Towards realistic simulations of lava dome growth using the level set method

The level set method has been implemented in a computational volcanology context. New techniques are presented to solve the advection equation and the reinitialisation equation. These techniques are based upon an algorithm developed in the finite difference context, but are modified to take advantage of the robustness of the finite element method. The resulting algorithm is tested on a well documented Rayleigh–Taylor instability benchmark [19], and on an axisymmetric problem where the analytical solution is known. Finally, the algorithm is applied to a basic study of lava dome growth.

Using the level set method to model endogenous lava dome growth

Modeling volcanic phenomena is complicated by free-surfaces often supporting large rheological gradients. Analytical solutions and analogue models provide explanations for fundamental characteristics of lava flows. But more sophisticated models are needed, incorporating improved physics and rheology to capture realistic events. To advance our understanding of the flow dynamics of highly viscous lava in Peléean lava dome formation, axi-symmetrical Finite Element Method (FEM) models of generic endogenous dome growth have been developed. We use a novel technique, the level-set method, which tracks a moving interface, leaving the mesh unaltered. The model equations are formulated in an Eulerian framework. In this paper we test the quality of this technique in our numerical scheme by considering existing analytical and experimental models of lava dome growth which assume a constant Newtonian viscosity. We then compare our model against analytical solutions for real lava domes extruded on Soufrière, St. Vincent, W.I. in 1979 and Mount St. Helens, USA in October 1980 using an effective viscosity. The level-set method is found to be computationally light and robust enough to model the free-surface of a growing lava dome. Also, by modeling the extruded lava with a constant pressure head this naturally results in a drop in extrusion rate with increasing dome height, which can explain lava dome growth observables more appropriately than when using a fixed extrusion rate. From the modeling point of view, the level-set method will ultimately provide an opportunity to capture more of the physics while benefiting from the numerical robustness of regular grids.

Incorporating level set methods in Geographical Information Systems (GIS) for land-surface process modelling

Land-surface processes include a broad class of models that operate at a landscape scale. Current modelling approaches tend to be specialised towards one type of process, yet it is the interaction of processes that is increasing seen as important to obtain a more integrated approach to land management. This paper presents a technique and a tool that may be applied generically to landscape processes. The technique tracks moving interfaces across landscapes for processes such as water flow, biochemical diffusion, and plant dispersal. Its theoretical development applies a Lagrangian approach to motion over a Eulerian grid space by tracking quantities across a landscape as an evolving front. An algorithm for this technique, called level set method, is implemented in a geographical information system (GIS). It fits with a field data model in GIS and is implemented as operators in map algebra. The paper describes an implementation of the level set methods in a map algebra programming language, called MapScript, and gives example program scripts for applications in ecology and hydrology.

Human Fatalities from Cyanobacteria: Chemical and Biological Evidence for Cyanotoxins

An outbreak of acute liver failure occurred at a dialysis center in Caruaru, Brazil (8 degrees 17 'S, 35 degrees 58 'W), 134 km from Recife, the state capital of Pernambuco. At the clinic, 116 (89%) of 131 patients experienced visual disturbances, nausea, and vomiting after routine hemodialysis treatment on 13-20 February 1996. Subsequently, 100 patients developed acute liver failure, and of these 76 died. As of December 1996, 52 of the deaths could be attributed to a common syndrome now called Caruaru syndrome. Examination of phytoplankton from the dialysis clinic's water source, analyses of the clinic's water treatment system, plus serum and liver tissue of clinic patients led to the identification of two groups of cyanobacterial toxins, the hepatotoxic cyclic peptide microcystins and the hepatotoxic alkaloid cylindrospermopsin. Comparison of victims' symptoms and pathology using animal studies of these two cyanotoxins leads us to conclude that the major contributing factor to death of the dialyses patients was intravenous exposure to microcystins, specifically microcystin-YR, -LR, and -AR. From liver concentrations and exposure volumes, it was estimated that 19.5 mug/L microcystin was in the water used for dialysis treatments. This is 19.5 times the level set as a guideline for safe drinking water supplies by the World. Health Organization.

Brief note on the variation of constants formula for fuzzy differential equations

This note gives a theory of state transition matrices for linear systems of fuzzy differential equations. This is used to give a fuzzy version of the classical variation of constants formula. A simple example of a time-independent control system is used to illustrate the methods. While similar problems to the crisp case arise for time-dependent systems, in time-independent cases the calculations are elementary solutions of eigenvalue-eigenvector problems. In particular, for nonnegative or nonpositive matrices, the problems at each level set, can easily be solved in MATLAB to give the level sets of the fuzzy solution. (C) 2002 Elsevier Science B.V. All rights reserved.

Simulation of the cake formation and growth in cake filtration

A computer model was developed to simulate the cake formation and growth in cake filtration at an individual particle level. The model was shown to be able to generate structural information and quantify the cake thickness, average cake solidosity, filtrate volume, filtrate flowrate for constant pressure filtration or pressure drop across the filter unit for constant rate filtration as a function of filtration time. The effects of particle size distribution and key operational variables such as initial filtration flowrate, maximum pressure drop and initial solidosity were examined based on the simulated results. They are qualitatively comparable to those observed in physical experiments. The need for further development in simulation was also discussed. (c) 2006 Elsevier Ltd. All rights reserved.

Kidney dysfunction and hypertension: Role for cadmium, P450 and heme oxygenases?

Cadmium (Cd) is a metal toxin of continuing worldwide concern. Daily intake of Cd, albeit in small quantities, is associated with a number of adverse health effects which are attributable to distinct pathological changes in a variety of tissues and organs. In the present review, we focus on its renal tubular effects in people who have been exposed environmentally to Cd at levels below the provisional tolerable intake level set for the toxin. We highlight the data linking such low-level Cd intake with tubular injury, altered abundance of cytochromes P450 (CYPs) in the kidney and an expression of a hypertensive phenotype. We provide updated knowledge on renal and vascular effects of the eicosanoids 20-hydroxyeicosatetraenoic acid (20-HETE) and eicosatrienoic acids (EETs), which are biologically active metabolites from arachidonate metabolism mediated by certain CYPs in the kidney. We note the ability of Cd to elicit oxidative stress and to alter metal homeostasis notably of zinc which may lead to augmentation of the defense mechanisms involving induction of the antioxidant enzyme heme oxygenase-1 (HO-1) and the metal binding protein metallothionein (MT) in the kidney. We hypothesize that renal Cd accumulation triggers the host responses mediated by HO-I and MT in an attempt to protect the kidney against injurious oxidative stress and to resist a rise in blood pressure levels. This hypothesis predicts that individuals with less active HO-1 (caused by the HO-1 genetic polymorphisms) are more likely to have renal injury and express a hypertensive phenotype following chronic ingestion of low-level Cd, compared with those having more active HO-1. Future analytical and molecular epidemiologic research should pave the way to the utility of induction of heme oxygenases together with dietary antioxidants in reducing the risk of kidney injury and hypertension in susceptible people.

Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) revelas a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an intersubspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

Simulation of the micro-physics of rocks using LSMearth

The particle-based Lattice Solid Model (LSM) was developed to provide a basis to study the physics of rocks and the nonlinear dynamics of earthquakes (MORA and PLACE, 1994; PLACE and MORA, 1999). A new modular and flexible LSM approach has been developed that allows different microphysics to be easily included in or removed from the model. The approach provides a virtual laboratory where numerical experiments can easily be set up and all measurable quantities visualised. The proposed approach provides a means to simulate complex phenomena such as fracturing or localisation processes, and enables the effect of different micro-physics on macroscopic behaviour to be studied. The initial 2-D model is extended to allow three-dimensional simulations to be performed and particles of different sizes to be specified. Numerical bi-axial compression experiments under different confining pressure are used to calibrate the model. By tuning the different microscopic parameters (such as coefficient of friction, microscopic strength and distribution of grain sizes), the macroscopic strength of the material and can be adjusted to be in agreement with laboratory experiments, and the orientation of fractures is consistent with the theoretical value predicted based on Mohr-Coulomb diagram. Simulations indicate that 3-D numerical models have different macroscopic properties than in 2-D and, hence, the model must be recalibrated for 3-D simulations. These numerical experiments illustrate that the new approach is capable of simulating typical rock fracture behaviour. The new model provides a basis to investigate nucleation, rupture and slip pulse propagation in complex fault zones without the previous model limitations of a regular low-level surface geometry and being restricted to two-dimensions.

Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set

The cell cycle is one of the most fundamental processes within a cell. Phase-dependent expression and cell-cycle checkpoints require a high level of control. A large number of genes with varying functions and modes of action are responsible for this biology. In a targeted exploration of the FANTOM2-Variable Protein Set, a number of mouse homologs to known cell-cycle regulators as well as novel members of cell-cycle families were identified. Focusing on two prototype cell-cycle families, the cyclins and the NIMA-related kinases (NEKs), we believe we have identified all of the mouse members of these families, 24 cyclins and 10 NEKs, and mapped them to ENSEMBL transcripts. To attempt to globally identify all potential cell cycle-related genes within mouse, the MGI (Mouse Genome Database) assignments for the RIKEN Representative Set (RPS) and the results from two homology-based queries were merged. We identified 1415 genes with possible cell-cycle roles, and 1758 potential paralogs. We comment on the genes identified in this screen and evaluate the merits of each approach.

Higher-level language deficits resulting from left primary cerebellar lesions

Background: Contemporary neuropsychological studies suggest that cerebellar lesions may impact upon higher-level cognitive functioning via mechanisms of crossed cerebello-cerebral diaschisis. Accordingly, right cerebellar lesions have been previously associated with linguistic impairments such as reduced word fluency and agrammatic output. Recently, however, neuroimaging investigations have also identified ipsilateral cerebral hypoperfusion as a consequence of cerebellar lesions, implicating a potential role for the left cerebellum in the mediation of language processes. Aims: The purpose of this research was to investigate the effects of left cerebellar lesions of vascular origin, on general as well as high-level language skills. Methods & Procedures: Linguistic profiles were compiled for five individuals with left primary cerebellar lesions utilising a comprehensive language test battery. Individual scores relevant to each subtest were compared to a group of non-neurologically impaired controls. The criterion for anomalous performance was established as greater than or equal to 1.5 SD below the mean of the control group. Outcomes & Results: The findings of this research suggest that higher-level language deficits may result from left primary cerebellar lesions. All participants demonstrated deficits on measures of word fluency, sentence construction within a set context, producing word definitions, and producing multiple definitions for the same word. Deficits were also noted for several participants on measures of understanding figurative language, forming word associations, identifying and correcting semantic absurdities, and producing synonyms and antonyms. Conclusions: The results presented challenge the notion of a lateralised linguistic cerebellum, supporting a potential role for the left as well as right cerebellar hemispheres in the regulation of language processes, presumably via cerebellar-basal ganglia/thalamo-cortical pathways.

Adverse Health Effects of Chronic Exposure to Low-Level Cadmium in Foodstuffs and Cigarette Smoke

Cadmium is a cumulative nephrotoxicant that is absorbed into the body from dietary sources and cigarette smoking. The levels of Cd in organs such as liver and kidney cortex increase with age because of the lack of an active biochemical process for its elimination coupled with renal reabsorption. Recent research has provided evidence linking Cd-related kidney dysfunction and decreases in bone mineral density in nonoccupationally exposed populations who showed no signs of nutritional deficiency. This challenges the previous view that the concurrent kidney and bone damage seen in Japanese itai-itai disease patients was the result of Cd toxicity in combination with nutritional deficiencies, notably, of zinc and calcium. Further, such Cd-linked bone and kidney toxicities were observed in people whose dietary Cd intakes were well within the provisional tolerable weekly intake (PTWI) set by the Joint Food and Agriculture Organization/World Health Organization Expert Committee on Food Additives of 1 mug/kg body weight/day or 70 mug/day. This evidence points to the much-needed revision of the current PTWI for Cd. Also, evidence for the carcinogenic risk of chronic Cd exposure is accumulating and Cd effects on reproductive outcomes have begun to emerge.

Phobic anxiety in 11 nations: part II. Hofstede's dimensions of national cultures predict national-level variations

Hofstede's dimensions of national cultures termed Masculinity-Femininity (MAS) and Uncertainty Avoidance (UAI) (Hofstede, 2001) are proposed to be of relevance for understanding national-level differences in self-assessed fears. The potential predictive role of national MAS was based on the classical work of Fodor (Fodor, 1974). Following Fodor, it was predicted that masculine (or tough) societies in which clearer differentiations are made between gender roles (high MAS) would report higher national levels of fears than feminine (or soft/modest) societies in which such differentiations are made to a clearly lesser extent (low MAS). In addition, it was anticipated that nervous-stressful-emotionally-expressive nations (high UAI) would report higher national levels of fears than calm-happy and low-emotional countries (low UAI), and that countries high on both MAS and UAI would report the highest national levels of fears. A data set comprising 11 countries (N > 5000) served as the basis for analyses. As anticipated, (a) high MAS predicted higher national levels of Agoraphobic fears and of Bodily Injury-Illness-Death fears; (b) higher scores on both UAI and MAS predicted higher national scores on Bodily Injury-Illness-Death fears, fears of Sexual and Aggressive Scenes, and Harmless Animals fears; (c) higher UAI predicted higher national levels of Harmless Animals, Bodily Injury-Illness-Death, and Agoraphobic fears. (C) 2003 Elsevier Ltd. All rights reserved.

Particle formation during soy protein precipitation

The current success of soy foods is driving soy ingredient manufacturers to develop innovative products for food manufacturers. One such innovation is separating the soy proteins glycinin and beta-conglycinin to take advantage of their individual functional and nutritional properties. Precipitation by acidification is a low-cost method for separating these two proteins. Separation is achieved by preferentially precipitating glycinin at pH ~ 6 while beta-conglycinin remains in solution. Understanding the particle formation during protein precipitation is important as it can influence the efficiency of the precipitation process as well as subsequent downstream processes such as the particle-liquid separation step, usually achieved by centrifugation. Most of the previous soy protein precipitation studies are limited to precipitation at pH 4 as this is the pH range most commonly used in the commercial manufacturing of soy protein isolates. To date, there have been no studies on the particle formation during precipitation at pH > 5.Precipitation of soy protein is generally thought to occur by the rapid formation of primary particles in the size range of 0.1 - 0.3 microns followed by aggregation of these particles via collision to aggregates of size about 1 - 50 microns. The formation of the primary particles occurs on a time scale much shorter than that of the overall precipitation process (Nelson and Glatz, 1985). This study shows that precipitation of soy protein is indeed rapid. At high pH levels, binary liquid-liquid separation occurs forming a protein-rich heavy phase. The protein-rich phase appears as droplets which can be coalesced to form a uniform bulk layer under centrifugation forces. Upon lowering the pH level by the addition of acid, further protein is precipitated as amorphous material which binds the droplets together to form aggregates of amorphous precipitates. Liquid-liquid separation has been observed in many protein solutions but this phenomenon has only scarcely been reported in the literature for soy proteins. It presents an exciting opportunity for an innovative product. Features of the liquid-phase protein such as protein yield and purity will be characterized.