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PubMed2006

Dynamic knowledge validation and verification for CBR teledermatology system.

OBJECTIVE: Case-based reasoning has been of great importance in the development of many decision support applications. However, relatively little effort has gone into investigating how new knowledge can be validated. Knowledge validation is important in dealing with imperfect data collected over time, because inconsistencies in data do occur and adversely affect the performance of a diagnostic system. METHODS: This paper consists of two parts. First, it describes methods that enable the domain expert, who may not be familiar with machine learning, to interactively validate knowledge base of a Web-based teledermatology system. The validation techniques involve decision tree classification and formal concept analysis. Second, it describes techniques to discover unusual relationships hidden in the dataset for building and updating a comprehensive knowledge base, because the diagnostic performance of the system is highly dependent on the content thereof. Therefore, in order to classify different kinds of diseases, it is desirable to have a knowledge base that covers common as well as uncommon diagnoses. RESULTS AND CONCLUSION: Evaluation results show that the knowledge validation techniques are effective in keeping the knowledge base consistent, and that the query refinement techniques are useful in improving the comprehensiveness of the case base.

Dermatology↗

PubMed2006

A novel screening assay for hydroxynitrile lyases suitable for high-throughput screening.

Hydroxynitrile lyases (Hnls) are important biocatalysts for the synthesis of optically pure cyanohydrins, which are used as precursors and building blocks for a wide range of high price fine chemicals. Although two Hnl enzymes, from the tropical rubber tree Hevea brasiliensis and from the almond tree Prunus amygdalus, are already used for large scale industrial applications, the enzymes still need to be improved and adapted to the special demands of industrial processes. In many cases directed evolution has been the method of choice to improve enzymes, which are applied as industrial biocatalysts. The screening procedure is the most crucial point in every directed evolution experiment. Herein, we describe the successful development of a novel screening assay for Hnls and its application in high-throughput screening of Escherichia coli mutant libraries. The new assay allows rapid screening of mutant libraries and facilitates the discovery of improved enzyme variants. Hnls catalyze the cleavage of cyanohydrins to hydrocyanic acid and the corresponding aldehyde or ketone. The enzyme assay is based on the detection of hydrocyanic acid produced, making it an all-purpose screening assay, without restriction to any kind of substrate. The gaseous HCN liberated within the Hnl reaction is detected by a visible colorimetric reaction. The facile, highly sensitive and reproducible screening method was validated by identifying new enzyme variants with novel substrate specificities.

Aldehyde-Lyases↗

PubMed2005

Classification of drugs in absorption classes using the classification and regression trees (CART) methodology.

Classification and regression trees (CART) were evaluated for their potential use in a quantitative structure-activity relationship (QSAR) context. Models were build using the published absorption values for 141 drug-like molecules as response variable and over 1400 molecular descriptors as potential explanatory variables. Both the role of two- and three-dimensional descriptors and their relative importance were evaluated. For the used dataset, CART models showed high descriptive and predictive abilities. The predictive abilities were evaluated based on both cross-validation and an external test set. Application of the variable ranking method to the models showed high importances for the n-octanol/water partition coefficient (logP) and polar surface area (PSA). This shows that CART is capable of selecting the most important descriptors, as known from the literature, for the absorption process in the intestinal tract.

Intestinal Mucosa↗

PubMed2005

A model-based approach for detecting coevolving positions in a molecule.

We present a new method for detecting coevolving sites in molecules. The method relies on a set of aligned sequences (nucleic acid or protein) and uses Markov models of evolution to map the substitutions that occurred at each site onto the branches of the underlying phylogenetic tree. This mapping takes into account the uncertainty over ancestral states and among-site rate variation. We then build, for each site, a "substitution vector" containing the posterior estimates of the number of substitutions in each branch. The amount of coevolution for a pair of sites is then measured as the Pearson correlation coefficient between the two corresponding substitution vectors and compared to the expectation under the null hypothesis of independence. We applied the method to a 79-species bacterial ribosomal RNA data set, for which extensive structural characterization has been done over the last 30 years. More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs.

Base Sequence↗

PubMed1977

An investigation into the health of kapok workers.

Kapok is a cotton-like fibre obtained from the fruits of Ceiba pentandra, a tree surgeon in tropical countries. In Sri Lanka ginning of kapok is usually done by machine in poorly ventilated buildings where workers are exposed to a great deal of dust. Forty-one workers in five ginneries in Colombo were examined. Mill fever occurred in 28 (77-8%) of the 36 workers who were able to give a history. Chronic bronchitis, which is an uncommon condition in Sri Lanka, was detected to seven workers with an average of 20-9 years' service in the industry. It is suggested that chronic bronchitis is an occupational hazard of workers who are exposed to kapok dust for long periods. Byssinosis was not found in any of the workers studied.

Adolescent↗

PubMed1987

Artificial intelligence--its use in nephrology.

Artificial intelligence techniques and expert systems are graduating from research laboratories to enter many human domains of activities. However, initial expectations of the seventies have been transformed with time to a more sober reality. Starting from examples in nephrology, this paper tries to give a balanced view of this new technology. Justification, indication and limitation of present expert systems are discussed as regards their possible goals. The respective roles of the experts and knowledge engineers are described. The need to integrate the artificial intelligence approach into present patient database management systems in order to build up expert database systems is evaluated.

Database Management Systems↗

PubMed2006

Practice parameters for sublingual immunotherapy.

The efficacy and safety of sublingual immunotherapy (SLIT) are currently supported by clinical trials, meta-analysis and post-marketing surveys. Practice parameters for clinical use of SLIT are proposed here by a panel of Italian specialists, with reference to evidence based criteria. Indications to SLIT include allergic rhinoconjunctivitis, asthma, and isolated conjunctivitis (strength of recommendation: grade A). As to severity of the disease, SLIT is indicated in moderate/severe intermittent rhinitis, persistent rhinitis and mild to moderate asthma (grade D). SLIT may be safely prescribed also in children aged three to five years (grade B), and its use in subjects aged more than 60 years is not prevented when the indications and contraindication are ascertained (grade D). The choice of the allergen to be employed for SLIT should be made in accordance with the combination of clinical history and results of skin prick tests (grade D). Polysensitisation, i.e. the occurrence of multiple positive response does not exclude SLIT, which may be done with the clinically most important allergens (grade D). As to practical administration, co-seasonal, pre co-seasonal, and continuous schedules are available, being the latter recommended for perennial allergens or for pollens with particularly prolonged pollination, such as Parietaria (grade D). For pollens with relatively short pollination, such as grasses and trees (cypress, birch, alder, hazelnut, olive) the pre co-seasonal and perennial schedules are preferred (grade C). The build-up phases suggested by manufacturers can be safely used (grade A), but they can be modified according to the patient's tolerance (grade C). A duration of SLIT of 3-5 years is recommended to ensure a long-lasting clinical effect after the treatment has been terminated (grade C).

Administration, Sublingual↗

PubMedDate not supplied

[Wood anatomy and uses of 7 tropical tree species from Mexico].

The wood anatomy of Coccoloba cozumelensis Hemsl., Coccoloba spicata Lundell, Gymnanthes lucida Sw., Blomia cupanioides Miranda, Canella winterana (L.) Gaertn., Aspidosperma megalocarpon Müell Arg. and Ehretia tinifolia L., is described. One tree per species was collected in the tropical rain forest of Quintana Roo, Mexico. Their wood has important traditional uses in furniture, tools, rural buildings, posts, fences, railroads and firewood. Macroscopic and microscopic characteristics were described and measured in wood samples, permanent slides and macerated material. These species have diffuse porosity, alternate vessel pits, simple perforation plates, numerous and small rays; libriform fibres are common, as well as ergastic material in gum forms, calcium carbonate and silica crystals. These characteristics explain aesthetical, weight, hardness and resistance (to mechanical and biological damage) characters that fit traditional use by the Maya.

Classification↗

PubMed2006

Linking clinical measurements and kinematic gait patterns of toe-walking using fuzzy decision trees.

Toe-walking is one of the most prevalent gait deviations and has been linked to many diseases. Three major ankle kinematic patterns have been identified in toe-walkers, but the relationships between the causes of toe-walking and these patterns remain unknown. This study aims to identify these relationships. Clearly, such knowledge would increase our understanding of this gait deviation, and could help clinicians plan treatment. The large quantity of data provided by gait analysis often makes interpretation a difficult task. Artificial intelligence techniques were used in this study to facilitate interpretation as well as to decrease subjective interpretation. Of the 716 limbs evaluated, 240 showed signs of toe-walking and met inclusion criteria. The ankle kinematic pattern of the evaluated limbs during gait was assigned to one of three toe-walking pattern groups to build the training data set. Toe-walker clinical measurements (range of movement, muscle spasticity and muscle strength) were coded in fuzzy modalities, and fuzzy decision trees were induced to create intelligible rules allowing toe-walkers to be assigned to one of the three groups. A stratified 10-fold cross validation situated the classification accuracy at 81%. Twelve rules depicting the causes of toe-walking were selected, discussed and characterized using kinematic, kinetic and EMG charts. This study proposes an original approach to linking the possible causes of toe-walking with gait patterns.

Biomechanical Phenomena↗

PubMed1996

Cellular sociology applied to neuroendocrine tumors of the lung: quantitative model of neoplastic architecture.

This paper reports on cellular sociology, which consists of modeling tissular architecture based on graph theory. Voronoi's diagram was chosen to build the models. This diagram derives from a cell neighborhood concept and generates parameters which objectively represent tissue architecture. Minimal spanning tree (MST) is probably the more frequently used among graphs and successfully discriminates different grades of pathological process. However, Voronoi's diagram is more comprehensive and a more complete representation of architecture with the advantage of stability. The lung neuroendocrine tumor classification is far from being consensual, especially for lesions which don't fall in with typical carcinoid and small cell carcinoma groups. By comparing architectural models of 20 neuroendocrine tumors of the lung, this work supports the morphologic spectrum concept of these tumors and also supports the recently proposed concept of large-cell neuroendocrine tumors of the lung. Finally, architectural parameters separate small-cell-lung carcinomas from neuroendocrine non-small-cell lung carcinomas.

Carcinoid Tumor↗

PubMed2005

Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis.

Many molecular phylogenies of viruses build upon the analysis of single genes. The study of whole-genomes, however, might yield more reliable information to infer tree topologies and a better approach for drawing the evolutionary history of virus families. In this study, we apply a novel comparative proteomic approach to seek whether incorporating information from the entire proteome would support the actual taxonomy of the family Bromoviridae. Our results suggest that the current taxonomic classification should be modified in several aspects to account for the genomic properties of the Bromoviridae. These differences are: i) Alfalfa mosaic virus (AMV) is a true Ilarvirus instead of constituting an independent genus; ii) Pelargonium zonate spot virus (PZSV) should be considered as a member of the Bromoviridae; and iii) the genus Ilarvirus should be divided into fewer phylogenetic subgroups than suggested by antigenic differences.

Bromoviridae↗

PubMed2001

Physicochemical and graph theoretical descriptors in developmental toxicity SAR: a comparative study.

Chemical insults to the developing fetus can lead to growth retardation, malformation, death, and functional deficits. The present study seeks to determine if physicochemical and/or graph theoretical parameters can be used to determine a structure-activity relationship (SAR) for developmental toxicity, and if consistency is observed among the selected features. The biological data utilized consists of a diverse series of compounds evaluated within the Chernoff-Kavlock in vivo mouse assay. Physicochemical parameters calculated correspond to electronic, steric, and transport properties. Graph theoretical parameters calculated include the simple, valence, and kappa indices. Both sets of parameters were independently applied to derive SARs in order to compare the quality of the respective models. Multiple random sampling, without replacement, was utilized to obtain ten training/test partitions. Models were built by linear discriminant analysis, decision trees, and neural networks respectively. Comparisons on identical sets of data were carried out to determine if any of the model building procedures had a significant advantage in terms of predictive performance. Furthermore, comparison of the features selected within and across the model building processes led to the determination of model consistency. Our results indicate that consistent features related to developmental toxicity are observed and that both physicochemical and graph theoretical parameters have equal utility.

Animals↗

PubMedDate not supplied

[Patient-centered consultation of "good practice guidelines": OncoDoc, a decision support system for the management of breast cancer patients].

Beyond considerations of cost-effectiveness, clinical practice guidelines (CPG) can reduce practice variations and thus improve the quality of care. However, despite the proliferation of implemented CPG and their wide diffusion thanks to Internet-based technologies, physicians' compliance with formal standards is weak. Developed according to a document-based paradigm, OncoDoc proposes an original framework for implementing CPG. Domain knowledge has been encoded as a decision tree whose branches are both exclusive and exhaustive. This generic knowledge is operationalized at the point of care by the interactive building, through hypertextual navigation, of a patient-based clinical context leading to specific therapeutic recommendations. OncoDoc has first been applied to the management of breast cancer patients and demonstrated within a full-scale experimentation in a clinical setting a compliance of 80 per cent.

Breast Neoplasms↗

PubMedDate not supplied

Use of recursion forests in the sequential screening process: consensus selection by multiple recursion trees.

The application of Cheminformatics to High-Throughput Screening (HTS) data requires the use of robust modeling methods. Robust models must be able to accommodate false positive and false negative data yet retain good explanatory and predictive power. Recursive Partitioning has been shown to accommodate false positive and false negative data in the model building phase but suffers from a high false positive rate in the prediction phase, especially with sparse data sets such as HTS data. Here, we introduce Consensus Selection as a procedure to decrease the false positive rate of Recursive Partitioning-based models. Consensus Selection by Multiple Recursion Trees can increase the hit rate of a High-Throughput Screen in excess of 30-fold while significantly reducing the false positive rate relative to single Recursion Tree models.

Combinatorial Chemistry Techniques↗

PubMed1975

Coronary and aortic atherosclerosis in relation to body-build factors.

The relationship between body-build factors and the severity of coronary and aortic atherosclerosis was estimated in a series of 193 men, aged 25 years or over, who had died of violent causes. Overweight showed a significant correlation with the extent of coronary and aortic fatty streaks but not with the extent of coronary or aortic raised lesions or calcifications. The stenosis score, which expressed the degree of obstruction in the coronary arterial tree, showed a slight tendency to a positive correlation with the degree of obesity but the finding was not consistent. Nor correlation was found between the sturdiness factor of body-build and the severity of atherosclerosis. The muscularity factor showed a significant correlation with the extent of coronary and aortic fatty streaks and an inverse correlation with aortic calcifcations.

Adipose Tissue↗

PubMed2004

Comparison of hospital charge prediction models for colorectal cancer patients: neural network vs. decision tree models.

Analysis and prediction of the care charges related to colorectal cancer in Korea are important for the allocation of medical resources and the establishment of medical policies because the incidence and the hospital charges for colorectal cancer are rapidly increasing. But the previous studies based on statistical analysis to predict the hospital charges for patients did not show satisfactory results. Recently, data mining emerges as a new technique to extract knowledge from the huge and diverse medical data. Thus, we built models using data mining techniques to predict hospital charge for the patients. A total of 1,022 admission records with 154 variables of 492 patients were used to build prediction models who had been treated from 1999 to 2002 in the Kyung Hee University Hospital. We built an artificial neural network (ANN) model and a classification and regression tree (CART) model, and compared their prediction accuracy. Linear correlation coefficients were high in both models and the mean absolute errors were similar. But ANN models showed a better linear correlation than CART model (0.813 vs. 0.713 for the hospital charge paid by insurance and 0.746 vs. 0.720 for the hospital charge paid by patients). We suggest that ANN model has a better performance to predict charges of colorectal cancer patients.

Algorithms↗

PubMed2007

Demonstrating freedom from disease using multiple complex data sources 1: a new methodology based on scenario trees.

Current methods to demonstrate zone or country freedom from disease are based on either quantitative analysis of the results of structured representative surveys, or qualitative assessments of multiple sources of evidence (including complex non-representative sources). This paper presents a methodology for objective quantitative analysis of multiple complex data sources to support claims of freedom from disease. Stochastic scenario tree models are used to describe each component of a surveillance system (SSC), and used to estimate the sensitivity of each SSC. The process of building and analysing the models is described, as well as techniques to take into account any lack of independence between units at different levels within a SSC. The combination of sensitivity estimates from multiple SSCs into a single estimate for the entire surveillance system is also considered, again taking into account lack of independence between components. A sensitivity ratio is used to compare different components of a surveillance system. Finally, calculation of the probability of country freedom from the estimated sensitivity of the surveillance system is illustrated, incorporating the use and valuation of historical surveillance evidence.

Animal Diseases↗

PubMed2000

Radionuclides in pinon pine (Pinus edulis) nuts from Los Alamos National Laboratory lands and the dose from consumption.

One of the dominant tree species growing within and around the eastern portion of Los Alamos National Laboratory (LANL), Los Alamos, NM, lands is the pinon pine (Pinus edulis). Pinon pine is used for firewood, fence posts, and building materials and is a source of nuts for food--the seeds are consumed by a wide variety of animals and are also gathered by people in the area and eaten raw or roasted. This study investigated the (1) concentration of 3H, 137Cs, 90Sr, totU, 238Pu, 239,240Pu, and 241Am in soils (0- to 12-in. [31 cm] depth underneath the tree), pinon pine shoots (PPS), and pinon pine nuts (PPN) collected from LANL lands and regional background (BG) locations, (2) committed effective dose equivalent (CEDE) from the ingestion of nuts, and (3) soil to PPS to PPN concentration ratios (CRs). Most radionuclides, with the exception of 3H in soils, were not significantly higher (p < 0.10) in soils, PPS, and PPN collected from LANL as compared to BG locations, and concentrations of most radionuclides in PPN fromLANL have decreased over time. The maximum net CEDE (the CEDE plus two sigma minus BG) at the most conservative ingestion rate (10 lb [4.5 kg]) was 0.0018 mrem (0.018 microSv); this is far below the International Commission on Radiological Protection (all pathway) permissible dose limit of 100 mrem (1000 microSv). Soil-to-nut CRs for most radionuclides were within the range of default values in the literature for common fruits and vegetables.

Animals↗