Calculation of line integrals in boundary integral methods

We propose quadrature rules for the approximation of line integrals possessing logarithmic singularities and show their convergence. In some instances a superconvergence rate is demonstrated.

Sampling phylogenetic tree space with the generalized Gibbs sampler

The generalized Gibbs sampler (GGS) is a recently developed Markov chain Monte Carlo (MCMC) technique that enables Gibbs-like sampling of state spaces that lack a convenient representation in terms of a fixed coordinate system. This paper describes a new sampler, called the tree sampler, which uses the GGS to sample from a state space consisting of phylogenetic trees. The tree sampler is useful for a wide range of phylogenetic applications, including Bayesian, maximum likelihood, and maximum parsimony methods. A fast new algorithm to search for a maximum parsimony phylogeny is presented, using the tree sampler in the context of simulated annealing. The mathematics underlying the algorithm is explained and its time complexity is analyzed. The method is tested on two large data sets consisting of 123 sequences and 500 sequences, respectively. The new algorithm is shown to compare very favorably in terms of speed and accuracy to the program DNAPARS from the PHYLIP package.

Ecosystem dynamics at disturbed and undisturbed sites in North Queensland wet tropical rain forest. III. Nutrient returns to the forest floor through litterfall

The nutrient contents and accessions in litterfall over a period of 3 y are reported for undisturbed areas and at two sites disturbed by selective harvesting in tropical rain forest in North Queensland, Australia. Mean concentrations (mg g(-1) dry weight) of nutrients in litterfall ranged from 10 to 12 for nitrogen; 0.33 to 0.43 for phosphorus; 3.6 to 4.3 for potassium; 6.0 to 10.5 for calcium and 1.7 to 2.6 for magnesium. These concentrations are in the middle to lower part of the spectrum of values recorded for tropical forest. Accessions of nutrients in litterfall (kg ha(-1) y(-1)) ranged from 59 to 64 N; 1.9 to 2.4 P; 20 to 24K; 34 to 63 Ca; and 9 to 16 Mg. These rates, particularly for IN and P, are among the lowest recorded for tropical forests. There were no consistent between-site differences in total nutrient accessions in small litterfall. In terms of the contribution of litterfall to the accessions of nutrients to the forest floor, this suggests that the logged sites have recovered from the effects of selective harvesting within 25 y. Nutrient accessions at each site were distinctly seasonal, with maximum accessions occurring in the late dry season to late in the wet season. Leaf-fall accounted for the largest proportion of nutrient accessions over the study period, although at certain times accessions in both reproductive material and wood were significant. A cyclone which crossed the coast near the study sites resulted in large nutrient accessions over a short period but had little effect on the total annual accession. A comparison with previous studies of litterfall in Australian tropical rainforests indicates that nutrient return in litterfall is directly related to soil fertility.

Bacteria in shrimp pond sediments: their role in mineralizing nutrients and some suggested sampling strategies

Strategies for sampling sediment bacteria were examined in intensive shrimp, Penaeus monodon (Fabricius), ponds in tropical Australia. Stratified sampling of bacteria at the end of the production season showed that the pond centre, containing flocculated sludge, had significantly higher bacterial counts (15.5 X 10(9) g(-1) dw) than the pond periphery (8.1 X 10(9) g(-1) dw), where the action of aerators had swept the pond floor. The variation in bacterial counts between these two zones within a pond was higher than that between sites within each zone or between ponds. Therefore, sampling effort should be focused within these zones: for example, sampling two ponds at six locations within each of the two zones resulted in a coefficient of variation of approximate to 5%. Bacterial numbers in the sediment were highly correlated with sediment grain size, probably because eroded soil particles and organic waste both accumulated in the centre of the pond. Despite high inputs of organic matter added to the ponds, principally as pelleted feeds, the mean bacterial numbers and nutrient concentrations (i.e. organic carbon, nitrogen and phosphorus) in the sediment were similar to those found in mangrove sediments. This suggests that bacteria are rapidly remineralizing particulates into soluble compounds. Bacterial numbers were highly correlated with organic carbon and total kjeldahl nitrogen in the sediment, suggesting that these were limiting factors to bacterial growth.

New techniques in nutritional assessment: body composition methods

New techniques in air-displacement plethysmography seem to have overcome many of the previous problems of poor reproducibility and validity. These have made body-density measurements available to a larger range of individuals, including children, elderly and sick patients who often have difficulties in being submerged underwater in hydrodensitometry systems. The BOD POD air-displacement system (BOD POD body composition system; Life Measurement Instruments, Concord, CA, USA) is more precise than hydrodensitometry, is simple and rapid to operate (approximately 1 min measurements) and the results agree closely with those of hydrodensitometry (e.g. +/-3.4% for estimation of body fat). Body line scanners employing the principles of three-dimensional photography are potentially able to measure the surface area and volume of the body and its segments even more rapidly (approximately 10 s), but the validity of the measurements needs to be established. Advances in i.r. spectroscopy and mathematical modelling for calculating the area under the curve have improved precision for measuring enrichment of (H2O)-H-2 in studies of water dilution (CV 0.1-0.9% within the range of 400-1000 mu l/l) in saliva, plasma and urine. The technique is rapid and compares closely with mass spectrometry (bias 1 (SD 2) %). Advances in bedside bioelectrical-impedance techniques are making possible potential measurements of skinfold thicknesses and limb muscle mass electronically. Preliminary results suggest that the electronic method is more reproducible (intra-and inter-individual reproducibility for measuring skinfold thicknesses) and associated with less bias (+ 12%), than anthropometry (+ 40%). In addition to these selected examples, the 'mobility' or transfer of reference methods between centres has made the distinction between reference and bedside or field techniques less distinct than in the past.

Habitat structure and egg distributions in the processionary caterpillar Ochrogaster lunifer: lessons for conservation and pest management

1. The spatial and temporal distribution of eggs laid by herbivorous insects is a crucial component of herbivore population stability, as it influences overall mortality within the population. Thus an ecologist studying populations of an endangered butterfly can do little to increase its numbers through habitat management without knowledge of its egg-laying patterns across individual host-plants under different habitat management regimes. At the other end of the spectrum, a knowledge of egg-laying behaviour can do much to control pest outbreaks by disrupting egg distributions that lead to rapid population growth. 2. The distribution of egg batches of the processionary caterpillar Ochrogaster lunifer on acacia trees was monitored in 21 habitats during 2 years in coastal Australia. The presence of egg batches on acacias was affected by host-tree 'quality' (tree size and foliar chemistry that led to increased caterpillar survival) and host-tree 'apparency' (the amount of vegetation surrounding host-trees). 3. In open homogeneous habitats, more egg batches were laid on high-quality trees, increasing potential population growth. In diverse mixed-species habitats, more egg batches were laid on low-quality highly apparent trees, reducing population growth and so reducing the potential for unstable population dynamics. The aggregation of batches on small apparent trees in diverse habitats led to outbreaks on these trees year after year, even when population levels were low, while site-wide outbreaks were rare. 4. These results predict that diverse habitats with mixed plant species should increase insect aggregation and increase population stability. In contrast, in open disturbed habitats or in regular plantations, where egg batches are more evenly distributed across high-quality hosts, populations should be more unstable, with site-wide outbreaks and extinctions being more common. 5. Mixed planting should be used on habitat regeneration sites to increase the population stability of immigrating or reintroduced insect species. Mixed planting also increases the diversity of resources, leading to higher herbivore species richness. With regard to the conservation of single species, different practices of habitat management will need to be employed depending on whether a project is concerned with methods of rapidly increasing the abundance of an endangered insect or concerned with the maintenance of a stable, established insect population that is perhaps endemic to an area. Suggestions for habitat management in these different cases are discussed. 6. Finally, intercropping can be highly effective in reducing pest outbreaks, although the economic gains of reduced pest attack may be outweighed by reduced crop yields in mixed-crop systems.

New methods for determining quasi-stationary distributions for Markov chains

We shall be concerned with the problem of determining quasi-stationary distributions for Markovian models directly from their transition rates Q. We shall present simple conditions for a mu-invariant measure m for Q to be mu-invariant for the transition function, so that if m is finite, it can be normalized to produce a quasi-stationary distribution. (C) 2000 Elsevier Science Ltd. All rights reserved.

Both beta(2)- and beta(1)-adrenergic receptors mediate hastened relaxation and phosphorylation of phospholamban and troponin I in ventricular myocardium of fallot infants, consistent with selective coupling of beta(2)-adrenergic receptors to G(s)-protein

Background-In adult human heart, both beta(1)- and beta(2)-adrenergic receptors mediate hastening of relaxation; however, it is unknown whether this also occurs in infant heart. We compared the effects of stimulation of beta(1)- and beta(2)-adrenergic receptors on relaxation and phosphorylation of phospholamban and troponin I in ventricle obtained from infants with tetralogy of Fallot. Methods and Results-Myocardium dissected from the right ventricular outflow tract of 27 infants (age range 2-1/2 to 35 months) with tetralogy of Fallot was set up to contract 60 times per minute. Selective stimulation of beta(1)-adrenergic receptors with (-)-norepinephrine (NE) and beta(2)-adrenergic receptors with (-)-epinephrine (EPI) evoked phosphorylation of phospholamban (at serine-16 and threonine-17) and troponin I and caused concentration-dependent increases in contractile force (-log EC50 [mol/L] NE 5.5+/-0.1, n=12; -EPI 5.6+/-0.1, n=13 patients), hastening of the time to reach peak force (-log EC50 [mol/L] NE 5.8+/--0.2; EPI 5.8+/-0.2) and 50% relaxation (-log EC50 [mol/L] NE 5.7+/-0.2: EPI 5.8+/-0.1), Ventricular membranes from Fallot infants, labeled with (-)-[I-125]-cyanopindolol, revealed a greater percentage of beta(1)- (71%) than beta(2)-adrenergic receptors (29%). Binding of (-)-epinephrine to beta(2)-receptors underwent greater GTP shifts than binding of (-)-norepinephrine to beta(1)-receptors. Conclusions-Despite their low density, beta(2)-adrenergic receptors are nearly as effective as beta(1)-adrenergic receptors of infant Fallot ventricle in enhancing contraction, relaxation, and phosphorylation of phospholamban and troponin I, consistent with selective coupling to G(s)-protein.

Assessing cost-effectiveness - Mental health: introduction to the study and methods

Objective: The Assessing Cost-Effectiveness - Mental Health (ACE-MH) study aims to assess from a health sector perspective, whether there are options for change that could improve the effectiveness and efficiency of Australia's current mental health services by directing available resources toward 'best practice' cost-effective services. Method: The use of standardized evaluation methods addresses the reservations expressed by many economists about the simplistic use of League Tables based on economic studies confounded by differences in methods, context and setting. The cost-effectiveness ratio for each intervention is calculated using economic and epidemiological data. This includes systematic reviews and randomised controlled trials for efficacy, the Australian Surveys of Mental Health and Wellbeing for current practice and a combination of trials and longitudinal studies for adherence. The cost-effectiveness ratios are presented as cost (A$) per disability-adjusted life year (DALY) saved with a 95% uncertainty interval based on Monte Carlo simulation modelling. An assessment of interventions on 'second filter' criteria ('equity', 'strength of evidence', 'feasibility' and 'acceptability to stakeholders') allows broader concepts of 'benefit' to be taken into account, as well as factors that might influence policy judgements in addition to cost-effectiveness ratios. Conclusions: The main limitation of the study is in the translation of the effect size from trials into a change in the DALY disability weight, which required the use of newly developed methods. While comparisons within disorders are valid, comparisons across disorders should be made with caution. A series of articles is planned to present the results.

Normal and anomalous classification of category exemplars in schizophrenia

Background Schizophrenia has been associated with semantic memory impairment and previous studies report a difficulty in accessing semantic category exemplars (Moelter et al. 2005 Schizophr Res 78:209–217). The anterior temporal cortex (ATC) has been implicated in the representation of semantic knowledge (Rogers et al. 2004 Psychol Rev 111(1):205–235). We conducted a high-field (4T) fMRI study with the Category Judgment and Substitution Task (CJAST), an analogue of the Hayling test. We hypothesised that differential activation of the temporal lobe would be observed in schizophrenia patients versus controls. Methods Eight schizophrenia patients (7M : 1F) and eight matched controls performed the CJAST, involving a randomised series of 55 common nouns (from five semantic categories) across three conditions: semantic categorisation, anomalous categorisation and word reading. High-resolution 3D T1-weighted images and GE EPI with BOLD contrast and sparse temporal sampling were acquired on a 4T Bruker MedSpec system. Image processing and analyses were performed with SPM2. Results Differential activation in the left ATC was found for anomalous categorisation relative to category judgment, in patients versus controls. Conclusions We examined semantic memory deficits in schizophrenia using a novel fMRI task. Since the ATC corresponds to an area involved in accessing abstract semantic representations (Moelter et al. 2005), these results suggest schizophrenia patients utilise the same neural network as healthy controls, however it is compromised in the patients and the different ATC activity might be attributable to weakening of category-to-category associations.

A family of perfect hashing methods

Minimal perfect hash functions are used for memory efficient storage and fast retrieval of items from static sets. We present an infinite family of efficient and practical algorithms for generating order preserving minimal perfect hash functions. We show that almost all members of the family construct space and time optimal order preserving minimal perfect hash functions, and we identify the one with minimum constants. Members of the family generate a hash function in two steps. First a special kind of function into an r-graph is computed probabilistically. Then this function is refined deterministically to a minimal perfect hash function. We give strong theoretical evidence that the first step uses linear random time. The second step runs in linear deterministic time. The family not only has theoretical importance, but also offers the fastest known method for generating perfect hash functions.

Local dispersion of the Eucalyptus leaf beetle Chrysophtharta bimaculata (Coleoptera: Chrysomelidae), and implications for forest protection

1. Chrysophtharta bimaculata is a native chrysomelid species that can cause chronic defoliation of plantation and regrowth Eucalyptus forests in Tasmania, Australia. Knowledge of the dispersion pattern of C. bimaculata was needed in order to assess the efficiency of an integrated pest management (IPM) programme currently used for its control. 2. Using data from yellow flight traps, local populations of C. bimaculata adults were monitored over a season at spatial scales relevant to commercial forestry: within a 50-ha operational management unit (a forestry 'coupe') and between coupes. In addition, oviposition was monitored over a season at a subset of the between-coupe sites. 3. Dispersion indices (Taylor's Power Law and Iwao's Mean Crowding regression method) demonstrated that C. bimaculata adults were spatially aggregated within and between coupes, although the number of egg-batches laid at the between-coupe scale was uniform. Spatial autocorrelation analysis showed that trap-catches at the within-coupe level were similar (positively autocorrelated) to a radius distance of approximately 110 m, and then dissimilar (negatively autocorrelated) at approximately 250 m. At the between-coupe scale, no repeatable spatial autocorrelation patterns were observed. 4. For any individual site, rapid changes in beetle density were observed to be associated with loosely aggregated flights of beetles into and out of that site. Peak adult catches (> the weekly mean plus standard deviation trap-catch) for a site occurred for a period of 2.0 +/- 0.22 weeks at a time (n = 37), with normally only one or two peaks per site per season. Peak oviposition events for a site occurred on average 1.4 +/- 0.11 times per season and lasted 1.5 +/- 0.12 weeks. 5. Analysis of an extensive data set (n = 417) demonstrated that adult abundance at a site was positively correlated with egg density, but negatively correlated with tree damage (caused by conspecifics) and the presence of conspecific larvae. There was no relationship between adult abundance and a visual estimate of the amount of young foliage on trees. 6. Adults of C. bimaculata are show n to occur in relatively small, mobile aggregations. This means that pest surveys must be both regular (less than 2 weeks apart) and intensive (with sampling points no more than 150 m apart) if beetle populations are to be monitored with confidence. Further refinement of the current IPM strategy must recognize the problems posed by this temporal and spatial patchiness, particularly with regard to the use of biological insecticides, such as Bacillus thuringiensis, for which only a very short operational window exists.

Chemical characterization of soils of a tropical humid forest zone: A methodology

A methodology, based on a combination of routinely performed analyses and investigation of fundamental charge and anion sorption properties, was used to characterize the soils of the humid forest zone of Cameroon, In general, the soils have about 2 cmol kg(-1) permanent negative charge, with about 1 cmol kg(-1) from variable-charge sources at current soil pH values, Furthermore, they are impoverished with respect to Ca, Mg, and K, while Al frequently dominates the exchange complex. Thus, the ability of these soils to retain base cations is more limited than is suggested by the cation-exchange capacity (CEC), Therefore we propose the concept of a degradation index (DI) defined as: DI = 100(CEC5.5 - sum of basic cations)/CEC5.5, where CEC5.5 is the CEC measured at pH 5.5, This index encompasses degradation a soil may have experienced from natural or man-made causes, Extractable PO4 concentrations are considered very low and the soils have a moderate to high capacity to fix added PO4. Surface soil SO4 concentrations are considered marginal to deficient for plant growth, though adequate reserves of SO4 are held in the subsoil by SO4 sorption, The approach used demonstrated that the five morphologically different soil profile classes identified in the zone have similar chemical characteristics. Thus, the results of experimentation conducted on one of the soil profile classes will be applicable throughout the zone, Furthermore, the approach has provided a means of identifying comparable soil types in other parts of the world and will guide technology transfer, The analytical methods used in this study are relatively simple and require no specialized equipment, and are therefore within the capabilities of many laboratories in the developing world.