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Knowledge discovery and data mining to assist natural language understanding.

As natural language processing systems become more frequent in clinical use, methods for interpreting the output of these programs become increasingly important. These methods require the effort of a domain expert, who must build specific queries and rules for interpreting the processor output. Knowledge discovery and data mining tools can be used instead of a domain expert to automatically generate these queries and rules. C5.0, a decision tree generator, was used to create a rule base for a natural language understanding system. A general-purpose natural language processor using this rule base was tested on a set of 200 chest radiograph reports. When a small set of reports, classified by physicians, was used as the training set, the generated rule base performed as well as lay persons, but worse than physicians. When a larger set of reports, using ICD9 coding to classify the set, was used for training the system, the rule base performed worse than the physicians and lay persons. It appears that a larger, more accurate training set is needed to increase performance of the method.

Artificial Intelligence↗

Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis.

Animals↗

Developing conceptual frameworks for the recovery of aquatic biota from acidification.

Surface water acidity is decreasing in large areas of Europe and North America in response to reductions in atmospheric S deposition, but the ecological responses to these water-quality improvements are uncertain. Biota are recovering in some lakes and rivers, as water quality improves, but they are not yet recovering in others. To make sense of these different responses, and to foster effective management of the acid rain problem, we need to understand 2 things: i) the sequence of ecological steps needed for biotic communities to recover; and ii) where and how to intervene in this process should recovery stall. Here our purpose is to develop conceptual frameworks to serve these 2 needs. In the first framework, the primarily ecological one, a decision tree highlights the sequence of processes necessary for ecological recovery, linking them with management tools and responses to bottlenecks in the process. These bottlenecks are inadequate water quality, an inadequate supply of colonists to permit establishment, and community-level impediments to recovery dynamics. A second, more management-oriented framework identifies where we can intervene to overcome these bottlenecks, and what research is needed to build the models to operationalize the framework. Our ability to assess the benefits of S emission reduction would be simplified if we had models to predict the rate and extent of ecological recovery from acidification. To build such models we must identify the ecological steps in the recovery process. The frameworks we present will advance us towards this goal.

Acid Rain↗

Decision-theoretic refinement planning: a new method for clinical decision analysis.

Clinical decision analysis seeks to identify the optimal management strategy by modelling the uncertainty and risks entailed in the diagnosis, natural history, and treatment of a particular problem or disorder. Decision trees are the most frequently used model in clinical decision analysis, but can be tedious to construct, cumbersome to use, and computationally prohibitive, especially with large, complex decision problems. We present a new method for clinical decision analysis that combines the techniques of decision theory and artificial intelligence. Our model uses a modular representation of knowledge that simplifies model building and enables more fully automated decision making. Moreover, the model exploits problem structures to yield better computational efficiency. As an example we apply our techniques to the problem of management of acute deep venous thrombosis.

Artificial Intelligence↗

[Structure and ecological benefits of urban forest in Shenyang build-up area].

Investigations were made in the sampling plots covering 243 km2 of the Shenyang urban area, and the results were used as the input for the Urban Forest Management Information System (UFMIS), which was developed based on the model of CITY green. With this system, and using tree species, tree density, tree height grade distribution, tree DBH (diameter at beast height) grade distribution, and tree health condition as parameters, the land use and forest structure in Shenyang City were analyzed. It was found that there were 1,914,500 trees in Shenyang, belonging to 136 species. The 25 dominant species accounted for 84.78% of the total number of trees, and the forest coverage was 9.765%. Trees with DBH < 0.25 m and > 0.5 m accounted for 82.8% of the total, and the young, middle-aged and old trees occupied 27%, 58% and 15% of the total, respectively. The healthy status of 84% of the trees was above middle level. Therefore, the forest in Shenyang urban is at a stable stage. According to the statistical results from UFMIS, the ecological value of forest in Shenyang urban is as high as 26,526,955. 1 USD in terms of economy.

China↗

[Light environment characteristics of forest gap in deciduous broad-leaved forest and its effects on growth features of Gynostemma pentaphyllum in Jianghuai watershed].

The daily total light intensity, various wave band light intensities, spectrum composition, and the growth characteristics and total saponia content of Gynostemma pentaphyllum in forest gap and under forest were studied in deciduous forest (Liquidambar formosana) in Jianghuai watershed. The results showed that the intensities of full wavelength daily total light, blue light(400-510 nm), yellow-green light(510-610 nm), red-orange light (610-720 nm) and near-infrared light(720-1100 nm) in forest gap were higher than those under forest. The intensities and spectra compositions of blue light and red-orange light in forest gaps were significantly higher than those under forest. Additionally, the differences between those in forest gap and under forest varied seasonally. The relative intensity of blue light in April, July and October in forest gap was 8.32%-28.83%, 30.00%-579.17% and 6.70%-88.74% more than those under forest, respectively, and that of red-orange light in April, July and October in forest gap was 8.72%-28.83%, 30.19%-502.69%, 6.76%-91.57% more than those under forest, respectively. The spectrum composition of blue light in forest gap in these 3 months was 5.76%, 33.14% and 17.29% higher than those under forest, respectively, and that of red-orange light in forest gap in these 3 months was 5.04%, 53.34% and 10.23% higher than those under forest, respectively. The net photosynthetic rate, total dry-matter weight, and total saponia content of Gynostemma pentaphyllum growing in forest gap were higher than those under forest. Gynostemma pentaphyllum growing in forest gap had more dry-matter distributed in stem. The results could be available to utilize the light environment of deciduous broad-leaved forest and further building comprehensive management model of Gynostemma pentaphyllum in Jianghuai watershed zone.

Environment↗

Protein family classification using sparse Markov transducers.

In this paper we present a method for classifying proteins into families using sparse Markov transducers (SMTs). Sparse Markov transducers, similar to probabilistic suffix trees, estimate a probability distribution conditioned on an input sequence. SMTs generalize probabilistic suffix trees by allowing for wild-cards in the conditioning sequences. Because substitutions of amino acids are common in protein families, incorporating wildcards into the model significantly improves classification performance. We present two models for building protein family classifiers using SMTs. We also present efficient data structures to improve the memory usage of the models. We evaluate SMTs by building protein family classifiers using the Pfam database and compare our results to previously published results.

Algorithms↗

ForestTreeDB: a database dedicated to the mining of tree transcriptomes.

ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (http://foresttree.org/ftdb). It currently encompasses 344,878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects.

Databases, Nucleic Acid↗

Long term fire scar monitoring with remote sensing in Northern Namibia: relations between fire frequency, rainfall, land cover, fire management and trees.

A cost-effective method was developed to map fire scars on Quicklooks of Landat TM imagery. The method was compared with a full resolution Landsat image using visual interpretation and supervised classification using the Maximum Likelihood procedure, resulting in a high degree of agreement between methods. A long time series of fire scars was developed using all available Landsat Quicklooks between 1989 and 2001 for an area of 63000 sq km in north-east Namibia. Between 27 and 51% of the study area burned annually, while only 10% of the area did not burn between 1989 and 2001. Not-burned areas were mainly settled areas and permanent wetlands. 33% of the area burned between 5 and 7 times during the 13 years indicating a high frequency overall. Rainfall and livestock had little influence on burned areas. In 1996 formal fire management started in a portion of the study area consisting of building firebreaks and holding awareness programs. A comparison of burned areas before and after the intervention started allowed evaluating its effectiveness. The area where the formal fire management program was undertaken showed a significant decrease in burned area. It is suggested that awareness campaigns rather than firebreaks contributed to this decrease. Selected tree population data were compared with fire frequencies. Differences in tree occurrence, regeneration, and stem diameter distributions between low and high fire frequencies could be detected and explained with known responses of the species to fire. This suggests that the observed time series is representative of a long-term fire regime in the area.

Biomass↗

Supertree construction in the genomic age.

Supertree construction is the process whereby overlapping phylogenetic trees, and not character data, are combined to yield a larger, more comprehensive phylogeny. In this chapter, I review the logic and methodology behind supertree construction and argue that it holds a necessary place in phylogenetic inference. Much of the justification for supertrees is admittedly practical. As I show with an empirical example, most large groups have insufficient sequence data to build complete phylogenies for them. By being able to indirectly combine diverse forms of phylogenetic information, supertrees are the best method for constructing complete phylogenies of groups with hundreds of species. However, supertree construction can also be justified on theoretical grounds. As whole genomic data are obtained for increasing numbers of species, the theoretical and practical advantages of supertrees together will ensure that the method will play a necessary analytical role as part of a divide-and-conquer strategy to reconstructing the Tree of Life.

Animals↗

Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms: implications for pathogenesis in avocado sunblotch disease.

Avocado sunblotch viroid (ASBVd) is a structured RNA molecule responsible for sunblotch disease of avocado, characterised by distinct chloroses of fruit, leaves, and stems. Despite its impact on avocado, the mechanism by which ASBVd elicits sunblotch symptoms remains unknown. Previous studies on other avsunviroids have shown that viroid-derived small RNAs (vd-sRNAs) with specific sequence mutations can trigger leaf chlorosis via RNA silencing of host genes. Building on this knowledge, we aimed to shed light on the molecular basis of ASBVd pathogenesis by analysing ASBVd sequence variants and ASBVd-sRNAs from bleached and asymptomatic leaf tissues of sunblotch-affected avocado trees. Sequencing of ASBVd clones revealed that variants carrying the pathogenic determinant for bleaching were present in both green and yellow leaf tissues. Next-generation sequencing (NGS) identified ASBVd-sRNAs that varied in abundance between symptomatic and asymptomatic leaf tissues, correlating with viroid titre. We discovered 64 vd-sRNAs spanning the pathogenic region of the ASBVd genome, which were almost exclusively found in yellow tissues. The ASBVd-sRNAs containing the bleaching-associated mutation were predicted to target numerous avocado transcripts for degradation, with 25 of these transcripts significantly downregulated in bleached tissues. Notably, one of these genes, encoding a chloroplastic protein, demonstrated strong evidence of ASBVd-sRNA-guided RNA silencing, presenting a promising candidate for future research into the molecular trigger for ASBVd-induced bleaching symptoms. This study is the first to investigate ASBVd-sRNAs in bleached leaves using NGS. Our findings support the role of RNA silencing in sunblotch symptom development and reveal a unique silencing trigger compared to other avsunviroids.

Persea↗

Impact of land use practices on faunal abundance, nutrient dynamics and biochemical properties of desert pedoecosystem.

Increased dependence of resource-poor rural communities on soils of low inherent fertility are the major problem of desert agroecosystem. Agrisilviculture practices may help to conserve the soil biota for maintaining essential soil properties and processes in harsh climate. Therefore, the impacts of different land use systems on faunal density, nutrient dynamics and biochemical properties of soil were studied in agrisilviculture system of Indian desert. The selected fields had trees (Zizyphus mauritiana, Prosopis cineraria, Acacia nilotica) and crops (Cuminum cyminum, Brassica nigra, Triticum aestivum) in different combinations. Populations of Acari, Myriapoda, Coleoptera, Collembola, other soil arthropods and total soil fauna showed significant changes with respect to different land use practices and tree species, indicating a strong relation between above and below ground biodiversity. The Coleoptera exhibited greatest association with all agrisilviculture fields. The Z. mauritiana system indicated highest facilitative effects (RTE value) on all groups of soil fauna. Soil temperature, moisture, organic carbon, nitrate- and ammonical-nitrogen, available phosphorus, soil respiration and dehydrogenase activity were greater under tree than that of tree plus cropping system. It showed accumulation of nitrate-nitrogen in tree field and more utilization by crops in cultivated lands. Positive and significant correlation among organic carbon, nitrate- and ammonical-nitrogen, phosphorus, soil respiration and dehydrogenase activity clearly reflects increase in soil nutrients with the increase in microbial and other biotic activity. P. cineraria field was the best pedoecosystem, while C. cyminum was the best winter crop for cultivation in desert agroforestry system for soil biological health and soil sustainability. The increase in organic carbon, soil nutrients and microbial activity is associated with the increase in soil faunal population which reflect role of soil fauna in fertility building. This suggests that strategies may be developed for nurturing fertility-building soil fauna and managing degraded pedoecosystem in desert just by adopting suitable agricultural practices.

Agriculture↗

Medical decision-making in membranous nephropathy: how to use limited clinical research evidence in patient management.

Evidence-based medicine (EBM) originally referred to the use of a combination of clinical expertise and research evidence to make medical decisions, while carefully considering the patient's preference. In Japan, however, EBM has been misunderstood as the more abstract pursuit of acquiring research evidence and building medical guidelines. This review aims to summarize the available data regarding therapy for membranous nephropathy (MN), a field in which no consensus has been reached, and to discuss medical decision-making by using a decision tree in several model cases. In clinical practice, we have to consider both the risks and benefits of treatment. These are evaluated by their therapeutic effect (the rate of improvement, no change, or worsening) and by the patients' quality of life (QOL). This process is compatible with the essential concept of EBM.

Adult↗

Solubility prediction by recursive partitioning.

PURPOSE: To build and test a computational model for predicting small molecule solubility, to improve the cost-effectiveness of the selection of vendor compounds suitable for nuclear magnetic resonance (NMR) screening. METHODS: A simple recursive partitioning decision tree-based classification model was generated utilizing "off-the-shelf" commercial software from Accelrys Inc., with a training set of 1992 compounds based on a series of calculated topologic and physical properties. The predictive ability of the decision tree was then assessed by employing it to classify a test set of 2851 vendor compounds, and the classification was subsequently used to guide the purchase of 686 compounds for the purpose of NMR screening. RESULTS: When the decision tree was used to guide purchasing, the percentage of "acceptable" compounds suitable for NMR screening doubled compared with the use of a simple cLogP cutoff, improving the successful selection rate from 25% to 50%. CONCLUSIONS: A simple recursive partitioning decision tree may successfully be used to improve cost-effectiveness by reducing the wastage associated with the unnecessary purchase of vendor compounds unsuitable for NMR screening because of insolubility.

Computer Simulation↗

A fast method to sample real protein conformational space.

A fast computer program, FOLDTRAJ, to generate plausible random protein structures is reported. All-atom proteins are made directly in continuous three-dimensional space starting from primary sequence with an N to C directed build-up method. The method uses a novel pipelined residue addition approach in which the leading edge of the protein is constructed three residues at a time for optimal protein geometry, including the placement of cis proline. Build-up methods represent a classic N-body problem, expected to scale as N(2). When proteins become more collapsed, build-up methods are susceptible to backtracking problems which can scale exponentially with the number of residues required to back out of a trapped walk. We have provided solutions to both these problems, using a multiway binary tree that makes the N-body problem of bump-checking scale as NlogN, and speeding up backtracking by varying the number of tries before backtracking based on available conformational space. FOLDTRAJ is independent of energy potentials, other than that implicit in the geometrical properties derived by statistical studies of known structures, and in atomic Van der Waals radii. WHAT-CHECK shows that the program generates chirally and physically valid proteins with all bond lengths, angles and dihedrals within allowable tolerances. Random structures built using sequences from PDB files 1SEM, 2HPR, and 1RTP typically have 5-15% alpha-helical content (according to DSSP) and on the order of 20% beta-strand/extended content. Ensembles of random structures are compared with polymer theory and with experimentally determined fluorescence resonance energy transfer distances. Reasonably sized structure ensembles do sample most of the conformational space available to proteins. The method is also capable of protein reconstruction using Calpha--Calpha direction vectors, and it compares favorably with methods that reconstruct protein backbones based on alpha-carbon coordinates, having an average backbone and Cbeta root mean square deviation of 0.63 A for nine different protein folds. Proteins 2000;39:112-131.

Algorithms↗

Relocalization of membrane enzymes accompanies biliary atresia in lamprey liver.

Light- and electron-microscopic histochemical procedures were used to show the distribution of the membrane-bound enzymes alkaline phosphatase (Alp), adenosine triphosphatase (ATPase), and 5'-nucleotidase (5'-nuc) in the livers of lamprey, Petromyzon marinus, throughout the life cycle. In larvae, the three enzymes are located at the biliary pole on the canalicular membranes of microvilli. At metamorphosis the enzymes become localized at all lateral cell surfaces of hepatocytes as bile canaliculi degenerate in the programmed regression of the entire biliary tree. This latter pattern of enzyme distribution persists during the parasitic adult phase but no activity is evident in individuals in the spawning migration. As the timing of the relocalization of enzymatic activity correlates well with a build-up of bile products and iron during metamorphosis, it is suggested that the lateral surface may be the new site for transport of these products.

5'-Nucleotidase↗

Tropical forest cover change in the 1990s and options for future monitoring.

Despite the importance of the world's humid tropical forests, our knowledge concerning their rates of change remains limited. Two recent programmes (FAO 2000 Forest Resources Assessment and TREES II), exploiting the global imaging capabilities of Earth observing satellites, have recently been completed to provide information on the dynamics of tropical forest cover. The results from these independent studies show a high degree of conformity and provide a good understanding of trends at the pan-tropical level. In 1990 there were some 1150 million ha of tropical rain forest with the area of the humid tropics deforested annually estimated at 5.8 million ha (approximately twice the size of Belgium). A further 2.3 million ha of humid forest is apparently degraded annually through fragmentation, logging and/or fires. In the sub-humid and dry tropics, annual deforestation of tropical moist deciduous and tropical dry forests comes to 2.2 and 0.7 million ha, respectively. Southeast Asia is the region where forests are under the highest pressure with an annual change rate of -0.8 to -0.9%. The annual area deforested in Latin America is large, but the relative rate (-0.4 to -0.5%) is lower, owing to the vast area covered by the remaining Amazonian forests. The humid forests of Africa are being converted at a similar rate to those of Latin America (-0.4 to -0.5% per year). During this period, secondary forests have also been established, through re-growth on abandoned land and forest plantations, but with different ecological, biophysical and economic characteristics compared with primary forests. These trends are significant in all regions, but the extent of new forest cover has proven difficult to establish. These results, as well as the lack of more detailed knowledge, clearly demonstrate the need to improve sound scientific evidence to support policy. The two projects provide useful guidance for future monitoring efforts in the context of multilateral environmental agreements and of international aid, trade and development partnerships. Methodologically, the use of high-resolution remote sensing in representative samples has been shown to be cost-effective. Close collaboration between tropical institutions and inter-governmental organizations proved to be a fruitful arrangement in the different projects. To properly assist decision-making, monitoring and assessments should primarily be addressed at the national level, which also corresponds to the ratification level of the multilateral environmental agreements. The Forest Resources Assessment 2000 deforestation statistics from countries are consistent with the satellite-based estimates in Asia and America, but are significantly different in Africa, highlighting the particular need for long-term capacity-building activities in this continent.

Conservation of Natural Resources↗

The role of the clinical research coordinator in multicenter clinical trials.

The clinical research coordinator plays a crucial role in organizing a site's participation in the expanding arena of multicenter medical and pharmacologic clinical trials. This summary clarifies the role of the clinical research coordinator for inexperienced staff members assuming these responsibilities and outlines planning procedures leading to successful implementation. Emphasis is placed on establishing an interdependent relationship with the principal investigator, careful protocol assessment, team building, and staff feedback. Useful tools such as study manuals and physicians' study orders are described.

Algorithms↗