Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Trees”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,333 records · Page 74Linked to original sources
PubMed2006

Seasonal variations in water relations in current-year leaves of evergreen trees with delayed greening.

We investigated seasonal patterns of water relations in current-year leaves of three evergreen broad-leaved trees (Ilex pedunculosa Miq., Ligustrum japonicum Thunb., and Eurya japonica Thunb.) with delayed greening in a warm-temperate forest in Japan. We used the pressure-volume method to: (1) assess the extent to which seasonal variation in leaf water relations is attributable to leaf development processes in delayed greening leaves versus seasonal variation in environmental variables; and (2) investigate variation in leaf water relations during the transition from the sapling to the adult tree stage. Leaf mass per unit leaf area was generally lowest just after completion of leaf expansion in May (late spring), and increased gradually throughout the year. Osmotic potential at full turgor (Psi(o) (ft)) and leaf water potential at the turgor loss point (Psi(w) (tlp)) were highest in May, and lowest in midwinter in all species. In response to decreasing air temperature, Psi(o) (ft) dropped at the rate of 0.037 MPa degrees C(-1). Dry-mass-based water content of leaves and the symplastic water fraction of total leaf water content gradually decreased throughout the year in all species. These results indicate that reductions in the symplastic water fraction during leaf development contributed to the passive concentration of solutes in cells and the resulting drop in winter Psi(o) (ft). The ratio of solutes to water volume increased in winter in current-year leaves of L. japonicum and E. japonica, indicating that osmotic adjustment (active accumulation of solutes) also contributed to the drop in winter in Psi(o) (ft). Bulk modulus of elasticity in cell walls fluctuated seasonally, but no general trend was found across species. Over the growing season, Psi(o) (ft) and Psi(w) (tlp) were lower in adult trees than in saplings especially in the case of I. pedunculosa, suggesting that adult-tree leaves are more drought and cold tolerant than sapling leaves. The ontogenetic increase in the stress resistance of I. pedunculosa may be related to its characteristic life form because I. pedunculosa grows taller than the other species studied.

Cell Wall↗
PubMed1989

Carbohydrate relations during propagation of cuttings from sexually mature Pinus banksiana trees.

Concentrations of glucose, sucrose, soluble reducing sugars, starch and total non-structural carbohydrate were determined during propagation of cuttings from sexually mature Pinus banksiana Lamb. trees. Such cuttings rarely initiate adventitious roots whatever the method or duration of propagation. Terminals, needles, and upper and basal stem segments of cuttings were analyzed at Day 0 and every 2 days for 18 days. Comparison of the results with those of earlier studies with cuttings of P. banksiana seedlings, which root readily, indicated pronounced differences in carbohydrate concentrations and partitioning between the two types of cutting. Compared with those from seedlings, cuttings from sexually mature trees exhibited: (1) more total non-structural carbohydrate in each tissue at Day 0; (2) decreasing rather than increasing total carbohydrate (mainly starch) concentrations in each tissue during propagation; (3) different carbohydrate concentration ratios in each tissue during propagation; and (4) higher sucrose concentrations in terminals during propagation, relative to concentrations at Day 0. Cuttings from sexually mature trees also differed from cuttings of seedlings in having a much lower rate of dry matter accumulation during propagation. These findings suggest that the poor rooting ability of cuttings from sexually mature P. banksiana is not attributable to a lack of total carbohydrate, but that the rooting abilities of cuttings from seedlings and from sexually mature trees differ because of differences between the two types of cutting in rates of net photosynthesis and starch metabolism. The difference in starch metabolism becomes apparent during the first 2 days of propagation.

Journal Article↗
PubMed1991

Sodium and chloride distribution in salt-stressed Prunus salicina, a deciduous tree species.

Measurements were made over four growing seasons of the Na(+) and Cl(-) content of leaves and woody tissues (twigs, branches, trunk and roots) of mature, fruit-bearing Prunus salicina Lindl. (on Marianna 2624 rootstock) trees irrigated during the growing season with water containing 3, 14 or 28 mM salt (2/1 molar ratio of NaCl and CaCl(2)). At the beginning of the study, the trees were 19 years old. Woody tissues of trees irrigated with water containing 14 or 28 mM salt accumulated Na(+) and Cl(-). Leaves of trees irrigated with water containing 14 or 28 mM salt accumulated Cl(-), but not Na(+), unless they had visible symptoms of salt injury. X-Ray microanalysis of leaf mesophyll cells indicated some ability of the cells to sequester Cl(-) in the vacuole. The data demonstrate a capacity for ion compartmentation among tissues and cell organelles in mature Prunus salicina, which may explain the ability of the species to survive low levels of salinity for several years in the field.

Journal Article↗
PubMed2003

Refractive state of tree shrew eyes measured with cortical visual evoked potentials.

PURPOSE: To determine the refractive state of tree shrew eyes using visual evoked potentials (VEP's) recorded from primary visual cortex and compare the values with those obtained with streak retinoscopy and with an autorefractor. METHODS: VEP's were recorded in seven normal tree shrews and three animals in which approximately 5 D of myopia (relative to control eye) was induced by monocular -5 D lens wear. While the animals were awake, refractive correction was measured with an autorefractor before and after cycloplegia (1% atropine and 2.5% phenylepherine). When anesthetized, cycloplegic refractive correction was measured with streak retinoscopy. Then VEP's were produced with square-wave counterphased (1 Hz) high-contrast checkerboard patterns near the animals' high spatial frequency cutoff. Spherical lenses (2 D steps) were placed before the eye, and the VEP (average of 128 sweeps) was measured to determine the lens that produced the largest first positive peak (P1). RESULTS: VEP's were obtained over a broad range of trial lenses. Tuning was narrower when check sizes were small. In normal and control eyes, the P1 amplitude was largest, on average, for a trial lens of (mean +/- SD) -0.6 +/- 1.6 D (corrected for working distance but not vertex distance). The mean streak retinoscopy value (spherical equivalent at the corneal plane) was 7.0 +/- 0.8 D, and mean autorefractor values were 4.0 +/- 1.1 D (cycloplegic) and 3.7 +/- 1.2 D (noncycloplegic). In the eyes that compensated for a -5 D lens, the largest P1 values occurred with lenses with a power of -6.3 +/- 3.2 D. Thus, the VEP measure showed a similar treated vs. control eye difference as did streak retinoscopy (treated eyes, 4.7 +/- 0.4 D myopic) and the autorefractor (treated eyes, 4.8 +/- 0.5 D myopic). CONCLUSIONS: Normal tree shrew eyes are approximately emmetropic. The hyperopic values obtained with streak retinoscopy and the autorefractor are consistent with the presence of a "small-eye artifact" in tree shrews. Eyes that have compensated for a -5 D lens are myopic by approximately the value of the lens.

Animals↗
PubMed2004

The subscapular arterial tree as a source of microvascular arterial grafts.

The subscapular arterial tree may be used as a source of microvascular grafts to replace damaged or diseased portions of arteries, particularly in the hand and forearm. By studying cadaver dissections, it is possible to estimate the number of branches that may be found at different arterial segment lengths from the origin of the subscapular artery. Fifty-five preserved cadaver subscapular arterial trees were dissected, and the branching patterns were documented. Three major arterial branching patterns of the subscapular artery were observed with one, two, and three major branches to the serratus anterior in 60 percent, 29 percent, and 9 percent of the cases, respectively. The authors determined the number of 1-mm-diameter, 1-cm-long branches arising from each of six 3-cm regions of the arterial tree measured from the origin of the subscapular artery to the end of the longest terminal branch. The probability of finding at least one usable terminal branch that is at least 12.0 cm in length was found to be 98 percent. Typically, there are two to five useful branches at this distance. Such information may help surgeons fine tune their process of selecting an appropriate arterial donor site for a particular arterial defect and supports the use of the subscapular arterial tree as a donor site for microvascular arterial grafts.

Arteries↗
PubMed2002

Inferring confidence sets of possibly misspecified gene trees.

The problem of inferring confidence sets of gene trees is discussed without assuming that the substitution model or the branching pattern of any of the investigated trees is correct. In this case, widely used methods to compare genealogies can give highly contradicting results. Here, three methods to infer confidence sets that are robust against model misspecification are compared, including a new approach based on estimating the confidence in a specific tree using expected-likelihood weights. The power of the investigated methods is studied by analysing HIV-1 and mtDNA sequence data as well as simulated sequences. Finally, guidelines for choosing an appropriate method to compare multiple gene trees are provided.

Animals↗
PubMed1998

Base-compositional biases and the bat problem. II. DNA-hybridization trees based on AT- and GC-enriched tracers.

We conducted a series of parallel DNA-hybridization experiments on a small group of bats (species of Pteropus, Rhinolophus, Noctilio and Pteronotus) and outgroups (Lemur, Cynocephalus, Didelphis), using whole-genome labels and tracers made from extracts enriched with AT and two levels of GC content. FITCH (additive phylogenetic trees) topologies were constructed from the four sets of comparisons, indexed as both delta Tmode and delta NPHs (normalized percentage of hybridization). Based on our previous work showing that the shared AT bias of pteropodids and some microchiropterans may affect the rank-ordering of taxa based on either AT- or GC-rich labels, our expectation was that the resulting trees would show differing topologies when generated from tracers made with the variously enriched DNA extracts. Whereas there was some variation among the trees, most of them grouped the bats together, and almost all paired the representative megachiropteran and rhinolophoid microchiropteran as sister-taxa in contrast to the other microchiropterans. As the pteropodid-rhinolophoid relationship is an unexpected and unlikely one, we attribute this association to an AT bias that was not obviated even by our most GC-rich labels, and suggest that such a bias may compromise the truth of some molecular trees. Accordingly, we believe the broader issue of bat monophyly remains unresolved by DNA-hybridization and probably also by gene-sequencing studies.

Animals↗
PubMed2001

Pattern formation on trees.

Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the nodes of a tree is described by a nonlinear map, giving rise to a coupled map lattice system. The coupling is expressed by a matrix whose eigenvectors constitute a basis on which spatial patterns on trees can be expressed by linear combination. The spectrum of eigenvalues of the coupling matrix exhibit a nonuniform distribution that manifests itself in the bifurcation structure of the spatially synchronized modes. These models may describe reaction-diffusion processes and several other phenomena occurring on heterogeneous media with hierarchical structure.

Journal Article↗
PubMed2002

Mutual learning in a tree parity machine and its application to cryptography.

Mutual learning of a pair of tree parity machines with continuous and discrete weight vectors is studied analytically. The analysis is based on a mapping procedure that maps the mutual learning in tree parity machines onto mutual learning in noisy perceptrons. The stationary solution of the mutual learning in the case of continuous tree parity machines depends on the learning rate where a phase transition from partial to full synchronization is observed. In the discrete case the learning process is based on a finite increment and a full synchronized state is achieved in a finite number of steps. The synchronization of discrete parity machines is introduced in order to construct an ephemeral key-exchange protocol. The dynamic learning of a third tree parity machine (an attacker) that tries to imitate one of the two machines while the two still update their weight vectors is also analyzed. In particular, the synchronization times of the naive attacker and the flipping attacker recently introduced in Ref. 9 are analyzed. All analytical results are found to be in good agreement with simulation results.

Journal Article↗
PubMed2004

Scale-free trees: the skeletons of complex networks.

We investigate the properties of the spanning trees of various real-world and model networks. The spanning tree representing the communication kernel of the original network is determined by maximizing the total weight of the edges, whose weights are given by the edge betweenness centralities. We find that a scale-free tree and shortcuts organize a complex network. Especially, in ubiquitous scale-free networks, it is found that the scale-free spanning tree shows very robust betweenness centrality distributions and the remaining shortcuts characterize the properties of the original network, such as the clustering coefficient and the classification of scale-free networks by the betweenness centrality distribution.

Journal Article↗
PubMed2005

Transport on randomly evolving trees.

The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant tau> or =0, the root produces v> or =0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to square root of 3/2 independently of the distributions of v and tau when q1-->1 and t-->infinity. Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.

Aging↗
PubMed1998

Segmentation of intrathoracic airway trees: a fuzzy logic approach.

Three-dimensional (3-D) analysis of airway trees extracted from computed tomography (CT) image data can provide objective information about lung structure and function. However, manual analysis of 3-D lung CT images is tedious, time consuming and, thus, impractical for routine clinical care. We have previously reported an automated rule-based method for extraction of airway trees from 3-D CT images using a priori knowledge about airway-tree anatomy. Although the method's sensitivity was quite good, its specificity suffered from a large number of falsely detected airways. We present a new approach to airway-tree detection based on fuzzy logic that increases the method's specificity without compromising its sensitivity. The method was validated in 32 CT image slices randomly selected from five volumetric canine electron-beam CT data sets. The fuzzy-logic method significantly outperformed the previously reported rule-based method (p < 0.002).

Animals↗
PubMed2005

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Algorithms↗
PubMed2004

Wavelet tree quantization for copyright protection watermarking.

This paper proposes a wavelet-tree-based blind watermarking scheme for copyright protection. The wavelet coefficients of the host image are grouped into so-called super trees. The watermark is embedded by quantizing super trees. The trees are so quantized that they exhibit a large enough statistical difference, which will later be used for watermark extraction. Each watermark bit is embedded in perceptually important frequency bands, which renders the mark more resistant to frequency based attacks. Also, the watermark is spread throughout large spatial regions. This yields more robustness against time domain geometric attacks. Examples of various attacks will be given to demonstrate the robustness of the proposed technique.

Algorithms↗
PubMed2004

Variable-branch tree-structured vector quantization.

Tree-structured vector quantizers (TSVQ) and their variants have recently been proposed. All trees used are fixed M-ary tree structured, such that the training samples in each node must be artificially divided into a fixed number of clusters. This paper proposes a variable-branch tree-structured vector quantizer (VBTSVQ) based on a genetic algorithm, which searches for the number of child nodes of each splitting node for optimal coding in VBTSVQ. Moreover, one disadvantage of TSVQ is that the searched codeword usually differs from the full searched codeword. Briefly, the searched codeword in TSVQ sometimes is not the closest codeword to the input vector. This paper proposes the multiclassification encoding method to select many classified components to represent each cluster, and the codeword encoded in the VBTSVQ is usually the same as that of the full search. VBTSVQ outperforms other TSVQs in the experiments presented here.

Algorithms↗
PubMed2005

Compression of map images by multilayer context tree modeling.

We propose a method for compressing color map images by context tree modeling and arithmetic coding. We consider multicomponent map images with semantic layer separation and images that are divided into binary layers by color separation. The key issue in the compression method is the utilization of interlayer correlations, and to solve the optimal ordering of the layers. The interlayer dependencies are acquired by optimizing the context tree for every pair of image layers. The resulting cost matrix of the interlayer dependencies is considered as a directed spanning tree problem and solved by an algorithm based on the Edmond's algorithm for optimum branching and by the optimal selection and removal of the background color. The proposed method gives results 50% better than JBIG and 25% better than a single-layer context tree modeling.

Algorithms↗
PubMed2005

Matching and anatomical labeling of human airway tree.

Matching of corresponding branchpoints between two human airway trees, as well as assigning anatomical names to the segments and branchpoints of the human airway tree, are of significant interest for clinical applications and physiological studies. In the past, these tasks were often performed manually due to the lack of automated algorithms that can tolerate false branches and anatomical variability typical for in vivo trees. In this paper, we present algorithms that perform both matching of branchpoints and anatomical labeling of in vivo trees without any human intervention and within a short computing time. No hand-pruning of false branches is required. The results from the automated methods show a high degree of accuracy when validated against reference data provided by human experts. 92.9% of the verifiable branchpoint matches found by the computer agree with experts' results. For anatomical labeling, 97.1% of the automatically assigned segment labels were found to be correct.

Algorithms↗
PubMed2004

An adaptive high-order neural tree for pattern recognition.

A new neural tree model, called adaptive high-order neural tree (AHNT), is proposed for classifying large sets of multidimensional patterns. The AHNT is built by recursively dividing the training set into subsets and by assigning each subset to a different child node. Each node is composed of a high-order perceptron (HOP) whose order is automatically tuned taking into account the complexity of the pattern set reaching that node. First-order nodes divide the input space with hyperplanes, while HOPs divide the input space arbitrarily, but at the expense of increased complexity. Experimental results demonstrate that the AHNT generalizes better than trees with homogeneous nodes, produces small trees and avoids the use of complex comparative statistical tests and/or a priori selection of large parameter sets.

Algorithms↗