SEARCH · PubMed Health

Results for “Tree building”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 415 records · Page 23Linked to original sources

PubMed2006

Ecology predicts large-scale patterns of phylogenetic diversification in birds.

One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.

Animals↗

PubMed2006

Classification and regression tree analysis for the prediction of aggressive prostate cancer on biopsy.

PURPOSE: Prostate cancer screening allows early cancer detection but not all patients benefit from subsequent therapy. Thus, identifying patients who are likely to harbor aggressive cancer could significantly decrease the number of prostate biopsies performed. MATERIALS AND METHODS: Data were collected on 1,563 consecutive referred men with serum PSA 10 ng/ml or less who underwent an initial prostate biopsy. Predictors of aggressive cancer (Gleason sum 7 or greater) were identified using CART analysis. Model building was done in a randomly selected training set (70% of the data) and validation was completed using the remaining data. RESULTS: Cancer was detected in 406 men (26.1%). Gleason 7 or greater cancer was found in 130 men (8.3%). CART created a decision tree that identified certain groups at risk for aggressive cancer, namely 1) PSAD greater than 0.165 ng/ml/cc, and 2) PSAD greater than 0.058 to 0.165 ng/ml/cc or less, age greater than 57.5 years and prostate volume greater than 22.7 cc. The incidence of aggressive prostate cancer was 1.1% when PSAD was 0.058 ng/ml/cc or less in the validation set. The sensitivity and specificity of CART for identifying men with aggressive cancer were 100% and 31.8% for model building data, and 91.5% and 33.5% for the validation data set, respectively. CONCLUSIONS: CART identified groups at risk for aggressive prostate cancer. Application of this CART could decrease unnecessary biopsies by 33.5% when only a diagnosis of high grade prostate cancer would lead to subsequent therapy.

Aged↗

PubMed2006

Formation of supramolecular hydrogels with controlled microstructures and stability via molecular assembling in a two-component system.

Two isomeric building units, 4-oxo-4-(2-pyridinylamino) butanoic acid (defined as G1) and 4-oxo-4-(3-pyridinylamino) butanoic acid (defined as G2) formed fiber- and tree-like crystals in aqueous solutions, respectively. The crystal formation process of G1 was suggested based on the layered cross section of an individual crystal and the single crystal structure. Through cooling the aqueous solutions of their mixtures under G1/G2 molar ratios ranged from 7/1 to 1/3, a series of supramolecular hydrogels were formed based on hydrogen bonds as the main driving force. As decreasing G1/G2 ratios, the first observed aggregates in solution changed from fiber to particle form, while the gelating time became longer and longer. At the collapsing temperature, the gels formed at G1/G2 ratio 3/1 kept the original gel shape but released water, while at G1/G2 ratio 2/1 they broke into pieces without releasing water. The "dropping ball" experiment indicated that the highest gel-to-sol dissociation temperature (T(gel)) is obtained at G1/G2 ratio of 2/1. As measured by UV-vis spectroscopy, the two building units distributed uniformly within the gel formed at G1/G2 ratio of 1/1, indicating they assembled together in forming hydrogel. The scanning electron microscope (SEM) and infrared spectrometer (FT-IR) analysis of the dried samples indicated that the backbone shape changed from fiber to sheet and the content of free carboxyl groups increased with decreasing G1/G2 ratios, therefore resulting in hydrogels with different stability. The simple gelator structures and the possibility in controlling gel structure and stability make the hydrogels suitable for various uses.

Crystallization↗

PubMed1998

Sleeping sites, sleeping places, and presleep behavior of gibbons (Hylobates lar).

The sleeping habits of wild white-handed gibbons (Hylobates lar) were investigated to assess the risk of predation and predation-avoidance behavior. Sleeping sites were distributed throughout home ranges, including areas where they overlapped with neighbors, and appeared to be selected independently of habitat characteristics. Individuals did not build night nests or otherwise manipulate the vegetation around the sleeping place but slept on open branches. Group members usually slept in separate trees, and, except for females with infants, they never shared a sleeping place. Sleeping trees were entered several hours before dusk and were used for about 14-17 h. The majority of sleeping trees were used only once, and fewer were selected repeatedly by the same or other group members. Usually females with infants went into a sleeping tree first, then juveniles, and last were mostly subadult and adult males. Intragroup competition over access to a sleeping place was observed once. Average time difference between the first and last group member to enter a sleeping tree was 13 min. The sequence of departure from sleeping trees was more variable. Gibbon sleeping habits seem to primarily reflect adaptations to minimize predation risk. The predation-risk hypothesis was indirectly supported by observations of mobbing pythons, alarm calls given in response to birdes of prey flying low over the canopy, and more importantly by 1) the predominant use of large sleeping trees, which were among the tallest trees available, particularly by adult females with small infants and juveniles, 2) an unpredictable long-term pattern of reuse of sleeping places, and 3) inconspicuous presleep behavior.

Animals↗

PubMed1998

GPCRDB: an information system for G protein-coupled receptors.

The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding constants as primary (experimental) data. Computationally derived data such as multiple sequence alignments, three dimensional models, phylogenetic trees and two dimensional visualization tools are added to enhance the database's usefulness. The GPCRDB is an EU sponsored project aimed at building a generic molecular class specific database capable of dealing with highly heterogeneous data. GPCRs were chosen as test molecules because of their enormous importance for medical sciences and due to the availability of so much highly heterogeneous data. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm

Computer Communication Networks↗

PubMed2006

Coronary vessel trees from 3D imagery: a topological approach.

We propose a simple method for reconstructing vascular trees from 3D images. Our algorithm extracts persistent maxima of the intensity on all axis-aligned 2D slices of the input image. The maxima concentrate along 1D intensity ridges, in particular along blood vessels. We build a forest connecting the persistent maxima with short edges. The forest tends to approximate the blood vessels present in the image, but also contains numerous spurious features and often fails to connect segments belonging to one vessel in low contrast areas. We improve the forest by applying simple geometric filters that trim short branches, fill gaps in blood vessels and remove spurious branches from the vascular tree to be extracted. Experiments show that our technique can be applied to extract coronary trees from heart CT scans.

Algorithms↗

PubMed2005

ARAMIS project: a comprehensive methodology for the identification of reference accident scenarios in process industries.

In the frame of the Accidental Risk Assessment Methodology for Industries (ARAMIS) project, this paper aims at presenting the work carried out in the part of the project devoted to the definition of accident scenarios. This topic is a key-point in risk assessment and serves as basis for the whole risk quantification. The first result of the work is the building of a methodology for the identification of major accident hazards (MIMAH), which is carried out with the development of generic fault and event trees based on a typology of equipment and substances. The term "major accidents" must be understood as the worst accidents likely to occur on the equipment, assuming that no safety systems are installed. A second methodology, called methodology for the identification of reference accident scenarios (MIRAS) takes into account the influence of safety systems on both the frequencies and possible consequences of accidents. This methodology leads to identify more realistic accident scenarios. The reference accident scenarios are chosen with the help of a tool called "risk matrix", crossing the frequency and the consequences of accidents. This paper presents both methodologies and an application on an ethylene oxide storage.

Accidents, Occupational↗

PubMed1993

Conformational properties of melatonin and two conformationally restricted agonists: a molecular mechanics and NMR spectroscopic study.

The hormone melatonin (N-acetyl-5-methoxytryptamine) has been implicated in the regulation of several neural and endocrine processes that are cued by the daily change in photoperiod. The conformational properties of melatonin and two conformationally restricted agonists, 8-methoxy-2-acetamidotetralin and cis-1-methyl-8-methoxy-2-acetamidotetralin, were examined as a starting point for SAR studies. The conformational analysis was carried out by means of molecular mechanics calculations (MM2-85 force field) using a step-wise build-up procedure and the molecular modelling program MacroModel (which has a modified version of the MM2 force field) for Monte Carlo and systematic tree searches. NMR spectroscopy was used to evaluate the conformational behaviour in solution. The three search methods were complementary and produced a good description of the conformational characteristics. The two force fields produced different geometries of some low energy conformations and also different relative steric energies. When using the MM2-85 force field, an intra-molecular interaction between the amide-H and the aromatic system lowers the relative energies of several conformations of both melatonin and the 2-amidotetralins. However, NMR experiments indicated that these interactions, which may be quite important in vacuo, are not important in solution.

Computer Simulation↗

PubMed2006

Changes in the pollen seasons of the early flowering trees Alnus spp. and Corylus spp. in Worcester, United Kingdom, 1996-2005.

Previous work on Betula spp. (birch) in the UK and at five sites in Europe has shown that pollen seasons for this taxon have tended to become earlier by about 5-10 days per decade in most regions investigated over the last 30 years. This pattern has been linked to the trend to warmer winters and springs in recent years. However, little work has been done to investigate the changes in the pollen seasons for the early flowering trees. Several of these, such as Alnus spp. and Corylus spp., have allergens, which cross-react with those of Betula spp., and so have a priming effect on allergic people. This paper investigates pollen seasons for Alnus spp. and Corylus spp. for the years 1996-2005 at Worcester, in the West Midlands, United Kingdom. Pollen data for daily average counts were collected using a Burkard volumetric trap sited on the exposed roof of a three-story building. The climate is western maritime. Meteorological data for daily temperatures (maximum and minimum) and rainfall were obtained from the local monitoring sites. The local area up to approximately 10 km surrounding the site is mostly level terrain with some undulating hills and valleys. The local vegetation is mixed farmland and deciduous woodland. The pollen seasons for the two taxa investigated are typically late December or early January to late March. Various ways of defining the start and end of the pollen seasons were considered for these taxa, but the most useful was the 1% method whereby the season is deemed to have started when 1% of the total catch is achieved and to have ended when 99% is reached. The cumulative catches (in grains/m(3)) for Alnus spp. varied from 698 (2001) to 3,467 (2004). For Corylus spp., they varied from 65 (2001) to 4,933 (2004). The start dates for Alnus spp. showed 39 days difference in the 10 years (earliest 2000 day 21, latest 1996 day 60). The end dates differed by 26 days and the length of season differed by 15 days. The last 4 years in the set had notably higher cumulative counts than the first 2, but there was no trend towards earlier starts. For Corylus spp. start days also differed by 39 days (earliest 1999 day 5, latest 1996 day 44). The end date differed by 35 days and length of season by 26 days. Cumulative counts and lengths of season showed a distinct pattern of alternative high (long) and low (short) years. There is some evidence of a synchronous pattern for Alnus spp.. These patterns show some significant correlations with temperature and rainfall through the autumn, winter and early spring, and some relationships with growth degree 4s and chill units, but the series is too short to discern trends. The analysis has provided insight to the variation in the seasons for these early flowering trees and will form a basis for future work on building predictive models for these taxa.

Acclimatization↗

PubMedDate not supplied

Further development of reduced graphs for identifying bioactive compounds.

Reduced graphs provide summary representations of chemical structures. Here, a variety of different types of reduced graphs are compared in similarity searches. The reduced graphs are found to give comparable performance to Daylight fingerprints in terms of the number of active compounds retrieved. However, no one type of reduced graph is found to be consistently superior across a variety of different data sets. Consequently, a representative set of reduced graphs was chosen and used together with Daylight fingerprints in data fusion experiments. The results show improved performance in 10 out of 11 data sets compared to using Daylight fingerprints alone. Finally, the potential of using reduced graphs to build SAR models is demonstrated using recursive partitioning. An SAR model consistent with a published model is found following just two splits in the decision tree.

Data Display↗

PubMed1999

The Diversity of Eukaryotes.

The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as "major building blocks." For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistologists to issues of nomenclature, ranking, and definitions of these groups are discussed, with particular reference to two groups-the stramenopiles and the Archezoa. The concept of "extended in-group" is introduced to refer to in-groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.

eukaryotes↗

PubMed2001

A short-term temperature forecaster based on a novel radial basis functions neural network.

Many applications dealing with electric load forecasting in buildings require temperature prediction. A new method for short-term temperature forecasting based on a Radial Basis Functions Neural Network, initialized by a Regression Tree, is presented. In this method, each terminal node of the tree contributes one hidden unit to the RBF network. The forecaster uses the current coded hour and the temperature as inputs, and predicts the next hour temperature. The results demonstrate this predictor can be used for load forecasting.

Neural Networks, Computer↗

PubMed2004

Ascomycete diversity in soil-feeding termite nests and soils from a tropical rainforest.

Molecular microbial ecology has revealed remarkable biodiversity - prokaryotic and eukaryotic - in numerous soil environments. However, no culture-independent surveys of the termitosphere exists, although termites dominate tropical rainforests. Here, we focused on soil feeders, building nests with their soil-born faeces, enriched with clay-organic complexes, thus contributing to the improvement of soil fertility. In order to assess the fungal community composition of these termitaries compared with soils not foraged by termites, samples of the two types were collected in the Lopé rainforest, Gabon, and processed for generation of fungal internal transcribed spacer (ITS) clone libraries. Although primers were universal, most of the recovered sequences represented Ascomycete that were previously uncharacterized and the proportions of which reached 72.5% in soils and 80% in termitaries. Their affiliation with identified fungi was analysed in performing a phylogenetic tree based on 5.8S rDNA. Furthermore, the ascomycete communities of soil-feeding termitaries and soils shared only 6.3% of sequences. This discrepancy of composition between soil and nest may result from the building behaviour of termites, as the organic matter in the nest is chemically modified, and some vacant ecological microniches are available for more specialized fungi.

Animals↗

PubMed2006

Personal recognition using hand shape and texture.

This paper proposes a new bimodal biometric system using feature-level fusion of hand shape and palm texture. The proposed combination is of significance since both the palmprint and hand-shape images are proposed to be extracted from the single hand image acquired from a digital camera. Several new hand-shape features that can be used to represent the hand shape and improve the performance are investigated. The new approach for palmprint recognition using discrete cosine transform coefficients, which can be directly obtained from the camera hardware, is demonstrated. None of the prior work on hand-shape or palmprint recognition has given any attention on the critical issue of feature selection. Our experimental results demonstrate that while majority of palmprint or hand-shape features are useful in predicting the subjects identity, only a small subset of these features are necessary in practice for building an accurate model for identification. The comparison and combination of proposed features is evaluated on the diverse classification schemes; naive Bayes (normal, estimated, multinomial), decision trees (C4.5, LMT), k-NN, SVM, and FFN. Although more work remains to be done, our results to date indicate that the combination of selected hand-shape and palmprint features constitutes a promising addition to the biometrics-based personal recognition systems.

Algorithms↗

PubMed2005

Automating genomic data mining via a sequence-based matrix format and associative rule set.

There is an enormous amount of information encoded in each genome--enough to create living, responsive and adaptive organisms. Raw sequence data alone is not enough to understand function, mechanisms or interactions. Changes in a single base pair can lead to disease, such as sickle-cell anemia, while some large megabase deletions have no apparent phenotypic effect. Genomic features are varied in their data types and annotation of these features is spread across multiple databases. Herein, we develop a method to automate exploration of genomes by iteratively exploring sequence data for correlations and building upon them. First, to integrate and compare different annotation sources, a sequence matrix (SM) is developed to contain position-dependant information. Second, a classification tree is developed for matrix row types, specifying how each data type is to be treated with respect to other data types for analysis purposes. Third, correlative analyses are developed to analyze features of each matrix row in terms of the other rows, guided by the classification tree as to which analyses are appropriate. A prototype was developed and successful in detecting coinciding genomic features among genes, exons, repetitive elements and CpG islands.

Base Sequence↗

PubMed2026

Phylogenomics reveals persistent gene-tree discordance in the Chenopodium album aggregate.

BACKGROUND AND AIMS: Complex genomic histories shaped by hybridisation and polyploidy can influence traits related to plant defence, stress tolerance and toxicity, particularly in Amaranthaceae, which includes crops such as quinoa and spinach. Within this family, white goosefoot (Chenopodium album), a widespread agricultural weed and traditional food resource, belongs to a diploid-polyploid aggregate with extensive phylogenetic discordance. Clarifying its evolutionary history provides context for interpreting ecologically and agronomically relevant trait variation across the aggregate. Building on the established genome-lineage framework, we tested whether discordance persists when constituent genome-lineage components are represented separately and whether the remaining signal is compatible with reticulate evolution. METHODS: We analysed 2,298 conserved nuclear BUSCO families across 27 assembly-level terminals using tree- and network-based approaches. Genome-lineage-aware analyses used 2,156 families after separating polyploid Chenopodium into A-H components, with Dysphania ambrosioides as outgroup. HyDe tested site-pattern asymmetry under global false-discovery-rate correction. KEY RESULTS: Assembly-level analyses grouped the Danish C. album aggregate accession Ca6-1 with hexaploid C. album sensu stricto dcCheAlbu1.1, whereas relationships among surrounding Chenopodium taxa were less stable. Genome-lineage-aware analyses recovered the expected B-, C- and D-affinity relationships, but substantial gene-family heterogeneity persisted. Reticulate network models fitted the assembly-level data better than bifurcating models, although inferred patterns differed between methods. HyDe detected significant site-pattern asymmetry in a small subset of loci, with most retained signal shared between the focal assemblies. CONCLUSIONS: Gene-tree discordance persists in the C. album aggregate after genome-lineage separation. The established genome-lineage framework captures the dominant phylogenomic structure, while residual heterogeneity is compatible with both tree-like and reticulate processes without identifying direct progenitors or a unique hybridisation history. This framework supports future analyses of lineage-specific and trait-associated loci related to plant defence, food quality and toxicity in C. album and related Amaranthaceae.

Chenopodium album↗

PubMed2000

Pollen availability for predaceous mites on apple: spatial and temporal heterogeneity.

It has been suggested that an abundance of alternate food early in the spring may be critical to the ability of generalist predaceous mites to suppress spider mite pests. One alternate food that is typically very abundant in spring is wind-dispersed pollen. Here we investigate, at several spatial scales, the heterogeneity in the availability of pollen to predaceous mites on apple. We found pollen to be abundant on apple leaves very soon after they opened (> 100 grains/cm2), and that the dominant pollen types at this time were wind-dispersed tree pollens (Betulaceae and Pinaceae). We found that most of the spatial variation in pollen abundance occurred at either small spatial scales (within trees) or very large spatial scales (among orchard blocks). Variability among orchards was clearly influenced by the surrounding vegetation, and probably also by the management regime (frequency of mowing). Spatial heterogeneity in pollen availability may affect the build-up of predatory mite populations in the spring, as we found early season abundances of Typhlodromus pyri (Phytoseiidae) and Zetzellia mali (Stigmaeidae) to be better correlated with early season pollen density than with abundance of mite prey (Aculus schlechtendali).

Animals↗

PubMed1996

On the interpretation of certainty factors in expert systems.

Despite the strong theoretical foundation the Bayesian probabilistic approach to model uncertainty in medicine meets many difficulties at the implementation step. One of these difficulties is related to a large amount of conditional probabilities to be assessed and in many cases this task was recognised to be practically insoluble. The MYCIN certainty factors model is a widely distributed pragmatical approach for modeling reasoning under uncertainty that substantially simplifies the problem, at the sacrifice of theoretical soundness. One can determine certainty factors as a function of prior and posterior probability. However, this approach is only consistent with the modularity axiom for certainty factors for tree-structure inference networks, which is rarely true for practical applications. In this paper we abandon the requirement of a direct probabilistic interpretation of certainty factors and build a model of propagation of uncertainty in terms of absolute belief and belief updates. We describe our model for propagating uncertainty in terms of matrix multiplication with specifically defined addition and multiplication which correspond to parallel and sequential combinations of certainty factors. It is possible to define these operations in such a manner that they form a field, and therefore to obtain some useful properties. Finally we present a method of determining certainty factors from statistical data using nonlinear regression and illustrate it with a leukemia diagnostics problem.

Artificial Intelligence↗