'Neighbourhood' size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods

Dispersal, or the amount of dispersion between an individual's birthplace and that of its offspring, is of great importance in population biology, behavioural ecology and conservation, however, obtaining direct estimates from field data on natural populations can be problematic. The prickly forest skink, Gnypetoscincus queenslandiae, is a rainforest endemic skink from the wet tropics of Australia. Because of its log-dwelling habits and lack of definite nesting sites, a demographic estimate of dispersal distance is difficult to obtain. Neighbourhood size, defined as 4 piD sigma (2) (where D is the population density and sigma (2) the mean axial squared parent-offspring dispersal rate), dispersal and density were estimated directly and indirectly for this species using mark-recapture and microsatellite data, respectively, on lizards captured at a local geographical scale of 3 ha. Mark-recapture data gave a dispersal rate of 843 m(2)/generation (assuming a generation time of 6.5 years), a time-scaled density of 13 635 individuals * generation/km(2) and, hence, a neighbourhood size of 144 individuals. A genetic method based on the multilocus (10 loci) microsatellite genotypes of individuals and their geographical location indicated that there is a significant isolation by distance pattern, and gave a neighbourhood size of 69 individuals, with a 95% confidence interval between 48 and 184. This translates into a dispersal rate of 404 m(2)/generation when using the mark-recapture density estimation, or an estimate of time-scaled population density of 6520 individuals * generation/km(2) when using the mark-recapture dispersal rate estimate. The relationship between the two categories of neighbourhood size, dispersal and density estimates and reasons for any disparities are discussed.

Repeatability of maximal voluntary force and of surface EMG variables during voluntary isometric contraction of quadriceps muscles in healthy subjects

The repeatability of initial values and rate of change of EMG signal mean spectral frequency (MNF), average rectified values (ARV), muscle fiber conduction velocity (CV) and maximal voluntary contraction (MVC) was investigated in the vastus medialis obliquus (VMO) and vastus lateralis (VL) muscles of both legs of nine healthy male subjects during voluntary, isometric contractions sustained for 50 s at 50% MVC. The values of MVC were recorded for both legs three times on each day and for three subsequent days, while the EMG signals have been recorded twice a day for three subsequent days. The degree of repeatability was investigated using the Fisher test based upon the ANalysis Of VAriance (ANOVA), the Standard Error of the Mean (SEM) and the Intraclass Correlation Coefficient (ICC). Data collected showed a high level of repeatability of MVC measurement (normalized SEM from 1.1% to 6.4% of the mean). MNF and ARV initial values also showed a high level of repeatability (ICC > 70% for all muscles and legs except right VMO). At 50% MVC level no relevant pattern of fatigue was observed for the VMO and VL muscles, suggesting that other portions of the quadriceps might have contributed to the generated effort. These observations seem to suggest that in the investigation of muscles belonging to a multi-muscular group at submaximal level, the more selective electrically elicited contractions should be preferred to voluntary contractions. (C) 2001 Elsevier Science Ltd. All rights reserved.

An aggregate sales model for consumer durables incorporating a time-varying mean replacement age

Forecasting category or industry sales is a vital component of a company's planning and control activities. Sales for most mature durable product categories are dominated by replacement purchases. Previous sales models which explicitly incorporate a component of sales due to replacement assume there is an age distribution for replacements of existing units which remains constant over time. However, there is evidence that changes in factors such as product reliability/durability, price, repair costs, scrapping values, styling and economic conditions will result in changes in the mean replacement age of units. This paper develops a model for such time-varying replacement behaviour and empirically tests it in the Australian automotive industry. Both longitudinal census data and the empirical analysis of the replacement sales model confirm that there has been a substantial increase in the average aggregate replacement age for motor vehicles over the past 20 years. Further, much of this variation could be explained by real price increases and a linear temporal trend. Consequently, the time-varying model significantly outperformed previous models both in terms of fitting and forecasting the sales data. Copyright (C) 2001 John Wiley & Sons, Ltd.

Patchy populations in stochastic environments: Critical number of patches for persistence

We introduce a model for the dynamics of a patchy population in a stochastic environment and derive a criterion for its persistence. This criterion is based on the geometric mean (GM) through time of the spatial-arithmetic mean of growth rates. For the population to persist, the GM has to be greater than or equal to1. The GM increases with the number of patches (because the sampling error is reduced) and decreases with both the variance and the spatial covariance of growth rates. We derive analytical expressions for the minimum number of patches (and the maximum harvesting rate) required for the persistence of the population. As the magnitude of environmental fluctuations increases, the number of patches required for persistence increases, and the fraction of individuals that can be harvested decreases. The novelty of our approach is that we focus on Malthusian local population dynamics with high dispersal and strong environmental variability from year to year. Unlike previous models of patchy populations that assume an infinite number of patches, we focus specifically on the effect that the number of patches has on population persistence. Our work is therefore directly relevant to patchily distributed organisms that are restricted to a small number of habitat patches.

Repeatability of surface EMG variables in the sternocleidomastoid and anterior scalene muscles

In this study we examined the repeatability and reliability of the surface electromyographic (sEMG) signal mean frequency (MNF), average rectified value (ARV) and conduction velocity (CV) measured for the sternocleidomastoid (SCM) and the anterior scalene (AS) muscles in nine healthy volunteers during 15-s isometric cervical flexion contractions at 50% of the maximal voluntary contraction level over 3 non-consecutive days. Repeatability and reliability estimates were obtained for the initial values and rates of change of each sEMG variable by using both the Intraclass Correlation Coefficient (ICC) and the normalised standard error of the mean (nSEM). Results from SCM indicated good levels of repeatability for the initial value and slope of ARV (ICC > 65%). For the AS, high levels of repeatability were identified for the initial value of MNF (ICC > 70%) and the slope of ARV (ICC > 75%). Values of nSEM in the range 2.8-7.2% were obtained for the initial values of MNF and CV for both SCM and AS, indicating clinically acceptable measurement precision. The low value obtained for the nSEM of the initial value of MNF for the AS, in combination with the high ICC, indicates that of all of the variables examined, this variable could offer the best normative index to distinguish between subjects with and without neck pain, and represents the sEMG variable of choice for future evaluation purposes.

Mapping glider habitat in dry eucalypt forests for Montreal Process indicator 1.1: Fragmentation of forest types

Accurate habitat mapping is critical to landscape ecological studies such as required for developing and testing Montreal Process indicator 1.1e, fragmentation of forest types. This task poses a major challenge to remote sensing, especially in mixedspecies, variable-age forests such as dry eucalypt forests of subtropical eastern Australia. In this paper, we apply an innovative approach that uses a small section of one-metre resolution airborne data to calibrate a moderate spatial resolution model (30 m resolution; scale 1:50 000) based on Landsat Thematic Mapper data to estimate canopy structural properties in St Marys State Forest, near Maryborough, south-eastern Queensland. The approach applies an image-processing model that assumes each image pixel is significantly larger than individual tree crowns and gaps to estimate crown-cover percentage, stem density and mean crown diameter. These parameters were classified into three discrete habitat classes to match the ecology of four exudivorous arboreal species (yellowbellied glider Petaurus australis, sugar glider P. breviceps, squirrel glider P. norfolcensis , and feathertail glider Acrobates pygmaeus), and one folivorous arboreal marsupial, the greater glider Petauroides volans. These species were targeted due to the known ecological preference for old trees with hollows, and differences in their home range requirements. The overall mapping accuracy, visually assessed against transects (n = 93) interpreted from a digital orthophoto and validated in the field, was 79% (KHAT statistic = 0.72). The KHAT statistic serves as an indicator of the extent that the percentage correct values of the error matrix are due to ‘true’ agreement verses ‘chance’ agreement. This means that we are able to reliably report on the effect of habitat loss on target species, especially those with a large home range size (e.g. yellow-bellied glider). However, the classified habitat map failed to accurately capture the spatial patterning (e.g. patch size and shape) of stands with a trace or sub-dominance of senescent trees. This outcome makes the reporting of the effects of habitat fragmentation more problematic, especially for species with a small home range size (e.g. feathertail glider). With further model refinement and validation, however, this moderateresolution approach offers an important, cost eff e c t i v e advancement in mapping the age of dry eucalypt forests in the region.

Empirical evidence for ultrametric structure in multi-layer perceptron error surfaces

Combinatorial optimization problems share an interesting property with spin glass systems in that their state spaces can exhibit ultrametric structure. We use sampling methods to analyse the error surfaces of feedforward multi-layer perceptron neural networks learning encoder problems. The third order statistics of these points of attraction are examined and found to be arranged in a highly ultrametric way. This is a unique result for a finite, continuous parameter space. The implications of this result are discussed.

The impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.

Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Comparison of two population pharmacokinetic programs, NONMEM and P-PHARM, for tacrolimus

Objectives: To compare the population modelling programs NONMEM and P-PHARM during investigation of the pharmacokinetics of tacrolimus in paediatric liver-transplant recipients. Methods: Population pharmacokinetic analysis was performed using NONMEM and P-PHARM on retrospective data from 35 paediatric liver-transplant patients receiving tacrolimus therapy. The same data were presented to both programs. Maximum likelihood estimates were sought for apparent clearance (CL/F) and apparent volume of distribution (V/F). Covariates screened for influence on these parameters were weight, age, gender, post-operative day, days of tacrolimus therapy, transplant type, biliary reconstructive procedure, liver function tests, creatinine clearance, haematocrit, corticosteroid dose, and potential interacting drugs. Results: A satisfactory model was developed in both programs with a single categorical covariate - transplant type - providing stable parameter estimates and small, normally distributed (weighted) residuals. In NONMEM, the continuous covariates - age and liver function tests - improved modelling further. Mean parameter estimates were CL/F (whole liver) = 16.3 1/h, CL/F (cut-down liver) = 8.5 1/h and V/F = 565 1 in NONMEM, and CL/F = 8.3 1/h and V/F = 155 1 in P-PHARM. Individual Bayesian parameter estimates were CL/F (whole liver) = 17.9 +/- 8.8 1/h, CL/F (cutdown liver) = 11.6 +/- 18.8 1/h and V/F = 712 792 1 in NONMEM, and CL/F (whole liver) = 12.8 +/- 3.5 1/h, CL/F (cut-down liver) = 8.2 +/- 3.4 1/h and V/F = 221 1641 in P-PHARM. Marked interindividual kinetic variability (38-108%) and residual random error (approximately 3 ng/ml) were observed. P-PHARM was more user friendly and readily provided informative graphical presentation of results. NONMEM allowed a wider choice of errors for statistical modelling and coped better with complex covariate data sets. Conclusion: Results from parametric modelling programs can vary due to different algorithms employed to estimate parameters, alternative methods of covariate analysis and variations and limitations in the software itself.

Evaluation of various pre-treatments for the dehydration of banana and selection of suitable drying models

The thin-layer drying behaviour of bananas in a beat pump dehumidifier dryer was examined. Four pre-treatments (blanching, chilling, freezing and combined blanching and freezing) were applied to the bananas, which were dried at 50 degreesC with an air velocity of 3.1 m s(-1) and with the relative humidity of the inlet air of 10-35%. Three drying models, the simple model, the two-term exponential model and the Page model were examined. All models were evaluated using three statistical measures, correlation coefficient, root means square error, and mean absolute percent error. Moisture diffusivity was calculated based on the diffusion equation for an infinite cylindrical shape using the slope method. The rate of drying was higher for the pre-treatments involving freezing. The sample which was blanched only did not show any improvement in drying rate. In fact, a longer drying time resulted due to water absorption during blanching. There was no change in the rate for the chilled sample compared with the control. While all models closely fitted the drying data, the simple model showed greatest deviation from the experimental results. The two-term exponential model was found to be the best model for describing the drying curves of bananas because its parameters represent better the physical characteristics of the drying process. Moisture diffusivities of bananas were in the range 4.3-13.2 x 10(-10) m(2)s(-1). (C) 2002 Published by Elsevier Science Ltd.

A study of five cervicocephalic relocation tests in three different subject groups

Objective: To compare head relocation accuracy in traumatic ( whiplash), insidious onset neck pain patients and asymptomatic subjects when targeting a natural head posture (NHP) and complex predetermined positions. Design: A case-control study. Setting: University-based musculoskeletal research clinic. Participants: Sixty-three volunteers divided into three groups of similar gender and age: Group 1 (n=21) an asymptomatic group; group 2 (n=20) insidious onset neck pain; group 3 (n=22) a history of whiplash injury. Intervention: Five randomly ordered tests designed to detect relocation accuracy of the head. Outcome measures: A 3-Space Fastrak system measured the mean absolute relocation error of three trials of each relocation test. Results: A significant difference was found between groups in one of the tests targeting the NHP (p=0.001). Post-hoc pairwise comparisons revealed a significant difference (pless than or equal to0.05) between the asymptomatic group and each symptomatic group. The difference between the symptomatic groups just failed to reach significance (p=0.07). None of the other four tests revealed significant differences. Conclusion: The test of targeting the NHP indicates that relocation inaccuracy exists in patients with neck pain with a trend to suggest that the deficit may be greater in whiplash patients. Tests employing unfamiliar postures or more complex movement were not successful in differentiating subject groups.