Electrochemical performance of a DNA-based sensor device for detecting toxic algae

This work illustrates the electrochemical performance of a DNA-based sensor device for detecting toxic algae. This biosensor uses an electrochemical detection of the species in a sandwich hybridisation. A thiol (biotin) labelled capture probe was immobilized onto gold (carbon) electrodes. Synthetic positive control DNA was applied to the sensor and allowed to hybridize to the capture probe. A signal probe with a horseradish peroxidase (HRP) label was then applied, followed by an antibody to the HRP and a substrate. The electrical signal obtained from the redox reaction was proportional to the amount of DNA applied to the biosensor, which in turn would be proportional to the number of cells harvested when applied to real samples. Optimization of the hybridization process was already achieved in a previous work. Elucidation of the different steps of the fabrication process from the electrochemical point of view, proof of concept with different algal species and evaluation of the influence of the transducer platform geometry and material in the biosensor analytical performance are the main achievements reported here.     

Chemical Genetic Programming – evolutionary optimization of the genotype-to-phenotype translation set

A new method of genetic programming, named chemical genetic programming (CGP), which enables evolutionary optimization of the mapping from genotypic strings to phenotypic trees is proposed. A cell is evolved which includes a DNA string that codes the fundamental mapping from the DNA code to computational functionality. Genetic modification of a cell's DNA allows the DNA code and the genotype-to-phenotype translation to coevolve. Building an optimal translation table enhances evolution within a population while maintaining the necessary diversity to explore the entire search space. This work was presented in part at the 9th International Symposium on Artificial Life and Robotics, Oita, Japan, January 28–30, 2004     

A novel ocean color index to detect floating algae in the global oceans

Various types of floating algae have been reported in open oceans and coastal waters, yet accurate and timely detection of these relatively small surface features using traditional satellite data and algorithms has been difficult or even impossible due to lack of spatial resolution, coverage, revisit frequency, or due to inherent algorithm limitations. Here, a simple ocean color index, namely the Floating Algae Index (FAI), is developed and used to detect floating algae in open ocean environments using the medium-resolution (250- and 500-m) data from operational MODIS (Moderate Resolution Imaging Spectroradiometer) instruments. FAI is defined as the difference between reflectance at 859 nm (vegetation “red edge”) and a linear baseline between the red band (645 nm) and short-wave infrared band (1240 or 1640 nm). Through data comparison and model simulations, FAI has shown advantages over the traditional NDVI (Normalized Difference Vegetation Index) or EVI (Enhanced Vegetation Index) because FAI is less sensitive to changes in environmental and observing conditions (aerosol type and thickness, solar/viewing geometry, and sun glint) and can “see” through thin clouds. The baseline subtraction method provides a simple yet effective means for atmospheric correction, through which floating algae can be easily recognized and delineated in various ocean waters, including the North Atlantic Ocean, Gulf of Mexico, Yellow Sea, and East China Sea. Because similar spectral bands are available on many existing and planned satellite sensors such as Landsat TM/ETM+ and VIIRS (Visible Infrared Imager/Radiometer Suite), the FAI concept is extendable to establish a long-term record of these ecologically important ocean plants.     

On the strict logic foundation of fuzzy reasoning

This paper focuses on the logic foundation of fuzzy reasoning. At first, a new complete first-order fuzzy predicate calculus system K^* corresponding to the formal system L^* is built. Based on the many-sort system K_ms^* corresponding to K^*, the triple I methods of FMP and FMT for fuzzy reasoning and their consistency are formalized, thus fuzzy reasoning is put completely and rigorously into the logic framework of fuzzy logic.The author is indebted to anonymous referee for his useful comments which have helped to improve the paper.     

Thermodynamic assessment of the ternary AgNO3-LiNO3-NaNO3 system

Based on the available experimental information, the AgNO₃-LiNO₃-NaNO₃ ternary system and its low order AgNO₃-LiNO₃, AgNO₃-NaNO₃ and LiNO₃-NaNO₃ binary systems are thermodynamically assessed using the Calphad method. A set of parameters describing the Gibbs energies of the different phases is presented. Ternary parameters are necessary to describe the liquid phase in a neutral species model where each nitrate is treated as a constituent. Calculated phase diagrams and thermodynamical functions for the three limiting binary systems show good agreement with experimental data. In the ternary AgNO₃-LiNO₃-NaNO₃ system we have calculated two vertical sections which are in reasonable agreement with the reported experimental data. Also, several isothermal sections are calculated.     

An exploratory study into whether to or not to include users in the development of industrial hypermedia applications

While there is agreement among both information system (IS) practitioners and IS researchers as to the value of user participation in IS development, the correlation between user participation and actual use or user satisfaction (surrogate measures of IS success) has been equivocal. A possible reason for the contradictory findings could be that user participation is being utilised, regardless of the levels of complexity of either the system or the task. This paper describes two exploratory case studies to test this hypothesis. Industrial hypermedia applications (IHA) were developed and qualitative data collected, through usability trials, to see the effect of user participation on user perception (extrinsic motivations of use) of the system, rather than IS success. The findings show that users should participate in the development when both the IS and the task are complex. On the other hand, when both the system and the task are not complex, user participation can be kept to a minimum. Furthermore, it is recommended that user participation should not be evaluated against IS success, but against system features.

Relationship between the attenuation of downwelling irradiance at 490 nm with the attenuation of PAR (400 nm-700 nm) in the Baltic Sea

The vertical attenuation coefficient of diffuse downwelling irradiance at 490 nm (K_d 490) is a parameter that we routinely derive from SeaWiFS images of the Baltic Sea. Here, through model simulations, we examine the relationship between K_d(490), and the vertical attenuation coefficient of PAR (K_d PAR), as this later coefficient determines the light available for aquatic photosynthesis. A simple semi-analytical model is used to predict K_d(490) and K_d(PAR), as a function of the concentrations of chlorophyll, colored dissolved organic material (CDOM), suspended inorganic, and suspended organic particulate material. A series of model simulations based on variations in these optically significant constituents over a range realistic for the Baltic Sea, are used to define the relationship between the two attenuation coefficients.

Kd(PAR)=0.6677Kd^0.6763(490).     

Structure and dynamics of the GH loop of the foot-and-mouth disease virus capsid

The GH loop of VP1 of the foot-and-mouth disease virus capsid is important because it is a major antigenic site and an integrin recognition site. The GH loop is disordered in all X-ray structures of the capsid except for serotype O under reduced conditions in which the loop lies on the capsid surface. Although the structure of the capsid–integrin complex has not yet been determined, the GH loop is known to protrude from the capsid surface when the capsid is bound with an antigen-binding fragment (Fab). To clarify the structure and dynamics of the GH loop under natural unreduced conditions before binding to integrins or Fab fragments, we performed molecular dynamics simulation of 16.3 ns long under rotational symmetry boundary conditions for the capsid of serotype O using the X-ray structure of the reduced capsid for the initial coordinates. When the disulfide bond at the base of the GH loop was formed by the molecular mutation method, the loop protruded into the surrounding water, as reported for Fab–capsid complexes, and fluctuated like a tentacle. After equilibration, the GH loop overlapped the surface of the capsid but continued to fluctuate, being directed toward a 2-fold axis. The conformational change of the GH loop after formation of the disulfide bond was explained by a model of elastic tube. The side chains of arginine and aspartic acid of the integrin recognition residues (RGD tripeptide) extended in opposite directions, and the residues on the C-terminal side of the RGD tripeptide formed a hydrophobic cluster in close proximity of the arginine residue of the tripeptide.     

Seasonal and spatial distribution of chlorophyll-a concentrations and water conditions in the Gulf of Tonkin, South China Sea

The Gulf of Tonkin is a semi-closed gulf northwest of the South China Sea, experiencing reversal seasonal monsoon. Previous studies of water conditions have been conducted in the western waters of the gulf, but very few studies of the Chlorophyll-a (Chl-a) distribution have been carried out for the entire gulf. The present study investigates seasonal and spatial distributions of Chl-a and water conditions in the Gulf of Tonkin by analyzing Sea-viewing Wide Field-of-View Scanner (SeaWiFS) derived Chlorophyll-a (Chl-a), in situ measurements, sea surface temperatures (SST), and other oceanographic data obtained in 1999 and 2000. The results show seasonality of Chl-a and SST variations in the Gulf of Tonkin, and reveal phytoplankton blooming events in the center part of the gulf during the northeast monsoon season. In summer, Chl-a concentrations were relatively low (<0.3 mg m⁻³) and distributed uniformly throughout most of the area, with a belt of higher Chl-a concentrations along the coast, particularly the coast of Qiongzhou Peninsula; in winter, Chl-a concentration increased (0.5 mg m⁻³) in the entire gulf, and phytoplankton blooms offshore-ward from the northeast coast to the center of the gulf, while Chl-a concentrations reached high levels (0.8-1 mg m⁻³) in the center of the blooms. One peak of Chl-a concentrations was observed during the northeast monsoon season in the year. SST were high (27-29 °C) and distributed uniformly in summer, but lower with a large gradient from northeast (17 °C) to southwest (25 °C) in winter, while strong northeast winds (8-10 m/s) were parallel to the east coast of the gulf. Comparison of Chl-a values shows that SeaWiFS derived Chl-a concentrations match well with in situ measurements in most parts of the gulf in May 1999, but SeaWiFS derived Chl-a are higher than in situ data in river mouth waters. The seasonal variation of Chl-a concentrations and SST distribution were associated with the seasonally reversing monsoon; the winter phytoplankton blooms were related to vertical mixing and upwelling nutrients drawn by the northeast wind.     

Electrical response of Sm2O3-doped SnO2 to C2H2 and effect of humidity interference

Pure and Sm₂O₃-doped SnO₂ are prepared through a sol–gel method and characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The sensor based on 6 wt% Sm₂O₃-doped SnO₂ displays superior response at an operating temperature of 180 °C, and the response magnitude to 1000 ppm C₂H₂ can reach 63.8, which is 16.8 times larger than that of pure SnO₂. This sensor also shows high sensitivity under various humidity conditions. These results make our product be a good candidate in fabricating C₂H₂ sensors.     

On the ω-language Expressive Power of Extended Petri Nets

In this paper, we study the expressive power of several monotonic extensions of Petri nets. We compare the expressive power of Petri nets, Petri nets extended with non-blocking arcs and Petri nets extended with transfer arcs, in terms of ω-languages. We show that the hierarchy of expressive powers of those models is strict. To prove these results, we propose original techniques that rely on well-quasi orderings and monotonicity properties.     

UppDMC: A Distributed Model Checker for Fragments of the μ-Calculus

We present UppDMC, a distributed model-checking tool. It is tailored for checking finite-state systems and μ-calculus specifications with at most one alternation of minimal and maximal fixed-point operators. This fragment is also known as . Recently, efficient game-based algorithms for this logic have been outlined.We describe the implementation of these algorithms within UppDMC and study their performance on practical examples. Running UppDMC on a simple workstation cluster, we were able to check liveness properties of the largest examples given in the VLTS Benchmark Suite, for which no answers were previously known.     

A Proof Search Specification of the π-Calculus

We present a meta-logic that contains a new quantifier (for encoding “generic judgments”) and inference rules for reasoning within fixed points of a given specification. We then specify the operational semantics and bisimulation relations for the finite π-calculus within this meta-logic. Since we restrict to the finite case, the ability of the meta-logic to reason within fixed points becomes a powerful and complete tool since simple proof search can compute this one fixed point. The quantifier helps with the delicate issues surrounding the scope of variables within π-calculus expressions and their executions (proofs). We shall illustrate several merits of the logical specifications we write: they are natural and declarative; they contain no side conditions concerning names of variables while maintaining a completely formal treatment of such variables; differences between late and open bisimulation relations are easy to see declaratively; and proof search involving the application of inference rules, unification, and backtracking can provide complete proof systems for both one-step transitions and for bisimulation.     

Gas sensitivity of Zn doped α-Fe2O3(SO4, Sn, Zn) to carbon monoxide

It is shown that the doping of Zn and Sn can improve the gas sensitivity of α-Fe₂O₃-based sensing material to CO. X-ray photo-electron spectroscopy analysis suggests that this is mainly due to the fact that the simultaneous doping of Zn and Sn can increase the S and hence SO₄²⁻ contents in the α-Fe₂O₃(SO₄²⁻, Sn, Zn) sensing material. The results also suggest that under a given condition, the gas sensitivity of α-Fe₂O₃(SO₄²⁻, Sn, Zn) to CO can be optimised by properly adjusting the doped Zn content.     

An H-minimax approach to the design of robust control systems, part II: All solutions, all-pass form solutions and the ‘best’ solution

We characterize all solutions to a robustness optimization problem as the solutions of a two-parameter interpolation problem. From this characterization it is easy to show that an all-pass form solution always exists as long as a solution exists. We also study the possibility of using non-all-pass form solutions and by introducing other optimization objectives (motivated by improvements in disturbance rejection and robust stability) we search for the 'best' solution.     

Development and application of the theory of parametric regulation of evolution of economic systems based on a neoclassical model of optimal growth

Presented were some results on roughness of the mathematical model of the neoclassical theory of optimal growth with and without parametric regulation, selection of the optimal law of parametric regulation, and the optimal law of parametric regulation vs. the uncontrollable parameters of this mathematical model based on the parametric regulation theory.     

Modelling β-1,3-exoglucanase–saccharide interactions: Structure of the enzyme–substrate complex and enzyme binding to the cell wall

Glycoside hydrolases are a class of enzymes that break/form the bond between sugar monomers (monosaccharides). Candida albicans's β-1,3-exoglucanase (Exg), a family 5 glycosidase, belongs to this class of enzymes. This small protein is an ideal computational model for its family of enzymes and was used here to create several enzyme–substrate models starting from a crystallographic glucanase-inhibitor structure. A series of enzyme–substrate complexes were generated using molecular docking, ranging from Exg–glucose (Exg–1Glc) to Exg–laminarihexaose (Exg–6Glc). Structure optimizations followed by molecular dynamics provided a picture of the way the enzyme and substrates interact.Molecular dynamics was conducted for each complex to assess the flexibility of the substrate, of the enzyme as a whole, and of enzyme–substrate interactions. The enzyme overall conformation was found to be quite rigid, although most enzyme residues increase mobility upon substrate binding. However, two surface loops stand out by having large fluctuations and becoming less flexible when the substrates were bound. These data point to a possible biological role for the mentioned loops, corresponding to amino acids 36–47 and 101–106.We propose that these loops could bind the enzyme to a glucan chain in the cell wall. The polysaccharide and enzyme structures have very complementary shapes and form numerous interactions; so it appears likely that the flexible loops connect the enzyme to the cell wall and allow it to navigate the wall to shape glucan structure.     

An evaluation of remote sensing techniques for enhanced detection of the toxic dinoflagellate, Karenia brevis

Optical techniques were investigated to enhance current bloom detection capabilities in support of an operational system for forecasting harmful Karenia brevis blooms along the west coast of Florida, within the Gulf of Mexico. Algorithms pertaining to backscatter and changes in spectral shape of remote-sensing reflectance were applied to SeaWiFS and MODIS imagery during known K. brevis and non-K. brevis events. A method to remove resuspended chlorophyll in Texas showed limited use when applied to several scenes following tropical storms off the west Florida coast. This analysis suggests that an ensemble image approach, wherein a combination of a chlorophyll anomaly, spectral shape at 490 nm and a backscatter ratio product would provide an improvement in satellite detection of K. brevis blooms. For southwest Florida, the combination of these methods through an ensemble approach may lead to an increase in user accuracy by 30-50%, as a result of correctly identifying non-K. brevis features. Where available, MODIS FLH scenes were analyzed to determine their use in K. brevis detection. However, insufficient imagery was available to make a fair assessment. Similar approaches could be applied to bloom tracking and monitoring in other regions.