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PubMed2007

Crop load affects maximum daily trunk shrinkage of plum trees.

We studied the effects of low fruit load (3-4 fruits cm(-2) of trunk cross-sectional area (TCSA), and high fruit load (6-7 fruits cm(-2) TCSA) on maximum daily trunk shrinkage (MDS) and trunk growth rates (TGR) over two seasons in plum (Prunus salicina Lindell) trees receiving full irrigation or deficit irrigation. Seasonal changes in MDS and TGR were compared with those in midday stem water potential (Psi(s)) and leaf stomatal conductance (g (s)). Crop load increased g (s) in fully irrigated trees approaching harvest. Although crop load did not affect plant water status in either watering regime, there were considerable differences in both MDS and TGR as a function of crop load. Compared with low-cropping [corrected] trees, MDS was 34% higher and TGR was 48% lower in high-cropping [corrected] trees. The differential responses of MDS and Psi(s) to crop load were a consequence of a higher MDS for a given Psi(s) in the high-cropping trees compared with the low-cropping trees. There was a linear increase in MDS with crop load, with a slope of 15.2 microm MPa(-1) per unit increment of crop load. In the fully irrigated trees, day-to-day variations in MDS were related to evaporative demand; however, the slope of the relationship between MDS and evaporative demand increased with crop load, indicating that different reference equations must be used to adjust for tree crop load when using MDS to determine plant water status and irrigation requirements.

Fruit↗

PubMed2005

A tree-decomposition approach to protein structure prediction.

This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction and protein side-chain prediction. To develop a unified tree-decomposition based approach to these two subproblems, we model them as a geometric neighborhood graph labeling problem. Theoretically, we can have a low-degree polynomial time algorithm to decompose a geometric neighborhood graph G = (V, E) into components with size O(|V|((2/3))log|V|). The computational complexity of the tree-decomposition based graph labeling algorithms is O(|V|Delta(tw+1)) where Delta is the average number of possible labels for each vertex and tw( = O(|V|((2/3))log|V|)) the tree width of G. Empirically, tw is very small and the tree-decomposition method can solve these two problems very efficiently. This paper also compares the computational efficiency of the tree-decomposition approach with the linear programming approach to these two problems and identifies the condition under which the tree-decomposition approach is more efficient than the linear programming approach. Experimental result indicates that the tree-decomposition approach is more efficient most of the time.

Algorithms↗

PubMedDate not supplied

Topological rearrangements and local search method for tandem duplication trees.

The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch . Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. In this paper, we deal with the topological rearrangement of these trees. Classical rearrangements used in phylogeny (NNI, SPR, TBR, ...) cannot be applied directly on duplication trees. We show that restricting the neighborhood defined by the SPR (Subtree Pruning and Regrafting) rearrangement to valid duplication trees, allows exploring the whole duplication tree space. We use these restricted rearrangements in a local search method which improves an initial tree via successive rearrangements. This method is applied to the optimization of parsimony and minimum evolution criteria. We show through simulations that this method improves all existing programs for both reconstructing the topology of the true tree and recovering its duplication events. We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our method than using any other program.

Algorithms↗

PubMedDate not supplied

Improved parameterized complexity of the maximum agreement subtree and maximum compatible tree problems.

Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively, maximum compatible tree problem (MCT), consists of finding a largest subset of taxa such that all input trees restricted to these taxa are isomorphic, respectively compatible. These problems have several applications in phylogenetics such as the computation of a consensus of phylogenies obtained from different data sets, the identification of species subjected to horizontal gene transfers and, more recently, the inference of supertrees, e.g., Trees Of Life. We provide two linear time algorithms to check the isomorphism, respectively, compatibility, of a set of trees or otherwise identify a conflict between the trees with respect to the relative location of a small subset of taxa. Then, we use these algorithms as subroutines to solve MAST and MCT on rooted or unrooted trees of unbounded degree. More precisely, we give exact fixed-parameter tractable algorithms, whose running time is uniformly polynomial when the number of taxa on which the trees disagree is bounded. The improves on a known result for MAST and proves fixed-parameter tractability for MCT.

Algorithms↗

PubMed2004

Top-down induction of model trees with regression and splitting nodes.

Model trees are an extension of regression trees that associate leaves with multiple regression models. In this paper, a method for the data-driven construction of model trees is presented, namely, the Stepwise Model Tree Induction (SMOTI) method. Its main characteristic is the induction of trees with two types of nodes: regression nodes, which perform only straight-line regression, and splitting nodes, which partition the feature space. The multiple linear model associated with each leaf is then built stepwise by combining straight-line regressions reported along the path from the root to the leaf. In this way, internal regression nodes contribute to the definition of multiple models and have a "global" effect, while straight-line regressions at leaves have only "local" effects. Experimental results on artificially generated data sets show that SMOTI outperforms two model tree induction systems, M5' and RETIS, in accuracy. Results on benchmark data sets used for studies on both regression and model trees show that SMOTI performs better than RETIS in accuracy, while it is not possible to draw statistically significant conclusions on the comparison with M5'. Model trees induced by SMOTI are generally simple and easily interpretable and their analysis often reveals interesting patterns.

Algorithms↗

PubMed2004

Cry j 1 isoforms derived from Cryptomeria japonica trees have different binding properties to monoclonal antibodies.

BACKGROUND: We identified five Cryptomeria japonica trees producing Cry j 1 isoforms that cannot be detected in a sandwich ELISA using two monoclonal antibodies, J1B01 and J1B07, suggesting that the binding affinity of these isoforms for both monoclonal antibodies is low. OBJECTIVES: The binding properties of the Cry j 1 isoforms produced by five trees to J1B07 and J1B01 were examined. The complementary DNA (cDNA) sequences of the Cry j 1 isoforms were also determined. METHODS: To clarify the binding properties of these Cry j 1 isoforms to J1B01 and J1B07, Cry j 1 was quantified in pollen samples collected from each of the five trees, by sandwich ELISAs using polyclonal antibodies and either J1B01 or J1B07. The cDNA sequences of isoforms with different binding properties were determined. To test the assumption that amino acid substitutions affect the binding affinities of Cry j 1 isoforms for monoclonal antibodies, cleaved amplified polymorphic sequences (CAPS) markers representing the putative polymorphisms were used to analyse additional trees. RESULTS: Four of the five trees produced Cry j 1 isoforms with extremely low binding affinity for J1B07, whereas the other tree produced two different isoforms with low binding affinity for either J1B01 or J1B07. Cry j 1-encoding cDNA sequences for one of the four trees and for the exceptional fifth tree indicate that amino acid substitutions at positions 55 and 352 in mature Cry j 1 affect its binding to J1B01 and J1B07, respectively. This was supported by the results of CAPS analysis. CONCLUSION: The existence of Cry j 1 isoforms with low binding affinity for either J1B01 or J1B07 was established. Furthermore, a single amino acid substitution is involved in this difference in binding affinity for each monoclonal antibody.

Allergens↗

PubMed1984

Contribution of tree structures in the lung to lung elastic recoil.

The direct contribution of forces in tree structures in the lung to lung recoil pressure and changes in recoil pressure induced by alterations of the forces are analyzed. The analysis distinguishes the contributions of axial and circumferential tensions in the trees and indicates that only axial tensions directly contribute to static recoil. This contribution is derived from analysis of the axial forces transmitted across a random plane transecting the lung. The change in recoil pressure induced by changes in axial tension is similarly derived. Alterations of circumferential tensions in the trees indirectly change recoil by causing nonuniform deformations of the surrounding lung parenchyma, and a continuum elasticity solution for the stress induced by the deformations is derived. Sample calculations are presented for the airway tree based on available data on airway morphometric and mechanical properties. The increase in recoil pressure accompanying increases in axial and circumferential tensions with contraction of airway smooth muscle is also analyzed. The calculations indicate that axial stresses in the airway tree out to bronchioles directly contribute only a small fraction of the static recoil pressure. However, it is found that contraction of smooth muscle in these airways can increase recoil pressure appreciably (10-20%), mainly by the deformation of the parenchyma with increases in circumferential tension in smaller airways. The results indicate that the geometric and mechanical properties of the airway tree are such that only peripheral elements of the tree can substantially affect the elastic properties of the lung. The possible contributions of vascular trees for which data on mechanical and morphometric properties are more limited are also discussed.

Lung↗

PubMed1983

Phylogeny through brain traits: trees generated by neural characters.

Phylogenetic trees were computed by the Wagner algorithm from data on up to 15 brain characters scored on 154 specimens of 134 mammalian species. Because the data were not complete on all specimens, only one tree, of 18 taxa, was generated on all 15 features; a tree of 99 species was computed from 10 characters, and trees of 38 species from 10 and 12. The 38-taxon trees were considered best because they preserved most completely the integrity of mammalian orders. All trees consistently separated the subclasses of mammals and suggested that rodents, insectivores, and the tree shrew were most derived on the basis of brain characters. The trees' shapes are sensitive to small alterations in character scorings, largely because of the relatively few characters available and small differences in the number of states among them.

Animals↗

PubMed2004

Pressure-induced changes in axial eye length of chick and tree shrew: significance of myofibroblasts in the sclera.

PURPOSE: To investigate the change in axial eye dimensions resulting from stretching the sclera by acute elevation of intraocular pressure (IOP). METHODS: IOP was increased to 100 mm Hg for 1 hour through an intravitreal cannula, while ocular component dimensions were monitored every 10 minutes with A-scan ultrasound in anesthetized animals (10 chicks and 10 tree shrews). In addition, immunocytochemical detection of alpha-smooth muscle actin (alpha-SMA) using a monoclonal antibody was conducted in the sclera of the tree shrew and the chick. RESULTS: In both species, axial eye length immediately and significantly (P < 0.0001) increased on elevation of IOP to 100 mm Hg: chick to 103.9%, tree shrew to 101.2% (mean percentage of original measured at 15 mm Hg). After 1 hour of maintained pressure, chick eyes showed a further significant increase in axial length (to 108.6%), but axial length of tree shrew eyes decreased (to 100.3%) to the point that it was not significantly different from the original value at 15 mm Hg. Immunocytochemical studies of age-matched tissue demonstrated the presence of alpha-SMA-containing fibroblasts (myofibroblasts) within tree shrew but not chick sclera. CONCLUSIONS: Elevation of IOP caused axial elongation of chick eyes, but a consistent reduction in axial length of tree shrew eyes. The presence of myofibroblasts, demonstrated in tree shrew but not chick sclera, suggests that the reduction in axial length of tree shrew eyes may have been caused by activation of a contractile mechanism involving scleral myofibroblasts. Such a mechanism may play a role in the regulation of eye size and refractive development.

Actins↗

PubMedDate not supplied

Stochastic trees: a new technique for temporal medical decision modeling.

This paper introduces stochastic trees, a new modeling approach for the class of medical decision problems in which risks of mortality and morbidity may extend over time. A stochastic tree may be regarded as a continuous-time version of a Markov-cycle tree, or alternately, as a multi-state DEALE model. Optimal decisions in stochastic trees can be determined by rollback, much in the same fashion as decision trees. The author discusses how age-dependent mortality rates and declining incidence rates may be modeled using stochastic trees. Concepts are illustrated using examples from the medical literature. It is argued that stochastic trees possess important advantages over Markov-cycle trees for medical decision modeling.

Age Factors↗

PubMed2004

Selection of informative clusters from hierarchical cluster tree with gene classes.

BACKGROUND: A common clustering method in the analysis of gene expression data has been hierarchical clustering. Usually the analysis involves selection of clusters by cutting the tree at a suitable level and/or analysis of a sorted gene list that is obtained with the tree. Cutting of the hierarchical tree requires the selection of a suitable level and it results in the loss of information on the other level. Sorted gene lists depend on the sorting method of the joined clusters. Author proposes that the clusters should be selected using the gene classifications. RESULTS: This article presents a simple method for searching for clusters with the strongest enrichment of gene classes from a cluster tree. The clusters found are presented in the estimated order of importance. The method is demonstrated with a yeast gene expression data set and with two database classifications. The obtained clusters demonstrated a very strong enrichment of functional classes. The obtained clusters are also able to present similar gene groups to those that were observed from the data set in the original analysis and also many gene groups that were not reported in the original analysis. Visualization of the results on top of a cluster tree shows that the method finds informative clusters from several levels of the cluster tree and indicates that the clusters found could not have been obtained by simply cutting the cluster tree. Results were also used in the comparison of cluster trees from different clustering methods. CONCLUSION: The presented method should facilitate the exploratory analysis of big data sets when the associated categorical data is available.

Cluster Analysis↗

PubMed2005

Genome trees from conservation profiles.

The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component "presence-absence" protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings.

Animals↗

PubMedDate not supplied

[Spatial distribution of Triatominae populations (Hemiptera: Reduviidae) in Mauritia flexuosa palm trees in Federal District of Brazil].

To determine and analyze the distribution of Triatominae sylvatic populations in the Federal District of Brazil, 150 Mauritia flexuosa palm trees were sampled in six veredas of different landscapes (sylvatic, rural and peri-urban) in the rainy season. Triatomines were morphologically identified and grouped by sex and nymphal stage and were examined to verify infection by Trypanosoma cruzi and Trypanosoma rangeli. Twenty eight (18.6%) palm trees were infested by Rhodnius neglectus and fourteen (9.5%) by Psammolestes tertius. The frequency of Triatominae in palm trees with and without nests was significantly different being higher in palm trees with bird and mammal nests in the crown. The higher average number of insects/palm tree was observed in rural areas with estimates of up to 838 insects/hectare. The species age makeup presented a different pattern, with nymphs predominant for Rhodnius neglectus and adults predominant for Psammolestes tertius. Also, many Rhodnius neglectus eggs were collected, which indicates a reproductive event in February 2003. Among the nests found in palm trees, that of the Phacellodomus ruber (Furnariidae) bird had the greatest abundance of Triatominae, occurring on 42% of palm trees. The relative abundance of Rhodnius neglectus and Psammolestes tertius was greater in rural areas which contained higher number of nests in palm trees and lesser density of palms per hectare. None of the 96 triatomines examined were infected by Trypanosoma cruzi or Trypanosoma rangeli, despite our finding of Rhodnius neglectus infection by those parasites in former studies.

Animals↗

PubMed2002

Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.

Evolutionary trees sit at the core of all realistic models describing a set of related sequences, including alignment, homology search, ancestral protein reconstruction and 2D/3D structural change. It is important to assess the stochastic error when estimating a tree, including models using the most realistic likelihood-based optimizations, yet computation times may be many days or weeks. If so, the bootstrap is computationally prohibitive. Here we show that the extremely fast "resampling of estimated log likelihoods" or RELL method behaves well under more general circumstances than previously examined. RELL approximates the bootstrap (BP) proportions of trees better that some bootstrap methods that rely on fast heuristics to search the tree space. The BIC approximation of the Bayesian posterior probability (BPP) of trees is made more accurate by including an additional term related to the determinant of the information matrix (which may also be obtained as a product of gradient or score vectors). Such estimates are shown to be very close to MCMC chain values. Our analysis of mammalian mitochondrial amino acid sequences suggest that when model breakdown occurs, as it typically does for sequences separated by more than a few million years, the BPP values are far too peaked and the real fluctuations in the likelihood of the data are many times larger than expected. Accordingly, several ways to incorporate the bootstrap and other types of direct resampling with MCMC procedures are outlined. Genes evolve by a process which involves some sites following a tree close to, but not identical with, the species tree. It is seen that under such a likelihood model BP (bootstrap proportions) and BPP estimates may still be reasonable estimates of the species tree. Since many of the methods studied are very fast computationally, there is no reason to ignore stochastic error even with the slowest ML or likelihood based methods.

Algorithms↗

PubMed1992

Evidence of cross-reactivity between olive, ash, privet, and Russian olive tree pollen allergens.

In a clinical investigation, 103 Michigan residents with symptoms suggestive of allergic rhinitis or asthma were skin tested with olive (Olea europaea) pollen extract. Nineteen had positive reactions. Since the olive tree is not native to nor grown in Michigan, this study was undertaken to determine whether the skin test reactivity was the result of cross-reactivity among tree pollen allergens. ELISAs were developed to measure olive, ash (Fraxinus americana), privet (Ligustrum vulgare), and Russian olive (Elaeagnus angustifolia) specific IgE antibodies. Inhibition studies were performed to determine whether pollen extracts from each of these tree species could inhibit IgE antibody binding to olive extracts. Eleven of the 19 skin test-positive patients were olive-ELISA positive, eight either were ELISA-positive to ash, seven to privet and ten to Russian olive. There were significant correlations between the ELISA results to olive and each of the other three pollens. The inhibition studies demonstrated that all three of the tree pollens were capable of inhibiting the binding of IgE to olive extract in a dose-response fashion. IgE-immunoblot studies demonstrated several proteins common to olive, ash, and privet. Twelve of the olive skin test-positive patients were contacted and 75% were exposed to one or more of the studied trees in their yards. Five patients had traveled to areas where olive trees are grown. We conclude that there is a high degree of cross-reactivity among allergens from native Michigan trees and from olive trees. This cross-reactivity is the most likely reason for skin test reactivity to olive pollen extract in Michigan.

Allergens↗

PubMed2004

[The use of family trees and the notion of heredity: a case study of hereditary chorea].

This paper analyzes the development and use of visual tools known as "family trees" that allow medical practitioners to see hereditary family diseases. Family trees, consisting of family names and a tree diagram on personal traits, became popular among neurologists during the late 19th century. However, social scientists have devoted only scant attention to the historical and social processes through which, before the rediscovery of Mendelian laws, medical practitioners came to use family trees as scientific devices for nosographical classification of hereditary diseases, such as hereditary chorea (one of the initial terms used to describe Huntington's disease). The purpose of this paper is to trace the complex processes by which family histories, namely the descriptive nosography of family members and family trees became distinct during the late 19th century. This paper argues that family trees of hereditary chorea became and important clinical tool, with the establishment of teaching hospitals, although, in the case of hereditary chorea, family trees were used to support different interpretations of the notion of heredity. The use of family trees was made possible by three conditions including the centralization of medical care, the standardization of medical records, and the circulation of medical information among medical practitioners.

Chorea↗

PubMed2005

A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization.

The computationally challenging problem of reconstructing the phylogeny of a set of contemporary data, such as DNA sequences or morphological attributes, was treated by an extended version of the neighbor-joining (NJ) algorithm. The original NJ algorithm provides a single-tree topology, after a cascade of greedy pairing decisions that tries to simultaneously optimize the minimum evolution and the least squares criteria. Given that some sub-trees are more stable than others, and that the minimum evolution tree may not be achieved by the original NJ algorithm, we propose a multi-neighbor-joining (MNJ) algorithm capable of performing multiple pairing decisions at each level of the tree reconstruction, keeping various partial solutions along the recursive execution of the NJ algorithm. The main advantages of the new reconstruction procedure are: 1) as is the case for the original NJ algorithm, the MNJ algorithm is still a low-cost reconstruction method; 2) a further investigation of the alternative topologies may reveal stable and unstable sub-trees; 3) the chance of achieving the minimum evolution tree is greater; 4) tree topologies with very similar performances will be simultaneously presented at the output. When there are multiple unrooted tree topologies to be compared, a visualization tool is also proposed, using a radial layout to uniformly distribute the branches with the help of well-known metaheuristics used in computer science.

Algorithms↗

PubMed1996

The M1 muscarinic antagonist pirenzepine reduces myopia and eye enlargement in the tree shrew.

PURPOSE: To determine the efficacy of the M1-selective muscarinic antagonist, pirenzepine, in preventing experimentally induced myopia in a mammalian model, the tree shrew. METHODS: Tree shrews were monocularly deprived (MD) using translucent goggles or negative lenses for a period of 12 days. In two of the MD groups, tree shrews received daily subconjunctival administration of either pirenzepine (17.7 mumol; n = 9) or vehicle control (n = 6). Control groups (n = 6) were used to assess the effects of MD, injection regimen, and drug effects. RESULTS: In sham-injected and saline-injected MD tree shrews, 12 days of MD produced-13.2 D +/- 0.8 D and -14.1 D +/- 0.5 D of axial myopia, respectively. In pirenzepine-injected MD tree shrews, 12 days of MD induced an axial myopia of only -2.1 D +/- 1.4 D. The significant reduction in myopia in pirenzepine-injected MD tree shrews was caused by significantly less vitreous chamber elongation of the deprived eye (0.05 mm +/- 0.04 mm) relative to the contralateral control eye when compared to sham-injected and saline-injected MD tree shrews (0.24 mm +/- 0.02 mm and 0.29 mm +/- 0.01 mm). Mean equatorial enlargement and increased eye weight were prevented in pirenzepine-injected MD tree shrews (P < 0.01). Pirenzepine also was found to reduce myopia and ocular enlargement in lens defocus-induced myopia. Control experiments demonstrated that pirenzepine did not cause a significant reduction in amplitude of carbachol-induced accommodation. CONCLUSIONS: Findings demonstrate that chronic administration of the M1-selective muscarinic antagonist, pirenzepine, prevents experimentally induced myopia in this mammalian model by a nonaccommodative mechanism.

Accommodation, Ocular↗