Development of a dietary supplement database

Data describing the composition of dietary supplements are not readily available to the public health community. As a result, intake from dietary supplements is generally not considered in most dietary surveys and, hence, little is known about the significance of supplement intake in relation to total diet or disease risk. To enable a more comprehensive analysis of dietary data, a database of the composition of various dietary supplements has been compiled. Active ingredients of all dietary supplements sold in Australia are included in the Australian Register of Therapeutic Goods (ARTG), maintained by the Therapeutic Goods Administration. Products included in the database were restricted to those vitamin, mineral and other supplements identified in dietary data collected from studies conducted in southeast Queensland and New South Wales (850 supplements). Conversion factors from ingredients compounds to active elements were compiled from standard sources. No account has been made for bioavailability, consistent with current practice for food composition databases. The database can be queried by ARTG identification number, brand, product title, or a variety of other fields. Expected future developments include development of standard formulations for use when supplements are incompletely specified, and expansion of products included for more widespread use.

MHCPEP, a database of MHC-binding peptides: update 1997

MHCPEP (http://wehih.wehi.edu.au/mhcpep/) is a curated database comprising over 13 000 peptide sequences known to bind MHC molecules, Entries are compiled from published reports as well as from direct submissions of experimental data, Each entry contains the peptide sequence, its MHC specificity and where available, experimental method, observed activity, binding affinity, source protein and anchor positions, as well as publication references, The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW or FTP.

Data partitioning for parallel spatial join processing

The cost of spatial join processing can be very high because of the large sizes of spatial objects and the computation-intensive spatial operations. While parallel processing seems a natural solution to this problem, it is not clear how spatial data can be partitioned for this purpose. Various spatial data partitioning methods are examined in this paper. A framework combining the data-partitioning techniques used by most parallel join algorithms in relational databases and the filter-and-refine strategy for spatial operation processing is proposed for parallel spatial join processing. Object duplication caused by multi-assignment in spatial data partitioning can result in extra CPU cost as well as extra communication cost. We find that the key to overcome this problem is to preserve spatial locality in task decomposition. We show in this paper that a near-optimal speedup can be achieved for parallel spatial join processing using our new algorithms.

A global marker database for Phytophthora infestans

A marker database was compiled for isolates of the potato and tomato late blight pathogen, Phytophthora infestans, originating from 41 locations which include 31 countries plus 10 regions within Mexico. Presently, the database contains information on 1,776 isolates for one or more of the following markers: restriction fragment length polymorphism (RFLP) fingerprint consisting of 23 bands; mating type; dilocus allozyme genotype; mitochondrial DNA haplotype; sensitivity to the fungicide metalaxyl; and virulence. In the database, 305 entries have unique RFLP fingerprints and 258 entries have unique multilocus genotypes based on RFLP fingerprint, dilocus allozyme genotype, and mating type. A nomenclature is described for naming multilocus genotypes based on the International Organization for Standardization (ISO) two-letter country code and a unique number, Forty-two previously published multilocus genotypes are represented in the database with references to publications. As a result of compilation of the database, seven new genotypes were identified and named. Cluster analysis of genotypes from clonally propagated populations worldwide generally confirmed a previously published classification of old and new genotypes. Genotypes from geographically distant countries were frequently clustered, and several old and new genotypes were found in two or more distant countries. The cluster analysis also demonstrated that A2 genotypes from Argentina differed from all others. The database is available via the Internet, and thus can serve as a resource for Phytophthora workers worldwide.

The spatial and temporal distribution of koala faecal pellets

Faecal pellets were collected under trees used by free-ranging koalas in south-western, central and southeastern Queensland to determine the spatial and temporal distribution of pellets with respect to the activity of koalas. Deposition of faecal pellets by koalas was analysed according to the time of day at which the tree was occupied. For free-ranging koalas, 47% of daily faecal pellet output was recovered using a collection mat of 8 x 8 m placed under a day-roost tree. The best predictor of pellet production was the presence of a koala in a tree between 1800 hours and midnight. For other periods, there was no relationship between period of tree occupancy and faecal pellet recovery. There was a significant relationship between the average length of tree occupancy and the time of day that a koala entered a tree.

X-ray computed tomography to quantify tree rooting spatial distributions

Poor root development due to constraining soil conditions could be an important factor influencing health of urban trees. Therefore, there is a need for efficient techniques to analyze the spatial distribution of tree roots. An analytical procedure for describing tree rooting patterns from X-ray computed tomography (CT) data is described and illustrated. Large irregularly shaped specimens of undisturbed sandy soil were sampled from Various positions around the base of trees using field impregnation with epoxy resin, to stabilize the cohesionless soil. Cores approximately 200 mm in diameter by 500 mm in height were extracted from these specimens. These large core samples were scanned with a medical X-ray CT device, and contiguous images of soil slices (2 mm thick) were thus produced. X-ray CT images are regarded as regularly-spaced sections through the soil although they are not actual 2D sections but matrices of voxels similar to 0.5 mm x 0.5 mm x 2 mm. The images were used to generate the equivalent of horizontal root contact maps from which three-dimensional objects, assumed to be roots, were reconstructed. The resulting connected objects were used to derive indices of the spatial organization of roots, namely: root length distribution, root length density, root growth angle distribution, root spatial distribution, and branching intensity. The successive steps of the method, from sampling to generation of indices of tree root organization, are illustrated through a case study examining rooting patterns of valuable urban trees. (C) 1999 Elsevier Science B.V. All rights reserved.

Differentiation of soil properties related to the spatial association of wheat roots and soil macropores

Under certain soil conditions, e.g. hardsetting clay B-horizons of South-Eastern Australia, wheat plants do not perform as well as would be expected given measurements of bulk soil attributes. In such soils, measurement indicates that a large proportion (80%) of roots are preferentially located in the soil within 1 mm of macropores. This paper addresses the question of whether there are biological and soil chemical effects concomitant with this observed spatial relationship. The properties of soil manually dissected from the 1-3 mm wide region surrounding macropores, the macropore sheath, were compared to those that are measured in a conventional manner on the bulk soil. Field specimens of two different soil materials were dissected to examine biological differentiation. To ascertain whether the macropore sheath soil differs from rhizosphere soil, wheat was grown in structured and repacked cores under laboratory conditions. The macropore sheath soil contained more microbial biomass per unit mass than both the bulk soil and the rhizosphere. The bacterial population in the macropore sheath was able to utilise a wider range of carbon substrates and to a greater extent than the bacterial population in the corresponding bulk soil. These differences between the macropore sheath and bulk soil were almost non-existent in the repacked cores. Evidence for larger numbers of propagules of the broad host range fungus Pythium in the macropore sheath soil were also obtained.

Regional-scale investigation of the spatial distribution and origin of soluble salts in central north Queensland

A method for regional assessment of the distribution of saline outbreaks is demonstrated for a large area (68 000 km(2)) in north Queensland, Australia. Soil samples were used in conjunction with a digital elevation model and a map of potentially saline discharge zones to examine the landscape distribution of soluble salts in the region. The hypothesis of atmospheric accession of salt was tested for the topographically defined catchment regions feeding into each potentially saline discharge area. Most catchments showed a salt distribution consistent with this hypothesis, i.e. %TSS was large near the discharge areas and decreased rapidly with distance uphill from the discharge areas. In some catchments, however, local saline outbreaks were apparent at significant distances uphill from discharge areas. The possibility of geological sources of this salt was examined by comparing random point distributions with the location of saline points with distance downhill from geological units (excluding points near discharge zones). The distribution of some saline outbreaks was consistent with the occurrence of Cambro-Ordovician metasediments, Devonian limestone, Upper Devonian-Lower Carboniferous volcanics, and Triassic sediments. Copyright (C) 2000 John Wiley & Sons, Ltd.

Effect of density on spatial distribution, pit formation and pit diameter of Myrmeleon acer Walker, (Neuroptera : Myrmeleontidae): patterns and processes

The effect of increasing population density on the formation of pits, their size and spatial distribution, and on levels of mortality was examined in the antlion Myrmeleon acer Walker. Antlions were kept at densities ranging from 0.4 to 12.8 individuals per 100 cm(2). The distribution of pits was regular or uniform across all densities, but antlions constructed proportionally fewer and smaller pits as density increased. Mortality through cannibalism was very low and only occurred at densities greater than five individuals per 100 cm(2). Antlions in artificially crowded situations frequently relocated their pits and when more space became available, individuals became more dispersed with time. Redistribution of this species results from active avoidance of other antlions and sand throwing associated with pit construction and maintenance, rather than any attempt to optimise prey capture per se.

Integrating attribute and space characteristics in choropleth display and spatial data mining

This paper develops an interactive approach for exploratory spatial data analysis. Measures of attribute similarity and spatial proximity are combined in a clustering model to support the identification of patterns in spatial information. Relationships between the developed clustering approach, spatial data mining and choropleth display are discussed. Analysis of property crime rates in Brisbane, Australia is presented. A surprising finding in this research is that there are substantial inconsistencies in standard choropleth display options found in two widely used commercial geographical information systems, both in terms of definition and performance. The comparative results demonstrate the usefulness and appeal of the developed approach in a geographical information system environment for exploratory spatial data analysis.

Disaggregation of polygons of surficial geology and soil maps using spatial modelling and legacy data

Examples from the Murray-Darling basin in Australia are used to illustrate different methods of disaggregation of reconnaissance-scale maps. One approach for disaggregation revolves around the de-convolution of the soil-landscape paradigm elaborated during a soil survey. The descriptions of soil ma units and block diagrams in a soil survey report detail soil-landscape relationships or soil toposequences that can be used to disaggregate map units into component landscape elements. Toposequences can be visualised on a computer by combining soil maps with digital elevation data. Expert knowledge or statistics can be used to implement the disaggregation. Use of a restructuring element and k-means clustering are illustrated. Another approach to disaggregation uses training areas to develop rules to extrapolate detailed mapping into other, larger areas where detailed mapping is unavailable. A two-level decision tree example is presented. At one level, the decision tree method is used to capture mapping rules from the training area; at another level, it is used to define the domain over which those rules can be extrapolated. (C) 2001 Elsevier Science B.V. All rights reserved.

MHCWeb: Converting a WWW database into a knowledge-based collaborative environment

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary, We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The 0 WEB environment allows for flexible access to the data by both users and computer programs.

Spatial data mining for enhanced soil map modelling

The principle of using induction rules based on spatial environmental data to model a soil map has previously been demonstrated Whilst the general pattern of classes of large spatial extent and those with close association with geology were delineated small classes and the detailed spatial pattern of the map were less well rendered Here we examine several strategies to improve the quality of the soil map models generated by rule induction Terrain attributes that are better suited to landscape description at a resolution of 250 m are introduced as predictors of soil type A map sampling strategy is developed Classification error is reduced by using boosting rather than cross validation to improve the model Further the benefit of incorporating the local spatial context for each environmental variable into the rule induction is examined The best model was achieved by sampling in proportion to the spatial extent of the mapped classes boosting the decision trees and using spatial contextual information extracted from the environmental variables.

A strategy to fill gaps in soil survey over large spatial extents: an example from the Murray-Darling basin of Australia

We re-mapped the soils of the Murray-Darling Basin (MDB) in 1995-1998 with a minimum of new fieldwork, making the most out of existing data. We collated existing digital soil maps and used inductive spatial modelling to predict soil types from those maps combined with environmental predictor variables. Lithology, Landsat Multi Spectral Scanner (Landsat MSS), the 9-s digital elevation model (DEM) of Australia and derived terrain attributes, all gridded to 250-m pixels, were the predictor variables. Because the basin-wide datasets were very large data mining software was used for modelling. Rule induction by data mining was also used to define the spatial domain of extrapolation for the extension of soil-landscape models from existing soil maps. Procedures to estimate the uncertainty associated with the predictions and quality of information for the new soil-landforms map of the MDB are described. (C) 2002 Elsevier Science B.V. All rights reserved.

Local-global processing in early-onset schizophrenia: Evidence for an impairment in shifting the spatial scale of attention

In this study we report the results of two experiments on visual attention conducted with patients with early-onset schizophrenia. These experiments investigated the effect of irrelevant spatial-scale information upon the processing of relevant spatial-scale information, and the ability to shift the spatial scale of attention, across consecutive trials, between different levels of the hierarchical stimulus. Twelve patients with early-onset schizophrenia and matched controls performed local-global tasks under: (1) directed attention conditions with a consistency manipulation and (2) divided-attention conditions. In the directed-attention paradigm, the early-onset patients exhibited the normal patterns of global advantage and interference, and were not unduly affected by the consistency manipulation. Under divided-attention conditions, however, the early-onset patients exhibited a local-processing deficit. The source of this local processing deficit lay in the prolonged reaction time to local targets, when these had been preceded by a global target, but not when preceded by a local target. These findings suggest an impaired ability to shift the spatial scale of attention from a global to a local spatial scale in early-onset schizophrenia. (C) 2003 Elsevier Science (USA). All rights reserved.