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PubMed2001

A multilingual medical thesaurus browser for patients and medical content managers.

This paper introduces a user-friendly browser interface which integrates multilingual search and browsing functionalities within medical thesauri via the internet. The tool is being developed as part of the GIN Austria Patient Information System and is based on an adapted datamodel of the MeSH thesaurus. A prototype offers the possibility to build up queries and export lists of MeSH main headings collected during browsing the relevant MeSH trees. The thesaurus browser can be used both by patients and citizens to build queries based on a controlled vocabulary to match them with existing documents within GIN and by medical information managers to find out appropriate keywords for interactive tagging or indexing of medical contents. A key component of this tool is the flexible choice of different languages of the MeSH datasource as well as of the user interface. Both can be changed independently at any point during a session. Another central aspect is the use of the UMLS Metathesaurus in combination with localized Thesaurus versions due to existing international character set problems.

Abstracting and Indexing↗

PubMed2003

Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs.

Related proteins with similar biological functions generally share common features, allowing us to extract the common sequence features. These common features enable us to build statistical models that can be used to classify proteins, to predict new members, and to study the sequence-function relationship of this protein function group. Although evolution underlies the basis of multiple sequence analysis methods, most methods ignore phylogenetic relationships and the evolutionary process in building these statistical models. Previously we have shown that a phylogenetic tree-based profile hidden Markov model (T-HMM) is superior in generating a profile for a group of similar proteins. In this study we used the method to generate common features of G protein-coupled receptors (GPCRs). The profile generated by T-HMM gives high accuracy in GPCR function classification, both by ligand and by coupled G protein.

Animals↗

PubMed2000

Comparing light interception with stand basal area for predicting tree growth.

Empirical and process-based tree growth models have been developedconcurrently; however, their growth predictions have rarely been compared directly. A major difference between the model types is the explicit quantification of foliage biomass as a key variable in process-based models. The aim of this work was to test if this difference has a significant impact on model behavior, especially when simulating silvicultural practices such as intensive thinning. A method was developed to evaluate leaf area and light interception of the mean tree of an even-aged stand from yield table data for Norway spruce (Picea abies (L.) Karst.) in the northern French Alps. Two scenarios were analyzed: (1) a closed stand where leaf area was limited by a maximum leaf area index-represented by young, dense stands, and (2) an open stand where leaf area was limited by the height of the crown base-represented by old, sparse stands. Light interception was calculated based on interpolation between a closed stand (Beer-Lambert law) and an isolated tree (light interception proportional to leaf area). This approach was then used to build a growth model in which competition was described by the ratio of light intercepted by a mean tree of the stand to light intercepted by an isolated tree of the same size. This process-based model was compared with a simpler empirical model in which competition was described by stand basal area. Both models fit well to yield table diameter increment data, the simpler model being slightly better. Simulation of long-term growth, interspersed with thinning, revealed differences between the models. The empirical model was sensitive to thinning and simulated a discontinuous growth pattern, whereas the model based on light calculation showed a smoother growth response to thinning. Simulations of heavy thinning in a dense stand highlighted these differences. The empirical model simulated heavy thinning in a dense stand unrealistically: after thinning, trees immediately grew as fast as trees of similar diameter in an unthinned stand at the same density. In contrast, leaf area played a regulatory role in the model based on light interception: trees with short crowns, as a result of a previous period of growth at high density, benefited little from an increase in light following thinning. It is concluded that models based on physiological or ecological processes have qualitative behaviors different from those of classical empirical models. This is especially important when models are used to make extrapolations far from reference data, for example, to forecast the long-term effect of a new silvicultural strategy.

Journal Article↗

PubMed2005

Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs.

Modular architecture is a hallmark of RNA structures, implying structural, and possibly functional, similarity among existing RNAs. To systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient RNA secondary structure comparison algorithm using a newly developed two-dimensional RNA graphical representation. Our survey of similarity among 14 pseudoknots and subtopologies within ribosomal RNAs (rRNAs) uncovers eight pairs of structurally related pseudoknots with non-random sequence matches and reveals modular units in rRNAs. Significantly, three structurally related pseudoknot pairs have functional similarities not previously known: one pair involves the 3' end of brome mosaic virus genomic RNA (PKB134) and the alternative hammerhead ribozyme pseudoknot (PKB173), both of which are replicase templates for viral RNA replication; the second pair involves structural elements for translation initiation and ribosome recruitment found in the viral internal ribosome entry site (PKB223) and the V4 domain of 18S rRNA (PKB205); the third pair involves 18S rRNA (PKB205) and viral tRNA-like pseudoknot (PKB134), which probably recruits ribosomes via structural mimicry and base complementarity. Additionally, we quantify the modularity of 16S and 23S rRNAs by showing that RNA motifs can be constructed from at least 210 building blocks. Interestingly, we find that the 5S rRNA and two tree modules within 16S and 23S rRNAs have similar topologies and tertiary shapes. These modules can be applied to design novel RNA motifs via build-up-like procedures for constructing sequences and folds.

Algorithms↗

PubMed2002

Defining the spatial impacts of poultry farm ammonia emissions on species composition of adjacent woodland groundflora using Ellenberg Nitrogen Index, nitrous oxide and nitric oxide emissions and foliar nitrogen as marker variables.

The marker variables, Ellenberg Nitrogen Index, nitrous oxide and nitric oxide fluxes and foliar nitrogen, were used to define the impacts of NH3 deposition from nearby livestock buildings on species composition of woodland ground flora, using a woodland site close to a major poultry complex in the UK. The study centred on 2 units in close proximity to each other, containing 350,000 birds, and estimated to emit around 140,000 kg N year(-1) as NH3. Annual mean concentrations of NH3 close to the buildings were very large (60 microg m(-3)) and declined to 3 microg m(-3) at a distance of 650 m from the buildings. Estimated total N deposition ranged from 80 kg N ha(-1) year(-1) at a distance of 30 m to 14 kg N ha(-1) year(-1) at 650 m downwind. Emissions of N2O and NO were 56 and 131 microg N m(-2) h(-1), respectively at 30 m and 13 and 80 microg N m(-2) h(-1), respectively at 250 m downwind of the livestock buildings. Species number in woodland ground flora downwind of the buildings remained fairly constant for a distance of 200 m from the units then increased considerably, doubling at a distance of 650 m. Within the first 200 m downwind, trends in plant species composition were hard to discern because of variations in tree canopy composition and cover. The mean Ellenberg N Index ranged from 6.0 immediately downwind of the livestock buildings to 4.8 at 650 m downwind. The mean abundance weighted Ellenberg N Index also declined with distance from the buildings. Tissue N concentrations in trees, herbs and mosses were all large, reflecting the substantial ammonia emissions at this site. Tissue N content of ectohydric mosses ranged from approximately 4% at 30 m downwind to 1.6% at 650 m downwind. An assessment of the relative merits of the three marker variables concludes, that while Ellenberg Index and trace gas fluxes of N2O and NO give broad indications of impacts of ammonia emissions on woodland vegetation, the application of a critical foliar N content for ectohydric mosses is the most useful method for providing spatial information which could be of value to policy developers and planners.

Agriculture↗

PubMed2005

Assembly models for Papovaviridae based on tiling theory.

A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can assume different local bonding structures in the capsid. This situation occurs, for example, for viruses in the family of Papovaviridae, which are linked to cancer and are hence of particular interest for the health sector. More specifically, the viral capsids of the (pseudo-) T = 7 particles in this family consist of pentamers that exhibit two different types of bonding structures. While this scenario cannot be described mathematically in terms of Caspar-Klug theory (Caspar D L D and Klug A 1962 Cold Spring Harbor Symp. Quant. Biol. 27 1), it can be modelled via tiling theory (Twarock R 2004 J. Theor. Biol. 226 477). The latter is used to encode the local bonding environment of the building blocks in a combinatorial structure, called the assembly tree, which is a basic ingredient in the derivation of assembly models for Papovaviridae along the lines of the equilibrium approach of Zlotnick (Zlotnick A 1994 J. Mol. Biol. 241 59). A phase space formalism is introduced to characterize the changes in the assembly pathways and intermediates triggered by the variations in the association energies characterizing the bonds between the building blocks in the capsid. Furthermore, the assembly pathways and concentrations of the statistically dominant assembly intermediates are determined. The example of Simian virus 40 is discussed in detail.

Capsid↗

PubMed2006

Insect antifeedants, pterocarpans and pterocarpol, in heartwood of Pterocarpus macrocarpus Kruz.

The insect antifeedant activities of pterocarpans and a sesquiterpene alcohol from the dichloromethane extract of Pterocarpus macrocarpus Kruz. (Leguminosae) were evaluated against the common cutworm, Spodoptera litura F. (Noctuidae), and the subterranean termite, Reticulitermes speratus (Kolbe)(Rhinotermitidae). Three pterocarpans, (-)-homopterocarpin (1), (-)-pterocarpin (2), and (-)-hydroxyhomopterocarpin (3) and the sesquiterpene alcohol, (+)-pterocarpol (5), were isolated from the dichloromethane extract of the heartwood of P. macrocarpus under guidance by a biological assay. Among these natural products, the most active insect antifeedant against both S. litura and R. speratus was 1. On the other hand, sesquiterpene alcohol 5 showed less insect antifeedant activity than the other pterocarpans against both insect species. While its methylated derivative, (-)-methoxyhomopterocarpin (4), showed high biological activity, 3 showed less insect antifeedant activity in this study. Interestingly, racemic 1 did not show insect antifeedant activity against S. litura. However, all of the test pterocarpans and isoflavones showed antifeedant activity against the test termites. Additionally, since these compounds were major constituents of P. macrocarpus, these antifeedant phenolics may act as chemical defense factors in this tree. In Thailand, lumber made from this tree is used to make furniture and in building construction due to its resistance to termite attack.

Alcohols↗

PubMed1998

Induction of diagnostic test strategies with multi-level information measures.

This paper presents a method for inducing clinical diagnostic test protocols or strategies from data. We represent testing strategies as a strategy tree. To support induction of strategy tree, we define three information measures: K-level information, K-level information gain, K-level gain ratio, and K-level cost index, for test selection during strategy building. These measures generalize Quinlan's information measures used in decision tree induction. We present theoretical and experimental results to show that the K-level cost index can be used to induce strategy trees in a practical domain.

Algorithms↗

PubMed2005

Modelling of classification rules on metabolic patterns including machine learning and expert knowledge.

Machine learning has a great potential to mine potential markers from high-dimensional metabolic data without any a priori knowledge. Exemplarily, we investigated metabolic patterns of three severe metabolic disorders, PAHD, MCADD, and 3-MCCD, on which we constructed classification models for disease screening and diagnosis using a decision tree paradigm and logistic regression analysis (LRA). For the LRA model-building process we assessed the relevance of established diagnostic flags, which have been developed from the biochemical knowledge of newborn metabolism, and compared the models' error rates with those of the decision tree classifier. Both approaches yielded comparable classification accuracy in terms of sensitivity (>95.2%), while the LRA models built on flags showed significantly enhanced specificity. The number of false positive cases did not exceed 0.001%.

Algorithms↗

PubMed2006

Bed-building in captive chimpanzees (Pan troglodytes): the importance of early rearing.

In the wild, great apes sleep in beds they make by successively bending branches into an interwoven platform. These beds are functionally more closely related to human beds than they are to the nests and tree-holes used by other primate species. The idea that bed-building by great apes is learned behavior that is dependent on appropriate early experiences has been proposed but never fully tested. In the present study this hypothesis was indirectly tested in 73 captive adult chimpanzees (Pan troglodytes; 27 wild-born and 46 captive-born). Bed-building and use were tested experimentally by the introduction of three sets of bedding materials. Over 200 hr of scan-sampling data were collected during 45-min observations following introduction of the bedding material. The wild-born subjects built and used beds significantly more often than the captive-born subjects. Also, wild-born subjects used more complex techniques during construction. Captive-born subjects that were mother-reared through early adolescence spent more time building and using beds than their nursery-reared counterparts. These differences remained consistent even when previous adult experience with bedding (measured as naturalistic vs. traditional housing) was accounted for. These results suggest that bed-building is a learned behavior that requires early experience and practice for acquisition.

Animals↗

PubMed2005

Analysis of the kinesin superfamily: insights into structure and function.

Kinesin superfamily proteins (KIFs) are key players or 'hub' proteins in the intracellular transport system, which is essential for cellular function and morphology. The KIF superfamily is also the first large protein family in mammals whose constituents have been completely identified and confirmed both in silico and in vivo. Numerous studies have revealed the structures and functions of individual family members; however, the relationships between members or a perspective of the whole superfamily structure until recently remained elusive. Here, we present a comprehensive summary based on a large, systematic phylogenetic analysis of the kinesin superfamily. All available sequences in public databases, including genomic information from all model organisms, were analyzed to yield the most complete phylogenetic kinesin tree thus far, comprising 14 families. This comprehensive classification builds on the recently proposed standardized nomenclature for kinesins and allows systematic analysis of the structural and functional relationships within the kinesin superfamily.

Amino Acid Sequence↗

PubMed2001

Building ICU artifact detection models with more data in less time.

As many as 86% of intensive care unit (ICU) alarms are false. Multiple signal integration of temporal monitor data by decision tree induction may improve artifact detection. We explore the effect of data granularity on model-building by comparing models made from 1-second versus 1-minute data. Models developed from 1-minute data remained effective when tested on 1-second data. Model development using 1-minute data means that more hours of ICU monitoring (including more artifacts) can be processed in less time. Compression of temporal data by arithmetic mean, therefore, can be an effective method for decreasing knowledge discovery processing time without compromising learning.

Artifacts↗

PubMed2003

Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.

Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687-705, 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Y. Pauplin (J. Mol. Evol. 51:41-47, 2000). Initial simulations suggested that FASTME, our program implementing the BME principle, was more accurate than or equivalent to all other distance methods we tested, with running time significantly faster than Neighbor-Joining (NJ). This article further explores the properties of the BME principle, and it explains and illustrates its impressive topological accuracy. We prove that the BME principle is a special case of the weighted least-squares approach, with biologically meaningful variances of the distance estimates. We show that the BME principle is statistically consistent. We demonstrate that FASTME only produces trees with positive branch lengths, a feature that separates this approach from NJ (and related methods) that may produce trees with branches with biologically meaningless negative lengths. Finally, we consider a large simulated data set, with 5,000 100-taxon trees generated by the Aldous beta-splitting distribution encompassing a range of distributions from Yule-Harding to uniform, and using a covarion-like model of sequence evolution. FASTME produces trees faster than NJ, and much faster than WEIGHBOR and the weighted least-squares implementation of PAUP*. Moreover, FASTME trees are consistently more accurate at all settings, ranging from Yule-Harding to uniform distributions, and all ranges of maximum pairwise divergence and departure from molecular clock. Interestingly, the covarion parameter has little effect on the tree quality for any of the algorithms. FASTME is freely available on the web.

Algorithms↗

PubMed2003

[Eco-value level classification and ecosystem management strategy of broad-leaved Korean pine forest in Changbai Mountain].

To realize the sustainable management of forest ecosystems, we should explicitly clarify the types and differences of the ecosystem services provided by different ecosystems under different conditions, with rethinking about the value of forest ecosystems; then solid management strategies and measurements will be enacted and applied to achieve the objects. The broad-leaved Korean pine forest (BLKPF) in Changbai Mountain is a unique and important forest type in China, owing to its many important ecosystem services such as preventing soil erosion, regulating climates, nutrient cycling, providing wood and non-timber forest products, etc. This paper is a preliminary study on the management strategy of BLKPF on the basis of analyzing the characters of the ecosystems and the relative importance of services they provided in this region. Based on the latest research of ecosystem services of BLKPF in Changbai Mountain, an idea of eco-value level (EVL) was introduced, and accordingly, management strategies were summarized by adopting the advanced theories in ecosystem management science and by analyzing field survey data. EVL means the relative amount of the value of ecosystem services provided by certain ecosystem, which can indicate the difference between services in given objects. The EVL classification of BLKPF implies the relative amount of the eco-value of different ecosystems including virgin forest, secondary forest, forest with human disturbance, and man-made forest in the clear-cutting sites. Analytical Hierarchical Processing method was used to formulate the equation for EVL index. Eight factors, namely, slope, soil depth, stability of soil maternal material, coverage of above-ground canopy, species diversity, regeneration rate of the stand, life span of dominant tree species, and intensity of human disturbance were chosen to build the formula. These factors belonged to three aspects affecting ecosystem services including the physical environment, community, and disturbance regime, and their selection and scaling were based on the previous studies on the BLKPF. The equation of EVL index (EI) was expressed as: EI = 0.542A1 + 0.171A2 + 0.072A3 + 0.067B1 + 0.043B2 + 0.014B3 + 0.010B4 + 0.081C1. According to the range of EI, ecosystems were classified into three types: low EVL type with EI from 1.000 to 1.874, medium EVL type with EI 1.874-2.749, and high EVL type with EI 2.749-3.623. Typical plots were surveyed and scaled with EI, and the predominant characters of each EVL type were summarized. Most forests of high EVL type were those in sites at high risk of soil erosion and hard to recover after disrupted. Forests of medium EVL type were those with worse community structure and composition, and were disturbed by human activities in relative steep sites. Forest of low EVL type were those in plane site with serious disruption or some young man-made stands. Based on the analyses of the characters of these three types, different management strategies were put forward. For high EVL type forest, strictly protection is most important to maintain the forest in natural succession and its eco-services. For medium EVL type forest, the key points of management are restoring their health and vigor by regulating their composition and structure in a seminatural way. For low EVL type forest, some area could be used to extensive exploration for economic benefits, and the rests should be reconstructed towards the original stand in composition and structure, based on the 'shadow ecosystem' in a close-to-nature way to promote the capacity of providing more eco-services.

Ecosystem↗

PubMed2004

Living in towers as risk factor of pollen allergy.

BACKGROUND: The effects of fluctuations in pollen counts have important implications for health services. Little research on the clinical implications of the vertical distribution of pollen in allergy symptoms has been carried out. METHODS: We have investigated the allergic symptoms of a population of 17 171 patients coming from our health area (Valladolid, Spain) and living in the city and villages. We compared the prevalence of sensitization to different pollens: Graminae, trees and shrub in relation with the floor of the building where they were living. RESULTS: Relative risk of pollen sensitization (confidence index, CI 95%) was higher in patients who were living at high floors than in those patients who were living in lower floors or at street level, independently of rural or urban conditions The chi-square showed a lineal trend in this relationship in the case of sensitization to grass pollen: chi(2): 1794, P > 0.00001 CONCLUSIONS: On the basis of our local investigations, natural pollen sensitization appears to increase with height where the patient lives. This paper reports clinical results on the influence of vertical pollen distribution in pollen allergy.

Adult↗

PubMed1999

Propagating distributions up directed acyclic graphs.

In a previous article, we considered game trees as graphical models. Adopting an evaluation function that returned a probability distribution over values likely to be taken at a given position, we described how to build a model of uncertainty and use it for utility-directed growth of the search tree and for deciding on a move after search was completed. In some games, such as chess and Othello, the same position can occur more than once, collapsing the game tree to a directed acyclic graph (DAG). This induces correlations among the distributions at sibling nodes. This article discusses some issues that arise in extending our algorithms to a DAG. We give a simply described algorithm for correctly propagating distributions up a game DAG, taking account of dependencies induced by the DAG structure. This algorithm is exponential time in the worst case. We prove that it is #P complete to propagate distributions up a game DAG correctly. We suggest how our exact propagation algorithm can yield a fast but inexact heuristic.

Algorithms↗

PubMed2001

Managing urban trees and their soil envelopes in a contiguously developed city environment.

Urban Hong Kong is covered by high building, road, and population densities. Its urban morphology is inherently not conducive to extensive or high-grade greening. Recent renewal of old areas has squeezed out some limited interstitial plantable space, although in new development areas modest spaces have been earmarked for greenery. The study aims at evaluating the major constraints to urban trees and their companion urban soil envelopes and at providing specific recommendations to improve tree management in the city. The analysis covers the above-ground confinements that dampen tree performance, the less tangible but rather difficult institutional restrictions that impose a somewhat unnecessary lid on tree planting, the multiplicity of players and stakeholders involved in urban-tree management that militates against coordination and cooperation, the widespread occupation of underground space by utility lines often to the exclusion of trees, and the extremely poor quality of urban soils that are often used without amelioration to support tree growth. The management recommendations furnish practical suggestions and hints to improve the short- and long-term welfare of trees in terms of quality, quantity, and spatial distribution. The conclusion enumerates some concrete measures for consideration by decision-makers to upgrade the city's greenery to close the gap between science and policy.

Cities↗

PubMed2001

Pattern recognition for road traffic accident severity in Korea.

An increasing number of road traffic accidents (RTA) in Korea has emerged as being harmful both for the economy and for safety. An accurately estimated classification model for several severity types of RTA as a function of related factors provides crucial information for the prevention of potential accidents. Here, three data-mining techniques (neural network, logistic regression, decision tree) are used to select a set of influential factors and to build up classification models for accident severity. The three approaches are then compared in terms of classification accuracy. The finding is that accuracy does not differ significantly for each model and that the protective device is the most important factor in the accident severity variation.

Accidents, Traffic↗