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.

Development of a physical and genetic map of the virulent Wolbachia strain wMelPop

We report here the construction of a physical and genetic map of the virulent Wolbachia strain, wMelPop. This map was determined by ordering 28 chromosome fragments that resulted from digestion with the restriction endonucleases FseI, ApaI, SmaI, and AscI and were resolved by pulsed-field gel electrophoresis. Southern hybridization was done with 53 Wolbachia-specific genes as probes in order to determine the relative positions of these restriction fragments and use them to serve as markers. Comparison of the resulting map with the whole genome sequence of the closely related benign Wolbachia strain, wMel, shows that the two genomes are largely conserved in gene organization with the exception of a single inversion in the chromosome.

A review of the use of the basic cation saturation ratio and the "ideal" soil

The use of 'balanced' Ca, Mg, and K ratios, as prescribed by the basic cation saturation ratio (BCSR) concept, is still used by some private soil-testing laboratories for the interpretation of soil analytical data. This review aims to examine the suitability of the BCSR concept as a method for the interpretation of soil analytical data. According to the BCSR concept, maximum plant growth will be achieved only when the soil’s exchangeable Ca, Mg, and K concentrations are approximately 65 % Ca, 10 % Mg, and 5 % K (termed the ‘ideal soil’). This ‘ideal soil’ was originally proposed by Firman Bear and co-workers in New Jersey (USA) during the 1940s as a method of reducing luxury K uptake by alfalfa (Medicago sativa L.). At about the same time, William Albrecht, working in Missouri (USA), concluded through his own investigations that plants require a soil with a high Ca saturation for optimal growth. Whilst it now appears that several of Albrecht’s experiments were fundamentally flawed, the BCSR (‘balanced soil’) concept has been widely promoted, suggesting that the prescribed cationic ratios provide optimum chemical, physical, and biological soil properties. Our examination of data from numerous studies (particularly those of Albrecht and Bear, themselves) would suggest that, within the ranges commonly found in soils, the chemical, physical, and biological fertility of a soil is generally not influenced by the ratios of Ca, Mg, and K. The data do not support the claims of the BCSR, and continued promotion of the BCSR will result in the inefficient use of resources in agriculture and horticulture.

High-resolution bulk density images, using calibrated X-ray radiography of impregnated soil slices

Bulk density of undisturbed soil samples can be measured using computed tomography (CT) techniques with a spatial resolution of about 1 mm. However, this technique may not be readily accessible. On the other hand, x-ray radiographs have only been considered as qualitative images to describe morphological features. A calibration procedure was set up to generate two-dimensional, high-resolution bulk density images from x-ray radiographs made with a conventional x-ray diffraction apparatus. Test bricks were made to assess the accuracy of the method. Slices of impregnated soil samples were made using hardsetting seedbeds that had been gamma scanned at 5-mm depth increments in a previous study. The calibration procedure involved three stages: (i) calibration of the image grey levels in terms of glass thickness using a staircase made from glass cover slips, (ii) measurement of ratio between the soil and resin mass attenuation coefficients and the glass mass attenuation coefficient, using compacted bricks of known thickness and bulk density, and (iii) image correction accounting for the heterogeneity of the irradiation field. The procedure was simple, rapid, and the equipment was easily accessible. The accuracy of the bulk density determination was good (mean relative error 0.015), The bulk density images showed a good spatial resolution, so that many structural details could be observed. The depth functions were consistent with both the global shrinkage and the gamma probe data previously obtained. The suggested method would be easily applied to the new fuzzy set approach of soil structure, which requires generation of bulk density images. Also, it would be an invaluable tool for studies requiring high-resolution bulk density measurement, such as studies on soil surface crusts.

Microsatellite instability and loss of heterozygosity at DNA mismatch repair gene loci occurs during hepatic carcinogenesis

DNA mismatch repair is an important mechanism involved in maintaining the fidelity of genomic DNA. Defective DNA mismatch repair is implicated in a variety of gastrointestinal and other turners; however, its role in hepatocellular carcinoma (HCC) has not been assessed. Formalin-fixed, paraffin-embedded archival pathology tissues from 46 primary liver tumors were studied by microdissection and microsatellite analysis of extracted DNA to assess the degree of microsatellite instability, a marker of defective mismatch repair, and to determine the extent and timing of allelic loss of two DNA mismatch repair genes, human Mut S homologue-2 (hMSH2) and human Mut L homologue-1 (hMLH1), and the tumor suppressor genes adenomatous polyposis coli gene (APC), p53, and DPC4. Microsatellite instability was detected in 16 of the tumors (34.8%). Loss of heterozygosity at microsatellites linked to the DNA mismatch repair genes, hMSH2 and/or hMLH1, was found in 9 cases (19.6%), usually in association with microsatellite instability. Importantly, the pattern of allelic loss was uniform in 8 of these 9 tumors, suggesting that clonal loss had occurred. Moreover, loss at these loci also occurred in nonmalignant tissue adjacent to 4 of these tumors, where it was associated with marked allelic heterogeneity. There was relatively infrequent loss of APC, p53, or DPC4 loci that appeared unrelated to loss of hMSH2 or hMLH1 gene loci. Loss of heterozygosity at hMSH2 and/or hMLH1 gene loci, and the associated microsatellite instability in premalignant hepatic tissues suggests a possible causal role in hepatic carcinogenesis in a subset of hepatomas.

Clinical measures of obesity and weight loss in men

OBJECTIVES: (?) To determine the relationship between waist circumference and body weight in overweight men both before and after participation in a weight loss program; and (2) to make recommendations for the appropriate use of these measures at various stages of weight toss. DESIGN: Weight and waist circumference measures were taken in two diverse groups of men both before and 1-2y after commencing a men's 'waist loss' program. Regression analyses were used to assess the relationship between weight and waist measures. SUBJECTS: One group of 42 retired Caucasian men from New South Wales, and one group of 45 indigenous men from the Torres Strait region of Northern Australia. RESULTS: There were differences in the relationships of weight and waist circumference before the program and change in weight and change in waist circumference after weight loss. These differences were similar in both groups of men (indigenous men and retired Caucasian men), with a 1 cm waist loss being on average equivalent to about 3/4 kg, but with wide variability, suggesting inter-individual variation in fat losses from different depots. This variation suggests that neither weight nor waist alone is a sufficient measure of fat loss for men. CONCLUSIONS: Weight and waist circumference should both be used at various stages in the clinical situation to assess change in body fat in men involved in obesity reduction.

Empirical catchment-wide rainfall erosivity models for two rivers in the humid tropics of Australia

The concept of rainfall erosivity is extended to the estimation of catchment sediment yield and its variation over time. Five different formulations of rainfall erosivity indices, using annual, monthly and daily rainfall data, are proposed and tested on two catchments in the humid tropics of Australia. Rainfall erosivity indices, using simple power functions of annual and daily rainfall amounts, were found to be adequate in describing the interannual and seasonal variation of catchment sediment yield. The parameter values of these rainfall erosivity indices for catchment sediment yield are broadly similar to those for rainfall erosivity models in relation to the R-factor in the Universal Soil Loss Equation.

Experimental examination of solute transport by surface runoff from low-angle slopes

The removal of chemicals in solution, by overland flow from agricultural land has the potential to be a significant source of chemical loss from zero-till and surface mulched farming systems. The objective of this study was to determine the magnitude of solute loss by surface runoff from agricultural systems. Previous experiments have enhanced the understanding of the exchange process, but the initial soil conditions together with the tracer application method in these experiments have meant that in some cases the results have limited applicability to field situations. In this study, two different sets of experiments were carried out to determine the magnitude of solute loss by surface runoff. These experiments entailed the surface application of bromide to (1) field scale plots 18 m long by 2 m wide and (2) repacked soil cores 236 mm in diameter; followed by the application of simulated rainfall in both cases. The most substantial finding of the field experiments was that the quantities of solute in surface runoff varied greatly with soil type and structure (0.07-14.9% of the applied bromide). Also, on some soils, large quantities of tracer were measured in the surface runoff even after several hours of infiltration. The experiments on soil cores showed that soil structure plays an important role in the quantity of chemical that may be transported in the surface runoff. These field results showed that, in certain systems, solute movement by overland flow is an important transport mechanism, which should be considered when budgeting for chemical loss. (C) 2000 Elsevier Science B.V. All rights reserved.

Soil carbon determination by high temperature combustion - A comparison with dichromate oxidation procedures and the influence of charcoal and carbonate carbon on the measured value

The measurement of organic carbon in soils has traditionally used dichromate oxidation procedures including the Wakley and Black and the Heanes methods. The measurement of carbon in soils by high temperature combustion is now widely used providing a rapid automated procedure without the use of toxic chemicals. This procedure however measures total carbon thus requiring some means of correction for soil samples containing carbonate and charcoal forms of carbon. This paper examines the effects of known additions of charcoal to a range of soil types on the results obtained by the Walkley and Black, Heanes and combustion methods. The results show, that while the charcoal carbon does not react under Walkley and Black conditions, some proportion does so with the Heanes method. A comparison of six Australian Soil and Plant Analysis Council reference soil samples by the three methods showed good agreement between the Heanes method, the combustion method and only slightly lower recoveries by the Walkley and Black procedure. Carbonate carbon will cause an overestimation of soil organic carbon by the combustion method thus requiring a separate determination of carbonate carbon to be applied as a correction. This work shows that a suitable acid pre-treatment of alkaline soils in the sample boats followed by a drying step eliminates the carbonate carbon prior to combustion and the need for an additional measurement. The measurement of carbon in soils by high temperature combustion in an oxygen atmosphere has been shown to be a rapid and reliable method capable of producing results in good agreement with one of the established dichromate oxidation procedures.

Allelic loss of cyclophilin 40, an estrogen receptor-associated immunophilin, in breast carcinomas

Purpose: Cyclophilin 40 (CyP40) is an estrogen receptor-associated protein which appears to modify receptor function. The aim of this study was to determine the extent of allelic loss at the CyP40 locus in a panel of breast carcinomas using a newly characterized microsatellite marker located upstream of the CyP40 gene and then to correlate this with losses at chromosomal sites for cancer-associated genes. Methods: Allelic loss at CyP40 was determined from patients' matched tumor and normal breast tissue using Genescan 672 software analysis of fluorescently labeled, PAGE-separated PCR products incorporating the marker. For each patient, allelic loss at CyP40 was then assessed and compared with losses at markers for various cancer-associated genes. Results: Allelic loss was detected in 30% of breast carcinomas from patients heterozygous for the CyP40 marker. All carcinomas demonstrating allelic loss were grade II or III invasive ductal carcinomas and generally showed multiple losses at other sites near known cancer-associated genes. Conclusions: The polymorphic marker which we characterized was useful in determining allelic loss at the CyP40 locus in breast cancer patients and when applied in these studies in conjunction with various cancer-associated gene markers, suggests that deletions in the region of the CyP40 gene might be a late event in breast tumor progression.

Plant growth limitation and nutrient loss following piled burning in slash and burn agriculture

In the forest zone of Cameroon, small-scale family farmers practicing traditional slash and burn practices achieve a clear field by piled burning of the branches and trunks of cleared vegetation. Plant growth inhibition on ash patches, and the risk of nutrient loss from these areas, was evaluated on field plots on which 0.5 t m(-2) or 1.0 t m(-2) of wood was piled and burnt, and in laboratory studies. The ash produced by burning was strongly alkaline, and laboratory bio-assessment studies showed that the saline, high pH conditions produced in ash patches prevented germination and plant growth for up to two wet seasons, as is observed in the field. Field and laboratory studies demonstrated rapid release (1 wet season) of K and S from the ash and the loss of a substantial portion of these nutrients from the soil profile by leaching. In contrast, leaching carries Mg from the ash gradually (3 to 4 wet seasons), while Ca, Cu, Zn and P are leached slowly. The nutrients contained in ash patches are considered at risk of loss both through leaching (K and S) and by erosion of ash (Ca, Mg, Cu, Zn and P). Farmers should be encouraged to spread ash patches prior to cultivation in order to exploit the nutrient content of ash and to lessen the risk of nutrient loss.

Degradation of phenanthrene and pyrene in soil slurry reactors with immobilized bacteria Zoogloea sp.

The environmental fate of polycyclic aromatic hydrocarbons (PAHs) in soils is motivated by their wide distribution, high persistence, and potentially deleterious effect on human health. Polycyclic aromatic hydrocarbons constitute the largest group of environmental contaminants released in the environment. Therefore, the potential biodegradation of these compounds is of vital importance. A biocarrier suitable for the colonization by micro-organisms for the purpose of purifying soil contaminated by polycyclic aromatic hydrocarbons was developed. The optimized composition of the biocarrier was polyvinyl alcohol (PVA) 10%, sodium alginate (SA) 0.5%, and powdered activated carbon (PAC) 5%. There was no observable cytotoxicity of biocarriers on immobilized cells and a viable cell population of 1.86 x 10(10) g(-1) was maintained for immobilized bacterium. Biocarriers made from chemical methods had a higher biodegradation but lower mechanical strengths. Immobilized bacterium Zoogloea sp. had an ideal capability of biodegradation for phenanthrene and pyrene over a relative wide concentration range. The study results showed that the biodegradation of phenanthrene and pyrene reached 87.0 and 75.4%, respectively, by using the optimal immobilized method of Zoogloea sp. cultivated in a sterilized soil. Immobilized Zoogloea sp. was found to be effective for biodegrading the soil contaminated with phenanthrene and pyrene. Even in natural (unsterilized) soil, the biodegradation of phenanthrene and pyrene using immobilized Zoogloea sp. reached 85.0 and 67.1%, respectively, after 168 h of cultivation, more than twice that achieved if the cells were not immobilized on the biocarrier. Therefore, the immobilization technology enhanced the competitive ability of introduced micro-organisms and represents an effective method for the biotreatment of soil contaminated with phenanthrene and pyrene.

Socioeconomic causes of loss of animal genetic diversity: Analysis and assessment

The number of breeds of domesticated animals, especially livestock, have declined rapidly. The proximate causes and processes involved in loss of breeds are outlined. The path-dependent effect and Swanson's dominance-effect are discussed in relation to breed selection. While these help to explain genetic erosion, they need to be supplemented to provide a further explanation of biodiversity loss. It is shown that the extension of markets and economic globalisation have contributed significantly to genetic loss of breeds. In addition, the decoupling of animal husbandry from surrounding natural environmental conditions is further eroding the stock of genetic resources, particularly industrialised intensive animal husbandry. Recent trends in animal husbandry raise very serious sustainability issues, apart from animal welfare concerns.

Sequestration of carbon by soil

Soil carbon is a major component of the terrestrial carbon cycle. The soils of the world contain more carbon than the combined total amounts occurring in vegetation and the atmosphere. Consequently, soils are a major reservoir of carbon and an important sink. Because of the relatively long period of time that carbon spends within the soil and is thereby withheld from the atmosphere, it is often referred to as being sequestered. Increasing the capacity of soils to sequester C provides a partial, medium-term countermeasure to help ameliorate the increasing CO2 levels in the atmosphere arising from fossil fuel burning and land clearing. Such action will also help to alleviate the environmental impacts arising from increasing levels of atmospheric CO2. The C sequestration potential of any soil depends on its capacity to store resistant plant components in the medium term and to protect and accumulate the humic substances (HS) formed from the transformations or organic materials in the soil environment. The sequestration potential of a soil depends on the vegetation it supports, its mineralogical composition, the depth of the solum, soil drainage, the availability of water and air, and the temperature of the soil environment. The sequestration potential also depends on the chemical characteristics of the soil organic matter and its ability to resist microbial decomposition. When accurate information for these features is incorporated in model systems, the potentials of different soils to sequester C can be reliably predicted. It is encouraging to know that improved soil and crop management systems now allow field yields to be maintained and soil C reserves to be increased, even for soils with depleted levels of soil C. Estimates of the soil C sequestration potential are discussed. Inevitably HS are the major components of the additionally sequestered C. It will be important to know more about the compositions and associations of these substances in the soil if we are able to predict reasonably accurately the ability of any soil type to sequester C in different cropping and soil management systems.