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PubMed2005

Time-resolved spectral studies of blue-green fluorescence of artichoke (Cynara cardunculus L. Var. Scolymus) leaves: identification of chlorogenic acid as one of the major fluorophores and age-mediated changes.

Synchrotron radiation and the time-correlated single-photon counting technique were used to investigate the spectral and time-resolved characteristics of blue-green fluorescence (BGF) of artichoke leaves. Leaves emitted BGF under ultraviolet (UV) excitation; the abaxial side was much more fluorescent than the adaxial side, and in both cases, the youngest leaves were much more fluorescent than the oldest ones. The BGF of artichoke leaves was dominated by the presence of hydroxycinnamic acids. A decrease in the percentage of BGF attributable to the very short kinetic component (from 42 to 20%), in the shape of the BGF excitation spectra, and chlorogenic acid concentrations indicate that there is a loss of hydroxycinnamic acid with leaf age. Studies on excitation, emission, and synchronized fluorescence spectra of leaves and trichomes and chlorogenic acid contents indicate that chlorogenic acid is one of the main blue-green fluorophores in artichoke leaves. Results of the present study indicate that 20-42% (i.e., the very short kinetic component) of the overall BGF is emitted by chlorogenic acid. Time-resolved BGF measurements could be a means to extract information on chlorogenic acid fluorescence from the overall leaf BGF.

Chlorogenic Acid↗
PubMed2001

Quantitative analysis of the time courses of enzyme-catalyzed reactions.

The catalytic properties of enzymes are usually evaluated by measuring and analyzing reaction rates. However, analyzing the complete time course can be advantageous because it contains additional information about the properties of the enzyme. Moreover, for systems that are not at steady state, the analysis of time courses is the preferred method. One of the major barriers to the wide application of time courses is that it may be computationally more difficult to extract information from these experiments. Here the basic approach to analyzing time courses is described, together with some examples of the essential computer code to implement these analyses. A general method that can be applied to both steady state and non-steady-state systems is recommended.

Biochemistry↗
PubMed2002

An additive genetic gamma frailty model for linkage analysis of diseases with variable age of onset using nuclear families.

Many late-onset complex diseases exhibit variable age of onset. Efficiently incorporating age of onset information into linkage analysis can potentially increase the power of dissecting complex diseases. In this paper, we treat age of onset as a genetic trait with censored observations. We use multiple markers to infer the inheritance vector at the disease susceptibility (DS) locus in order to extract information about the inheritance pattern of the disease allele in a pedigree. Given the inheritance distribution at the DS locus, we define the genetic frailty for each individual within a nuclear family as the sum of frailties due to a putative major disease gene and a polygenic effect due to any remaining DS loci. Conditioning on these frailties we use the proportional hazards model for the risk of developing disease. We show that a test of linkage can be formulated as a test of zero variance due to a specific locus of the additive gamma frailties. Maximum likelihood estimation, using the EM algorithm, and likelihood ratio tests are employed for parameter estimation and tests of linkage. A simulation study presented indicates that the proposed method is well behaved and can be more powerful than the currently available allele-sharing based linkage methods. A breast cancer data example is used for illustration.

Adult↗
PubMed2002

An overview on predicting the subcellular location of a protein.

The present paper overviews the issue on predicting the subcellular location of a protein. Five measures of extracting information from the global sequence based on the Bayes discriminant algorithm are reviewed. 1) The auto-correlation functions of amino acid indices along the sequence; 2) The quasi-sequence-order approach; 3) the pseudo-amino acid composition; 4) the unified attribute vector in Hilbert space, 5) Zp parameters extracted from the Zp curve. The actual performance of the predictive accuracy is closely related to the degree of similarity between the training and testing sets or to the average degree of pairwise similarity in dataset in a cross-validated study. Many scholars considered that the current higher predictive accuracy still cannot ensure that some available algorithms are effective in practice prediction for the higher pairwise sequence identity of the datasets, but some of them declared that construction of the dataset used for developing software should base on the reality determined by the Mother Nature that some subcellular locations really contain only a minor number of proteins of which some even have a high percentage of sequence similarity. Owing to the complexity of the problem itself, some very sophisticated and special programs are needed for both constructing dataset and improving the prediction. Anyhow finding the target information in mature protein sequence and properly cooperating it with sorting signals in prediction may further improve the overall predictive accuracy and make the prediction into practice.

Algorithms↗
PubMed2007

A self-paced brain interface system that uses movement related potentials and changes in the power of brain rhythms.

Movement execution results in the simultaneous generation of movement-related potentials (MRP) as well as changes in the power of Mu and Beta rhythms. This paper proposes a new self-paced multi-channel BI that combines features extracted from MRPs and from changes in the power of Mu and Beta rhythms. We developed a new algorithm to classify the high-dimensional feature space. It uses a two-stage multiple-classifier system (MCS). First, an MCS classifies each neurological phenomenon separately using the information extracted from specific EEG channels (EEG channels are selected by a genetic algorithm). In the second stage, another MCS combines the outputs of MCSs developed in the first stage. Analysis of the data of four able-bodied subjects shows the superior performance of the proposed algorithm compared with a scheme where the features were all combined in a single feature vector and then classified.

Brain↗
PubMed2004

Manual versus powered toothbrushes: a summary of the Cochrane Oral Health Group's Systematic Review. Part II.

PURPOSE: A systematic review examining the clinical effectiveness of power versus manual toothbrushes was conducted by the Cochrane Collaborations Oral Health Group. Their review examined clinical trials conducted through 2001 and used international standards to identify, access, evaluate, analyze, and report the data. Part I of this series discussed distinguishing characteristics of evidence-based publications, such as systematic reviews, whereas this report provides a summary of the Cochrane Review, its importance to the profession, and discusses the strengths and limitations of systematic reviews. METHODS: Search strategies to identify published clinical trials on power toothbrushes were developed, and manufacturers were contacted for additional published and unpublished information. Trials were selected based on pre-established criteria; including whether they compared power versus manual toothbrushes used a randomized research design tested products in the general population without disabilities, provided data on plaque and gingivitis, and were at least 28 days in length. Six reviewers independently extracted information in duplicate. Indices for plaque and gingivitis levels were expressed as standardized mean differences for data distillation. Data distillation was accomplished using a meta-analysis, with a mean difference between power and manual toothbrushes as the measure of effectiveness. RESULTS: Searches identified 354 trials, of which 29 met inclusion criteria. These trials involved 2.547 participants who provided data for meta-analysis. Results indicated that for both plaque and gingivitis, all types of power toothbrushes worked as well as manual toothbrushes, however only the rotating oscillating toothbrush consistently provided a statistically significant though modest benefit over manual toothbrushes in reducing plaque (7%) and gingivitis (17%). None of the battery powered toothbrush studies met the inclusion criteria. CONCLUSION: The Cochrane systematic review used international standards to examine more than 30 years of published studies. A concern is that only one type of electric toothbrush, the rotating oscillating toothbrush consistently demonstrated a statistically significant benefit over manual toothbrushes, and the majority of studies did not meet the standards for inclusion in moving forward it will be important to conduct methodologically sound studies demonstrating the ability of power toothbrushes to reduce the incidence and prevalence of caries and periodontal disease.

Decision Making↗
PubMed1985

Digital processing in cardiac imaging.

In recent years, imaging modalities have realized the potential for digitizing images of the heart. These modalities include nuclear cardiology, echocardiography, digital subtraction angiography, computed tomography, positron emission tomography, and magnetic resonance imaging. Once the cardiac images have been digitized by the computer and formatted in a pixel array of data, the computer can perform mathematical operations on the input (original) images for the purpose of providing improved output (processed) images. The computer can also analyze the original (or processed) images for the purpose of extracting global, regional, or temporal measurements of cardiac perfusion and function. These processes include the restoration, enhancement, analysis, manipulation, and coding of images. These basic processes are implemented by a combination of image processing operations. These operations include pixel point processing, pixel group processing, frame processing, geometric processing, and information extraction. This article describes how these operations are used to perform processes, and how these processes are applied to cardiac imaging, currently and in the future.

Algorithms↗
PubMed1998

Applied cognitive task analysis (ACTA): a practitioner's toolkit for understanding cognitive task demands.

Cognitive task analysis (CTA) is a set of methods for identifying cognitive skills, or mental demands, needed to perform a task proficiently. The product of the task analysis can be used to inform the design of interfaces and training systems. However, CTA is resource intensive and has previously been of limited use to design practitioners. A streamlined method of CTA, Applied Cognitive Task Analysis (ACTA), is presented in this paper. ACTA consists of three interview methods that help the practitioner to extract information about the cognitive demands and skills required for a task. ACTA also allows the practitioner to represent this information in a format that will translate more directly into applied products, such as improved training scenarios or interface recommendations. This paper will describe the three methods, an evaluation study conducted to assess the usability and usefulness of the methods, and some directions for future research for making cognitive task analysis accessible to practitioners. ACTA techniques were found to be easy to use, flexible, and to provide clear output. The information and training materials developed based on ACTA interviews were found to be accurate and important for training purposes.

Cognition↗
PubMed2001

Haploid chromosomes in molecular ecology: lessons from the human Y.

We review the potential use of haploid chromosomes in molecular ecology, using recent work on the human Y chromosome as a paradigm. Chromosomal sex-determination systems, and hence constitutively haploid chromosomes, which escape from recombination over much of their length, have evolved multiple times in the animal kingdom. In mammals, where males are the heterogametic sex, the patrilineal Y chromosome represents a paternal counterpart to mitochondrial DNA. Work on the human Y chromosome has shown it to contain the same range of polymorphic markers as the rest of the nuclear genome and these have rendered it the most informative haplotypic system in the human genome. Examples from research on the human Y chromosome are used to illustrate the common interests of anthropologists and ecologists in investigating the genetic impact of sex-specific behaviours and dispersals, as well as patterns of global diversity. We present some methodologies for extracting information from these uniquely informative yet under-utilized loci.

Animals↗
PubMed1999

Wrapping SRS with CORBA: from textual data to distributed objects.

MOTIVATION: Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data. RESULTS: This paper presents a CORBA interface to the SRS system which manages databanks in a flat file format. SRS Object Servers are CORBA wrappers for SRS. They allow client applications (visualisation tools, data mining tools, etc.) to access and query SRS servers remotely through an Object Request Broker (ORB). They provide loader objects that contain the information extracted from the databanks by SRS. Loader objects are not hard-coded but generated in a flexible way by using loader specifications which allow SRS administrators to package data coming from distinct databanks. AVAILABILITY: The prototype may be available for beta-testing. Please contact the SRS group (http://srs.ebi.ac.uk).

Computer Systems↗
PubMed1980

The persistences of vision.

Human observers continue to experience a visual stimulus for some time after the offset that stimulus. The neural activity evoked by a visual stimulus continues for some time after its offset. The information extracted from a visual stimulus continues to be registered in a visual form of memory ('iconic memory') for some time after its offset. We may thus distinguish three distinct senses in which a visual stimulus may be said to persist after its physical offset: there is phenomenological persistence, neural persistence and informational persistence. Various assumptions have been made about the relation between these forms of visual persistence. The most frequent assumption is that they correspond simply to three different methods for studying a single entity. Detailed consideration of what is known about the properties of these three forms of persistence suggests, however, that this assumption is not correct. It can reasonably be proposed that visible persistence is the phenomenological correlate of neural persistence occurring at various stages of the visual system: photoreceptors, ganglion cells and the stereopsis system. Iconic memory on the other hand, does not correspond to visible persistence, nor to neural persistence in any stage of the visual system. Recent work, in fact, suggests that iconic memory is a property of some relatively late stage in the visual information-processing system, rather than being a peripheral sensory buffer store. This suggestion raises some fundamental theoretical issues concerning the psychology of visual perception, issues with which cognitive psychology has yet to come to grips.

Afterimage↗
PubMed1991

Linkage disequilibrium and linkage information from one-child families.

In linkage analysis a single-child family is usually considered to be completely uninformative. This article shows that such a family can provide information on linkage disequilibrium, even if it provides no information on linkage equilibrium. A transition matrix consisting of the recombination fraction and the phase proportion is proposed to study the genetic transmission from a pair of parents to their single child. The information about linkage for a single-child family is shown to be confounded by the phase proportion. This explains why such a family used to be considered uninformative under the assumption of linkage equilibrium. By reparametrizing the recombination fraction and the phase proportion into one parameter, it is demonstrated that extracting information on linkage disequilibrium is feasible. The study of power of the testing method proposed here is carried out by simulation.

Child↗
PubMed2006

Imitating manual curation of text-mined facts in biomedicine.

Text-mining algorithms make mistakes in extracting facts from natural-language texts. In biomedical applications, which rely on use of text-mined data, it is critical to assess the quality (the probability that the message is correctly extracted) of individual facts--to resolve data conflicts and inconsistencies. Using a large set of almost 100,000 manually produced evaluations (most facts were independently reviewed more than once, producing independent evaluations), we implemented and tested a collection of algorithms that mimic human evaluation of facts provided by an automated information-extraction system. The performance of our best automated classifiers closely approached that of our human evaluators (ROC score close to 0.95). Our hypothesis is that, were we to use a larger number of human experts to evaluate any given sentence, we could implement an artificial-intelligence curator that would perform the classification job at least as accurately as an average individual human evaluator. We illustrated our analysis by visualizing the predicted accuracy of the text-mined relations involving the term cocaine.

Abstracting and Indexing↗
PubMed2004

Enhancing access to the Bibliome: the TREC Genomics Track.

The growing amount of scientific discovery in genomics and related biomedical disciplines has led to a corresponding increase in the amount of on-line data and information. A new challenge for biomedical researchers has been how to access and manage this ever-increasing quantity of information. The Text Retrieval Conference (TREC) has implemented a Genomics Track to create an experimental environment for research in the use of information retrieval systems in the genomics domain. In the first year of the track, an ad hoc document retrieval task and an information extraction task were carried out by 29 research groups. Future work will focus on more complex data sources, searching tasks, and types of experiments.

Computational Biology↗
PubMed2005

The effectiveness of self-performed mechanical plaque control with triclosan containing dentifrices.

OBJECTIVE: To assess the effectiveness of self-performed mechanical plaque control with triclosan (5-chloro-2-(2,4 dichlorophenoxy)phenol) containing dentifrice. SEARCH STRATEGY: An electronic search of the National Library of Medicine, Washington DC (Medline-PubMed; up to and including March 2005) was performed using specific search terms to identify clinical trials of >or=6 months in duration, which assessed the effect of various forms of plaque control in gingivitis subjects. In those trials the manual toothbrush group (frequently the control group) served to provide data for the assessment of the effectiveness of self-performed mechanical plaque control with a triclosan-containing dentifrice. The data were analysed depending on the (baseline) intervention, being either a professional oral hygiene instructions, a prophylaxis, or both. DATA COLLECTION AND ANALYSIS: Two reviewers extracted information (KPKJH and GAW). Where appropriate plaque and gingivitis data for baseline and end-trial were used to calculate weighted mean differences (WMD) with the appropriate 95% confidence intervals (CI) using a random effect models. MAIN RESULTS: Of 105 titles and abstracts, 18 trials were found suitable for clinical data were extracted. Meta-analysis were conducted. In studies (n=9) evaluating a triclosan/copolymer dentifrice, plaque control [Quigley and Hein (1962) Journal of American Dental Association, Vol. 65: pp. 26-29] was significantly improved compared with a control fluoride dentifrice, with a WMD of -0.48 (95% CI: -0.73 to -0.24). For gingival inflammation as assessed with the gingival index [Löe and Silness (1963) Acta Odontologica Scandinavica, Vol. 21: pp. 533-551] a significant WMD of -0.24 (95% CI: -0.35 to -0.13) was found. From studies (n=6) evaluating the Triclosan zinc/citrate dentifrices a small but significant WMD for plaque control [Silness and Löe (1964) Acta Odontologica Scandinavica, Vol. 22: pp. 121-135] was observed in favour of the test group as compared with the standard fluoride dentifrice formulations (WMD -0.07, 95% CI: -0.10 to 0.05). While at baseline the proportion of bleeding was comparable, at the end of the studies a significant -10.81% WMD (95% CI: -12.69 to -8.93) in favour of the triclosan/zinc citrate dentifrice was observed. CONCLUSION: This systematic review indicates, based on studies >or=6 months of duration in adults with gingivitis, that the effectiveness of self-performed mechanical plaque control with a triclosan-containing dentifrice, had a significant albeit small positive effect on the reduction of plaque and gingivitis.

Anti-Infective Agents, Local↗
PubMed2003

PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine.

BACKGROUND: The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND. RESULTS: Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high throughput interactions present in another yeast-protein interaction database. Finally, this system was applied to a real-world curation problem and its use was found to reduce the task duration by 70% thus saving 176 days. CONCLUSIONS: Machine learning methods are useful as tools to direct interaction and pathway database back-filling; however, this potential can only be realized if these techniques are coupled with human review and entry into a factual database such as BIND. The PreBIND system described here is available to the public at http://bind.ca. Current capabilities allow searching for human, mouse and yeast protein-interaction information.

Algorithms↗
PubMed1997

Factors associated with elective Norplant removal in black and white women.

Premature removal of contraceptive implants (Norplant [levonorgestrel implants], Wyeth-Ayerst Laboratories, Philadelphia, Pennsylvania) is a cause of a sizable national medical expenditure in the United States. Understanding the factors that influence the decision to remove the implants and being able to predict which users are likely to elect discontinuation prematurely could provide useful information for counseling patients as they are considering contraceptive implants so that potentially enormous long-term savings could be achieved. This study surveyed 98 women who had Norplant inserted and removed between January 1991 and December 1994. Data were collected from chart review, and when necessary, a questionnaire was used to extract information not found in the chart. The chi-squared statistic and t-test were used to compare demographic variables. All but one subject received comprehensive pre-implant counseling. The main reason given for electively removing the Norplant prematurely was irregular menstrual bleeding (60%). Pre-implant counseling did not influence the decision for removal. These results indicate the importance of clarifying patients' doubts regarding menstrual bleeding irregularities during follow-up visits rather than relying on the information patients received during preimplant counseling.

Adult↗
PubMed1991

Analysis of the health condition of the children born to the personnel exposed to cytostatics at an oncology unit.

The health condition of the children born to the health personnel exposed to cytostatics at a specialized oncology unit, Faculty Hospital, Olomouc, was analyzed. Questionnaires and interviews were used to examine on the whole 44 workers (23 nurses, 7 physicians, 8 auxiliary nurses and 6 cleaners). The average age of the group was 34.8 years. By the time of the follow-up, 25 persons had worked at the unit for up to 5 years, 14 persons for 6 to 10 years, and 5 persons for 10 to 20 years. The nurses were exposed to cytostatics for 8 and more hours daily. The information extracted in the questionnaires concerned the course of delivery, obstetrical complications, birth weight and length, maturity, incidence of developmental defects. Data was further obtained concerning the postnatal health condition of the child, its well-being and further development. The exposed workers were asked about spontaneous abortions, course of deliveries, or risk pregnancies. Information on the exposure to cytostatics at the time of conception and pregnancy was considered as important. Of the 61 children under study, 10 were born to workers exposed to cytostatics at the time of conception or in the course of pregnancy. Two developmental defects were found among the 61 children, one of them being serious and not compatible with life, probably in connection with occupational exposure of the mother to ionizing radiation. Ten spontaneous abortions (8 early, 2 late abortions) and 12 risk pregnancies requiring hospitalization occurred in the group of 23 nurses in connection with physical effort. On the whole, the health condition of the children born to the exposed workers at the oncology unit studied has been found satisfactory. This is likely due to the good knowledgeability of the personnel of the character and actions of cytostatics and the introduction of technological safety measures as well as sticking to the guidelines for safe handling of cytostatics.

Adult↗