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A new scoring system in Cystic Fibrosis : Statistical tools for database analysis - A preliminary report

  • Authors: Hafen, Gaudenz , Hurst, Cameron , Yearwood, John , Smith, Julie , Dzalilov, Zari , Robinson, P. J.
  • Date: 2008
  • Type: Text , Journal article
  • Relation: BMC Medical Informatics and Decision Making Vol. 8, no. 44 (2008), p.1-11
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  • Description: Background. Cystic fibrosis is the most common fatal genetic disorder in the Caucasian population. Scoring systems for assessment of Cystic fibrosis disease severity have been used for almost 50 years, without being adapted to the milder phenotype of the disease in the 21st century. The aim of this current project is to develop a new scoring system using a database and employing various statistical tools. This study protocol reports the development of the statistical tools in order to create such a scoring system. Methods. The evaluation is based on the Cystic Fibrosis database from the cohort at the Royal Children's Hospital in Melbourne. Initially, unsupervised clustering of the all data records was performed using a range of clustering algorithms. In particular incremental clustering algorithms were used. The clusters obtained were characterised using rules from decision trees and the results examined by clinicians. In order to obtain a clearer definition of classes expert opinion of each individual's clinical severity was sought. After data preparation including expert-opinion of an individual's clinical severity on a 3 point-scale (mild, moderate and severe disease), two multivariate techniques were used throughout the analysis to establish a method that would have a better success in feature selection and model derivation: 'Canonical Analysis of Principal Coordinates' and 'Linear Discriminant Analysis'. A 3-step procedure was performed with (1) selection of features, (2) extracting 5 severity classes out of a 3 severity class as defined per expert-opinion and (3) establishment of calibration datasets. Results. (1) Feature selection: CAP has a more effective "modelling" focus than DA. (2) Extraction of 5 severity classes: after variables were identified as important in discriminating contiguous CF severity groups on the 3-point scale as mild/moderate and moderate/severe, Discriminant Function (DF) was used to determine the new groups mild, intermediate moderate, moderate, intermediate severe and severe disease. (3) Generated confusion tables showed a misclassification rate of 19.1% for males and 16.5% for females, with a majority of misallocations into adjacent severity classes particularly for males. Conclusion. Our preliminary data show that using CAP for detection of selection features and Linear DA to derive the actual model in a CF database might be helpful in developing a scoring system. However, there are several limitations, particularly more data entry points are needed to finalize a score and the statistical tools have further to be refined and validated, with re-running the statistical methods in the larger dataset. © 2008 Hafen et al; licensee BioMed Central Ltd.

Does Geijera parviflora Lindl. (Rutaceae) facilitate understorey species in semi-arid Australia?

  • Authors: Warnock, Andrew , Westbrooke, Martin , Florentine, Singarayer , Hurst, Cameron
  • Date: 2007
  • Type: Text , Journal article
  • Relation: Rangeland Journal Vol. 29, no. 2 (2007), p. 207-216
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  • Description: Species composition under tree canopies often differs from that of surrounding micro-environments. In arid and semi-arid zones, trees can be beneficial to understorey vegetation. This study examined zones of vegetation composition and soil physiochemical parameters associated with Geijera parviflora Lindl. The importance of shade, rainfall redistribution, seed bank and soil moisture were examined. Species abundance, soil moisture, seed bank composition, rainfall redistribution and soil nutrient concentration were measured under five randomly selected mature G. parviflora trees in south-western New South Wales, Australia. To complement the findings from this study, artificial shade plots were constructed in a canopy-free area and species abundance measured seven months after shade construction. The study demonstrated that G. parviflora was associated with zonation of understorey vegetation. Two zones of understorey vegetation were found in relation to G. parviflora: (i) under the tree canopy with high species diversity, and (ii) beyond the canopy, this community being dominated by Dissocarpus paradoxus throughout the year with Crassula colorata appearing after rainfall. The zone beyond the canopy also had lower soil nutrient concentrations. Soil moisture, nutrient concentration and the seed bank density were significantly higher under the canopy. However, the canopy reduced precipitation reaching the soil surface. The effects of the canopy on understorey species composition and soil moisture were enhanced after winter rainfall. Artificial shade increased species abundance and richness under a 90%-shading treatment. The results indicated that G. parviflora generated spatial heterogeneity over the broader plant community increasing species richness, abundance and diversity under the canopy. This emphasises the importance of arid zone trees in conserving understorey plant diversity. Shading, soil nutrient concentration and increased seed bank density and soil moisture appeared to be key influences on the plant communities under the canopy. © Australian Rangeland Society 2007.
  • Description: C1
  • Description: 2003004817

Quantification of intermarket influence on the Australian All Ordinary Index based on optimization techniques

Dry lakes and drifting seed-heads : The ecology of fairy grass Lachnagrostis filiformis

Macroinvertebrate communities in Phragmites australis (Cav.) Trin. ex Steud. reed beds and open bank habitats in central Victorian streams in Australia

  • Authors: Jayawardana, Chandamali , Westbrooke, Martin , Wilson, Michael , Hurst, Cameron
  • Date: 2006
  • Type: Text , Journal article
  • Relation: Hydrobiologia Vol. 568, no. 1 (2006), p. 169-185
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  • Description: Reed invasion is a common phenomenon of open streams with disturbed riparian vegetation in river catchments. Knowledge of the effects of such vegetation change on aquatic communities is fundamental to river management. Macroinvertebrate fauna in Phragmites australis (Cav.) Trin. ex Steud. and open bank habitats were examined in three rivers in central Victoria in order to understand the effect of such littoral habitat on macroinvertebrates. Data were analysed using Partially Nested Factorial ANOVA with season, river and habitats as main effects. Habitat structure had a significant effect (p < 0.05) on macroinvertebrate species richness, however this was not seasonally consistent across the three rivers. There was a significant increase (p < 0.05) in macroinvertebrate taxa richness in Phragmites habitats during winter and spring seasons. Total abundance of taxa showed no consistent significant differences in the two habitats. Results of Canonical Analysis of Principle Coordinates indicated significant differences (p < 0.05) in macroinvertebrate assemblages between Phragmites and bare bank habitats in all seasons. Habitat selection by taxa could be related to the microphysical environment of the habitats. This study suggests that reed beds create important littoral habitat structures which support diverse macroinvertebrate assemblages. © Springer 2006.
  • Description: C1
  • Description: 2003001589

Macroinvertebrate communities in willow (Salix spp.) and reed beds (Phragmites australis) in central Victorian streams in Australia

  • Authors: Jayawardana, Chandamali , Westbrooke, Martin , Wilson, Michael , Hurst, Cameron
  • Date: 2006
  • Type: Text , Journal article
  • Relation: Marine and Freshwater Research Vol. 57, no. 4 (2006), p. 429-439
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  • Description: Exotic willows (Salix spp.) are widespread riparian tree species of rivers in temperate Australia and New Zealand. Despite being considered as a weed of national significance, little is known about the habitat value of willows and the impact on aquatic biota of vegetation change following willow management programmes. Macroinvertebrate fauna in root habitats of willows and Phragmites australis habitats were examined in three central Victorian rivers to understand the effect of such littoral habitat changes on macroinvertebrates. Data were analysed using Partially Nested Factorial ANOVA with season, river and habitat as main effects. Habitat structure had a significant effect (P < 0.05) on macroinvertebrate community assemblage. However, effect of habitat was not consistent among seasons. The greatest community differences among habitats were observed during winter and least separation during autumn. Taxa responsible for community differences among habitats were also identified. Species richness and abundance did not show consistent variation among habitats over different rivers or seasons. This study provided some indication of the macroinvertebrate community changes that would take place in situations where riparian vegetation changes takes place from willows to P. australis. © CSIRO 2006.
  • Description: C1
  • Description: 2003001620

Quantification of intermarket influence based on the global optimization and its application for stock market prediction

  • Authors: Tilakaratne, Chandima , Mammadov, Musa , Hurst, Cameron
  • Date: 2006
  • Type: Text , Conference paper
  • Relation: Paper presented at Integrating AI and Data Mining, 1st International Workshop Proceedings, Hobart, Tasmania : 4th - 5th December, 2006
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  • Description: This study investigates how intermarket influences can be used to help the prediction of the direction (up or down) of the next day's close price of the Australian All Ordinary Index (AORD). First, intermarket influences from the potential influential markets on the AORD are quantified by assigning weights for all influential markets. The weights were defined as a solution to an optimization problem which aims to maximise rank correlation between the current day's relative return of the AORD and the weighted sum of lagged relative returns of the potential influential markets. Then, the next day's relative return of the AORD is predicted by applying the neural networks as a classifier. Two different scenarios were compared: 1) using the current day's relative returns of different sets of influential markets as separate inputs; and, 2) using only the weighted sum of these relative returns as a "combined market". The results revealed that the second approach provides better predictions in all cases. This shows the effectiveness of the proposed approach for quantifying intermarket influences and the potential of using the "weighted combined markets" for the prediction
  • Description: E1
  • Description: 2003001609

Simulated power of the discrete Cramer-von Mises goodness-of-fit tests

  • Authors: Steele, Mike , Chaseling, Janet , Hurst, Cameron
  • Date: 2005
  • Type: Text , Conference paper
  • Relation: Paper presented at MODSIM 2005: International Congress of Modelling and Simulation, Advances and Applications for Management and Decision Making, Melbourne : 12th -15th December, 2005 p. 1300-1304
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  • Description: The use of goodness-of-fit test statistics for discrete or categorical data is widespread throughout the research community with the Chi- Square the most popular when a researcher aims to determine if observed categorical data differs from a hypothesized multinomial distribution. Even for ordinal categorical data, the use of empirical distribution function (EDF) test statistics such as the Kolmogorov-Smirnov, the three Cramér-von Mises (A2, W2 and U2 as defined below) and various modifications of these are limited in the literature. Power studies of the EDF type test statistics are even more limited. This paper compares the simulated power of the three Cramér-von Mises test statistics with that of the Chi-Square test statistic for a uniform null hypothesis against a variety of alternative distributions which are summarized in Figure 1. Recommendations are made on which is the most powerful test statistic for the predefined alternative distributions.
  • Description: E1
  • Description: 2003001375

Asymmetrical dependence test for intermarket influence analysis

Observations on survival and early growth of natural regeneration in floodplain coolibah Eucalyptus victrix (Myrtaceae) in the Pilbara, Western Australia

  • Authors: Fox, John , Florentine, Singarayer , Westbrooke, Martin , Hurst, Cameron
  • Date: 2004
  • Type: Text , Journal article
  • Relation: Rangeland Journal Vol. 26, no. 2 (2004), p. 150-160
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  • Description: Observations are presented on the natural regeneration of Eucalyptus victrix L. Johnson and K. Hill (coolibah), the dominant tree species of grassy woodlands on the floodplain of the Fortescue River, north of Newman in the Pilbara district of Western Australia. The main objectives of this study were to examine: (i) survival of newly recruited E. victrix seedlings on flooded and burnt sites, and (ii) growth and survival of established plants in a gilgaied landscape. Populations of newly-recruited seedlings following flooding or fire were monitored opportunistically at 'Marillana' and 'Ethel Creek' stations, for up to two years from tagging. A population of saplings at 'Roy Hill' station was observed over eight years. Seedling densities of E. victrix in flooded sites were 0.32 and 1.03 plants/m2 in 1995 and 1997 respectively. Locally high densities reached from 1.2 to 17.7 plants/m2 on areas of 28 and 6 m2 respectively. At the burnt site at 'Ethel Creek', 1.30 plants/m2 were observed where 58 seedlings were recorded on an area of 445 m2 a year after a natural fire. Many of these persisted well into their second year, whereas seedlings recruited in the flooded sites generally lasted less than a year (250-376 days). In contrast, persistence of a cohort of 100 established saplings <2 m tall in a gilgaied landscape at 'Roy Hill' was high. During 8 years of observations, only one sapling was lost. Those found at the edges of gilgais had attained greater heights (3.91 ± 1.14 m) than saplings located inside (3.16 ± 0.95 m) or on top (3.12 ± 0.93 m) of the gilgais. This study demonstrates that the seedling stage in E. victrix is critical, in that once newly recruited individuals reach the sapling stage (0.6-1 m), mortality rates are much reduced. Unfortunately, it was not possible during the course of this study to locate a cohort of young seedlings that did survive and so any consideration of the conditions necessary for their survival is speculative.
  • Description: C1
  • Description: 2003000725
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