Scaling up data mining techniques to large datasets using parallel and distributed processing

Advances in hardware and software technology enable us to collect, store and distribute large quantities of data on a very large scale. Automatically discovering and extracting hidden knowledge in the form of patterns from these large data volumes is known as data mining. Data mining technology is not only a part of business intelligence, but is also used in many other application areas such as research, marketing and financial analytics. For example medical scientists can use patterns extracted from historic patient data in order to determine if a new patient is likely to respond positively to a particular treatment or not; marketing analysts can use extracted patterns from customer data for future advertisement campaigns; finance experts have an interest in patterns that forecast the development of certain stock market shares for investment recommendations. However, extracting knowledge in the form of patterns from massive data volumes imposes a number of computational challenges in terms of processing time, memory, bandwidth and power consumption. These challenges have led to the development of parallel and distributed data analysis approaches and the utilisation of Grid and Cloud computing. This chapter gives an overview of parallel and distributed computing approaches and how they can be used to scale up data mining to large datasets.

Accessing biodiversity resources in computational environments from workflow applications

In the Biodiversity World (BDW) project we have created a flexible and extensible Web Services-based Grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. The current Web Servicesbased Grid environment enables execution of the BDW workflow tasks in remote nodes but with a limited scope. The next step in the evolution of the BDW architecture is to enable workflow tasks to utilise computational resources available within and outside the BDW domain. We describe the present BDW architecture and its transition to a new framework which provides a distributed computational environment for mapping and executing workflows in addition to bringing together heterogeneous resources and analytical tools.

Determining the influence of rainfall patterns and carbendazim on the surface activity of the earthworm Lumbricus terrestris

Carbendazim is highly toxic to earthworms and is used as a standard control substance when running field-based trials of pesticides, but results using carbendazim are highly variable. In the present study, impacts of timing of rainfall events following carbendazim application on earthworms were investigated. Lumbricus terrestris were maintained in soil columns to which carbendazim and then deionized water (a rainfall substitute) were applied. Carbendazim was applied at 4 kg/ha, the rate recommended in pesticide field trials. Three rainfall regimes were investigated: initial and delayed heavy rainfall 24 h and 6 d after carbendazim application, and frequent rainfall every 48 h. Earthworm mortality and movement of carbendazim through the soil was assessed 14 d after carbendazim application. No detectable movement of carbendazim occurred through the soil in any of the treatments or controls. Mortality in the initial heavy and frequent rainfall was significantly higher (approximately 55%) than in the delayed rainfall treatment (approximately 25%). This was due to reduced bioavailability of carbendazim in the latter treatment due to a prolonged period of sorption of carbendazim to soil particles before rainfall events. The impact of carbendazim application on earthworm surface activity was assessed using video cameras. Carbendazim applications significantly reduced surface activity due to avoidance behavior of the earthworms. Surface activity reductions were least in the delayed rainfall treatment due to the reduced bioavailability of the carbendazim. The nature of rainfall events' impacts on the response of earthworms to carbendazim applications, and details of rainfall events preceding and following applications during field trials should be made at a higher level of resolution than is currently practiced according to standard International Organization for Standardization protocols.

Fragmentation or creative diversity? Options in the provision of land management advisory services

Rural land managers need access to sound advice and information to respond to pressures from environmental regulations, declining farm incomes, changing patterns in international trade and new institutional arrangements within the domestic food chain. Governments have cut back their provision of advisory services but need more than ever to influence land managers' decisions to achieve a growing array of policy objectives: The paper develops a conceptual framework for analysing advisory services and concludes, through a review of sixteen case studies, that the needs of both governments and land managers can be met by a diverse mixture of private and public sector provision. (C) 2003 Elsevier Ltd. All rights reserved.

Fungicide and cultivar affect post-anthesis patterns of nitrogen uptake, remobilization and utilization efficiency in wheat

Three successive field experiments (2000/01-2002/03) assessed the effect of wheat cultivar (Consort.. Hereward and Shamrock) and fungicide (epoxiconazole and azoxystrobin) applied at and after flag leaf emergence on the nitrogen in the above-ground crop (Total N) and grain (Grain N), net nitrogen remobilization from non-grain tissues (Remobilized N). grain dry matter (Grain Dill), and nitrogen utilization efficiency (NUtE(g) = Grain DM/Total N). Ordinary logistic curves were fitted to the accumulation of Grain N, Grain DM and Remobilized N against thermal time after anthesis and used to simultaneously derive fits for Total N and NUtE(g). When disease was controlled, Consort achieved the greatest Grain DM, Total N, Grain N and NUtEg; in each case due mostly to longer durations, rather than quicker rates, of accumulation. Fungicide application increased final Grain Dill.. Grant N, Total N and Remobilized N, also mostly through effects on duration rather than rate of accumulation. Completely senesced leaf laminas retained less nitrogen when fungicide had been applied compared with leaf laminas previously infected severely with brown rust (Puccinia recondita) and Septoria tritici, or with just S. tritici. Late movement of nitrogen out of fungicide-treated laminas contributed to extended duration of both nitrogen remobilization and grain N filling, and meant that increases in NUtE(g) could occur without simultaneous reductions in grain N concentration.

Landscape effects on crop pollination services: are there general patterns?

Pollination by bees and other animals increases the size, quality, or stability of harvests for 70% of leading global crops. Because native species pollinate many of these crops effectively, conserving habitats for wild pollinators within agricultural landscapes can help maintain pollination services. Using hierarchical Bayesian techniques, we synthesize the results of 23 studies - representing 16 crops on five continents - to estimate the general relationship between pollination services and distance from natural or semi-natural habitats. We find strong exponential declines in both pollinator richness and native visitation rate. Visitation rate declines more steeply, dropping to half of its maximum at 0.6 km from natural habitat, compared to 1.5 km for richness. Evidence of general decline in fruit and seed set - variables that directly affect yields - is less clear. Visitation rate drops more steeply in tropical compared with temperate regions, and slightly more steeply for social compared with solitary bees. Tropical crops pollinated primarily by social bees may therefore be most susceptible to pollination failure from habitat loss. Quantifying these general relationships can help predict consequences of land use change on pollinator communities and crop productivity, and can inform landscape conservation efforts that balance the needs of native species and people.

Microbe-associated molecular pattern (MAMP) signatures, synergy, size and charge: influences on perception or mobility and host defence responses

Triggering of defences by microbes has mainly been investigated using single elicitors or microbe-associated molecular patterns (MAMPs), but MAMPs are released in planta as complex mixtures together with endogenous oligogalacturonan (OGA) elicitor. We investigated the early responses in Arabidopsis of calcium influx and oxidative burst induced by non-saturating concentrations of bacterial MAMPs, used singly and in combination: flagellin peptide (flg22), elongation factor peptide (elf18), peptidoglycan (PGN) and component muropeptides, lipo-oligosaccharide (LOS) and core oligosaccharides. This revealed that some MAMPs have additive (e.g. flg22 with elf18) and even synergistic (flg22 and LOS) effects, whereas others mutually interfere (flg22 with OGA). OGA suppression of flg22-induced defences was not a result of the interference with the binding of flg22 to its receptor flagellin-sensitive 2 (FLS2). MAMPs induce different calcium influx signatures, but these are concentration dependent and unlikely to explain the differential induction of defence genes [pathogenesis-related gene 1 (PR1), plant defensin gene 1.2 (PDF1.2) and phenylalanine ammonia lyase gene 1 (PAL1)] by flg22, elf18 and OGA. The peptide MAMPs are potent elicitors at subnanomolar levels, whereas PGN and LOS at high concentrations induce low and late host responses. This difference might be a result of the restricted access by plant cell walls of MAMPs to their putative cellular receptors. flg22 is restricted by ionic effects, yet rapidly permeates a cell wall matrix, whereas LOS, which forms supramolecular aggregates, is severely constrained, presumably by molecular sieving. Thus, MAMPs can interact with each other, whether directly or indirectly, and with the host wall matrix. These phenomena, which have not been considered in detail previously, are likely to influence the speed, magnitude, versatility and composition of plant defences.

A middleware independent grid workflow builder for scientific applications

Grid workflow authoring tools are typically specific to particular workflow engines built into Grid middleware, or are application specific and are designed to interact with specific software implementations. g-Eclipse is a middleware independent Grid workbench that aims to provide a unified abstraction of the Grid and includes a Grid workflow builder to allow users to author and deploy workflows to the Grid. This paper describes the g-Eclipse Workflow Builder and its implementations for two Grid middlewares, gLite and GRIA, and a case study utilizing the Workflow Builder in a Grid user's scientific workflow deployment.

Urban mammals: what does the future hold? An analysis of the factors affecting patterns of use of residential gardens in Great Britain

1Urban areas are predicted to grow significantly in the foreseeable future because of increasing human population growth. Predicting the impact of urban development and expansion on mammal populations is of considerable interest due to possible effects on biodiversity and human-wildlife conflict. 2The British government has recently announced a substantial housing programme to meet the demands of its growing population and changing socio-economic profile. This is likely to result in the construction of high-density, low-cost housing with small residential gardens. To assess the potential effects of this programme, we analysed the factors affecting the current pattern of use of residential gardens by a range of mammal species using a questionnaire distributed in wildlife and gardening magazines and via The Mammal Society. 3Twenty-two species/species groups were recorded. However, the pattern of garden use by individual species was limited, with only six species/species groups (bats, red fox Vulpes vulpes, grey squirrel Sciurus carolinensis, hedgehog Erinaceus europaeus, mice, voles) recorded as frequent visitors to > 20% of gardens in the survey. 4There was a high degree of association between the variables recorded in the study, such that it was difficult to quantify the effects of individual variables. However, all species/species groups appeared to be negatively affected by the increased fragmentation and reduced proximity of natural and semi-natural habitats, decreasing garden size and garden structure, but to differing degrees. Patterns of garden use were most clearly affected by house location (city, town, village, rural), with garden use declining with increasing urbanization for the majority of species/species groups, except red foxes and grey squirrels. Increasing urbanization is likely to be related to a wide range of interrelated factors, any or all of which may affect a range of mammal species. 5Overall, the probable effects of the planned housing development programme in Britain are not likely to be beneficial to mammal populations, although the pattern of use examined in this study may represent patterns of habitat selection by species rather than differences in distribution or abundance. Consequently, additional data are required on the factors affecting the density of species within urban environments.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Computer modelling and estimation of recruitment patterns of non-branching coral colonies at three sites in Wakatobi Marine Park, S.E. Sulawesi, Indonesia; implications for coral reef conservation

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function, where dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curaçao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village.

Patterns of peristome reduction and ornamentation in African Entodontaceae

The Entodontaceae is characterised by erect capsules with inset and substantially reduced peristomes. Differences in peristome morphology and ornamentation delimit both genera and species within the family. The Entodontaceae, as presently recognised, consists of four genera, Entodon, Erythrodontium, Mesonodon and Pylaisiobryum, which show a variety of peristome ornamentation patterns, and exhibit differing levels of peristome reduction. This variation encompasses an unusual combination of structurally reduced peristomes, which retain massive exostome ornamentation, and residual peristome function. As part of a taxonomic revision of the family in Africa, generic patterns of peristome reduction and ornamentation are described. Inter- and intra-specific variation patterns of both the exostome and endostome have been investigated using detailed SEM studies of material from Africa and beyond. Structural reduction of the peristome is associated with high levels of intra-specific variation in peristome ornamentation patterns. Common trends in these patterns of variation are identified within the family. Putative hybrid sporophytes have been identified in Entodon, and the taxonomic implications of these observations are considered for a family where species delimitation has in the past often depended on minor variation in peristome structure or ornamentation patterns. (author abst.)