Reliability measures for local nodes assessment in classification trees

Most of the modem developments with classification trees are aimed at improving their predictive capacity. This article considers a curiously neglected aspect of classification trees, namely the reliability of predictions that come from a given classification tree. In the sense that a node of a tree represents a point in the predictor space in the limit, the aim of this article is the development of localized assessment of the reliability of prediction rules. A classification tree may be used either to provide a probability forecast, where for each node the membership probabilities for each class constitutes the prediction, or a true classification where each new observation is predictively assigned to a unique class. Correspondingly, two types of reliability measure will be derived-namely, prediction reliability and classification reliability. We use bootstrapping methods as the main tool to construct these measures. We also provide a suite of graphical displays by which they may be easily appreciated. In addition to providing some estimate of the reliability of specific forecasts of each type, these measures can also be used to guide future data collection to improve the effectiveness of the tree model. The motivating example we give has a binary response, namely the presence or absence of a species of Eucalypt, Eucalyptus cloeziana, at a given sampling location in response to a suite of environmental covariates, (although the methods are not restricted to binary response data).

Mechanical alloying of MoSi2 with ternary alloying elements. Part 1: Experimental

Phase evolution during the mechanical alloying of Mo and Si elemental powders with a ternary addition of Al, Mg, Ti or Zr was monitored using X-ray diffraction. Rietveld analysis was used to quantify the phase proportions. When Mo and Si are mechanically alloyed in the absence of a ternary element, the tetragonal C11b polymorph of MoSi2 (t-MoSi2) forms by a self-propagating combustion reaction. With additional milling, the tetragonal phase transforms to the hexagonal C40 structure (h-MoSi2). The mechanical alloying of Al, Mg and Ti additions with Mo and Si tend to promote a more rapid transformation of t-MoSi2 to h-MoSi2. In high concentrations, the addition of these ternary elements inhibits the initial combustion reaction, instead promoting the direct formation of h-MoSi2. The addition of Zr tends to stabilise the tetragonal phase.

Mechanical alloying of MoSi2 with ternary alloying elements. Part 2 - computer simulation

A computer model of the mechanical alloying process has been developed to simulate phase formation during the mechanical alloying of Mo and Si elemental powders with a ternary addition of Al, Mg, Ti or Zr. Using the Arhennius equation, the model balances the formation rates of the competing reactions that are observed during milling. These reactions include the formation of tetragonal C11(b) MOSi2 (t-MoSi2) by combustion, the formation of the hexagonal C40 MoSi2 polymorph (h-MoSi2), the transformation of the tetragonal to the hexagonal form, and the recovery of t-MoSi2 from h-MoSi2 and deformed t-MoSi2. The addition of the ternary additions changes the free energy of formation of the associated MoSi2 alloys, i.e. Mo(Si, Al)(2), Mo(Mg, Al)(2), (Mo, Ti)Si-2 (Mo, Zr)Si-2 and (Mo, Fe)Si-2, respectively. Variation of the energy of formation alone is sufficient for the simulation to accurately model the observed phase formation. (C) 2003 Elsevier B.V. All rights reserved.

Cambial meristem dormancy in trees involves extensive remodelling of the transcriptome

The establishment of the dormant state in meristems involves considerable physiological and metabolic alterations necessary for surviving unfavourable growth conditions. However, a global molecular analysis of dormancy in meristems has been hampered by the difficulty in isolating meristem cells. We used cryosectioning to isolate purified cambial meristem cells from the woody plant Populus tremula during active growth and dormancy. These samples were used to generate meristem-specific cDNA libraries and for cDNA microarray experiments to define the global transcriptional changes underlying cambial dormancy. The results indicate a significant reduction in the complexity of the cambial transcriptome in the dormant state. Although cell division is terminated in the dormant cambium, the cell cycle machinery appears to be maintained in a skeletal state as suggested by the continued presence of transcripts for several cell cycle regulators. The downregulation of PttPIN1 and PttPIN2 transcripts explains the reduced basipetal polar auxin transport during dormancy. The induction of a member of the SINA family of ubiquitin ligases implicated in auxin signalling indicates a potential mechanism for modulation of auxin sensitivity during cambial dormancy. The metabolic alterations during dormancy are mirrored in the induction of genes involved in starch breakdown and the glyoxysomal cycle. Interestingly, the induction of RGA1 like gene suggests modification of gibberellin signalling in cambial dormancy. The induction of genes such as poplar orthologues of FIE and HAP2 indicates a potential role for these global regulators of transcription in orchestrating extensive changes in gene expression during dormancy.

Pseudo-ternary phase diagrams of aqueous mixtures of Quil A, cholesterol and phospholipid prepared by the lipid-film hydration method

Pseudo-ternary phase diagrams of the polar lipids Quil A, cholesterol (Chol) and phosphatidylcholine (PC) in aqueous mixtures prepared by the lipid film hydration method (where dried lipid film of phospholipids and cholesterol are hydrated by an aqueous solution of Quil A) were investigated in terms of the types of particulate structures formed therein. Negative staining transmission electron microscopy and polarized light microscopy were used to characterize the colloidal and coarse dispersed particles present in the systems. Pseudo-ternary phase diagrams were established for lipid mixtures hydrated in water and in Tris buffer (pH 7.4). The effect of equilibration time was also studied with respect to systems hydrated in water where the samples were stored for 2 months at 4degreesC. Depending on the mass ratio of Quil A, Chol and PC in the systems, various colloidal particles including ISCOM matrices, liposomes, ring-like micelles and worm-like micelles were observed. Other colloidal particles were also observed as minor structures in the presence of these predominant colloids including helices, layered structures and lamellae (hexagonal pattern of ring-like micelles). In terms of the conditions which appeared to promote the formation of ISCOM matrices, the area of the phase diagrams associated with systems containing these structures increased in the order: hydrated in water/short equilibration period < hydrated in buffer/short equilibration period < hydrated in water/prolonged equilibration period. ISCOM matrices appeared to form over time from samples, which initially contained a high concentration of ring-like micelles suggesting that these colloidal structures may be precursors to ISCOM matrix formation. Helices were also frequently found in samples containing ISCOM matrices as a minor colloidal structure. Equilibration time and presence of buffer salts also promoted the formation of liposomes in systems not containing Quil A. These parameters however, did not appear to significantly affect the occurrence and predominance of other structures present in the pseudo-binary systems containing Quil A. Pseudo-ternary phase diagrams of PC, Chol and Quil A are important to identify combinations which will produce different colloidal structures, particularly ISCOM matrices, by the method of lipid film hydration. Colloidal structures comprising these three components are readily prepared by hydration of dried lipid films and may have application in vaccine delivery where the functionality of ISCOMs has clearly been demonstrated. (C) 2003 Elsevier B.V. All rights reserved.

A comparison of pseudo-ternary diagrams of aqueous mixtures of Quil A, cholesterol and phospholipid prepared by lipid-film hydration and dialysis

Pseudo-ternary diagrams for Quil A, phospholipid (phosphatidylcholine (PC) or phosphatidylethanolamine (PE)) and cholesterol were established in order to identify combinations that result in the formation of immune-stimulating complex (ISCOM) matrices and other colloidal structures produced by these three components in aqueous systems following lipid-film hydration or dialysis (methods that can be used to produce ISCOMs). In addition, the effect of equilibration time (1 month at 4degreesC) on the structures formed by the various combinations of the three components was investigated. Depending on the ratio of Quil A, cholesterol and phospholipid, different colloidal particles, including ISCOM matrices, liposomes and ring-like micelles, were found irrespective of the preparation method used. In contrast, worm-like micelles were only observed in systems prepared by lipid-film hydration. For samples prepared by dialysis, ISCOM matrices were predominantly found near the Quil A apex of the pseudo-ternary diagram (> 50% Quil A). On the other hand, for samples prepared by lipid-film hydration, ISCOM matrices were predominantly found near the phospholipid apex of the pseudo-ternary diagram (> 50% phospholipid). The regions in the pseudo-ternary diagrams in which ISCOM matrices were observed increased following an extended equilibration time, particularly for samples prepared by lipid-film hydration. Differences were also observed between pseudoternary diagrams prepared using either PE or PC as phospholipids.

The status of hollow-bearing trees required for the conservation of arboreal marsupials in the dry sclerophyll forests of south-east Queensland, Australia

At 38 sites in the dry sclerophyll forests of south-east Queensland, Australia, hollow-bearing trees were studied to determine the effects of past forestry practices on their density, size and spatial distribution. The density of hollow-bearing trees was reduced at sites that had been altered by poisoning and ringbarking of unmerchantable trees. This was especially the case for living hollow-bearing trees that were now at densities too low to support the full range of arboreal marsupials. Although there are presently enough hollow-bearing stags (i.e., dead hollow-bearing trees) to provide additional denning and nesting opportunities, the standing life of these hollow-bearing stags is lower than the living counterparts which means denning and nesting sites may be limited in the near future. The mean diameter at breast height (DBH) of hollow-bearing stags was significantly less than that of living hollow-bearing trees. This indicated that many large hollow-bearing stags may have a shorter standing life than smaller hollow-bearing stags. Hollow-bearing trees appear to be randomly distributed throughout the forest in both silviculturally treated and untreated areas. This finding is at odds with the suggestion by some forest managers that hollow-bearing trees should have a clumped distribution in dry sclerophyll forests of south-east Queensland.

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Monitoring genetic diversity in tropical trees with multilocus dominant markers

Since no universal codominant markers are currently available, dominant genetic markers, such as amplified fragment length polymorphism (AFLP), are valuable tools for assessing genetic diversity in tropical trees. However, the measurement of genetic diversity (H) with dominant markers depends on the frequency of null homozygotes (Q) and the fixation index (F) of populations. While Q can be estimated for AFLP loci, F is less accessible. Through a modelling approach, we show that the monolocus estimation of genetic diversity is strongly dependent on the value of F, but that the multilocus diversity estimate is surprisingly robust to variations in F. The robustness of the estimate is due to a mechanistic effect of compensation between negative and positive biases of H by different AFLP loci exhibiting contrasting frequency profiles of Q. The robustness was tested across contrasting theoretical frequency profiles of Q and verified for 10 neotropical species. Practical recommendations for the implementation of this analytical method are given for genetic surveys in tropical trees, where such markers are widely applied.

To self, or not to self ... A review of outcrossing and pollen-mediated gene flow in neotropical trees

Despite the typically low population densities and animal-mediated pollination of tropical forest trees, outcrossing and long-distance pollen dispersal are the norm. We reviewed the genetic literature on mating systems and pollen dispersal for neotropical trees to identify the ecological and phylogenetic correlates. The 36 studies surveyed found >90% outcrossed mating for 45 hermaphroditic or monoecious species. Self-fertilization rates varied inversely with population density and showed phylogenetic and geographic trends. The few direct measures of pollen flow (N = 11 studies) suggest that pollen dispersal is widespread among low-density tropical trees, ranging from a mean of 200 m to over 19 km for species pollinated by small insects or bats. Future research needs to examine (1) the effect of inbreeding depression on observed outcrossing rates, (2) pollen dispersal in a wide range of pollination syndromes and ecological classes, (3) and the range of variation of mating system expression at different hierarchical levels, including individual, seasonal, population, ecological, landscape and range wide.

Enhanced dust deposition by trees recently established on degraded rangeland

Results from 2 years of dust deposition monitoring in a 10-year-old Pinus nigra plantation near Lake Tekapo are presented. They show that recently established plantations significantly enhance dust deposition rates. This could reverse a cycle of soil loss and enhance vertical accretion of soil, which would provide more options for future land use. However, observations indicate that even under such enhanced conditions for soil formation, it would take several thousand years to replace the soil lost to erosion since European farming practices were first introduced to the northern section of the Mackenzie Basin.

Sampling tissue for DNA analysis of trees: Trunk cambium as an alternative to canopy leaves

The number of studies of tropical tree species that use molecular tools is increasing, most of which collect leaf tissue for genomic DNA extraction. In tropical trees the canopy is not only frequently inaccessible, but also, once reached, the leaf tissue is often heavily defended against herbivory by high concentrations of anti-predation compounds, which may inhibit downstream applications, particularly PCR. Cambium tissue, accessed directly from the tree trunk at ground level, offers a readily accessible resource that is less hampered by the presence of defensive chemicals than leaf tissue. Here we describe a simple method for obtaining tissue from the cambial zone for DNA extraction and test the applicability of the method in a range of tropical tree species. The method was used successfully to extract DNA from 11 species in nine families. A subset of the DNA extracts was tested in more detail and proved to be highly suitable for AFLP analysis.