Showing papers by "University of Sydney published in 1996"

Experiments in Ecology: Their Logical Design and Interpretation Using Analysis of Variance

Abstract: Ecological theories and hypotheses are usually complex because of natural variability in space and time, which often makes the design of experiments difficult. The statistical tests we use require data to be collected carefully and with proper regard to the needs of these tests. This book, first published in 1996, describes how to design ecological experiments from a statistical basis using analysis of variance, so that we can draw reliable conclusions. The logical procedures that lead to a need for experiments are described, followed by an introduction to simple statistical tests. This leads to a detailed account of analysis of variance, looking at procedures, assumptions and problems. One-factor analysis is extended to nested (hierarchical) designs and factorial analysis. Finally, some regression methods for examining relationships between variables are covered. Examples of ecological experiments are used throughout to illustrate the procedures and examine problems. This book will be invaluable to practising ecologists as well as advanced students involved in experimental design.

Enhancing Teaching through Constructive Alignment.

Abstract: Two lines of thinking are becoming increasingly important in higher educational practice. The first derives from constructivist learning theory, and the second from the instructional design literature. Constructivism comprises a family of theories but all have in common the centrality of the learner's activities in creating meaning. These and related ideas have important implications for teaching and assessment. Instructional designers for their part have emphasised alignment between the objectives of a course or unit and the targets for assessing student performance. “Constructive alignment” represents a marriage of the two thrusts, constructivism being used as a framework to guide decision-making at all stages in instructional design: in deriving curriculum objectives in terms of performances that represent a suitably high cognitive level, in deciding teaching/learning activities judged to elicit those performances, and to assess and summatively report student performance. The “performances of understanding” nominated in the objectives are thus used to systematically align the teaching methods and the assessment. The process is illustrated with reference to a professional development unit in educational psychology for teachers, but the model may be generalized to most units or programs in higher education.

Flavonoids—Chemistry, metabolism, cardioprotective effects, and dietary sources

Abstract: Flavonoids are a group of polyphenolic compounds, diverse in chemical structure and characteristics, found ubiquitously in plants. Therefore, flavonoids are part of the human diet. Over 4,000 different flavonoids have been identified within the major flavonoid classes which include flavonols, flavones, flavanones, catechins, anthocyanidins, isoflavones, dihydroflavonols, and chalcones. Flavonoids are absorbed from the gastrointestinal tracts of humans and animals and are excreted either unchanged or as flavonoid metabolites in the urine and feces. Flavonoids are potent antioxidants, free radical scavengers, and metal chelators and inhibit lipid peroxidation. The structural requirements for the antioxidant and free radical scavenging functions of flavonoids include a hydroxyl group in carbon position three, a double bond between carbon positions two and three, a carbonyl group in carbon position four, and polyhydroxylation of the A and B aromatic rings. Epidemiological studies show an inverse correlation between dietary flavonoid intake and mortality from coronary heart disease (CHD) which is explained in part by the inhibition of low density lipoprotein oxidation and reduced platelet aggregability. Dietary intake of flavonoids range between 23 mg/day estimated in The Netherlands and 170 mg/day estimated in the USA. Major dietary sources of flavonoids determined from studies and analyses conducted in The Netherlands include tea, onions, apples, and red wine. More research is needed for further elucidation of the mechanisms of flavonoid absorption, metabolism, biochemical action, and association with CHD.

Improved use of continuous attributes in C4.5

Abstract: A reported weakness of C4.5 in domains with continuous attributes is addressed by modifying the formation and evaluation of tests on continuous attributes. An MDL-inspired penalty is applied to such tests, eliminating some of them from consideration and altering the relative desirability of all tests. Empirical trials show that the modifications lead to smaller decision trees with higher predictive accuracies. Results also confirm that a new version of C4.5 incorporating these changes is superior to recent approaches that use global discretization and that construct small trees with multi-interval splits.

Bagging, boosting, and C4.S

Abstract: Breiman's bagging and Freund and Schapire's boosting are recent methods for improving the predictive power of classifier learning systems Both form a set of classifiers that are combined by voting, bagging by generating replicated bootstrap samples of the data, and boosting by adjusting the weights of training instances This paper reports results of applying both techniques to a system that learns decision trees and testing on a representative collection of datasets While both approaches substantially improve predictive accuracy, boosting shows the greater benefit On the other hand, boosting also produces severe degradation on some datasets A small change to the way that boosting combines the votes of learned classifiers reduces this downside and also leads to slightly better results on most of the datasets considered

Structural Equation Modeling: Concepts, Issues, and Applications

Abstract: Foreword - Kenneth A Bollen Preface - Rick H Hoyle The Structural Equation Modeling Approach - Rick H Hoyle Basic Concepts and Fundamental Issues Model Specification - Robert C MacCallum Procedures, Strategies, and Related Issues Estimates and Tests in Structural Equation Modeling - Chih-Ping Chou and Peter M Bentler Structural Equation Models with Nonnormal Variables - Stephen G West, John F Finch and Patrick J Curran Problems and Remedies Evaluating Model Fit - Li-tze Hu and Peter M Bentler Statistical Power in Structural Equation Modeling - David Kaplan Objectivity and Reasoning in Science and Structural Equation Modeling - Stanley A Mulaik and Lawrence R James One Application of Structural Equation Modeling from Two Perspectives - Barbara M Byrne Exploring the EQS and LISREL Strategies Writing about Structural Equation Models - Rick H Hoyle and Abigail T Panter Latent Variable Models for Multitrait-Multimethod Data - Herbert W Marsh and David Grayson Sex-Race Differences in Social Support and Depression in Older Low-Income Adults - Jane A Scott-Lennox and Richard D Lennox Modeling the Relation of Personality Variables to Symptom Complaints - Jay G Hull, Judith C Tedlie and Daniel A Lehn The Unique Role of Negative Affectivity Predictors of Change in Antisocial Behavior during Elementary School for Boys - Mike Stoolmiller, Terry E Duncan and Gerald Patterson

Progress with Proteome Projects: Why all Proteins Expressed by a Genome Should be Identified and How To Do It

Abstract: (1996). Progress with Proteome Projects: Why all Proteins Expressed by a Genome Should be Identified and How To Do It. Biotechnology and Genetic Engineering Reviews: Vol. 13, No. 1, pp. 19-50.

The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis.

Abstract: Objective. —Multiple endocrine neoplasia type 2 (MEN 2) is an autosomal dominant disorder. The 3 recognized subtypes include MEN 2A, characterized by medullary thyroid carcinoma (MTC), pheochromocytoma (pheo), and hyperparathyroidism (HPT); MEN 2B, by MTC, pheo, and characteristic stigmata; and familial MTC (FMTC), by the presence of MTC only. The purpose of this study was to establish the relationship between specific mutations and the presence of certain disease features in MEN 2 which could help in clinical decision making. Design. —Correlative survey study of 477 MEN 2 families. Setting. —Eighteen tertiary referral centers worldwide. Patients. —A total of 477 independent MEN 2 families. Main Outcome Measures. —Association between the position and type of germline mutation in the RET proto-oncogene and the presence or absence of MTC, pheo, HPT, and/or other features in a family. Results. —There is a statistically significant association between the presence of any mutation at a specific position (codon 634) and the presence of pheo and HPT. The presence of a specific mutation, CGC at codon 634, has yet to be associated with FMTC. Conversely, mutations at codons 768 and 804 are thus far seen only with FMTC, while codon 918 mutation is MEN 2B-specific. Rare families with both MEN 2 and Hirschsprung disease were found to have MEN 2-specific codon mutations. Patients with Hirschsprung disease presenting with such mutations should be monitored for the possible development of MEN 2 tumors. Conclusions. —This consortium analysis suggests that genotype-phenotype correlations do exist and, if made reliably absolute, could prove useful in the future in clinical management with respect to screening, surveillance, and prophylaxis, as well as provide insight into the genetic effects of particular mutations.

From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Amino Acid Analysis

Abstract: Separation and identification of proteins by two-dimensional (2-D) electrophoresis can be used for protein-based gene expression analysis In this report single protein spots, from polyvinylidene difluoride blots of micropreparative E coli 2-D gels, were rapidly and economically identified by matching their amino acid composition, estimated pI and molecular weight against all E coli entries in the SWISS-PROT database Thirty proteins from an E coli 2-D map were analyzed and identities assigned Three of the proteins were unknown By protein sequencing analysis, 20 of the 27 proteins were correctly identified Importantly, correct identifications showed unambiguous “correct” score patterns While incorrect protein identifications also showed distinctive score patterns, indicating that protein must be identified by other means These techniques allow large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states The computer program described here is accessible via the World Wide Web at URL address (http://expasyhcugech/)

Characterization of wheat-alien translocations conferring resistance to diseases and pests: current status

Abstract: Wild relatives of common wheat, Triticum aestivum, and related species are an important source of disease and pest resistance and several useful traits have been transferred from these species to wheat. C-banding and in situ hybridization analyses are powerful cytological techniques allowing the detection of alien chromatin in wheat. C-banding permits identification of the wheat and alien chromosomes involved in wheat-alien translocations, whereas genomic in situ hybridization analysis allows determination of their size and breakpoint positions. The present review summarizes the available data on wheat-alien transfers conferring resistance to diseases and pests. Ten of the 57 spontaneous and induced wheat-alien translocations were identified as whole arm translocations with the breakpoints within the centromeric regions. The majority of transfers (45) were identified as terminal translocations with distal alien segments translocated to wheat chromosome arms. Only two intercalary wheat-alien transloctions were identified, one induced by radiation treatment with a small segment of rye chromosome 6RL (H25) inserted into the long arm of wheat chromosome 4A, and the other probably induced by homoeologous recombination with a segment derived from the long arm of a group 7 Agropyron elongatum chromosome with Lr19 inserted into the long arm of 7D. The presented information should be useful for further directed chromosome engineering aimed at producing superior germplasm.

Spasticity and muscle contracture following stroke

Abstract: Summary It has become increasingly recognized that the major functional deficits following brain damage are largely due to 'negative' features such as weakness and loss of dexterity rather than spasticity. A variety of studies suggest that spasticity is a distinct problem and separate from the loss of dexterity, but that it may be implicated in the formation of muscle contracture and even in the recovery of strength. In order to address these issues, we examined the relationship between spasticity, contracture, strength and dexterity in the affected upper limb following stroke. Spasticity was measured both as increased tonic stretch reflexes and increased resistance to passive stretch (hypertonia). Twenty-four patients were recruited non-selectively from three rehabilitation units within 13 months of their stroke. Few patients exhibited increased tonic reflexes but half were found to have muscle contracture, the earliest at 2 months following stroke. Hypertonia was associated with contracture but not with reflex hyperexcitability. Increased tonic stretch reflexes were observed only in a subgroup of those with contracture and where present could usually be elicited only at the end of muscle range. This finding suggests that instead of spasticity causing contracture, contracture may actually potentiate spasticity in some patients. However, the majority of patients with contracture did not have increased tonic stretch reflexes. In addition, we found no relationship between spasticity and either weakness or loss of dexterity. Therefore, while hypertonia remains an important problem following cerebral lesions, it would appear that the amount of attention directed to reflex hyperexcitability associated with spasticity is out of proportion with its effects. Consequently, hypertonia needs to be clearly distinguished from reflex hyperexcitability in patients with spasticity.

Presence of hypochlorite-modified proteins in human atherosclerotic lesions.

Abstract: Oxidation of LDL may contribute to atherogenesis, though the nature of the in vivo oxidant(s) remains obscure. Myeloperoxidase, the enzyme responsible for hypochlorous acid/hypochlorite (HOCl) production in vivo, is present in active form in human atherosclerotic lesions, and HOCl aggregates and transforms LDL into a high-uptake form for macrophages in vitro. Here we demonstrate HOCl-modified proteins in human lesions using an mAb raised against HOCl-modified LDL that recognizes HOCl-oxidized proteins but does not cross-react with Cu2+-, malondialdehyde-, or 4-hydroxynonenal-modified LDL. This antibody detected significantly more material in advanced atherosclerotic lesions than normal arteries, even though azide and methionine were included during sample work-up to inhibit myeloperoxidase and to scavenge HOCl. The epitope(s) recognized was predominantly cell associated and present in monocyte/macrophages, smooth muscle, and endothelial cells. The intima and cholesterol clefts stained more heavily than the center of the thickened vessels; adventitial staining was apparent in some cases. Immunostaining was also detected in a very early lesion from an accident victim, beside healthy areas that were unreactive. LDL oxidized by HOCl in vitro, but not native LDL, effectively competed with the epitopes in lesions for antibody binding. Density centrifugation of plaque homogenates and Western blot analysis showed that, in the apo B-containing lipoprotein fraction, the mAb recognized protein(s) of molecular mass greater than apo B, similar to those produced during oxidation of LDL with HOCl in vitro. Three major proteins were recognized by the anti-HOCl-modified protein antibody but not by an anti-apo B antibody in the apo B-free fraction. Together, these results demonstrate HOCl-oxidized proteins in human atherosclerotic lesions, implicating this oxidant in LDL modification in vivo.

Efficient nonlinear algorithm for envelope detection in white light interferometry

Abstract: A compact and efficient algorithm for digital envelope detection in white light interferograms is derived from a well-known phase-shifting algorithm. The performance of the new algorithm is compared with that of other schemes currently used. Principal criteria considered are computational efficiency and accuracy in the presence of miscalibration. The new algorithm is shown to be near optimal in terms of computational efficiency and can be represented as a second-order nonlinear filter. In combination with a carefully designed peak detection method the algorithm exhibits exceptionally good performance on simulated interferograms.

Bragg Grating Solitons

Abstract: We report the first experimental observation of nonlinear propagation effects in fiber Bragg gratings, resulting in nonlinear optical pulse compression and soliton propagation. The solitons occur at frequencies near the photonic band gap of the grating; they are due to a combination of the negative dispersion of the grating, which dominates the material dispersion, and self-phase modulation. The solitons propagate at velocities well below the speed of light in the uniform medium.

Prevalence and associations of retinal vein occlusion in Australia : The blue mountains eye study

Abstract: Objective: To determine the prevalence and associations of retinal vein occlusion (RVO) in a defined older Australian population. Design: Participants (N=3654; age, ≥49 years), representing 88% of the permanent residents from an area west of Sydney, Australia, underwent a detailed eye examination, including stereophotography (Zeiss). The diagnosis of RVO was made clinically and from photographic grading. Results: Signs of RVO were found in 59 participants (1.6%; 95% confidence interval, 1.3-1.9). The prevalence for each age-specific participant was as follows: 0.7%, younger than 60 years; 1.2%, 60 to 69 years; 2.1%, 70 to 79 years; and 4.6%, 80 years or older. There was no significant sex difference in prevalence. Branch RVO was observed in 41 subjects (69.5%); of this number, 10 subjects had branch RVO outside the vascular arcade or in the nasal fundus and 3 subjects developed new vessels. Hemispheric RVO was found in 3 subjects (5.1%), and central RVO was observed in 15 (25%); RVO was bilateral in 3 subjects (5.1%). Visual acuity was affected most in the people with central RVO, with a visual acuity of 20/200 or less in 60% compared with 14% among the people with branch RVO. Retinal vein occlusion was the fifth most frequent cause of unilateral blindness in this population. Significant associations with RVO were found with glaucoma, hypertension, stroke, and angina. Conclusions: This study emphasizes RVO as an important cause of unilateral visual loss in an older population. The proportion of the 3 vein occlusion sites shows some differences from those of clinic-based reports and suggests a likely selection bias in previous clinic studies.

House dust mite allergens. A major risk factor for childhood asthma in Australia.

Abstract: If house dust mite allergen (Der p I) is an important cause of asthma, there should be a direct relationship between level of exposure to this allergen and asthma severity. To examine this, we studied six large random samples of children in different regions of New South Wales, Australia. We measured recent wheeze by questionnaire, airway hyperresponsiveness (AHR) by histamine inhalation test and sensitization to house dust mites by skin prick tests. Current asthma was defined as the presence of recent wheeze and AHR. We measured Der p I levels in the beds of approximately 80 children in each region. In regions where Der p I levels were high, more children were sensitized to house dust mites, and these children had significantly more AHR and recent wheeze. After adjusting for sensitization to other allergens, we found that the risk of house dust mite-sensitized children having current asthma doubled with every doubling of Der p I level. There was a modest correlation between AHR and Der p I exposure in in...

Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid.

Abstract: Colanic acid (CA) is an extracellular polysaccharide produced by most Escherichia coli strains as well as by other species of the family Enterobacteriaceae. We have determined the sequence of a 23-kb segment of the E. coli K-12 chromosome which includes the cluster of genes necessary for production of CA. The CA cluster comprises 19 genes. Two other sequenced genes (orf1.3 and galF), which are situated between the CA cluster and the O-antigen cluster, were shown to be unnecessary for CA production. The CA cluster includes genes for synthesis of GDP-L-fucose, one of the precursors of CA, and the gene for one of the enzymes in this pathway (GDP-D-mannose 4,6-dehydratase) was identified by biochemical assay. Six of the inferred proteins show sequence similarity to glycosyl transferases, and two others have sequence similarity to acetyl transferases. Another gene (wzx) is predicted to encode a protein with multiple transmembrane segments and may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The first three genes of the cluster are predicted to encode an outer membrane lipoprotein, a phosphatase, and an inner membrane protein with an ATP-binding domain. Since homologs of these genes are found in other extracellular polysaccharide gene clusters, they may have a common function, such as export of polysaccharide from the cell.

Scales of spatial patterns of distribution of intertidal invertebrates.

Abstract: Few comparative studies of spatial patterns at different scales have examined several species in the same habitat or the same species over a range of habitats. Therefore, variability in patterns among species or among habitats has seldom been documented. This study quantifies spatial patterns of a suite of intertidal snails and a species of barnacle using a range of statistical techniques. Variability in densities was quantified from the scale of adjacent quadrats (over a distance of centimeters) to tens of kilometers. Significant differences in abundances occurred primarily at two spatial scales. Small-scale differences were found at the scales of centimeters or 1-2 m and, for many species on many shores, these accounted for most of the variability in abundances from place to place. These are likely to be determined by behavioural responses to small-scale patches of microhabitat. Large-scale differences in abundance were also found in most species at the scale of hundreds of meters alongshore. These are likely to be due to variation in recruitment (and/or mortality) because of limited dispersal by adults of these species. There was little or no additional variation among shores, separated by tens of kilometers, than was shown among patches of shore separated by hundreds of meters. Identification of the scale(s) at which significant differences in abundance are found focus attention on the processes (and the scales at which these processes operate) that influence patterns of distribution and abundance. Some of the advantages and disadvantages of various procedures are discussed.

Frequency and Morphologic Characteristics of Invasive Melanomas Lacking Specific Surface Microscopic Features

Abstract: Objectives: To create a simple diagnostic method for invasive melanoma with in vivo cutaneous surface microscopy (epiluminescence microscopy, dermoscopy, dermatoscopy) and to analyze the incidence and characteristics of those invasive melanomas that had no diagnostic features by means of hand-held surface microscopes. Design: Pigmented skin lesions were photographed in vivo with the use of immersion oil. All were excised and reviewed for histological diagnosis. A training set of 62 invasive melanomas and 159 atypical nonmelanomas and a test set of 45 invasive melanomas and 119 atypical nonmelanomas were used. Images from the training set were scored for 72 surface microscopic features. Those features with a low sensitivity (0%) and high specificity (>85%) were used to create a simple diagnostic model for invasive melanoma. Setting: All patients were recruited from the Sydney (Australia) Melanoma Unit (a primary case and referral center). Patients: A random sample of patients whose lesions were excised, selected from a larger database. Main Outcome Measures: Sensitivity and specificity of the model for diagnosis of invasive melanona. Results: The model gave a sensitivity of 92% (98/107) and specificity of 71%. Of the 9 "featureless" melanomas the model failed to detect, 6 were pigmented and thin and had a pigment network. The other 3 were thicker, hypomelanotic lesions lacking a pigment network, some with prominent telangiectases, and all with only small areas of pigment. All featureless melanomas noted by the patients had a history of change in color, shape, or size. Conclusions: Surface microscopy does not allow 100% sensitivity in diagnosing invasive melanoma and therefore cannot be used as the sole indicator for excision. Clinical history is an important consideration when featureless lesions are diagnosed. Arch Dermatol. 1996;132:1178-1182

Tetrahedral bonding in amorphous carbon

Abstract: Electron configurations close to the tetrahedral hybridization are found in pure amorphous carbon at a concentration which depends on preparation conditions. Tetrahedral bonding at levels of approximately 80% is found in amorphous carbons formed from beams of carbon ions with energies in a `window' between 20 eV and approximately 500 eV. Suitable techniques for its formation include cathodic arc deposition, ion beam deposition and laser ablation. Similar material appears to be formed by pressure treatment of fullerene precursors and by displacement damage in diamond. Highly tetrahedral forms of amorphous carbon (ta-C) show electronic, optical and mechanical properties which approach those of diamond and are quite different from amorphous carbons with low content. Useful techniques for determining the content include electron energy loss spectroscopy, electron and neutron diffraction and Raman spectroscopy. Considerable progress has been made in the understanding of this material by simulating its structure in the computer with a range of techniques from empirical potentials to ab initio quantum mechanics. The structure shows departures from an idealized glassy state of diamond which would have a random tetrahedral network structure as used to describe amorphous silicon and germanium. A surprising feature of the structure simulated using ab initio methods is the presence of small rings containing three or four carbon atoms. The electronic and optical properties are strongly influenced by the residual of carbon. Applications to electronic devices are at an early stage with the demonstration of photoconductivity and some simple junction devices. Applications as a wear resistant coating are promising, since the theoretically predicted high values of elastic constants, comparable to but less than those of diamond, are achieved experimentally, together with low friction coefficients.

Differential Rotation and Dynamics of the Solar Interior

Abstract: Splitting of the sun's global oscillation frequencies by large-scale flows can be used to investigate how rotation varies with radius and latitude within the solar interior. The nearly uninterrupted observations by the Global Oscillation Network Group (GONG) yield oscillation power spectra with high duty cycles and high signal-to-noise ratios. Frequency splittings derived from GONG observations confirm that the variation of rotation rate with latitude seen at the surface carries through much of the convection zone, at the base of which is an adjustment layer leading to latitudinally independent rotation at greater depths. A distinctive shear layer just below the surface is discernible at low to mid-latitudes.

The Maximum Entropy Distribution of an Asset Inferred from Option Prices

Abstract: This paper describes the application ofthe Principle of Maximum Entropy to the estimation of the distribution of an underlying asset from a set of option prices. The resulting distri? bution is least committal with respect to unknown or missing information and is, hence, the least prejudiced. The maximum entropy distribution is the only information about the asset that can be inferred from the price data alone. An extension to the Principle of Mini? mum Cross-Entropy allows the inclusion of prior knowledge of the asset distribution. We show that the maximum entropy distribution is able to accurately fit a known density, given simulated option prices at different strikes.