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PubMed2005

Selection of orthogonal reversed-phase HPLC systems by univariate and auto-associative multivariate regression trees.

In order to select chromatographic starting conditions to be optimized during further method development of the separation of a given mixture, so-called generic orthogonal chromatographic systems could be explored in parallel. In this paper the use of univariate and multivariate regression trees (MRT) was studied to define the most orthogonal subset from a given set of chromatographic systems. Two data sets were considered, which contain the retention data of 68 structurally diversive drugs on sets of 32 and 38 chromatographic systems, respectively. For both the univariate and multivariate approaches no other data but the measured retention factors are needed to build the decision trees. Since multivariate regression trees are used in an unsupervised way, they are called auto-associative multivariate regression trees (AAMRT). For all decision trees used, a variable importance list of the predictor variables can be derived. It was concluded that based on these ranked lists, both for univariate and multivariate regression trees, a selection of the most orthogonal systems from a given set of systems can be obtained in a user-friendly and fast way.

Chromatography, High Pressure Liquid↗

PubMed2005

Reconstruction of large phylogenetic trees: a parallel approach.

Reconstruction of phylogenetic trees for very large datasets is a known example of a computationally hard problem. In this paper, we present a parallel computing model for the widely used Multiple Instruction Multiple Data (MIMD) architecture. Following the idea of divide-and-conquer, our model adapts the recursive-DCM3 decomposition method [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] to divide datasets into smaller subproblems. It distributes computation load over multiple processors so that each processor constructs subtrees on each subproblem within a batch in parallel. It finally collects the resulting trees and merges them into a supertree. The proposed model is flexible as far as methods for dividing and merging datasets are concerned. We show that our method greatly reduces the computational time of the sequential version of the program. As a case study, our parallel approach only takes 22.1h on four processors to outperform the best score to date (Found at 123.7h by the Rec-I-DCM3 program [Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T, 2004a. Performance of suptertree methods on various dataset decompositions. In: Binida-Emonds, O.R.P. (Eds.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, vol. 3 of Computational Biology, Kluwer Academics, pp. 301-328; Roshan, U., Moret, B.M.E., Williams, T.L., Warnow, T., 2004b. Rec-I-DCM3: A Fast Algorithmic Technique for reconstructing large phylogenetic trees, Proceedings of the IEEE Computational Systems Bioinformatics Conference (ICSB)] on one dataset. Developed with the standard message-passing library, MPI, the program can be recompiled and run on any MIMD systems.

Journal Article↗

PubMed2005

Tree age dependence and within-canopy variation of leaf gas exchange and antioxidative defence in Fagus sylvatica under experimental free-air ozone exposure.

We characterized leaf gas exchange and antioxidative defence of two-year-old seedlings and 60-year-old trees of Fagus sylvatica exposed to ambient (1 x O3) or two-fold ambient (2 x O3) O3 concentrations (maximum of 150 ppb) in a free-air canopy exposure system throughout the growing season. Decline in photosynthesis from sun-exposed to shaded conditions was more pronounced in adult than juvenile trees. Seedling leaves and leaves in the sun-exposed canopy had higher stomatal conductance and higher internal CO2 concentrations relative to leaves of adult trees and leaves in shaded conditions. There was a weak overall depression of photosynthesis in the 2 x O3 variants across age classes and canopy positions. Pigment and tocopherol concentrations of leaves were significantly affected by canopy position and tree age, whereas differences between 1 x O3 and 2 x O3 regimes were not observed. Glutathione concentrations were significantly increased under 2 x O3 across both age classes and canopy levels. Seedlings differed from adult trees in relevant physiological and biochemical traits in ozone response. The water-soluble antioxidative systems responded most sensitively to 2 x O3 without regard of tree age or canopy position.

Acclimatization↗

PubMed2006

Wall shear stress in normal left coronary artery tree.

Despite the fact that the role of wall shear stress (WSS) as a local mechanical factor in atherogenesis is well established, its distribution over the entire normal human left coronary artery (LCA) tree has not yet been studied. A three-dimensional computer generated model of the epicardial LCA tree, based on averaged human data set extracted from angiographies, was adopted for finite-element analysis of the Navier-Stokes flow equations treating blood as non-Newtonian fluid. The LCA tree includes the left main coronary artery (LMCA), the left anterior descending (LAD), the left circumflex artery (LCxA) and their major branches. In proximal LCA tree regions where atherosclerosis frequently occurs, low WSS appears. Low WSS regions occur at bifurcations in regions opposite the flow dividers, which are anatomic sites predisposed for atherosclerotic development. On the LMCA bifurcation, at regions opposite to the flow divider, dominant low WSS values occur ranging from 0.75 to 2.25 N/m2. High WSS values are encountered at all flow dividers. This work determines, probably for the first time, the topography of the WSS in the entire normal human LCA epicardial tree. It is also the first work determining the spatial WSS differentiation between proximal and distal normal human LCA parts. The haemodynamic analysis of the entire epicardial LCA tree further verifies the implications of the WSS in atherosclerosis mechanisms.

Angiography↗

PubMed2006

Spatial embedding of neuronal trees modeled by diffusive growth.

The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees based on diffusion-limited aggregation process. The model reproduces diverse neuronal shapes (i.e., granule cells, Purkinje cells, the basal and apical dendrites of pyramidal cells, and the axonal trees of interneurons) by changing only the size of the growth area, the time span of pruning, and the spatial concentration of 'neurotrophic particles'. Moreover, the presented model shows how competition between neurons can affect the shape of the dendritic trees. The model reveals that the creation of complex (but reproducible) dendrite-like trees does not require precise guidance or an intrinsic plan of the dendrite geometry. Instead, basic environmental factors and the simple rules of diffusive growth adequately account for the spatial embedding of different types of dendrites observed in the cortex. An example demonstrating the broad applicability of the algorithm to model diverse types of tree structures is also presented.

Animals↗

PubMed2004

Effect of selection on the topology of genealogical trees.

Selection is one of the factors that most influence the shape of genealogical trees. Here we report results of simulations of the infinite-sites version of Moran's model of population genetics aiming at quantifying how the presence of selection affects the branching pattern (topology) of binary genealogical trees. In particular, we consider a scenario of purifying or negative selection in which all mutations are deleterious and each new mutation reduces the fitness of the individual by the same fraction. Analysis of five statistical measures of tree balance or symmetry borrowed from taxonomy indicates that the genealogical trees of samples of populations in which selection is actuating are in the average more asymmetric than neutral trees and that this effect is enhanced by increasing the sample size. However, a quantitative evaluation of the power of these balance measures to detect a tree topology significantly distinct from the neutral one indicates that they are not useful as tests of neutrality of mutations.

Animals↗

PubMed2005

Wall pressure gradient in normal left coronary artery tree.

The three-dimensional wall pressure gradient (WPG) of the normal human left coronary artery (LCA) tree is quantitatively analysed. A model LCA tree, based on averaged human data set extracted from angiographies was adopted for finite-element analysis. The LCA tree includes the left main coronary artery (LMCA), the left anterior descending (LAD), the left circumflex artery (LCxA) and their major branches. The WPG is calculated using 44,452 nodes throughout the tree extension. The governing flow equations were solved using a validated numerical code. WPG as well as wall shear stress gradient (WSSG) were calculated at all available bifurcation regions. In proximal LCA tree regions where atherosclerosis frequently occurs, low WPG appears. At distal segments, WPG increases substantially due to increased velocity resulted from increased vessel tapering. Low WPG occurs at bifurcations in regions opposite the apexes, which are anatomic sites predisposed for atherosclerotic development. Endothelial cells respond to the combined effects of locally low WPG and low WSSG and provide a mechanism promoting atherosclerosis. This computational work determines probably for the first time the topography of the WPG in the normal human LCA tree. Spatial WPG differentiation indicates that locally low values of this physical parameter probably correlate to atherosclerosis localization.

Animals↗

PubMed1999

Localization of dopamine receptors in the tree shrew brain using [3H]-SCH23390 and [125I]-epidepride.

The tree shrew is a mammalian species, which is phylogenetically related to insectivores and primates. The aim of the present study was to investigate the distribution of dopamine receptor D1- and D2-like binding sites in the brain of this non-rodent, non-primate mammal. Using in vitro autoradiography and employing the radioligands [3H]-SCH23390 and [125I]-epidepride, dopamine receptors were mapped and quantified. Significant findings with regard to the D1-like binding pattern include the presence of a "patchy" binding in the striatum. In the cortex, D1-like binding sites were observed in both the superficial and the deep layers. In the hippocampal formation, D1-like binding sites were seen primarily in the CAI region and not in the dentate gyrus. These characteristics of the D1 pattern in the tree shrew brain are shared by cat and monkey and human brain, but not by rodent brain. Significant findings with regard to the D2-like binding pattern include the presence of D2-like binding in the claustrum. In addition, the striatum demonstrated "patchy" D2-like binding. These characteristics of the D2 pattern in the tree shrew brain are shared by cat and monkey and human brain, but not by rodent brain. On the other hand, the significant densities of D2-like binding sites in the glomerular layer of the tree shrew olfactory bulb is a finding that discriminates tree shrews from higher evolutionary species who lack such binding. Overall, the evidence coincides with the view that tree shrews are phylogenetically related to primates.

Animals↗

PubMed1996

Full reconstruction of Markov models on evolutionary trees: identifiability and consistency.

A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a specification of probability transition matrices on the edges of the tree. Previous work has shown that, under mild conditions, the tree topology may be reconstructed, in the sense that the topology is identifiable from knowledge of the joint distribution of character states at pairs of terminal nodes of the tree. Also, the method of maximum likelihood is statistically consistent for inferring the tree topology. In this article we answer the analogous questions for reconstructing the full model, including the edge transition matrices. Under mild conditions, such full reconstruction is achievable, not by using pairs of terminal nodes, but rather by using triples of terminal nodes. The identifiability result generalizes previous results that were restricted either to characters having two states or to transition matrices having special structure. The proof develops matrix relationships that may be exploited to identify the model. We also use the identifiability result to prove that the method of maximum likelihood is consistent for reconstructing the full model.

Animals↗

PubMed2001

A phylogenetic comparison of gene trees constructed from plastid, mitochondrial and genomic DNA of Plasmodium species.

Gene trees of Plasmodium species have been reported for the nuclear encoded genes (e.g. the Small Subunit rRNA) and a mitochondrial encoded gene, cytochrome b. Here, we have analyzed a plastid gene coding for caseinolytic protease ClpC, whose structure, function and evolutionary history have been studied in various organisms. This protein possesses a 220-250 amino acid long AAA domain (ATPases associated with a variety of cellular activities) that belongs to the Walker super family of ATPases and GTPases. We have sequenced the AAA motif of this gene, encoding the protein from nine different species of Plasmodium infecting rodents, birds, monkeys, and humans. The codon usage and GC content of each gene were nearly identical in contrast to the widely varying nucleotide composition of genomic DNAs. Phylogenetic trees derived from both DNA and inferred protein sequences have consistent topologies. We have used the ClpC sequence to analyze the phylogenetic relationship among Plasmodium species and compared it with those derived from mitochondrial and genomic sequences. The results corroborate well with the trees constructed using the mitochondrially encoded cytochrome b. However, an important element distinguishes the trees: the placement of Plasmodium elongatum near the base of the plastid tree, indicating an ancient lineage of parasites in birds that branches from the tree prior to other lineages of avian malaria and the human parasite, P. falciparum.

Adenosine Triphosphatases↗

PubMed2003

Comparative study of HP-27 gene promoter activities between the chipmunk and tree squirrel.

The chipmunk hibernation-specific protein HP-27 is a component of the 140-kDa complex that decreases in the blood during hibernation. Although the HP-27 gene is detected in both the chipmunk, a hibernating species of the squirrel family, and the tree squirrel, a nonhibernating species, it is expressed only in the chipmunk, in a liver-specific manner. To understand the difference in HP-27 gene expression between the chipmunk and tree squirrel, we isolated chipmunk and tree squirrel HP-27 genomic clones, and compared their promoter activities. Transient transfection studies in HepG2 cells revealed that the 170 bp 5'-flanking sequence of the chipmunk HP-27 gene was sufficient for liver-specific promoter activity and that deletion of the sequence from -170 to -140 reduced the promoter activity by 90%. Although the corresponding 170 bp 5'-flanking sequence of the tree squirrel HP-27 gene had 89% nucleotide sequence homology to that of the chipmunk, it showed almost no promoter activity in HepG2 cells. In a gel retardation assay using HepG2 or chipmunk liver nuclear extracts, the 5'-flanking sequence of the chipmunk HP-27 gene from -170 to -140 showed a shifted band, but the corresponding tree squirrel sequence did not. Taken together, these data indicate that a transcription factor that binds to this 5'-flanking sequence of the chipmunk HP-27 gene plays an important role in HP-27 gene expression, and the failure of this factor to bind in the case of the tree squirrel HP-27 gene could be responsible for this animal's lack of HP-27 gene expression.

5' Flanking Region↗

PubMed2001

The use of classification and regression trees in clinical epidemiology.

A critique is presented of the use of tree-based partitioning algorithms to formulate classification rules and identify subgroups from clinical and epidemiological data. It is argued that the methods have a number of limitations, despite their popularity and apparent closeness to clinical reasoning processes. The issue of redundancy in tree-derived decision rules is discussed. Simple rules may be unlikely to be "discovered" by tree growing. Subgroups identified by trees are often hard to interpret or believe and net effects are not assessed. These problems arise fundamentally because trees are hierarchical. Newer refinements of tree technology seem unlikely to be useful, wedded as they are to hierarchical structures.

Algorithms↗

PubMed2006

Consumption and portion sizes of tree nuts, peanuts and seeds in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohorts from 10 European countries.

Tree nuts, peanuts and seeds are nutrient dense foods whose intake has been shown to be associated with reduced risk of some chronic diseases. They are regularly consumed in European diets either as whole, in spreads or from hidden sources (e.g. commercial products). However, little is known about their intake profiles or differences in consumption between European countries or geographic regions. The objective of this study was to analyse the population mean intake and average portion sizes in subjects reporting intake of nuts and seeds consumed as whole, derived from hidden sources or from spreads. Data was obtained from standardised 24-hour dietary recalls collected from 36 994 subjects in 10 different countries that are part of the European Prospective Investigation into Cancer and Nutrition (EPIC). Overall, for nuts and seeds consumed as whole, the percentage of subjects reporting intake on the day of the recall was: tree nuts = 4. 4%, peanuts = 2.3 % and seeds = 1.3 %. The data show a clear northern (Sweden: mean intake = 0.15 g/d, average portion size = 15.1 g/d) to southern (Spain: mean intake = 2.99 g/d, average portion size = 34.7 g/d) European gradient of whole tree nut intake. The three most popular tree nuts were walnuts, almonds and hazelnuts, respectively. In general, tree nuts were more widely consumed than peanuts or seeds. In subjects reporting intake, men consumed a significantly higher average portion size of tree nuts (28.5 v. 23.1 g/d, P<0.01) and peanuts (46.1 v. 35.1 g/d, P<0.01) per day than women. These data may be useful in devising research initiatives and health policy strategies based on the intake of this food group.

Arachis↗

PubMed2001

Agrammatism and the psychological reality of the syntactic tree.

Syntactic trees, or phrase markers, have originally been suggested as a representation of syntax in the mind based on purely linguistic grounds. In this paper, the psychological reality of syntactic trees and hierarchical ordering is explored from another perspective--that of the neuropsychology of language breakdown. The study reported here examined several syntactic domains that rely on different nodes in the tree--tense and agreement verb inflection, subordinations, interrogatives, and verb movement, through a study of 14 Hebrew- and Palestinian Arabic-speaking agrammatic aphasics and perusal of the cross-linguistic literature. The results show that the impairment in agrammatic production is highly selective and lends itself to characterization in terms of a deficit in the syntactic tree. The complex pattern of dissociations follows from one underlying deficit--the inaccessibility of high nodes of the syntactic tree to agrammatic speakers. Structures that relate to high nodes of the tree are impaired, while "lower" structures are spared.

Aphasia, Broca↗

PubMed2002

Does size really matter--using a decision tree approach for comparison of three different databases from the medical field of acute appendicitis.

Decision trees have been successfully used for years in many medical decision making applications. Transparent representation of acquired knowledge and fast algorithms made decision trees one of the most often used symbolic machine learning approaches. This paper concentrates on the problem of separating acute appendicitis, which is a special problem of acute abdominal pain, from other diseases that cause acute abdominal pain by use of an decision tree approach. Early and accurate diagnosing of acute appendicitis is still a difficult and challenging problem in everyday clinical routine. An important factor in the error rate is poor discrimination between acute appendicitis and other diseases that cause acute abdominal pain. This error rate is still high, despite considerable improvements in history-taking and clinical examination, computer-aided decision-support, and special investigation such as ultrasound. We investigated three databases of different size with cases of acute abdominal pain to complete this task as successful as possible. The results show that the size of the database does not necessary directly influence the success of the decision tree built on it. Surprisingly we got the best results from the decision trees built on the smallest and the biggest database, where the database with medium size (relative to the other two) was not so successful. Despite this we were able to produce decision tree classifiers that were capable of producing correct decisions on test data sets with accuracy up to 84%, sensitivity to acute appendicitis up to 90%, and specificity up to 80% on the same test set.

Acute Disease↗

PubMed2004

The effects of seed quality and pipecolic and djenkolic acids on bruchid beetle infestation in water deficit-stressed Acacia trees.

Acacia trees in the Negev desert and the Arava valley of Israel are suffering high levels of mortality due to water stress. Additionally, recruitment is negatively affected by bruchid beetles. We hypothesized that water-stressed trees would be less able to produce secondary defense compounds, such as the nonprotein amino acids, pipecolic acid and djenkolic acid, in their seeds to decrease seed herbivory. We further hypothesized that the high seed infestation reported is due to increased fitness of beetles infesting trees that are in a poor physiological state. Contrary to our prediction, pipecolic acid concentration was higher in water-stressed Acacia raddiana trees. We found that infestation rates and beetle fitness were higher in trees in a poor physiological state, despite the higher levels of pipecolic acid in these trees. There was a significant positive correlation between infestation level and the amounts of djenkolic acid in the seeds, indicating that the beetles may have found a means of utilizing djenkolic acid for their own benefit.

Acacia↗

PubMed2003

The tree shrews: adjuncts and alternatives to primates as models for biomedical research.

The tree shrews are non-rodent, primate-like, small animals. There is increasing interest in using them to establish animal models for medical and biological research. This review focuses on the use of the tree shrews in in vivo studies on viral hepatitis, hepatocellular carcinoma (HCC), myopia, and psychosocial stress. Because of the susceptibility of the tree shrews (Tupaia belangeri) and their hepatocytes to infection with human hepatitis B virus (HBV) in vivo and in vitro, these animals have been used to establish human hepatitis virus-induced hepatitis and human HBV- and aflatoxin B1-associated HCC models. As these animals are phylogenetically close to primates in evolution and have a well-developed visual system and color vision in some species, they have been utilized to establish myopia models. Because dramatic behavioral, physiological, and neuroendocrine changes in subordinate male tree shrews are similar to those observed in depressed human patients, the tree shrews have been successfully employed to experimentally study psychosocial stress. However, the tree shrews holds significant promise as research models and great use could be made of these animals in biomedical research.

Animals↗

PubMed2004

An optimal bronchial tree may be dangerous.

The geometry and dimensions of branched structures such as blood vessels or airways are important factors in determining the efficiency of physiological processes. It has been shown that fractal trees can be space filling and can ensure minimal dissipation. The bronchial tree of most mammalian lungs is a good example of an efficient distribution system with an approximate fractal structure. Here we present a study of the compatibility between physical optimization and physiological robustness in the design of the human bronchial tree. We show that this physical optimization is critical in the sense that small variations in the geometry can induce very large variations in the net air flux. Maximum physical efficiency therefore cannot be a sufficient criterion for the physiological design of bronchial trees. Rather, the design of bronchial trees must be provided with a safety factor and the capacity for regulating airway calibre. Paradoxically, our results suggest that bronchial malfunction related to asthma is a necessary consequence of the optimized efficiency of the tree structure.

Asthma↗