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PubMed2006

Effect of tapping activity on the dynamics of radial growth of Hevea brasiliensis trees.

Rubber tree (Hevea brasiliensis Müll. Arg.) radial growth dynamics were monitored with displacement sensors, together with latex production, to investigate three aspects of the dual production of latex and wood: (1) the usefulness of fine-scale dendrometric measurements as a physiological tool to detect water shortage through radial growth; (2) the dynamic aspects, both at the seasonal and at the multi-year scale, of the competition between latex and wood production; and (3) the spatial distribution of radial growth rates around the tapping cut. Radial growth of untapped control trees started with the onset of the rainy season and lasted until the onset of the dry season, ceasing completely during the driest period. Displacement sensors provided a sensitive means of detecting water shortage, with a clear correlation between diameter variations and changes in water availability (both daily evapotranspiration and monthly rainfall) over the whole annual cycle. However, the correlation was significantly disturbed in tapped trees. After resumption of tapping, the radial growth rate dropped sharply within two weeks and the effect persisted throughout the whole season, so that the cumulative growth of tapped trees was about half that of untapped trees, with the cumulative growth deficit reaching 80% for the period from mid-June to November. This long-known negative impact of tapping on growth was much stronger in the second year of tapping than in the first, whereas latex production increased significantly between the first and second year of tapping. The increased latex production, which could not be ascribed to climatic conditions, shows that the establishment of an artificial latex sink is a progressive, long-term process likely involving many aspects of metabolism. As expected, ethylene significantly increased latex production in both years; however, ethylene had no effect on the growth rates of tapped trees. Radial growth was differentially affected at different locations around the tapping cut, with growth rates significantly lower in the tapped panel than in the untapped panel, and higher above the cut than below the cut. Thus, caution is needed when deriving whole stem wood production from girth measurements at one location on the stem, especially from girth measurements made close to the tapping cut. This also provides new evidence for the location of the latex regeneration area in the tapped panel, below the cut.

Agriculture↗

PubMed2007

Variability with xylem depth in sap flow in trunks and branches of mature olive trees.

Knowledge of sap flow variability in tree trunks is important for up-scaling transpiration from the measuring point to the whole-tree and stand levels. Natural variability in sap flow, both radial and circumferential, was studied in the trunks and branches of mature olive trees (Olea europea L., cv Coratina) by the heat field deformation method using multi-point sensors. Sapwood depth ranged from 22 to 55 mm with greater variability in trunks than in branches. Two asymmetric types of sap flow radial patterns were observed: Type 1, rising to a maximum near the mid-point of the sapwood; and Type 2, falling continuously from a maximum just below cambium to zero at the inner boundary of the sapwood. The Type 1 pattern was recorded more often in branches and smaller trees. Both types of sap flow radial patterns were observed in trunks of the sample trees. Sap flow radial patterns were rather stable during the day, but varied with soil water changes. A decrease in sap flow in the outermost xylem was related to water depletion in the topsoil. We hypothesized that the variations in sap flow radial pattern in a tree trunk reflects a vertical distribution of water uptake that varies with water availability in different soil layers.

Circadian Rhythm↗

PubMed1988

A dynamic model for water flow in a single tree: evidence that models must account for hydraulic architecture.

A model is presented for the dynamics of water flow in a single eastern white cedar tree (Thuja occidentalis L.). The model takes into account the spatial and temporal dependence of the evaporative flux from leaves in the crown. It also accounts for the quantitative hydraulic architecture of the tree, i.e., the model characterizes the tree as a branched catena of > 4000 stem segments in which account is taken of the segment length, diameter, hydraulic resistance, and the total area of leaves attached to the segment. Input values needed to run the model are measurements of evaporative flux, hydraulic conductance of stems versus stem diameter, and leaf and stem water storage capacitances. Output parameters are the spatial and temporal characterization of stem and leaf water potentials, stem and leaf water deficits, sap flow rate, and relative sap velocity. The input and output values of the branched catena model are compared and contrasted to that of an unbranched catena model. It is shown that the branched catena model fits independently measured field parameters better than an unbranched catena model. Close correspondence is found between model predictions and field measurements of shoot water potential, pressure gradients in stems, hysteresis in sap velocity between the lower and upper parts of the tree, and diurnal changes in stem and leaf water deficits. This model is discussed in terms of both the hydraulic architecture of trees and the potential application of the model to questions of tree morphology, ecology, physiology and evolution.

Journal Article↗

PubMed2006

Prognostic variables and prognostic groups for malignant melanoma. The information from Cox and Classification And Regression Trees analysis: an Italian population-based study.

The common way to analyse the prognostic role of selected variables in cutaneous melanoma patients is by means of Cox proportional hazard model. The prognostic effect of the simultaneous presence of more than one independent variable in the same patient is, however, difficult to establish. This hampers the possibility of tailoring a survival expectance for a selected patient as well as to communicate it to the patient himself/herself. The objectives of the study were to compare information on cutaneous melanoma prognosis from multivariate Cox proportional hazard model and from Classification And Regression Trees analysis. Classification And Regression Trees analysis is an automatic method that splits data by means of a binary recursive process creating a 'tree' of groups with different profiles according to the analysed outcome, for example, the risk of death. This approach automatically produces data that is easily interpreted by clinicians. A total of 1403 invasive cutaneous melanoma patients, 1110 from the Tuscan Cancer Registry and 293 from the Reggio Emilia Cancer Registry, Italy, were included. Cases were incident during 1996-2001 and followed up at the end of 2003. Cox proportional hazard model and Classification And Regression Trees analysis were applied to the following variables: age, sex, Breslow thickness, Clark level, registry, subsite and morphologic type. The Classification And Regression Trees analysis identified 10 categories with statistically different survival; this results were summarized into six classes of different risks based on Breslow thickness, age and sex. The best prognostic group (5-year observed survival, 98.1%) included those subjected with Breslow less than 0.94 mm and age 19-44 years. The same thickness but an older age (50-69 years) was associated with a statistically significant different prognosis (5-year observed survival, 92.8%). The Cox proportional hazard model found sex, age, Breslow thickness, Clark and morphologic type to have a significant independent prognostic value. In conclusion, compared with the conventional approach based on Cox hazard model, Classification And Regression Trees analysis produces data closer to the clinical need of defining the prognostic profile of a specific patient. This may help the clinician both in the communication of risk and in the follow-up strategy.

Adult↗

PubMed2002

Bantu language trees reflect the spread of farming across sub-Saharan Africa: a maximum-parsimony analysis.

Linguistic divergence occurs after speech communities divide, in a process similar to speciation among isolated biological populations. The resulting languages are hierarchically related, like genes or species. Phylogenetic methods developed in evolutionary biology can thus be used to infer language trees, with the caveat that 'borrowing' of linguistic elements between languages also occurs, to some degree. Maximum-parsimony trees for 75 Bantu and Bantoid African languages were constructed using 92 items of basic vocabulary. The level of character fit on the trees was high (consistency index was 0.65), indicating that a tree model fits Bantu language evolution well, at least for the basic vocabulary. The Bantu language tree reflects the spread of farming across this part of sub-Saharan Africa between ca. 3000 BC and AD 500. Modern Bantu subgroups, defined by clades on parsimony trees, mirror the earliest farming traditions both geographically and temporally. This suggests that the major subgroups of modern Bantu stem from the Neolithic and Early Iron Age, with little subsequent movement by speech communities.

Africa South of the Sahara↗

PubMed2001

Topological classification of binary trees using the Horton-Strahler index.

The Horton-Strahler (HS) index r=max(i,j)+delta(i,j) has been shown to be relevant to a number of physical (such as diffusion limited aggregation) geological (river networks), biological (pulmonary arteries, blood vessels, various species of trees), and computational (use of registers) applications. Here we revisit the enumeration problem of the HS index on the rooted, unlabeled, plane binary set of trees, and enumerate the same index on the ambilateral set of rooted, plane binary set of trees of n leaves. The ambilateral set is a set of trees whose elements cannot be obtained from each other via an arbitrary number of reflections with respect to vertical axes passing through any of the nodes on the tree. For the unlabeled set we give an alternate derivation to the existing exact solution. Extending this technique for the ambilateral set, which is described by an infinite series of nonlinear functional equations, we are able to give a double exponentially converging approximant to the generating functions in a neighborhood of their convergence circle, and derive an explicit asymptotic form for the number of such trees.

Journal Article↗

PubMed2005

Minimum spanning trees and random resistor networks in d dimensions.

We consider minimum-cost spanning trees, both in lattice and Euclidean models, in d dimensions. For the cost of the optimum tree in a box of size L , we show that there is a correction of order L(theta) , where theta< or =0 is a universal d -dependent exponent. There is a similar form for the change in optimum cost under a change in boundary condition. At nonzero temperature T , there is a crossover length xi approximately T(-nu) , such that on length scales larger than xi, the behavior becomes that of uniform spanning trees. There is a scaling relation theta=-1/nu, and we provide several arguments that show that nu and -1/theta both equal nu(perc) , the correlation length exponent for ordinary percolation in the same dimension d , in all dimensions d> or =1 . The arguments all rely on the close relation of Kruskal's greedy algorithm for the minimum spanning tree, percolation, and (for some arguments) random resistor networks. The scaling of the entropy and free energy at small nonzero T , and hence of the number of near-optimal solutions, is also discussed. We suggest that the Steiner tree problem is in the same universality class as the minimum spanning tree in all dimensions, as is the traveling salesman problem in two dimensions. Hence all will have the same value of theta=-3/4 in two dimensions.

Journal Article↗

PubMed1990

Comparison of lodging safety factor of untreated and succinic Acid 2,2-dimethylhydrazide-treated shoots of mulberry tree.

This study examined the lodging resistance of mulberry tree (Morus bombycis Koidz. cv Kenmochi) shoots treated or not treated with succinic acid 2,2-dimethylhydrazide (SADH). The lodging safety factor, an indicator of lodging resistance, was defined as the ratio of critical lodging load to the leaf fresh weight observed, provided that the distribution of the critical lodging load along the stem was similar to that of the leaf fresh weight observed. The critical lodging load was experimentally estimated by loading weights onto the stems. In the untreated trees, the lodging safety factor was maintained at about 3.2. In the SADH-treated trees, the stem elongation was inhibited to about 80% of that in the untreated trees, and the percentage of shoot dry matter partitioned into the leaves was always larger than that of the untreated trees. This dwarfing of the stem caused by SADH increased the critical lodging load supported by the unit stem dry weight, while this large investment of materials in leaves increased the leaf fresh weight supported by the unit stem dry weight. Since the increments canceled each other, the lodging safety factor of the SADH-treated shoots was similar to that of the untreated ones. These results suggest that the shoot formation of the mulberry tree is controlled to maintain the lodging safety factor at a constant level.

Journal Article↗

PubMed2005

Vessel tree reconstruction in thoracic CT scans with application to nodule detection.

Vessel tree reconstruction in volumetric data is a necessary prerequisite in various medical imaging applications. Specifically, when considering the application of automated lung nodule detection in thoracic computed tomography (CT) scans, vessel trees can be used to resolve local ambiguities based on global considerations and so improve the performance of nodule detection algorithms. In this study, a novel approach to vessel tree reconstruction and its application to nodule detection in thoracic CT scans was developed by using correlation-based enhancement filters and a fuzzy shape representation of the data. The proposed correlation-based enhancement filters depend on first-order partial derivatives and so are less sensitive to noise compared with Hessian-based filters. Additionally, multiple sets of eigenvalues are used so that a distinction between nodules and vessel junctions becomes possible. The proposed fuzzy shape representation is based on regulated morphological operations that are less sensitive to noise. Consequently, the vessel tree reconstruction algorithm can accommodate vessel bifurcation and discontinuities. A quantitative performance evaluation of the enhancement filters and of the vessel tree reconstruction algorithm was performed. Moreover, the proposed vessel tree reconstruction algorithm reduced the number of false positives generated by an existing nodule detection algorithm by 38%.

Adult↗

PubMed2005

Classifiability-based omnivariate decision trees.

Top-down induction of decision trees is a simple and powerful method of pattern classification. In a decision tree, each node partitions the available patterns into two or more sets. New nodes are created to handle each of the resulting partitions and the process continues. A node is considered terminal if it satisfies some stopping criteria (for example, purity, i.e., all patterns at the node are from a single class). Decision trees may be univariate, linear multivariate, or nonlinear multivariate depending on whether a single attribute, a linear function of all the attributes, or a nonlinear function of all the attributes is used for the partitioning at each node of the decision tree. Though nonlinear multivariate decision trees are the most powerful, they are more susceptible to the risks of overfitting. In this paper, we propose to perform model selection at each decision node to build omnivariate decision trees. The model selection is done using a novel classifiability measure that captures the possible sources of misclassification with relative ease and is able to accurately reflect the complexity of the subproblem at each node. The proposed approach is fast and does not suffer from as high a computational burden as that incurred by typical model selection algorithms. Empirical results over 26 data sets indicate that our approach is faster and achieves better classification accuracy compared to statistical model select algorithms.

Algorithms↗

PubMed2006

Inducing NNC-Trees with the R4-rule.

An NNC-Tree is a decision tree (DT) with each non-terminal node containing a nearest neighbor classifier (NNC). Compared with the conventional axis-parallel DTs (APDTs), the NNC-Trees can be more efficient, because the decision boundary made by an NNC is more complex than an axis-parallel hyperplane. Compared with single-layer NNCs, the NNC-Trees can classify given data in a hierarchical structure that is often useful for many applications. This paper proposes an algorithm for inducing NNC-Trees based on the R4-rule, which was proposed by the author for finding the smallest nearest neighbor based multilayer perceptrons (NN-MLPs). There are mainly two contributions here. 1) A heuristic but effective method is given to define the teacher signals (group labels) for the data assigned to each nonterminal node. 2) The R4-rule is modified so that an NNC with proper size can be designed automatically in each nonterminal node. Experiments with several public databases show that the proposed algorithm can produce NNC-Trees effectively and efficiently.

Algorithms↗

PubMed2005

Pine microsatellite markers allow roots and ectomycorrhizas to be linked to individual trees.

Linking roots and ectomycorrhizas (EcM) to individual host trees in the field is required to test whether individual trees support different ectomycorrhizal communities. Here we describe a method that identifies the source of EcM roots by PCR of polymorphic pine nuclear microsatellite loci using fluorescently labelled primers and high-throughput fragment analysis. ITS-PCR can also be performed on the same EcM DNA extract for fungal identification. The method was tested on five neighbouring Scots pine (Pinus sylvestris var scotica) trees in native woodland. Successful host tree identification from DNA extracts of EcM root tips was achieved for 93% of all root fragments recovered from soil cores. It was estimated that each individual mature pine sampled was colonised by between 15 and 19 EcM fungi. The most abundant fungal species were found on all five trees, and within the constraints of the sampling scheme, no differences between trees in EcM fungal community structure or composition were detected.

DNA Fingerprinting↗

PubMed2006

Hydrogen exchange during cellulose synthesis distinguishes climatic and biochemical isotope fractionations in tree rings.

The abundance of the hydrogen isotope deuterium (D) in tree rings is an attractive record of climate; however, use of this record has proved difficult so far, presumably because climatic and physiological influences on D abundance are difficult to distinguish. Using D labelling, we created a D gradient in trees. Leaf soluble sugars of relatively low D abundance entered cellulose synthesis in stems containing strongly D-labelled water. We used nuclear magnetic resonance (NMR) spectroscopy to quantify D in the C-H groups of leaf glucose and of tree-ring cellulose. Ratios of D abundances of individual C-H groups of leaf glucose depended only weakly on leaf D labelling, indicating that the D abundance pattern was determined by physiological influences. The D abundance pattern of tree-ring cellulose revealed C-H groups that exchanged strongly (C(2)-H) or weakly (C(6)-H2) with water during cellulose synthesis. We propose that strongly exchanging C-H groups of tree-ring cellulose adopt a climate signal stemming from the D abundance of source water. C-H groups that exchange weakly retain their D abundance established in leaf glucose, which reflects physiological influences. Combining both types of groups may allow simultaneous reconstruction of climate and physiology from tree rings.

Cellulose↗

PubMed1980

Dendritic trees and cutaneous receptive fields of adjacent spinocervical tract neurones in the cat.

1. The relationship between the dendritic trees and the receptive fields of adjacent spinocervical tract neurones were studied using the intracellular injection of horseradish peroxidase in chloralose-anaesthetized, paralysed, cats. 2. Fourteen pairs of neurones were successfully stained and the receptive fields of twelve pairs were also defined. Five of the pairs were 'rostrocaudal pairs', i.e. in line within +/- 50 micrometer of each other in the rostrocaudal axis of the cord. Nine of the pairs were 'mediolateral pairs', i.e. in line within +/- 50 micrometer of each other in the mediolateral axis of the cord. 3. For twelve pairs of stained neurones, for which the receptive fields were described, a correspondence was found between the organization of their dendritic trees and their receptive fields. 4. All five rostrocaudal pairs of neurones had interdigitating dendritic trees together with overlapping receptive fields. 5. Of the seven mediolateral pairs, four had receptive fields which overlapped and interdigitating dendritic trees. The remaining three had separate receptive fields and non-interdigitating dendritic trees. 6. The results are discussed in relation to previous work on the columnar organization of the receptive fields of s.c.t. neurones and the columnar organization of hair follicle afferent fibre terminals in the spinal cord. The hypothesis is advanced that the receptive fields of most s.c.t. neurones are defined by their connexions with hair follicle afferent fibres such that along the mediolateral axis spatial separation of the dendritic trees of s.c.t. neurones is crucial for receptive field separation.

Animals↗

PubMed2005

New genotype of avian influenza H5N1 viruses isolated from tree sparrows in China.

The 2004 outbreaks of highly pathogenic avian influenza H5N1 disease in China led to a great poultry loss and society attention. A survey of avian influenza viruses was conducted on tree sparrows (Passer montanus) collected in China in 2004. Four viruses were isolated from free-living tree sparrows. The results of the whole-genome analysis indicated that an H5N1 virus with a new genotype is circulating among tree sparrows. The hemagglutinin and neuraminidase genes of the new genotype were derived from Gs/Gd/96-like viruses and the nuclear protein gene descended from the 2001 genotype A H5N1 viruses, while the other inner genes originated from an unknown influenza virus. In experimental infection, all four viruses were highly pathogenic to chickens but not pathogenic to ducks or mice. The four tree sparrow viruses were different from the 2003 tree sparrow strain (genotype Z) in Hong Kong. The results suggested that H5N1 viruses might be distributed widely in tree sparrows.

Animals↗

PubMed2004

CT-based geometry analysis and finite element models of the human and ovine bronchial tree.

The interpretation of experimental results from functional medical imaging is complicated by intersubject and interspecies differences in airway geometry. The application of computational models in understanding the significance of these differences requires methods for generation of subject-specific geometric models of the bronchial airway tree. In the current study, curvilinear airway centerline and diameter models have been fitted to human and ovine bronchial trees using detailed data segmented from multidetector row X-ray-computed tomography scans. The trees have been extended to model the entire conducting airway system by using a volume-filling algorithm to generate airway centerline locations within detailed volume descriptions of the lungs or lobes. Analysis of the geometry of the scan-based and model-based airways has verified their consistency with measures from previous anatomic studies and has provided new anatomic data for the ovine bronchial tree. With the use of an identical parameter set, the volume-filling algorithm has produced airway trees with branching asymmetry appropriate for the human and ovine lung, demonstrating the dependence of the method on the shape of the lung or lobe volume. The modeling approach that has been developed can be applied to any level of detail of the airway tree and into any volume shape for the lung; hence it can be used directly for different individuals or animals and for any number of scan-based airways. The resulting models are subject-specific computational meshes with anatomically consistent geometry, suitable for application in simulation studies.

Algorithms↗

PubMed2006

A quantitative analysis of secondary RNA structure using domination based parameters on trees.

BACKGROUND: It has become increasingly apparent that a comprehensive database of RNA motifs is essential in order to achieve new goals in genomic and proteomic research. Secondary RNA structures have frequently been represented by various modeling methods as graph-theoretic trees. Using graph theory as a modeling tool allows the vast resources of graphical invariants to be utilized to numerically identify secondary RNA motifs. The domination number of a graph is a graphical invariant that is sensitive to even a slight change in the structure of a tree. The invariants selected in this study are variations of the domination number of a graph. These graphical invariants are partitioned into two classes, and we define two parameters based on each of these classes. These parameters are calculated for all small order trees and a statistical analysis of the resulting data is conducted to determine if the values of these parameters can be utilized to identify which trees of orders seven and eight are RNA-like in structure. RESULTS: The statistical analysis shows that the domination based parameters correctly distinguish between the trees that represent native structures and those that are not likely candidates to represent RNA. Some of the trees previously identified as candidate structures are found to be "very" RNA like, while others are not, thereby refining the space of structures likely to be found as representing secondary RNA structure. CONCLUSION: Search algorithms are available that mine nucleotide sequence databases. However, the number of motifs identified can be quite large, making a further search for similar motif computationally difficult. Much of the work in the bioinformatics arena is toward the development of better algorithms to address the computational problem. This work, on the other hand, uses mathematical descriptors to more clearly characterize the RNA motifs and thereby reduce the corresponding search space. These preliminary findings demonstrate that graph-theoretic quantifiers utilized in fields such as computer network design hold significant promise as an added tool for genomics and proteomics.

Algorithms↗

PubMed2005

Genomic variability within an organism exposes its cell lineage tree.

What is the lineage relation among the cells of an organism? The answer is sought by developmental biology, immunology, stem cell research, brain research, and cancer research, yet complete cell lineage trees have been reconstructed only for simple organisms such as Caenorhabditis elegans. We discovered that somatic mutations accumulated during normal development of a higher organism implicitly encode its entire cell lineage tree with very high precision. Our mathematical analysis of known mutation rates in microsatellites (MSs) shows that the entire cell lineage tree of a human embryo, or a mouse, in which no cell is a descendent of more than 40 divisions, can be reconstructed from information on somatic MS mutations alone with no errors, with probability greater than 99.95%. Analyzing all approximately 1.5 million MSs of each cell of an organism may not be practical at present, but we also show that in a genetically unstable organism, analyzing only a few hundred MSs may suffice to reconstruct portions of its cell lineage tree. We demonstrate the utility of the approach by reconstructing cell lineage trees from DNA samples of a human cell line displaying MS instability. Our discovery and its associated procedure, which we have automated, may point the way to a future "Human Cell Lineage Project" that would aim to resolve fundamental open questions in biology and medicine by reconstructing ever larger portions of the human cell lineage tree.

Animals↗