The value of a desk study for building a national river obstacle inventory

This study evaluates two desk‐based approaches for building an inventory of man‐made river obstacles. The creation of a river obstacle inventory is a vital first step in developing a prioritization process for obstacle removal and/or modification. In this study, a desktop geographical information system analysis of two rivers and their tributary network was undertaken, using two different approaches. The first involved analysing historical maps, satellite imagery, and Ordnance Survey Ireland Discovery Series maps and producing a geo‐referenced layer of all the potential river obstacles. The second involved developing a geo‐referenced layer of potential river obstacles based on the intersections between elements of the transport network (roads and railways) and river systems. To determine the effectiveness of the desk studies, the located obstacles were cross‐referenced with actual obstacles verified through a field survey. The desk studies identified several thousand potential obstacles. The study utilizing a range of maps consistently located a greater number of actual obstacles than the desk study based on intersections between the transport and river networks. The results indicate that desk‐based research offers an efficient and effective method for locating river obstacles and can guide subsequent field surveys aimed at confirming the presence of obstacles. This is particularly useful for eliminating from study large stretches of rivers that would otherwise need to be walked to confirm the presence, or otherwise, of potential river obstacles. In this regard, desk‐based exercises can offer opportunities to save on both time and cost in larger river assessments.     

Clonal plasticity: an autonomic mechanism for multi-agent systems to self-diversify

Diversity has long been used as a design tactic in computer systems to achieve various properties. Multi-agent systems, in particular, have utilized diversity to achieve aggregate properties such as efficiency of resource allocations, and fairness in these allocations. However, diversity has usually been introduced manually by the system designer. This paper proposes a decentralized technique, clonal plasticity, that makes homogeneous agents self-diversify, in an autonomic way. We show that clonal plasticity is competitive with manual diversification, at achieving efficient resource allocations and fairness.     

An automated framework for verifying or refuting trace properties of extended finite state machines

Model checkers and interactive proof assistants are both used in the assurance of critical systems. Where theorem proving involves the use of axioms and inference rules to mathematically prove defined properties, model checkers can be used to provide concrete counterexamples to refute them. Thus, the two techniques can be thought of as complementary, and it is helpful to use both in tandem to take advantage of their respective strengths. However, this requires us to translate our system model and our desired properties between the two tools which is a time-consuming and error prone process if done manually. The key contribution of this work is a set of automated tools to translate between the Isabelle/HOL proof assistant and the Symbolic Analysis Laboratory (SAL) model checker. We focus on systems specified as extended finite state machines (EFSMs) and on properties specified in linear temporal logic (LTL). We present our representations in the two tools and demonstrate the applicability of our system with respect to an academic example and two realistic case studies. This is a significant contribution to broadening the applicability of these formal approaches, since it allows two powerful verification tools to be easily used in tandem without the risk of human error.

     

Model-based cross-layer monitoring and adaptation of multilayer systems

With the vision of "Internet as a computer", complex software-intensive systems running on the Internet, or the "Internetwares", can be also divided into multiple layers. Each layer has a different focus, implementation technique, and stakeholders. Monitoring and adaptation of such multilayer systems are challenging, because the mismatches and adaptations are interrelated across the layers. This interrelation makes it difficult to find out: 1) When a system change causes mismatches in one layer, how to identify all the cascaded mismatches on the other layers? 2) When an adaptation is performed at one layer, how to find out all the complementary adaptations required in other layers? This paper presents a model-based approach towards cross-layer monitoring and adaptation of multilayer systems. We provide standard meta-modelling languages for system experts to specify the concepts and constraints separately for each layer, as well as the relations among the concepts from different layers. Within each individual layer, we use run-time models to represent the system state specific to this layer, monitor the systems by evaluating model changes according to specified constraints, and support manual or semi-automated adaption by modifying the models. When a change happens in the run-time model for one layer, either caused by system changes or by the adaptation, we synchronize the models for other layers to identify cascaded mismatches and complementary adaptations across the layers. We illustrate the approach on a simulated crisis management system, and are using it on a number of ongoing projects.     

Fate of prions in soil: adsorption and extraction by electroelution of recombinant ovine prion protein from montmorillonite and natural soils

Prions, the infectious agents thought to be responsible for transmissible spongiform encephalopathies, may contaminate soils and have been reported to persist there for years. We have studied the adsorption and desorption of a model recombinant prion protein on montmorillonite and natural soil samples in order to elucidate mechanisms of prion retention in soils. Clay minerals, such as montmorillonite, are known to be strong adsorbents for organic molecules, including proteins. Montmorillonite was found to have a large and selective adsorption capacity for both the normal and the aggregated prion protein. Adsorption occurred mainly via the N-terminal domain of the protein. Incubation with standard buffers and detergents did not desorb the full length protein from montmorillonite, emphasizing the largely irreversible trapping of prion protein by this soil constituent. An original electroelution method was developed to extract prion protein from both montmorillonite and natural soil samples, allowing quantification when coupled with rapid prion detection tests. This easy-to-perform method produced concentrated prion protein extracts and allowed detection of protein at levels as low as 0.2 ppb in natural soils.     

Effect of Hypergravity and Phytohormones on Isoflavonoid Accumulation in Soybean (Glycine max. L.) Callus

The objective of this study was to explore the potential interaction between gravity and growth hormones on isoflavonoid accumulation. Soybean callus (Glycine max (L.) Merr. cv. ‘Acme’) was grown in the dark for 16 days at 22 °C in a growth medium supplemented with four different combinations of phytohormones and subjected to 4-g and 8-g forces simulated in a centrifuge and 1-g in an adjacent stationary control. Isoflavonoid aglycones and their glycoside concentrations (daidzein, genistein, daidzin, 6″-O-malonyl-7-O-glucosyl daidzein, genistin, 6″-O-malonyl-7-O-glucosyl genistein) were determined in the resulting tissues. Although gravity had no significant impact on callus growth, increasing gravity reduced isoflavonoid accumulation in three out of the four phytohormone-supplemented culture media. The ratio of the auxin naphthalene acetic acid (NAA) to the cytokinin benzylaminopurine (BAP) was found to have profound effect on both callus growth and isoflavonoid accumulation. The cytokinin BAP promoted callus tissue growth, but reduced callus isoflavonoid suggesting the isoflavonoid accumulation was not keeping pace with the cell growth in the elevated concentration of BAP. On the other hand, NAA had little or no effect on callus growth, but greatly enhanced isoflavonoid accumulation. Interactive effects of gravity and hormone on isoflavonoid accumulation were evident and its implication to the mechanism by which gravity exerts the effect on plant secondary metabolites is discussed.     

Z2SAL: a translation-based model checker for Z

Despite being widely known and accepted in industry, the Z formal specification language has not so far been well supported by automated verification tools, mostly because of the challenges in handling the abstraction of the language. In this paper we discuss a novel approach to building a model-checker for Z, which involves implementing a translation from Z into SAL, the input language for the Symbolic Analysis Laboratory, a toolset which includes a number of model-checkers and a simulator. The Z2SAL translation deals with a number of important issues, including: mapping unbounded, abstract specifications into bounded, finite models amenable to a BDD-based symbolic checker; converting a non-constructive and piecemeal style of functional specification into a deterministic, automaton-based style of specification; and supporting the rich set-based vocabulary of the Z mathematical toolkit. This paper discusses progress made towards implementing as complete and faithful a translation as possible, while highlighting certain assumptions, respecting certain limitations and making use of available optimisations. The translation is illustrated throughout with examples; and a complete working example is presented, together with performance data.     

Comparing the anaerobic digestion of Ascophyllum nodosum,the organic fraction of municipal solid waste and white rice in batch reactors

The biogas potential of marine macroalga Ascophyllum nodosum was compared with the organic fraction of municipal solid waste (OFMSW) and white rice to determine the applicability of the feedstock for anaerobic digestion. For OFMSW three dry matter contents were compared, 3%, 10% and 25%, to determine the effect of dry matter on methane yield. Biogas was evolved in each system, but the rate of evolution of biogas changed with moisture content. The highest total methane yield was obtained from 3% OFMSW but A. nodosum yielded more methane at 176±37.62 L/kg VS than white rice and the drier anaerobic digestion of OFMSW. The substrates were digested using wastewater treatment plant inoculum to determine gas yield and gas quality under batch mesophilic digestion conditions.     

Bacterial pathogens in Hawaiian coastal streams--associations with fecal indicators, land cover, and water quality

This work aimed to understand the distribution of five bacterial pathogens in O’ahu coastal streams and relate their presence to microbial indicator concentrations, land cover of the surrounding watersheds, and physical-chemical measures of stream water quality. Twenty-two streams were sampled four times (in December and March, before sunrise and at high noon) to capture seasonal and time of day variation. Salmonella, Campylobacter, Staphylococcus aureus, Vibrio vulnificus, and V. parahaemolyticus were widespread —12 of 22 O’ahu streams had all five pathogens. All stream waters also had detectable concentrations of four fecal indicators and total vibrio with log mean ± standard deviation densities of 2.2 ± 0.8 enterococci, 2.7 ± 0.7 Escherichia coli, 1.1 ± 0.7 Clostridium perfringens, 1.2 ± 0.8 F⁺ coliphages, and 3.6 ± 0.7 total vibrio per 100 ml. Bivariate associations between pathogens and indicators showed enterococci positively associated with the greatest number of bacterial pathogens. Higher concentrations of enterococci and higher incidence of Campylobacter were found in stream waters collected before sunrise, suggesting these organisms are sensitive to sunlight. Multivariate regression models of microbes as a function of land cover and physical-chemical water quality showed positive associations between Salmonella and agricultural and forested land covers, and between S. aureus and urban and agricultural land covers; these results suggested that sources specific to those land covers may contribute these pathogens to streams. Further, significant associations between some microbial targets and physical-chemical stream water quality (i.e., temperature, nutrients, turbidity) suggested that organism persistence may be affected by stream characteristics. Results implicate streams as a source of pathogens to coastal waters. Future work is recommended to determine infectious risks of recreational waterborne illness related to O’ahu stream exposures and to mitigate these risks through control of land-based runoff sources.