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PubMed2005

Decision-making tree for women considering hysterectomy.

AIMS: This paper reports on a study carried out to establish a decision tree model to describe how women in Taiwan make the decision whether or not to have a hysterectomy. In addition, we examined the predictability of the decision-tree model. BACKGROUND: Hysterectomy is the second most common surgical procedure performed worldwide. Medical professionals believe that the operation can relieve pain and prevent cervical cancer, thus improving a woman's quality of life. While most physicians advise hysterectomy even for benign uterine conditions, feminists decry the belief that the uterus has no purpose, believing that it is an important symbol of womanhood. METHODS: The study was conducted in two phases. Phase I, the model development phase, was carried out to generalize data from a qualitative study of 14 women and to establish a tree model outlining their decision to proceed with hysterectomy. The second phase was the model prediction phase that applied inductive and deductive methods to data analysis and development of the decision-tree model. The model tree was then tested with 18 women who were deciding whether or not to undergo hysterectomy. Using the decision-making tree, we studied the women's thought processes and analysed their primary concerns. The study was carried out in 1999-2001. RESULTS: The study determined 13 criteria that Taiwanese women use when deciding about having a hysterectomy. Developed in accordance with Gladwin's methodology, the model tree successfully predicted 90% of decisions whether or not to have a hysterectomy. CONCLUSIONS: Nurses working in gynaecological services should understand how women decide to undergo hysterectomy so that the proper counselling and follow-up can be provided. With further testing, our decision tree may help in this process.

Adult↗

PubMed2006

The importance of local tree resources around Gombe National Park, Western Tanzania: implications for humans and chimpanzees.

Miombo woodlands and associated habitats provide a vital resource for both humans and chimpanzees in western Tanzania. A baseline survey was conducted to determine the perceived relative value of different woody species to local people in the six villages adjacent to Gombe National Park. This area also provides direct comparison of tree utilization by humans and chimpanzees since it has been the site of a long-term behavioral study on chimpanzees. Four hundred and fifty-two people, all over 30 years old, were interviewed and asked to select the 10 trees that they considered to be the most important in their everyday lives: 77% of the 4520 responses (represented by 260 species) were native and 23% (represented by 35 species) were exotic trees. In this study, particular focus was paid to the 25 tree species most frequently listed. Of these trees, 19 (representing 50% of all responses) were native, and 6 were exotic. There was a marked difference in the choices, especially with respect to native trees, by men and women. Many of the trees highly prized by humans are also of great importance in the diet of chimpanzees. It is recommended that a major effort be made to maintain the usage and availability of native trees outside the park boundary, which, in conjunction with the balanced planting of exotics for meeting local needs, should contribute to protecting the biodiversity of Gombe and the local ethnobotanical heritage.

Animals↗

PubMed2001

Tomicus piniperda (Coleoptera: Scolytidae) shoot-feeding characteristics and overwintering behavior in Scotch pine Christmas trees.

Overwintering behavior of Tomicus piniperda (L.) was studied in a Scotch pine (Pinus sylvestris L.) Christmas tree plantation in Indiana (1992-1994) and a plantation in Michigan (1994). In general, adults feed inside shoots during summer, then move to overwintering sites at the base of trees in autumn. In early autumn, adults were most often found in shoot-feeding tunnels that were still surrounded by green needles, whereas few were in tunnels surrounded by yellow or brown needles. For all years and sites combined, the range in the percentage of recently tunneled shoots that contained live T. piniperda adults decreased from 89 to 96% in mid-October, to 15- 66% in early November, to 2-10% in mid-November, and to 0-2% by late November to early December. In each year, the first subfreezing temperatures in autumn occurred in October, before most adults left the shoots. Of 1,285 T. piniperda-tunneled shoots, one to seven tunnels (mean = 1.6) and zero to three adults were found per infested shoot. Of these 1,285 attacked shoots, 55% of the shoots had one tunnel, 33% had two, 9% had three, 3% had four, and <1% had five to seven tunnels each. When two or more tunnels occurred in a single shoot, adults were most commonly found in the innermost (most basal) tunnel. For the 2,070 tunnels found in the 1,285 shoots, average shoot thickness at the tunnel entrance was 6.0 mm, average distance from the tunnel entrance to the shoot tip was 6.3 cm, and average tunnel length was 2.3 cm. Four Scotch pine Christmas trees were dissected in January 1993. Eighty percent of the tunneled shoots were in the upper quarter of the tree crown and 98% were in the upper half. For the four trees inspected in January, one live adult was found in a shoot and 85 adults were found in the outer bark along the lower trunk from 1 cm below the soil line to 19 cm above the soil line. No overwintering adults were found outside the trunk in the duff or soil near the base of each test tree. Implications of these results are discussed in terms of surveying, timing the cutting of Christmas trees, and cutting height for Christmas trees.

Animals↗

PubMed2006

Architecture of 54 moist-forest tree species: traits, trade-offs, and functional groups.

Tree architecture is an important determinant of the height extension, light capture, and mechanical stability of trees, and it allows species to exploit the vertical height gradient in the forest canopy and horizontal light gradients at the forest floor. Tropical tree species partition these gradients through variation in adult stature (Hmax) and light demand. In this study we compare 22 architectural traits for 54 Bolivian moist-forest tree species. We evaluate how architectural traits related to Hmax vary with tree size, and we present a conceptual scheme in which we combine the two axes into four different functional groups. Interspecific correlations between architecture and Hmax varied strongly from negative to positive, depending on the reference sizes used. Stem height was positively related to Hmax at larger reference diameters (14-80 cm). Species height vs. diameter curves often flattened toward their upper ends in association with reproductive maturity for species of all sizes. Thus, adult understory trees were typically shorter than similar-diameter juveniles of larger species. Crown area was negatively correlated with Hmax at small reference heights and positively correlated at larger reference heights (15-34 m). Wide crowns allow the small understory species to intercept light over a large area at the expense of a reduced height growth. Crown length was negatively correlated with Hmax at intermediate reference heights (4-14 m). A long crown enables small understory species to maximize light interception in a light-limited environment. Light-demanding species were characterized by orthotropic stems and branches, large leaves, and a monolayer leaf arrangement. They realized an efficient height growth through the formation of narrow and shallow crowns. Light demand turned out to be a much stronger predictor of tree architecture than Hmax, probably because of the relatively low, open, and semi-evergreen canopy at the research site. The existence of four functional groups (shade-tolerant, partial-shade-tolerant, and long- and short-lived pioneer) was confirmed by the principal component and discriminant analysis. Both light demand and Hmax capture the major variation in functional traits found among tropical rain forest tree species, and the two-way classification scheme provides a straightforward model to understand niche differentiation in tropical forests.

Adaptation, Physiological↗

PubMed2000

Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data.

Renal cell carcinoma is characterized by an accumulation of complex chromosomal alterations during tumor progression. Chromosome 3p deletions are known to occur early in the carcinogenesis, but the nature of subsequent events, their interrelationships, and their sequence is poorly understood, as one usually only obtains a single "view" of the dynamic process of tumor development in a particular cancer patient. To address this limitation, we used comparative genomic hybridization analysis in combination with a distance-based and a branching-tree method to search for tree models of the oncogenesis process of 116 conventional (clear cell) renal carcinomas. This provides a means to analyze and model cancer development processes based on a more dynamic model, including the presence of multiple pathways, as compared with the fixed linear model first proposed by Vogelstein et al. (N. Engl. J. Med., 319: 525-532, 1988) for colorectal cancer. The most common DNA losses involved 3p (61%), 4q (50%), 6q (40%), 9p (35%), 13q (37%), and Xq (21%). The most common gains were seen at chromosome 17p and 17q (20%). The tree model derived from the distance-based method is consistent with the established theory that -3p is an important early event in conventional (clear cell) renal cancer and supports the prediction made from the branching tree that -4q is another important early event. Both tree models suggest that there may be two groups of clear cell renal cancers: one characterized by -6q, +17q, and + 17p, and another by -9p, -13q, and -18q. Putative prognostic parameters were -9p and -13q. The distance-based tree clarifies that -8p (present in 12% of tumors) is a late event, largely independent of other events. In summary, tree modeling of comparative genomic hybridization data provided new information on the interrelationships of genetic changes in renal cancer and their possible order, as well as a clustering of these events. Using tree analysis, one can derive a more in-depth understanding of the renal cancer development process than is possible by simply focusing on the frequencies of genetic events in a given cancer type.

Carcinoma, Renal Cell↗

PubMed1996

On the nearest neighbour interchange distance between evolutionary trees.

We present some new results on a well-known distance measure between evolutionary trees. The trees we consider are free 3-trees having n leaves labeled 0,...,n - 1 (representing species), and n - 2 internal nodes of degree 3. The distance between two trees is the minimum number of nearest neighbour interchange (NNI) operations required to transform one into the other. First, we improve an upper bound on the nni-distance between two arbitrary n-node trees from 4n log n (Culik & Wood, 1982, Inf. Pro. Letts. 15, 39-42) to n log n. Second, we present a counterexample disproving several theorems in (Waterman & Smith, 1978, J. theor. Biol. 73, 789-800). Roughly speaking, finding an equal partition between two trees does not imply decomposability of the distance finding problem. Third, we present a polynomial-time approximation algorithm that, given two trees, finds a transformation between them of length O(log n) times their distance. We also present some results of computations we performed on small size trees.

Algorithms↗

PubMed1999

On fractal properties of arterial trees.

The question of fractal properties of arterial trees is considered in light of data from the extensive tree structure of the right coronary artery of a human heart. Because of the highly non-uniform structure of this tree, the study focuses on the purely geometrical rather than statistical aspects of fractal properties. The large number of arterial bifurcations comprising the tree were found to have a mixed degree of asymmetry at all levels of the tree, including the depth of the tree where it has been generally supposed that they would be symmetrical. Cross-sectional area ratios of daughter to parent vessels were also found to be highly mixed at all levels, having values both above and below 1.0, rather than consistently above as has been generally supposed in the past. Calculated values of the power law index which describes the theoretical relation between the diameters of the three vessel segments at an arterial bifurcation were found to range far beyond the two values associated with the cube and square laws, and not clearly favoring one or the other. On the whole the tree structure was found to have what we have termed "pseudo-fractal" properties, in the sense that vessels of different calibers displayed the same branching pattern but with a range of values of the branching parameters. The results suggest that a higher degree of fractal character, one in which the branching parameters are constant throughout the tree structure, is unlikely to be attained in non-uniform vascular structures.

Arteries↗

PubMed1982

Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species.

The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.

Base Sequence↗

PubMed1990

Iterative character weighting based on mutation frequency: a new method for constructing phyletic trees.

In this paper we present an iterative character weighting method for the construction of phyletic trees. An initial tree is used to calculate the character weights, which are the number of mutations normalized so that the possible range is corrected for. The weights obtained are used to adjust the tree; this process is iterated until a stable tree is found. Using data generated according to a model tree, we show that the trees constructed by the iterative character weighting method converge to the true underlying tree. Using biological data, the trees become closer to the systematic classification of the species concerned, and patterns conflicting with the phylogenetic pattern can be singled out. The method involves a combination of minimal length methods and similarity methods, whereby the strict parsimony criterion is relaxed.

Animals↗

PubMed2003

Probabilistic analysis indicates discordant gene trees in chloroplast evolution.

Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue-green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.

Chloroplasts↗

PubMed1999

Defining the ancestral karyotype of all primates by multidirectional chromosome painting between tree shrews, lemurs and humans.

We used multidirectional chromosome painting with probes derived by bivariate fluorescence-activated flow sorting of chromosomes from human, black lemur (Eulemur macaco macaco) and tree shrew (Tupaia belangeri, order Scandentia) to better define the karyological relationship of tree shrews and primates. An assumed close relationship between tree shrews and primates also assists in the reconstruction of the ancestral primate karyotype taking the tree shrew as an "outgroup" species. The results indicate that T. belangeri has a highly derived karyotype. Tandem fusions or fissions of chromosomal segments seem to be the predominant mechanism in the evolution of this tree shrew karyotype. The 22 human autosomal painting probes delineated 40 different segments, which is in the range found in most mammals analyzed by chromosome painting up to now. There were no reciprocal translocations that would distinguish the karyotype of the tree shrew from an assumed primitive primate karyotype. This karyotype would have included the chromosomal forms 1a, 1b, 2a, 2b, 3/21, 4-11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y and had a diploid chromosome number of 2n=50. Of these forms, chromosomes 1a, 1b, 4, 8, 12a/22a, and 12b/22b may be common derived characters that would link the tree shrew with primates. To define the exact phylogenetic relationships of the tree shrews and the genomic rearrangements that gave rise to the primates and eventually to humans further chromosome painting in Rodentia, Lagomorpha, Dermoptera and Chiroptera is needed, but many of the landmarks of genomic evolution are now known.

Animals↗

PubMed2005

Soil modification by different tree species influences the extent of seedling ectomycorrhizal infection.

Established vegetation can facilitate the ectomycorrhizal infection of seedlings, but it is not known whether this interaction is limited by the phylogenetic relatedness of trees and seedlings. We use a series of bioassay experiments to test whether soil modification by different ectomycorrhizal tree species causes different levels of seedling infection, whether the extent of seedling infection is a function of the relatedness of tree and seedling, and whether the effect of trees on seedlings is mediated by biotic or abiotic soil factors. We found that soils from under different tree species do vary in their mycorrhizal infectiveness. However, this variation is not related to the genetic relatedness of trees and seedlings but instead, appears to be an attribute of the overstory species, irrespective of seedling species, mediated through a suite of humus- and base-cation-related abiotic effects on soils. Modification of abiotic soil properties by overstory trees should be considered as an important factor in the effect of different overstory trees on the extent of seedling mycorrhizal infection.

Ecosystem↗

PubMed2005

A computer reconstruction of the entire coronary arterial tree based on detailed morphometric data.

A rigorous analysis of blood flow must be based on the branching pattern and vascular geometry of the full vascular circuit of interest. It is experimentally difficult to reconstruct the entire vascular circuit of any organ because of the enormity of the vessels. The objective of the present study was to develop a novel method for the reconstruction of the full coronary vascular tree from partial measurements. Our method includes the use of data on those parts of the tree that are measured to extrapolate the data on those parts that are missing. Specifically, a two-step approach was employed in the reconstruction of the entire coronary arterial tree down to the capillary level. Vessels > 40 microm were reconstructed from cast data while vessels < 40 microm were reconstructed from histological data. The cast data were reconstructed one-bifurcation at a time while histological data were reconstructed one-sub-tree at a time by "cutting" and "pasting" of data from measured to missing vessels. The reconstruction algorithm yielded a full arterial tree down to the first capillary bifurcation with 1.9, 2.04 and 1.15 million vessel segments for the right coronary artery (RCA), left anterior descending (LAD) and left circumflex (LCx) trees, respectively. The node-to-node connectivity along with the diameter and length of every vessel segment was determined. Once the full tree was reconstructed, we automated the assignment of order numbers, according to the diameter-defined Strahler system, to every vessel segment in the tree. Consequently, the diameters, lengths, number of vessels, segments-per-element ratio, connectivity and longitudinal matrices were determined for every order number. The present model establishes a morphological foundation for future analysis of blood flow in the coronary circulation.

Algorithms↗

PubMed1994

The agreement metric for labeled binary trees.

Let S be a set of n objects. A binary tree of S is a binary tree whose leaves are labeled without repetition from S. The operation of pruning a tree T is that of removing some leaves from T and suppressing all inner vertices of degree 2 which are formed by this deletion. Given two trees T and U, an agreement tree is a tree that can be obtained from T as well as from U by pruning the fewest number of leaves from the two trees. A quadratic algorithm is presented for doing this and two metrics are defined based on agreement trees.

Algorithms↗

PubMed2006

Effect of age on the distribution of oil in Eastern redcedar tree segments.

Eastern redcedar is widespread in the US and produces significant amount of biomass. Open-grown trees invade abandoned fields and compete with valuable forage species in pastures and rangelands. Value-added product development from redcedar is vital for management of eastern redcedar. Cedarwood oil is a valuable component which can be used for further value-added product development. This study examined the effect of age on the distribution of oil in redcedar tree segments. Trunks of eastern redcedar (Juniperus virginiana L.) trees at different stages of growth (26-63 years old) were divided into three sections (top, center and lower). Each section was fractionated separately into bark, heartwood and sapwood segments. Heartwood and sapwood samples from each tree section were analyzed for oil content and composition. A hydrodistillation method was used for oil extraction. Volatile components of tree segments were examined by using a Gas Chromatograph-headspace analysis technique. The heartwood of eastern redcedar contained significantly higher oil than sapwood. Older trees had more oil in the heartwood than younger trees. Both redcedar bark and leaves contained significantly lower oil content than the cedarwood. There were also significant differences in the oil composition of bark, leaves and wood fractions. Cedarwood oil extraction may benefit from prior separation of tree segments prior to oil extraction. However, the economic feasibility of separation prior to an extraction process needs to be further studied. Required extra capital investment and operating costs need to be examined, as well as whether sapwood is worth processing.

Juniperus↗

PubMed2004

Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees.

The molecular phylogeny of parabasalids has mainly been inferred from small subunit (SSU) rRNA sequences and has conflicted substantially with systematics based on morphological and ultrastructural characters. This raises the important question, how congruent are protein and SSU rRNA trees? New sequences from seven diverse parabasalids (six trichomonads and one hypermastigid) were added to data sets of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), enolase, alpha-tubulin and beta-tubulin and used to construct phylogenetic trees. The GAPDH tree was well resolved and identical in topology to the SSU rRNA tree. This both validates the rRNA tree and suggests that GAPDH should be a valuable tool in further phylogenetic studies of parabasalids. In particular, the GAPDH tree confirmed the polyphyly of Monocercomonadidae and Trichomonadidae and the basal position of Trichonympha agilis among parabasalids. Moreover, GAPDH strengthened the hypothesis of secondary loss of cytoskeletal structures in Monocercomonadidae such as Monocercomonas and Hypotrichomonas. In contrast to GAPDH, the enolase and both tubulin trees are poorly resolved and rather uninformative about parabasalian phylogeny, although two of these trees also identify T. agilis as representing the basal-most lineage of parabasalids. Although all four protein genes show multiple gene duplications (for 3-6 of the seven taxa examined), most duplications appear to be relatively recent (i.e., species-specific) and not a problem for phylogeny reconstruction. Only for enolase are there more ancient duplications that may confound phylogenetic interpretation.

Animals↗

PubMed2002

Taxol content in the bark of Himalayan Yew in relation to tree age and sex.

Taxol content in the bark of Taxus baccata trees growing in a homogenous (uniform) environment at Jageshwar, District Almora in Central Himalaya has been quantified. The average taxol concentration in the bark of sampled trees was 0.0558+/-0.008% (of dry wt.) and was about 64% higher for male plants (averaged across tree age) in comparison to female trees. Maximum taxol content was recorded in the bark samples collected from trees of >110 yrs age. ANOVA indicates a significant difference in the taxol content of bark from trees of different ages, however, differences were not significant between sexes. Taxol was quantified by HPLC using a standard curve prepared with authentic taxol; the identification of bark taxol was confirmed by UV and mass spectrometry. The total taxol content of the bark of Taxus trees across an age series was found to range between 0.064 to 8.032 g/tree, and a tree of about 100 yrs age can yield 5.74 kg dry bark.

Chromatography, High Pressure Liquid↗

PubMed2003

A cytoarchitectonic study of the hippocampal formation of the tree shrew (Tupaia belangeri).

Tree shrews constitute an interesting animal model to study the impact of stress or aging on the hippocampal formation, a brain structure known to be affected under such environmental or internal influences. To perform detailed investigations of the hippocampal formation, adequate knowledge of its anatomy should be present. Until now, the hippocampal formation of the tree shrew has not yet been studied extensively. The main objective of this study, therefore, was to describe the subfield boundaries in various levels of the dorsoventral hippocampal axis of the tree shrew (Tupaia belangeri) in detail. The secondary aim was to clarify whether a separate CA2 field can actually be distinguished in the tree shrew hippocampus, a fact that was denied in former reports. In addition, we aimed at investigating whether or not a CA4 subfield can be identified in the tree shrew's hippocampus. The immunocytochemical distribution of microtubule-associated protein 2 and the calcium-binding proteins, parvalbumin and calbindin, and the characteristics of Nissl staining in adjacent sections were compared. Because of the rather dorsoventral orientation of the long hippocampal axis in tree shrews, staining patterns were analyzed mainly in horizontal sections. The subiculum and the hippocampal CA1 and CA3 areas were easily identified. Moreover, we were able to demonstrate the existence of a distinct CA2 subfield in the tree shrew's Ammon's horn, contrary to previous reports. However, our results indicate that a CA4 field in the tree shrew hippocampal formation cannot be identified with the methods that we used. Therefore, supposed CA4 pyramidal neurons should be included into the CA3 field.

Animals↗