂ production.