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 865 records · Page 48Linked to original sources
PubMed1990

Indications of physical, sexual, and verbal victimization in projective tree drawings.

Several facets of the Tree-Scar-Trauma hypothesis were addressed. The first inquiry was whether scars, knotholes, and/or broken branches on a drawn tree are indicative of previous victimization. A statistically significant relationship between these variables was found. The study also examined differences between mental health patients (N = 56) and control subjects (N = 215) with regard to their abuse history and tree drawings. No significant differences between these two populations were found. A modification of Buck's (1948) hypothesis with regard to the relationship between the location of traumatic indicators on projective tree drawings and age of traumatization was tested and not validated. However, the association between the duration of physical abuse and the number of indicators on the tree was statistically significant.

Adolescent↗
PubMed2004

Improved prediction of recurrence after curative resection of colon carcinoma using tree-based risk stratification.

BACKGROUND: Patients who are at high risk of recurrence after undergoing curative (R0) resection for colon carcinoma may benefit most from adjuvant treatment and from intensive follow-up for early detection and treatment of recurrence. However, in light of new clinical evidence, there is a need for continuous improvement in the calculation of the risk of recurrence. METHODS: Six hundred forty-one patients with R0-resected colon carcinoma who underwent surgery between January 1, 1984 and December 31, 1996 were recruited from the Erlangen Registry of Colorectal Carcinoma. The study end point was time until first locoregional or distant recurrence. The factors analyzed were: age, gender, site in colon, International Union Against Cancer (UICC) pathologic tumor classification (pT), UICC pathologic lymph node classification, histologic tumor type, malignancy grade, lymphatic invasion, venous invasion, number of examined lymph nodes, number of lymph node metastases, emergency presentation, intraoperative tumor cell spillage, surgeon, and time period. The resulting prognostic tree was evaluated by means of an independent sample using a measure of predictive accuracy based on the Brier score for censored data. Predictive accuracy was compared with several proposed stage groupings. RESULTS: The prognostic tree contained the following variables: pT, the number of lymph node metastases, venous invasion, and emergency presentation. Predictive accuracy based on the validation sample was 0.230 (95% confidence interval [95% CI], 0.227-0.233) for the prognostic tree and 0.212 (95% CI, 0.209-0.215) for the UICC TNM sixth edition stage grouping. CONCLUSIONS: The prognostic tree showed superior predictive accuracy when it was validated using an independent sample. It is interpreted easily and may be applied under clinical circumstances. Provided that their classification system can be validated successfully in other centers, the authors propose using the prognostic tree as a starting point for studies of adjuvant treatment and follow-up strategies.

Adenocarcinoma↗
PubMed1982

Dendritic tree structure and dendritic hypertrophy during growth of the crucian carp eye.

The areas of the ganglion cell dendritic trees were determined in Golgi-stained, flatmounted retinas of crucian carp ranging in age from one summer to 7 years. The dendritic trees of small ganglion cells (S-GC), forming the majority of retinal ganglion cells, add new branches as the retina grows. The increase in dendritic tree area exactly compensates for the decrease in ganglion cell density during growth of the eye so that the number of dendritic trees covering a particular point remains constant. While the retinal diameter increases by a factor of 2.5, the mean diameter of the S-GC dendritic fields increases by a factor of 1.9 and the visual angle covered by one S-GC dendritic tree decreases from 1.6 degrees to 1.2 degrees. The number of branching points of the S-GC dendrites is significantly higher in the ventral retina than in the dorsal. In general the dendrites of the S-GCs tend to grow towards the retinal margin. Dendritic orientation patterns of large (LGC) and large displaced (LDGC) ganglion cells closely resemble those of the amacrines, being oriented parallel to the retinal margin over a wide peripheral region, while the SGCs rapidly lose their tangential orientation. The dendrites of the SGCs are restricted mainly to the proximal sublayer of the inner plexiform layer, suggesting they are ON-cells, while LGC, LDGC, and amacrine cell dendrites are distributed in depth bimodally. As determined from Golgi-stained sections the crucian carp has the same basic IPL organization as the carp and cat.

Animals↗
PubMed2007

Deriving evolutionary tree models of the oncogenesis of endometrial adenocarcinoma.

Endometrial adenocarcinoma (EAC) is the fourth leading cause of cancer death in women worldwide, but not much is known about the underlying genetic factors involved in the development of this complex disease. In the present work, we used 3 different algorithms to derive tree models of EAC oncogenesis from data on the frequencies of genomic alterations in rat chromosome 10 (RNO10). The tumor material was derived from progenies of crosses between the EAC susceptible BDII inbred rat strain and two non susceptible inbred rat strains. Data from allelic imbalance scans of RNO10 with microsatellite markers on solid tumor material and corresponding tissue cultures were used. For the analysis, RNO10 was divided into 24 segments containing a total of 59 informative microsatellite markers. The derived tree models show that genomic alterations have occurred in 11 of the 24 segments. In addition, the models provide information about the likely order of the alterations as well as their relationship with each other. Interestingly, there was a high degree of consistency among the different tree models and with the results of previous studies, which supports the reliability of the tree models. Our results may be extended into a general approach for tree modeling of whole genome alterations during oncogenesis.

Adenocarcinoma↗
PubMed2005

A tree-based model for homogeneous groupings of multinomials.

The motivation of this paper is to provide a tree-based method for grouping multinomial data according to their classification probability vectors. We produce an initial tree by binary recursive partitioning whereby multinomials are successively split into two subsets and the splits are determined by maximizing the likelihood function. If the number of multinomials k is too large, we propose to order the multinomials, and then build the initial tree based on a dramatically smaller number k-1 of possible splits. The tree is then pruned from the bottom up. The pruning process involves a sequence of hypothesis tests of a single homogeneous group against the alternative that there are two distinct, internally homogeneous groups. As pruning criteria, the Bayesian information criterion and the Wilcoxon rank-sum test are proposed. The tree-based model is illustrated on genetic sequence data. Homogeneous groupings of genetic sequences present new opportunities to understand and align these sequences.

Animals↗
PubMed1996

Thyroid dysfunction and thyroxine-dependent programming of photoinduced ovarian growth in American tree sparrows (Spizella arborea).

The time course of thyroid dysfunction after injecting 0.30 mCi Na131I was charted in female American tree sparrows (Spizella arborea) transferred to long days on Day 0 and challenged with 30 micrograms bovine thyroid-stimulating hormone on Postinjection Days 4, 7, 46, and 105. Serum T4 (L-thyroxine) was not detectable in thyroidectomized birds, indicating complete thyroid dysfunction by Day 4 and no restoration of thyroid function by Day 105. By contrast, serum T4 concentrations in similarly challenged thyroid-intact controls greatly exceeded assay sensitivity. To determine whether a single injection of T4 can program thyroidectomized female tree sparrows for seasonal reproduction and postnuptial molt, as it can thyroidectomized male tree sparrows, thyroidectomized females were injected with T4 (100 micrograms) or alkaline vehicle (V) either on the first day of photostimulation or 1 week before photostimulation (during which time injected T4 likely was cleared metabolically). Females injected with T4 on the first day of photostimulation showed robust ovarian growth similar to that reported for photostimulated euthyroid females. Both groups of V-injected females, as well as females injected with T4 1 week before photostimulation, showed slow, but reliable, ovarian growth, indicating that thyroidectomized birds can detect an increase in day length. When birds were moved at Week 7.5 or 9 to constant light and given T4 in drinking water (a qualitative assay for absolute photorefractoriness), only one tested photorefractory and molted. The remaining birds, including those injected with T4 1 week before photostimulation and both groups of V-injected controls, tested photosensitive and did not molt. Taken together, these results indicate that T4, or one of its metabolites, programs thyroidectomized female tree sparrows for ovarian growth early during photostimulation. A single T4 injection (100 micrograms) on the first day of photostimulation usually also programs thyroidectomized male tree sparrows for photorefractoriness and molt. Such an injection is far less effective in programming females for these two late-season events.

Animals↗
PubMed1996

Addition of Darwin's third dimension to phyletic trees.

A three-dimensional (3D) approach for visualizing the phyletic relationship of living animals is proposed and developed as an alternative to current two-dimensional (2D) evolutionary trees. The 3D tree enhances visualization and qualitative analysis since it simultaneously provides topological (tree-structure) and spatial information (based upon genetically measured distances). However, the meaning of the third dimension, particularly its relationship to temporal processes, and further quantitative analyses emerge as open questions. Our method consists of two phases. First, a 3D representation of the genetic relationships of a related group of extant animals is produced using an optimization algorithm developed here. Second, linear connections are added to suggest a visual representation of the differing evolutionary trajectories of the organisms involved on the basis of a 2D tree algorithm. The method is applied to a set of distantly related Caenophidian snakes, and the resulting relationships are analysed. The discussions here are meant to stimulate the generation of 3D trees in the goal of complementing standard 2D views and, perhaps ultimately, improving our classification of evolutionary relationships.

Algorithms↗
PubMed1998

Scaling properties of the placenta's arterial tree.

The purpose of the present work is to establish a basic knowledge about the scaling properties of the placenta's arterial tree. For this end we have analysed X-ray angiograms of 22 normal arterial trees by box counting. All the investigated arterial trees scale closely according to a power-law over a one decade wide range of scales. Perfectly self-similar fractals, of the same resolution as our representation of the arterial tree, do not follow a power-law more closely. The results support the hypothesis that a mechanism or rule--as regular as those which dictate the structure of perfectly self-similar fractals--also determines fundamental aspects of the arterial tree's morphology.

Angiography↗
PubMed2002

Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk's method.

Measurement of the degree of asymmetry in phylogenetic trees is important because a tree's shape reflects the process by which it has grown. For example, highly asymmetric trees are evidence that species have had different potential for diversification. Of the tree shape measures in the literature, that proposed by Fusco & Cronk (J. theor. Biol.175, 235-243) appears to be particularly useful, because it does not require fully-resolved trees whose terminals are of equal taxonomic rank. The value of the asymmetry or imbalance at a node is intended to be independent of the number of species ultimately descended from the node. In this paper, however, we point out that the value does depend upon species number. We propose two modifications that remove the dependency and so increase the measure's usefulness. We illustrate the use of the modified measures, which are implemented in a freely-available program, MESA.

Animals↗
PubMed1993

Phylogenetic tree and sequence similarity of beta-lactamases.

beta-Lactamases are the main cause of beta-lactam resistance in many pathogenic bacteria. These enzymes can be detected in a variety of pathogenic as well as non-pathogenic bacteria. The cyanobacteria are also known to produce a beta-lactamase. Recently, the amino acid sequences and the three-dimensional structures of some of these beta-lactamases have been clarified. On the basis of the amino acid sequences of 47 beta-lactamases and the computer-aided analysis, a phylogenetic tree is proposed in this paper. According to the tree, beta-lactamases are classified into six groups. Group 1 beta-lactamases are mainly composed of plasmid-mediated enzymes from gram-negative bacteria. However, chromosome-derived beta-lactamases from Klebsiella pneumoniae and Rhodopseudomonas capsulata take part in this group. Group 2 enzymes consist of a part of the chromosome-encoded beta-lactamases from Streptomyces, and chromosome-mediated enzymes from Yersinia enterocolitica, Citrobacter diversus, and Klebsiella oxytoca. Chromosome-encoded beta-lactamases from gram-negative bacteria form group 3. Group 4 is composed of metalloenzymes, whereas group 5 consists of OXA type beta-lactamases. Chromosome-encoded beta-lactamases from gram-positive bacteria form group 6. Comparison of the amino acid sequences among these groups confirmed the phylogenetic tree and the classification: the beta-lactamases in each group have its particular conserved amino acid sequences. In addition, the tree provides more detailed classification and time-scale mutual relationships and predicts new types of beta-lactamases that may be found. Furthermore, the classification deduced from the tree is generally in accord with the one based on the amino acid sequences reported previously. However, the class A beta-lactamases are clearly divided into three groups: groups 1, 2, and 6. RDF2 analysis shows that some combinations between beta-lactamases and beta-lactam-interacting proteins as well as eukaryotic proteins have a low but significant evolutionary relatedness.

Amino Acid Sequence↗
PubMed1994

Jackknifing of weighted trees: validation of phylogenies reconstructed from distance matrices.

The jackknife strict consensus has been used to detect topological incompatibilities in phylogenetic trees derived from distance data. We here extend this approach to account for branch lengths, as well as topological relationships, when comparing jackknife pseudoreplicates. The average consensus procedure is used to derive a tree reflecting the agreement among the jackknife phylogenies. Combining the average tree with a minimum and a maximum consensus provides information about jackknife tree variability; the range consensus between the minimum and the maximum represents the topological agreement among them. We also demonstrate the effect of the number of pseudoreplicates on the resulting consensus trees by considering single and multiple deletions. The jackknife extensions that we propose are applied to both hypothetical and DNA-DNA hybridization distance data. Consideration of branch lengths reveals greater stability of the jackknife phylogeny than would be demonstrated by a strict consensus based on topology alone.

Animals↗
PubMed2005

Automatic vascular tree formation using the Mahalanobis distance.

We present a novel technique for the automatic formation of vascular trees from segmented tubular structures. Our method combines a minimum spanning tree algorithm with a minimization criterion of the Mahalanobis distance. First, a multivariate class of connected junctions is defined using a set of trained vascular trees and their corresponding image volumes. Second, a minimum spanning tree algorithm forms the tree using the Mahalanobis distance of each connection from the "connected" class as a cost function. Our technique allows for the best combination of the discrimination criteria between connected and non-connected junctions and is also modality, organ and segmentation specific.

Algorithms↗
PubMed1986

A continuous cable method for determining the transient potential in passive dendritic trees of known geometry.

Models using cable equations are increasingly employed in neurophysiological analyses, but the amount of computer time and memory required for their implementation are prohibitively large for many purposes and many laboratories. A mathematical procedure for determining the transient voltage response to injected current or synaptic input in a passive dendritic tree of known geometry is presented that is simple to implement since it is based on one equation. It proved to be highly accurate when results were compared to those obtained analytically for dendritic trees satisfying equivalent cylinder constraints. In this method the passive cable equation is used to express the potential for each interbranch segment of the dendritic tree. After applying boundary conditions at branch points and terminations, a system of equations for the Laplace transform of the potential at the ends of the segments can be readily obtained by inspection of the dendritic tree. Except for the starting equation, all of the equations have a simple format that varies only with the number of branches meeting at a branch point. The system of equations is solved in the Laplace domain, and the result is numerically inverted back to the time domain for each specified time point (the method is independent of any time increment delta t). The potential at any selected location in the dendritic tree can be obtained using this method. Since only one equation is required for each interbranch segment, this procedure uses far fewer equations than comparable compartmental approaches. By using significantly less computer memory and time than other methods to attain similar accuracy, this method permits extensive analyses to be performed rapidly on small computers. One hopes that this will involve more investigators in modeling studies and will facilitate their motivation to undertake realistically complex dendritic models.

Dendrites↗
PubMed1991

Robustness of maximum likelihood tree estimation against different patterns of base substitutions.

In the maximum likelihood (ML) method for estimating a molecular phylogenetic tree, the pattern of nucleotide substitutions for computing likelihood values is assumed to be simpler than that of the actual evolutionary process, simply because the process, considered to be quite devious, is unknown. The problem, however, is that there has been no guarantee to endorse the simplification. To study this problem, we first evaluated the robustness of the ML method in the estimation of molecular trees against different nucleotide substitution patterns, including Jukes and Cantor's, the simplest ever proposed. Namely, we conducted computer simulations in which we could set up various evolutionary models of a hypothetical gene, and define a true tree to which an estimated tree by the ML method was to be compared. The results show that topology estimation by the ML method is considerably robust against different ratios of transitions to transversions and different GC contents, but branch length estimation is not so. The ML tree estimation based on Jukes and Cantor's model is also revealed to be resistant to GC content, but rather sensitive to the ratio of transitions to transversions. We then applied the ML method with different substitution patterns to nucleotide sequence data on tax gene from T-cell leukemia viruses whose evolutionary process must have been more complicated than that of the hypothetical gene. The results are in accordance with those from the simulation study, showing that Jukes and Cantor's model is as useful as a more complicated one for making inferences about molecular phylogeny of the viruses.

Base Composition↗
PubMed1986

Statistical properties of molecular tree construction methods under the neutral mutation model.

The statistical properties of three molecular tree construction methods--the unweighted pair-group arithmetic average clustering (UPG), Farris, and modified Farris methods--are examined under the neutral mutation model of evolution. The methods are compared for accuracy in construction of the topology and estimation of the branch lengths, using statistics of these two aspects. The distribution of the statistic concerning topological construction is shown to be as important as its mean and variance for the comparison. Of the three methods, the UPG method constructs the tree topology with the least variation. The modified Farris method, however, gives the best performance when the two aspects are considered simultaneously. It is also shown that a topology based on two genes is much more accurate than that based on one gene. There is a tendency to accept published molecular trees, but uncritical acceptance may lead one to spurious conclusions. It should always be kept in mind that a tree is a statistical result that is affected strongly by the stochastic error of nucleotide substitution and the error intrinsic to the tree construction method itself.

Biological Evolution↗
PubMed1996

On the pressure and flow-rate distributions in tree-like and arterial-venous networks.

A solution algorithm yielding the pressure and flow-rate distributions for steady flow in an arbitrary, tree-like network is provided. Given the tree topology, the conductance of each segment and the pressure distribution at the boundary nodes, the solution is obtained from a simple recursion based on perfect Gauss elimination. An iterative solution method using this algorithm is suggested to solve for the pressure and flow-rate distributions in an arbitrary diverging-converging (arterial-venous) network consisting of two tree-like networks which are connected to each other at the capillary nodes. A number of special solutions for tree-like networks are obtained for which the general algorithm is either simplified or can be replaced by closed form solutions of the pressure and flow-rate distributions. These special solutions can also be obtained for each tree of diverging-converging networks having particular topologies and conductance distributions. Sample numerical results are provided.

Algorithms↗
PubMed1998

The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery.

The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed SRalpha for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between the N-terminal half of SRP54(Ffh) and the C-terminal half of SRalpha(Ftsy). This enables a universal phylogeny based on either protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment (220 amino acid positions) of the shared SRP54(Ffh) and SRalpha(Ftsy) regions generate two reciprocally rooted universal trees corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.

Algorithms↗
PubMed2002

Using homolog groups to create a whole-genomic tree of free-living organisms: an update.

Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27 complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders, and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to these lineages. Finally, artificial "partial genomes" were generated by randomly selecting ORFs from the complete genomes in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available. The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole genome sequences.

Animals↗