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PubMed2001

Using decision tree induction to model oculomotor data.

Decision tree induction is a machine learning method used to generate classification models from data sets. Numerous decision trees were constructed to examine relationships between oculomotor test parameters and lesion sites in a data set containing cases with operated cerebello-pontine angle tumour, operated hemangioblastoma, infarction of cerebello-brainstem and Ménière's disease, and control subjects. The aim was to find useful parameter combinations with discriminatory power. Decision trees constructed using both pursuit eye movements and saccadic eye movements yielded the best classification results. This is reasonable: oculomotor test results vary according to the site of the lesion and so the performance ability of subjects has to be taken into account in the classification. The decision tree program was able to generate classification models from the oculomotor data set. Generated decision trees were intelligible and can be utilized in physicians' research work.

Decision Making↗
PubMed2003

A waveguide irradiation chamber for destruction of red palm weevils (Rhynchophorus ferrugineus) inside a block sample of a palm tree trunk.

A simple waveguide irradiation chamber at 2.45 GHz. was locally constructed for controlled laboratory experiments to assess the potentiality of using microwave heating for irradiation of weevils (RPW) inside healthy and infected palm tree trunks. The chamber consists of an aluminum rectangular waveguide with one of its broad sides removed for easy insertion of the block samples of the palm tree trunk. A rectangular aluminum plate, with the same dimensions as the removed wall section was made to slide-in and cover the tree block sample after its insertion in the waveguide to insure continuity of metallic walls. Temperature rise in the samples were monitored by thermocouples inserted through holes drilled at different positions along one of the waveguide side walls. Results showed that 100% mortality rate could be obtained with the RPW samples at distances not more than 2-3 cm from the leading edge of healthy tree block samples and 4-5 cm from leading edge of infected samples. Hot spots were observed at the leading edge of the tree samples due to high absorption of microwave at these regions.

Animals↗
PubMed2001

Headspace constituents of the tree remain of Cinnamomum camphora.

The volatile ingredients isolated from a fresh tree of Cinnamomum camphora (camphor tree) and from a tree remain of C. camphora were collected by using headspace techniques and analyzed by means of gas chromatography/mass spectrometry (GC/MS). 99.77% of the constituents consisting 23 components from the fresh tree, 98.68% of the constituents consisting 24 components from the tree remain were identified. Of these ingredients, camphor was obtained as the most abundant component.

Gas Chromatography-Mass Spectrometry↗
PubMed2002

Inferring the root of a phylogenetic tree.

Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.

Bayes Theorem↗
PubMed2002

An approximately unbiased test of phylogenetic tree selection.

An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.

Animals↗
PubMed2002

Tree balance, time slices, and evolutionary turnover in cretaceous planktonic foraminifera.

Studies of phylogenetic tree shape often concentrate on the balance of phylogenies of extant taxa. Paleontological phylogenies (which include extinct taxa) can contain additional useful information and can directly document changes in tree shape through evolutionary time. Unfortunately, the inclusion of extinct taxa lowers the power of direct examinations of tree balance because it increases the range of tree shapes expected under null models of evolution (with equal rates of speciation and extinction across lineages). A promising approach for the analysis of tree shape in paleontological phylogenies is to break the phylogeny down into time slices, examining the shape of the phylogeny of taxa alive at each time slice and changes in that shape between successive time slices. This method was illustrated with 57 time slices through a stratophenetic phylogeny of the Cretaceous planktonic foraminiferal superfamily Globotruncanacea. At 3 of 56 intervals between time slices, 93-92.5 million years ago (MYA), 89-88.5 MYA, and 85.5-84 MYA, the group showed steep increases in imbalance. Although none of these increases were significant after Bonferroni correction, these points in the history of the Globotruncanacea were nevertheless identified as deserving of further macroevolutionary investigation. The 84 MYA time slice coincides with a peak in species turnover for the superfamily. Time slices through phylogenies may prove useful for identifying periods of time when evolution was proceeding in a nonstochastic manner.

Biological Evolution↗
PubMed2005

Isolation of Cryptococcus gattii and Cryptococcus neoformans var. grubii from the flowers and bark of Eucalyptus trees in India.

The association of Cryptococcus gattii with Eucalyptus trees has been well established. Here we report the isolation of both C. gattii and Cryptococcus neoformans var. grubii from the flowers and bark of Eucalyptus trees in India. We investigated a total of 233 samples of Eucalyptus trees: 120 flowers, 81 fragments of bark, and 32 leaves. C. gattii was isolated from two samples of flowers of Eucalyptus terreticornis. C. neoformans var. grubii was recovered twice from the bark of Eucalyptus camaldulensis, initially from one of three samples, and again 2 months later, from one of four samples collected beneath the canopy of the tree. The primary isolation medium was Nigerseed agar, and brown colonies were presumptively identified as C. gattii or C. neoformans. The species identification was confirmed by morphological and biochemical characteristics. Using the Crypto-Check kit (Iatron, Tokyo, Japan), the first two isolates were identified as serotype B (C. gattii) and the other two were serotype A (C. neoformans var. grubii). PCR analysis of the isolates of C. neoformans var. grubii revealed that they possessed the MATalpha mating type allele. Molecular typing by amplified fragment length polymorphism markers indicated that both isolates of C. neoformans var. grubii possessed the same genotype. This study demonstrates that C. neoformans var. grubii, as well as C. gattii, may be associated with Eucalyptus trees.

Cryptococcus neoformans↗
PubMed2006

Analyses of rear-end crashes based on classification tree models.

OBJECTIVE: Signalized intersections are accident-prone areas especially for rear-end crashes due to the fact that the diversity of the braking behaviors of drivers increases during the signal change. The objective of this article is to improve knowledge of the relationship between rear-end crashes occurring at signalized intersections and a series of potential traffic risk factors classified by driver characteristics, environments, and vehicle types. METHODS: Based on the 2001 Florida crash database, the classification tree method and Quasi-induced exposure concept were used to perform the statistical analysis. Two binary classification tree models were developed in this study. One was used for the crash comparison between rear-end and non-rear-end to identify those specific trends of the rear-end crashes. The other was constructed for the comparison between striking vehicles/drivers (at-fault) and struck vehicles/drivers (not-at-fault) to find more complex crash pattern associated with the traffic attributes of driver, vehicle, and environment. RESULTS: The modeling results showed that the rear-end crashes are over-presented in the higher speed limits (45-55 mph); the rear-end crash propensity for daytime is apparently larger than nighttime; and the reduction of braking capacity due to wet and slippery road surface conditions would definitely contribute to rear-end crashes, especially at intersections with higher speed limits. The tree model segmented drivers into four homogeneous age groups: < 21 years, 21-31 years, 32-75 years, and > 75 years. The youngest driver group shows the largest crash propensity; in the 21-31 age group, the male drivers are over-involved in rear-end crashes under adverse weather conditions and the 32-75 years drivers driving large size vehicles have a larger crash propensity compared to those driving passenger vehicles. CONCLUSIONS: Combined with the quasi-induced exposure concept, the classification tree method is a proper statistical tool for traffic-safety analysis to investigate crash propensity. Compared to the logistic regression models, tree models have advantages for handling continuous independent variables and easily explaining the complex interaction effect with more than two independent variables. This research recommended that at signalized intersections with higher speed limits, reducing the speed limit to 40 mph efficiently contribute to a lower accident rate. Drivers involved in alcohol use may increase not only rear-end crash risk but also the driver injury severity. Education and enforcement countermeasures should focus on the driver group younger than 21 years. Further studies are suggested to compare crash risk distributions of the driver age for other main crash types to seek corresponding traffic countermeasures.

Acceleration↗
PubMed1997

Limited bifurcation asymmetry in coronary arterial tree models generated by constrained constructive optimization.

Models of coronary arterial trees are generated by the algorithm of constrained constructive optimization (CCO). In a given perfusion area a binary branching network of straight cylindrical tubes is generated by successively adding terminal segments to the growing structure. In each step the site of connection is chosen according to an optimization target function (total intravascular volume), and in any stage of development the tree fulfills physiologic boundary conditions (constraints involving pressures, flows and bifurcation rules). CCO generates structures which in many aspects resemble real coronary arterial trees, except for very asymmetric bifurcations, occurring when a large branch gives off a tiny terminal segment. In the present work we evaluate an additional constraint within CCO, namely imposing a limit on the asymmetry of bifurcations during the construction process. Model trees are grown with different limits imposed, and the effects on structure are studied both phenomenologically and via statistical descriptors. As the limit to asymmetry is tightened, blood is conveyed to the perfusion sites via detours rather than directly and the comparison with measured data shows that the structure to change from a conveying to a delivering type of function. Simultaneously total intravascular volume, surface and sum of segments' lengths increase. It is shown why and how local bifurcation asymmetry is able to determine the global structure of the optimized arterial tree model. Surprisingly, the pressure profile from inlet to terminals, being a functional characteristic, remains unaffected.

Algorithms↗
PubMed2000

Strategy Space and the Disturbance Spectrum: A Life-History Model for Tree Species Coexistence.

The disturbance spectrum consists of disturbance patterns differing in type, size, intensity, and frequency. It is proposed that tree life-history traits are adaptations to particular disturbance regimes. Four independent axes are proposed to define the dominant dimensions of tree strategy space: shade tolerance, tree height, capacity for vegetative reproduction, and seed dispersal distance. A fitness model was developed to elucidate interactions between the proposed life-history traits. The model shows how alternate life-history sets can coexist when disturbance patterns fluctuate in space and time. Variable disturbance regimes were shown, based on data and simulation results, to enhance species coexistence, as predicted. The strategy space model accurately predicts the number of common tree species for the eastern United States, boreal Canada, and southwestern piñon-juniper woodlands. The model also provides an explanation for latitudinal gradients in tree species richness in North America and Europe. The proposed model predicts a relationship between disturbance characteristics and the species composition of a forest that allows for the coexistence of large numbers of species. The life-history traits of size, growth rate, life span, shade tolerance, age of reproduction, seed dispersal distance, and vegetative reproduction are all incorporated into the model.

biodiversity↗
PubMed1998

Primary Mycobacterium avium complex infections correlate with lowered cellular immune reactivity in Matschie's tree kangaroos (Dendrolagus matschiei).

The National Zoological Park has maintained a breeding colony of Matschie's tree kangaroos (Dendrolagus matschiei) since 1975 with a documented history and continued prevalence of Mycobacterium avium complex (MAC) infections. No evidence of immunosuppressive retrovirus infections or loss of heterozygosity that may have led to an immune dysfunction in these animals was found. Isolates of MAC organisms from affected tree kangaroos and from their environment had no common restriction fragment DNA types. Cellular immune reactivity in apparently healthy tree kangaroos was 3- to 6-fold lower than in humans and other marsupial and eutherian mammals, as determined by lymphocyte proliferative assays. Thus, while MAC infections are typically opportunistic in humans and other mammals, tree kangaroos commonly develop primary progressive disease with MAC from random sources. Comparative information derived from this study should benefit both the endangered tree kangaroo and humans with immunosuppressive disorders that lead to mycobacterial infections.

Animals↗
PubMed2003

Protection of tree shrews by pVAX-PS DNA vaccine against HBV infection.

The immunological protection of pVAX-PS, a DNA vaccine, was assessed in the tree shrews model. pVAX-PS was constructed by inserting the gene encoding the middle (pre-S2 plus S) envelope protein of HBV into a plasmid vector pVAX1. Tree shrews (Tupaia belangeri chinenesis) were experimentally infected with human HBV by inoculation with human serum positive for HBV markers. DNA vaccination-induced seroconversion and antibody to HBV surface antigen (anti-HBs) were analyzed by ELISA, and protective effects elicited by pVAX-PS vaccination against subsequent HBV challenge were evaluated by detection of HBV seromarkers and observation of hepatic lesions in HBV-infected tree shrews. The results shown that anti-HBs were detectable in serum at week 2 after pVAX-PS vaccination and peaked at week 4, and immunization with pVAX-PS decreased the positive conversion rate of HBV seromarkers and relieved hepatic lesions in tree shrews challenged with HBV. These results indicated that pVAX-PS immunization could induce remarkable humoral immune response and prevent the experimental tree shrews from infection of HBV.

Animals↗
PubMed2002

Fast recovery of evolutionary trees with thousands of nodes.

We present a novel distance-based algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n(2)) time using O(n) working space. In the general Markov model of evolution, the algorithm recovers the topology successfully with (1 - o(1)) probability from sequences with polynomial length in n. Moreover, for almost all trees, our algorithm achieves the same success probability on polylogarithmic sample sizes. The theoretical results are supported by simulation experiments involving trees with 500, 1,895, and 3,135 leaves. The topologies of the trees are recovered with high success from 2,000 bp DNA sequences.

Algorithms↗
PubMedDate not supplied

Disk-covering, a fast-converging method for phylogenetic tree reconstruction.

The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.

Algorithms↗
PubMed1994

The effects of sequence length, tree topology, and number of taxa on the performance of phylogenetic methods.

Simulations were used to study the performance of several character-based and distance-based phylogenetic methods in obtaining the correct tree from pseudo-randomly generated input data. The study included all the topologies of unrooted binary trees with from 4 to 10 pendant vertices (taxa) inclusive. The length of the character sequences used ranged from 10 to 10(5) characters exponentially. The methods studied include Closest Tree, Compatibility, Li's method, Maximum Parsimony, Neighbor-joining, Neighborliness, and UPGMA. We also provide a modification to Li's method (SimpLi) which is consistent with additive data. We give estimations of the sequence lengths required for given confidence in the output of these methods under the assumptions of molecular evolution used in this study. A notation for characterizing all tree topologies is described. We show that when the number of taxa, the maximum path length, and the minimum edge length are held constant, there it little but significant dependence of the performance of the methods on the tree topology. We show that those methods that are consistent with the model used perform similarly, whereas the inconsistent methods, UPGMA and Li's method, perform very poorly.

Base Sequence↗
PubMed1996

Hunting for trees in binary character sets: efficient algorithms for extraction, enumeration, and optimization.

We describe a useful and efficient tree building technique that is closely related to the maximum compatible subset method. Given a set of binary characters C and a degree bound d, the algorithm we describe counts the number of trees T that satisfy (1) the edges of T correspond to characters contained in C, and (2) the vertices of T have degree bounded by d. If the characters are weighted then we can efficiently determine which of these trees have maximum summed edge weight, where the weight of an edge equals the weight of the corresponding binary character in C. The complexity of the algorithms equals O(nk + ndK(d-1), where n is the number of taxa, k is the number of characters, and K is the number of distinct characters. A number of new tree consensus methods based on the algorithm are introduced, including one that uses edge weighted trees. As well, we illustrate the applicability of the algorithm for large sequence data sets by analyzing sequences from the "Out of Africa" mtDNA data set.

Algorithms↗
PubMed1997

Towards integration of multiple alignment and phylogenetic tree construction.

A central problem in the study of molecular evolution is the reconstruction of the history of a set of biological sequences in the form of a phylogenetic tree. One step in calculating this tree is the computation of a multiple alignment. Most existing approaches treat the two problems of multiple alignment and tree construction as separate while in fact they influence each other. Based on three-way alignments of pre-aligned groups of sequences we adapt a commonly used tree construction procedure to produce both tree and multiple alignment simultaneously. In contrast to existing iterative algorithms the new method can change alignments made early in the course of the computation at a later stage. A sufficient criterion to prevent the introduction of edges with negative length reduces the number of three-way alignments that need to be computed. Applications of the new approach to the alignment of protein and of nucleic acid sequences are presented.

Amino Acid Sequence↗
PubMed2005

Survival trees for analyzing clinical outcome in lung adenocarcinomas based on gene expression profiles: identification of neogenin and diacylglycerol kinase alpha expression as critical factors.

We present survival trees as an exploratory tool for revealing new insights into gene expression profiles in combination with clinical patient data. Survival trees partition the patient data studied into groups with similar survival outcomes and identify characteristic genetic profiles within these groups. We demonstrate the application of survival trees in a study involving the expression profiles of 3,588 genes in 211 lung adenocarcinoma patients. The survival tree identified a group of early-stage cancer patients with relatively low survival rates and another group of advanced-stage patients with remarkably good survival outcome. For both groups, the tree identified characteristic expression profiles of genes that might play a role in cancerogenesis and disease progression, notably the genes for the netrin receptor neogenin and the Ras/Rho kinase modulator diacylglycerol kinase alpha.

Adenocarcinoma↗