Spatial analysis of the error in a model of soil nitrogen

Models of the dynamics of nitrogen in soil (soil-N) can be used to aid the fertilizer management of a crop. The predictions of soil-N models can be validated by comparison with observed data. Validation generally involves calculating non-spatial statistics of the observations and predictions, such as their means, their mean squared-difference, and their correlation. However, when the model predictions are spatially distributed across a landscape the model requires validation with spatial statistics. There are three reasons for this: (i) the model may be more or less successful at reproducing the variance of the observations at different spatial scales; (ii) the correlation of the predictions with the observations may be different at different spatial scales; (iii) the spatial pattern of model error may be informative. In this study we used a model, parameterized with spatially variable input information about the soil, to predict the mineral-N content of soil in an arable field, and compared the results with observed data. We validated the performance of the N model spatially with a linear mixed model of the observations and model predictions, estimated by residual maximum likelihood. This novel approach allowed us to describe the joint variation of the observations and predictions as: (i) independent random variation that occurred at a fine spatial scale; (ii) correlated random variation that occurred at a coarse spatial scale; (iii) systematic variation associated with a spatial trend. The linear mixed model revealed that, in general, the performance of the N model changed depending on the spatial scale of interest. At the scales associated with random variation, the N model underestimated the variance of the observations, and the predictions were correlated poorly with the observations. At the scale of the trend, the predictions and observations shared a common surface. The spatial pattern of the error of the N model suggested that the observations were affected by the local soil condition, but this was not accounted for by the N model. In summary, the N model would be well-suited to field-scale management of soil nitrogen, but suited poorly to management at finer spatial scales. This information was not apparent with a non-spatial validation. (c),2007 Elsevier B.V. All rights reserved.

Behavioral and spatial analysis of extraterritorial movements in red foxes (Vulpes vulpes)

Abstract: Movements away from the natal or home territory are important to many ecological processes, including gene flow, population regulation, and disease epidemiology, yet quantitative data on these behaviors are lacking. Red foxes exhibit 2 periods of extraterritorial movements: when an individual disperses and when males search neighboring territories for extrapair copulations during the breeding season. Using radiotracking data collected at 5-min interfix intervals, we compared movement parameters, including distance moved, speed of movement, and turning angles, of dispersal and reproductive movements to those made during normal territorial movements; the instantaneous separation distances of dispersing and extraterritorial movements to the movements of resident adults; and the frequency of locations of 95%, 60%, and 30% harmonic mean isopleths of adult fox home territories to randomly generated fox movements. Foxes making reproductive movements traveled farther than when undertaking other types of movement, and dispersal movements were straighter. Reproductive and dispersal movements were faster than territorial movements and also differed in intensity of search and thoroughness. Foxes making dispersal movements avoided direct contact with territorial adults and moved through peripheral areas of territories. The converse was true for reproductive movements. Although similar in some basic characteristics, dispersal and reproductive movements are fundamentally different both behaviorally and spatially and are likely to have different ultimate purposes and contrasting effects on spatial processes such as disease transmission

Performance analysis of data transmissions in MPLS and non-MPLS networks

Basic Network transactions specifies that datagram from source to destination is routed through numerous routers and paths depending on the available free and uncongested paths which results in the transmission route being too long, thus incurring greater delay, jitter, congestion and reduced throughput. One of the major problems of packet switched networks is the cell delay variation or jitter. This cell delay variation is due to the queuing delay depending on the applied loading conditions. The effect of delay, jitter accumulation due to the number of nodes along transmission routes and dropped packets adds further complexity to multimedia traffic because there is no guarantee that each traffic stream will be delivered according to its own jitter constraints therefore there is the need to analyze the effects of jitter. IP routers enable a single path for the transmission of all packets. On the other hand, Multi-Protocol Label Switching (MPLS) allows separation of packet forwarding and routing characteristics to enable packets to use the appropriate routes and also optimize and control the behavior of transmission paths. Thus correcting some of the shortfalls associated with IP routing. Therefore MPLS has been utilized in the analysis for effective transmission through the various networks. This paper analyzes the effect of delay, congestion, interference, jitter and packet loss in the transmission of signals from source to destination. In effect the impact of link failures, repair paths in the various physical topologies namely bus, star, mesh and hybrid topologies are all analyzed based on standard network conditions.

Fine-root turnover rates of European forests revisited: an analysis of data from sequential coring and ingrowth cores

Background and Aims Forest trees directly contribute to carbon cycling in forest soils through the turnover of their fine roots. In this study we aimed to calculate root turnover rates of common European forest tree species and to compare them with most frequently published values. Methods We compiled available European data and applied various turnover rate calculation methods to the resulting database. We used Decision Matrix and Maximum-Minimum formula as suggested in the literature. Results Mean turnover rates obtained by the combination of sequential coring and Decision Matrix were 0.86 yr−1 for Fagus sylvatica and 0.88 yr−1 for Picea abies when maximum biomass data were used for the calculation, and 1.11 yr−1 for both species when mean biomass data were used. Using mean biomass rather than maximum resulted in about 30 % higher values of root turnover. Using the Decision Matrix to calculate turnover rate doubled the rates when compared to the Maximum-Minimum formula. The Decision Matrix, however, makes use of more input information than the Maximum-Minimum formula. Conclusions We propose that calculations using the Decision Matrix with mean biomass give the most reliable estimates of root turnover rates in European forests and should preferentially be used in models and C reporting.

The Representative Soil Sampling Scheme of England and Wales: the spatial variation of topsoil nutrient status and pH between 1971 and 2001

The Representative Soil Sampling Scheme (RSSS) has monitored the soil of agricultural land in England and Wales since 1969. Here we describe the first spatial analysis of the data from these surveys using geostatistics. Four years of data (1971, 1981, 1991 and 2001) were chosen to examine the nutrient (available K, Mg and P) and pH status of the soil. At each farm, four fields were sampled; however, for the earlier years, coordinates were available for the farm only and not for each field. The averaged data for each farm were used for spatial analysis and the variograms showed spatial structure even with the smaller sample size. These variograms provide a reasonable summary of the larger scale of variation identified from the data of the more intensively sampled National Soil Inventory. Maps of kriged predictions of K generally show larger values in the central and southeastern areas (above 200 mg L-1) and an increase in values in the west over time, whereas Mg is fairly stable over time. The kriged predictions of P show a decline over time, particularly in the east, and those of pH show an increase in the east over time. Disjunctive kriging was used to examine temporal changes in available P using probabilities less than given thresholds of this element. The RSSS was not designed for spatial analysis, but the results show that the data from these surveys are suitable for this purpose. The results of the spatial analysis, together with those of the statistical analyses, provide a comprehensive view of the RSSS database as a basis for monitoring the soil. These data should be taken into account when future national soil monitoring schemes are designed.

The sequential analysis of repeated binary responses: a score test for the case of three time points

In this paper a robust method is developed for the analysis of data consisting of repeated binary observations taken at up to three fixed time points on each subject. The primary objective is to compare outcomes at the last time point, using earlier observations to predict this for subjects with incomplete records. A score test is derived. The method is developed for application to sequential clinical trials, as at interim analyses there will be many incomplete records occurring in non-informative patterns. Motivation for the methodology comes from experience with clinical trials in stroke and head injury, and data from one such trial is used to illustrate the approach. Extensions to more than three time points and to allow for stratification are discussed. Copyright © 2005 John Wiley & Sons, Ltd.

Spatio-temporal analysis of an invasive plant pathogen (Phytophthora ramorum) in England and Wales

Phytophthora ramorum is a damaging invasive plant pathogen and was first discovered in the UK in 2002. Spatial point analyses were applied to the occurrence of this disease in England and Wales during the period of 2003-2006 in order to assess its spatio-temporal spread. Out of the 4301 garden centres and nurseries (GCN) surveyed, there were 164, 105, 123 and 41 sites with P. ramorum in 2003, 2004, 2005 and 2006, respectively. Spatial analysis of the observed point patterns of GCN outbreaks suggested that these sites were significantly clumped within a radius of ca 60 km in 2003, but not in later years. Further analyses were conducted to determine the relationship of GCN outbreak sites over two consecutive years and thus to infer possible disease spread over time. This analysis suggested that disease spread among GCN sites was most likely to have occurred within a distance of 60 km for 2003-2004, but not for the later years. There were 35, 63, 81 and 58 sites with P. ramorum in the semi-natural environment (SNE). Analyses were carried out to assess whether infected GCN sites could act as an inoculum source of infected SNE plants or vice versa. In all years, there was a significant spatial closeness among GCN and SNE outbreak sites within a distance of 1 km. But a significant relationship over a longer distance (within 60 km) was only observed between cases in 2003 and 2004. These analyses suggest that statutory actions taken so far appear to have reduced the extent of long-distance spread of P. ramorum among garden centres and nurseries, but not the disease spread at a shorter distance between GCN and SNE sites.

An analysis of verbal responses to music in a group of adult non-specialists

In a workshop setting, two pieces of recorded music were presented to a group of adult non-specialists; a key feature was to set up structured discussion within which the respondents considered each piece of music as a whole and not in its constituent parts. There were two areas of interest, namely to explore whether the respondents were likely to identify the musical features or to make extra-musical associations and, to establish the extent to which there would be commonality and difference in their approach to formulating the verbal responses. An inductive approach was used in the analysis of data to reveal some of the working theories underpinning the intuitive musicianship of the adult non-specialist listener. Findings have shown that, when unprompted by forced choice responses, the listeners generated responses that could be said to be information-poor in terms of musical features but rich in terms of the level of personal investment they made in formulating their responses. This is evidenced in a number of connections they made between the discursive and the non-discursive, including those which are relational and mediated by their experiences. Implications for music education are considered.

A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

Background: Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity. Results: The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data. Conclusion: After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.

Casein-derived lactotripeptides reduce systolic and diastolic blood pressure in a meta-analysis of randomised clinical trials

There is an urgent need to treat individuals with high blood pressure (BP) with effective dietary strategies. Previous studies suggest a small, but significant decrease in BP after lactotripeptides (LTP) ingestion, although the data are inconsistent. The study aim was to perform a comprehensive meta-analysis of data from all relevant randomised controlled trials (RCT). Medline, Cochrane library, EMBASE and Web of Science were searched until May 2014. Eligibility criteria were RCT that examined the effects of LTP on BP in adults, with systolic BP (SBP) and diastolic BP (DBP) as outcome measures. Thirty RCT met the inclusion criteria, which resulted in 33 sets of data. The pooled treatment effect for SBP was −2.95 mmHg (95% CI: −4.17, −1.73; p < 0.001), and for DBP was −1.51 mmHg (95% CI: −2.21, −0.80; p < 0.001). Sub-group analyses revealed that reduction of BP in Japanese studies was significantly greater, compared with European studies (p = 0.002 for SBP and p < 0.001 for DBP). The 24-h ambulatory BP (AMBP) response to LTP supplementation was statistically non-significant (p = 0.101 for SBP and p = 0.166 for DBP). Both publication bias and “small-study effect” were identified, which shifted the treatment effect towards less significant SBP and non-significant DBP reduction after LTP consumption. LTP may be effective in BP reduction, especially in Japanese individuals; however sub-group, meta-regression analyses and statistically significant publication biases suggest inconsistencies.

Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood

The variogram is essential for local estimation and mapping of any variable by kriging. The variogram itself must usually be estimated from sample data. The sampling density is a compromise between precision and cost, but it must be sufficiently dense to encompass the principal spatial sources of variance. A nested, multi-stage, sampling with separating distances increasing in geometric progression from stage to stage will do that. The data may then be analyzed by a hierarchical analysis of variance to estimate the components of variance for every stage, and hence lag. By accumulating the components starting from the shortest lag one obtains a rough variogram for modest effort. For balanced designs the analysis of variance is optimal; for unbalanced ones, however, these estimators are not necessarily the best, and the analysis by residual maximum likelihood (REML) will usually be preferable. The paper summarizes the underlying theory and illustrates its application with data from three surveys, one in which the design had four stages and was balanced and two implemented with unbalanced designs to economize when there were more stages. A Fortran program is available for the analysis of variance, and code for the REML analysis is listed in the paper. (c) 2005 Elsevier Ltd. All rights reserved.

Estimating the spatial scale of herbicide and soil interactions by nested sampling, hierarchical analysis of variance and residual maximum likelihood

An unbalanced nested sampling design was used to investigate the spatial scale of soil and herbicide interactions at the field scale. A hierarchical analysis of variance based on residual maximum likelihood (REML) was used to analyse the data and provide a first estimate of the variogram. Soil samples were taken at 108 locations at a range of separating distances in a 9 ha field to explore small and medium scale spatial variation. Soil organic matter content, pH, particle size distribution, microbial biomass and the degradation and sorption of the herbicide, isoproturon, were determined for each soil sample. A large proportion of the spatial variation in isoproturon degradation and sorption occurred at sampling intervals less than 60 m, however, the sampling design did not resolve the variation present at scales greater than this. A sampling interval of 20-25 m should ensure that the main spatial structures are identified for isoproturon degradation rate and sorption without too great a loss of information in this field.

A geostatistical analysis of soil, vegetation, and image data characterizing land surface variation

The elucidation of spatial variation in the landscape can indicate potential wildlife habitats or breeding sites for vectors, such as ticks or mosquitoes, which cause a range of diseases. Information from remotely sensed data could aid the delineation of vegetation distribution on the ground in areas where local knowledge is limited. The data from digital images are often difficult to interpret because of pixel-to-pixel variation, that is, noise, and complex variation at more than one spatial scale. Landsat Thematic Mapper Plus (ETM+) and Satellite Pour l'Observation de La Terre (SPOT) image data were analyzed for an area close to Douna in Mali, West Africa. The variograms of the normalized difference vegetation index (NDVI) from both types of image data were nested. The parameters of the nested variogram function from the Landsat ETM+ data were used to design the sampling for a ground survey of soil and vegetation data. Variograms of the soil and vegetation data showed that their variation was anisotropic and their scales of variation were similar to those of NDVI from the SPOT data. The short- and long-range components of variation in the SPOT data were filtered out separately by factorial kriging. The map of the short-range component appears to represent the patterns of vegetation and associated shallow slopes and drainage channels of the tiger bush system. The map of the long-range component also appeared to relate to broader patterns in the tiger bush and to gentle undulations in the topography. The results suggest that the types of image data analyzed in this study could be used to identify areas with more moisture in semiarid regions that could support wildlife and also be potential vector breeding sites.

Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood

The variogram is essential for local estimation and mapping of any variable by kriging. The variogram itself must usually be estimated from sample data. The sampling density is a compromise between precision and cost, but it must be sufficiently dense to encompass the principal spatial sources of variance. A nested, multi-stage, sampling with separating distances increasing in geometric progression from stage to stage will do that. The data may then be analyzed by a hierarchical analysis of variance to estimate the components of variance for every stage, and hence lag. By accumulating the components starting from the shortest lag one obtains a rough variogram for modest effort. For balanced designs the analysis of variance is optimal; for unbalanced ones, however, these estimators are not necessarily the best, and the analysis by residual maximum likelihood (REML) will usually be preferable. The paper summarizes the underlying theory and illustrates its application with data from three surveys, one in which the design had four stages and was balanced and two implemented with unbalanced designs to economize when there were more stages. A Fortran program is available for the analysis of variance, and code for the REML analysis is listed in the paper. (c) 2005 Elsevier Ltd. All rights reserved.