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At least 685 records · Page 38Linked to original sources
PubMed2005

Implementing the iHOP concept for navigation of biomedical literature.

MOTIVATION: The World Wide Web has profoundly changed the way in which we access information. Searching the internet is easy and fast, but more importantly, the interconnection of related contents makes it intuitive and closer to the associative organization of human memory. However, the information retrieval tools currently available to researchers in biology and medicine lag far behind the possibilities that the layman has come to expect from the internet. RESULTS: By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource. iHOP (Information Hyperlinked over Proteins) is an online service that provides this gene-guided network as a natural way of accessing millions of PubMed abstracts and brings all the advantages of the internet to scientific literature research. Navigating across interrelated sentences within this network is closer to human intuition than the use of conventional keyword searches and allows for stepwise and controlled acquisition of information. Moreover, this literature network can be superimposed upon experimental interaction data to facilitate the simultaneous analysis of novel and existing knowledge. The network presented in iHOP currently contains5 million sentences and 40 000 genes from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Danio rerio, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. AVAILABILITY: iHOP is freely accessible at http://www.pdg.cnb.uam.es/UniPub/iHOP/

Biomedical Engineering↗
PubMed2006

Insights into latent class analysis of diagnostic test performance.

Latent class analysis is used to assess diagnostic test accuracy when a gold standard assessment of disease is not available but results of multiple imperfect tests are. We consider the simplest setting, where 3 tests are observed and conditional independence (CI) is assumed. Closed-form expressions for maximum likelihood parameter estimates are derived. They show explicitly how observed 2- and 3-way associations between test results are used to infer disease prevalence and test true- and false-positive rates. Although interesting and reasonable under CI, the estimators clearly have no basis when it fails. Intuition for bias induced by conditional dependence follows from the analytic expressions. Further intuition derives from an Expectation Maximization (EM) approach to calculating the estimates. We discuss implications of our results and related work for settings where more than 3 tests are available. We conclude that careful justification of assumptions about the dependence between tests in diseased and nondiseased subjects is necessary in order to ensure unbiased estimates of prevalence and test operating characteristics and to provide these estimates clinical interpretations. Such justification must be based in part on a clear clinical definition of disease and biological knowledge about mechanisms giving rise to test results.

Algorithms↗
PubMed2003

Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase.

Understanding of the evolutionary histories of many genes has not yet allowed us to predict the evolutionary potential of those genes. Intuition suggests that current biochemical activity of gene products should be a good predictor of the potential to evolve related activities; however, we have little evidence to support that intuition. Here we use our in vitro evolution method to evaluate biochemical activity as a predictor of future evolutionary potential. Neither the class C Citrobacter freundii CMY-2 AmpC beta-lactamase nor the class A TEM-1 beta-lactamase confer resistance to the beta-lactam antibiotic cefepime, nor do any of the naturally occurring alleles descended from them. However, the CMY-2 AmpC enzyme and some alleles descended from TEM-1 confer high-level resistance to the structurally similar ceftazidime. On the basis of the comparison of TEM-1 and CMY-2, we asked whether biochemical activity is a good predictor of the evolutionary potential of an enzyme. If it is, then CMY-2 should be more able than the TEMs to evolve the ability to confer higher levels of cefepime resistance. Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles.

Bacterial Proteins↗
PubMed2005

A qualitative examination of primary care providers' and physician managers' uses and views of research evidence.

OBJECTIVE: To examine the reasons and search strategies related to physicians' search for evidence and to compare clinician and physician manager approaches. DESIGN: Qualitative analysis of verbatim transcripts of four focus groups in 2002. Study setting. Clinicians and managers in community practices in Southern California. PARTICIPANTS: Pediatricians, family practitioners, and general internists (i.e. child and adult primary care providers) in non-academic practice and physician managers whose primary responsibility involved making management decisions within a moderate to large sized health care delivery system (e.g. health plan, community hospital, large group practice). MAIN OUTCOME MEASURES: Themes related to clinician and manager reasons for using evidence and approach to selecting among evidence sources. RESULTS: Clinicians and managers differed substantially in their reasons for using evidence. Whereas clinicians consistently invoked clinical intuition as a guide to most routine clinical decisions, managers articulated both motivation and interest in using medical research to guide decision-making, most commonly prompted by cost. Both clinicians and managers rated trustworthiness as a paramount consideration in arbitrating between evidence sources, because neither group evinced comfort with the complexity of primary literature. Both groups expressed a preference for tested, convenient, and respected evidence sources such as expert colleagues and professional societies. CONCLUSIONS: Because clinicians invoke intuition in confronting the challenges of daily practice, evidence-based medicine interventions that target managers are likely to have larger effects on health outcomes than those that target primary care providers and individual patient treatment. Ensuring trustworthiness of evidence is of the utmost importance. Because both groups express discomfort with the format of primary evidence sources, strategies should probably not rely on individual appraisal.

Adult↗
PubMed2005

The resistance ratchet: theoretical implications of cyclic selection pressure.

OBJECTIVES: To investigate the effects of cyclic antibiotic selection pressure on resistance in a simple mathematical model. METHODS: The model assumed that resistance in microbial ecologies changes slowly with changing selection pressure, at a rate proportional to the difference between the current resistance level and the resistance level that would be in equilibrium with current selection pressure. The maximum rate of increase in resistance during periods of increasing selection was assumed to be greater than the maximum rate of decrease during decreased selection. RESULTS: Under a simulated annual cyclic selection pressure variation of 40%, with maximum resistance rise and fall rates of 10 and 0.5%, respectively, resistance rose above the level expected from the mean selection pressure by small ratchet-like increments. Over 50 simulated years, resistance increased to 62%, rather than the 50% expected from the mean level of selection. Welsh community prescribing for a selection of antibiotics showed a seasonal cyclic variation of 13-45%. CONCLUSIONS: The intuitive assumption that cyclic selective pressure would produce resistance levels commensurate with the mean selection pressure was contradicted; rather resistance drifted towards a level commensurate with maximum selection pressure. If the ratchet effect exists in reality, it may produce unexpected excess resistance, particularly in the community for antibiotics used in respiratory infection, where cycling is pronounced, or in ITU antibiotic rotation. It should be most pronounced for resistance systems with strong asymmetry between rates of adaptation under rising and falling selection pressure. Non-linear dynamic systems in physics and ecology are notorious for producing counter-intuitive effects; resistance epidemiology may be similar.

Anti-Bacterial Agents↗
PubMed1981

Bridging clinical distance: an empathic rediscovery of the known.

In this essay, I argue that traditional medical views of illness systematically exclude intuitive knowledge from their description of disease and thus result in a functionally impressive but humanly ungrounded medicine. Physicians trained in a technologized anatomico-pathologic view of disease find themselves cut off from much of what they knew about illness when they began their training. Not only do they lack a rigorous or formal way to confront the non-technical aspects of medical practice, but many have even lost sight of the motives for medicine. I argue here for an intuitively based humanly grounded ontology of illness. Such an ontology begins in an understanding of the experience of the sick person rather than in a "objective" description of pathology. It is only through a science of illness-as-lived that one may achieve a truly humanistic medicine.

Disease↗
PubMed1983

Bioethical decision-making: a reply to Ackerman.

Terrence Ackerman has suggested that we ought to view general bioethical principles as generalizations which summarize our previous bioethical decisions rather than as moral rules. He would have us derive our ethical views instead principally from the facts of the cases in question and our intuitions about them. The proposal is attractive because of its similarity to medical decision-making, but it fails because it allows for no higher order standard of reference against which conflicting ethical intuitions may be judged.

Bioethics↗
PubMed2006

GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

In order to understand the evolution, structure and function of genomes, it is important to know the general compositional features of DNA sequences. Based on the quadratic divergence, a new segmentation algorithm to partition a given genome or DNA sequence into compositionally distinct domains has been put forward. With the aid of the technique of cumulative GC profile, the distribution of segmentation points can be displayed intuitively. We have therefore developed them into GC-Profile, an interactive web-based software system, which can be used to segment prokaryotic and eukaryotic genomes. GC-Profile provides a quantitative and qualitative view of genome organization. Based on the obtained results, the relationships between the G+C content and other genomic features, such as distributions of genes and CpG islands, can be analyzed in a perceivable manner. It shows that GC-Profile would be an appropriate starting point for analyzing the isochore structure of higher eukaryotic genomes, and an intuitive tool for identifying genomic islands in prokaryotic genomes. GC-Profile is freely available at the website http://tubic.tju.edu.cn/GC-Profile/. In addition, precompiled binaries, together with examples and documentation, can also be freely downloaded for a local execution.

Algorithms↗
PubMed1999

Classifying the empathic understanding of the nurse psychotherapist.

The purpose of this article is to identify types of verbal communication approaches to empathic understanding, and to consider the way of psychological support for cancer patients based on those types. These types were derived from the nurse psychotherapy process used with 46 Japanese cancer patients involved in the author's practice as a nurse psychotherapist. The psychotherapy process was interpreted by the phenomenologic approach. These types are as follows: Type A: Reflecting the perceived meaning of the verbalized experiencing of the patient. Type B: Anticipatively communicating the intuitively perceived meaning of the patient's experiencing, not verbalized, but now aware. Type C: Communicating the intuitively perceived meaning of the patient's experiencing, indifferent now, but usually aware. Type D: Facilitating the patient in focusing on her or his implicit felt sense. Type E: Communicating definitely the insight of the patient's implicit felt sense. These approaches indicated that when both a patient and a nurse psychotherapist have a deep level of empathic understanding, the patient could interpret personal meaning clearly and change the previous meaning. This experience helps the patient recover his or her own way of being, while helping the patient to live in the here and now.

Adolescent↗
PubMedDate not supplied

Nearest neighbor phase synchronization as a measure to detect seizure activity from scalp EEG recordings.

The author presents results from the application of a particular measure for synchronization between brain areas (i.e., phase synchronization) in its behavior to detect epileptic seizure activity from scalp EEG recordings. The primary motivation for the current study was to contribute to the development of physiologic measures that both transform the EEG to a visual domain that allows a more intuitive interpretation of the interictal and ictal EEG and allows automated analysis, both relevant for real-time monitoring. EEGs from 16 patients experiencing temporal lobe and generalized seizures were analyzed. Nearest neighbor phase synchronization (NNPS) values for several frequency bands were determined. Additional analysis of the NNPS in the delta band, using different thresholds, allows construction of receiver operating characteristics (ROC) curves for each EEG analyzed. The common value for the sensitivity and the specificity, Q*, was used as a measure for the test accuracy, with values of Q* near 1.0, indicating ROC curves with sensitivity and specificity both approaching 1.0. It was found that Q* = 0.48 to 0.87, depending on the EEG analyzed, indicating that the proposed method allows seizure detection in a significant portion of the EEGs studied. Nearest neighbor phase synchronization was typically increased during seizure activity and seems to be a promising method to detect seizure activity from scalp EEG recordings. The proposed visualization allows an intuitive interpretation of the EEG and may assist in real-time monitoring.

Cortical Synchronization↗
PubMed1998

A preliminary evaluation of diagnostic odds in lung scan reporting.

Reporting of lung scans for pulmonary embolism (PE) using a descriptive probability notation is tried and tested. Subjectivity in interpretation of this jargon can be a problem for internists. Parallel descriptive and numerical probability reporting has been recommended, but the numerical probability scale is less precise than likelihood ratios expressed as odds. We therefore assessed internists' intuitive understanding of lung scan reports in the odds format compared to the descriptive probability notation. A questionnaire was sent to Scotland's 217 internists to assess their intuitive understanding of odds reporting and to compare their management strategies when confronted by lung scan reports in both an odds and a descriptive probability notation. There was a broad understanding of numerical odds. Internists used 'normal' and '100:1 against PE' identically; similarly, 'low probability' and '10:1 against PE'. There was a statistically significant preference for the diagnosis of PE when internists were given the '1:1 evens' report compared with the 'indeterminate' report. There does appear to be a greater awareness of the risk of PE when non-diagnostic lung scans are reported in numerical odds as compared with the descriptive probability format.

Diagnosis, Differential↗
PubMed1993

Understanding the diffractive bifocal contact lens.

How a diffractive bifocal contact lens works is not intuitively obvious. This is because the diffractive bifocal operates by an unusual blend of refraction and interference. The present article seeks to clarify how it achieves its two focal powers. Most of this article, however, is devoted to the conceptually simpler case of diffraction gratings in order to develop an intuition for how a double focus is produced. Single slit, double slit, and multiple slit gratings are considered using two formalisms: Feynman's "arrow" method (also called phasors) and the Fourier method. When dealing with linear diffraction gratings we are interested in the light intensity in the focal plane. By a simple redefinition of variables, all of the mathematics for diffraction gratings can be applied to circular lenses. For this latter case instead of looking at the light intensity in the focal plane, we look at light intensity on the optic axis. The appearance of two focal points is a simple consequence of a combined interference and diffraction pattern. The goal of this article is to present an introduction to Fourier optics and an analysis of the bifocal contact lens in a reader-friendly manner.

Contact Lenses↗
PubMed2007

Incorporating principles and practical wisdom in research ethics education: a preliminary study.

PURPOSE: Researchers are faced with daily ethical decisions that are subtle and nuanced. However, research ethics training has primarily focused on formal guidelines, general ethical principles, and historically noteworthy cases of research abuse, which may not prepare researchers to respond to everyday dilemmas in research. This study characterized researchers' responses to ethical dilemmas with the goal of aligning research ethics education programs with the demands of practice. METHOD: As a preliminary study, the authors conducted 23 semistructured interviews with senior researchers and research administrators engaged in research with human subjects at the University of Washington and affiliated institutions in 2004. Transcripts were reviewed for research conflicts and strategies used to resolve conflicts identified by participants. RESULTS: Participants referenced two distinct methods of reasoning when faced with conflicts: formal guidelines and practical wisdom. Formal guidelines include established goals, boundaries, and absolutes. Practical wisdom, an Aristotelian concept involving intuitions developed through experience, facilitates responses to everyday dilemmas and new situations. Developing practical wisdom requires researchers to calibrate their own intuitions about right and wrong. Three practices were reported to contribute to this development: self-reflection, sincere skepticism, and open dialogue with colleagues. CONCLUSIONS: These reflections from the senior researchers suggest a need to expand the scope of ethics education programs to include a focus on the development of researchers' pragmatic decision making in addition to the formal rules that govern research. Further research should explore effective educational and institutional strategies that can foster researchers' development in ethical decision making and conduct.

Authorship↗
PubMed2003

Network bipartivity.

Systems with two types of agents with a preference for heterophilous interaction produce networks that are more or less close to bipartite. We propose two measures quantifying the notion of bipartivity. The two measures-one well known and natural, but computationally intractable, and the other computationally less complex, but also less intuitive-are examined on model networks that continuously interpolate between bipartite graphs and graphs with many odd circuits. We find that the bipartivity measures increase as we tune the control parameters of the test networks to intuitively increase the bipartivity, and thus conclude that the measures are quite relevant. We also measure and discuss the values of our bipartivity measures for empirical social networks (constructed from professional collaborations, Internet communities, and field surveys). Here we find, as expected, that networks arising from romantic online interaction have high, and professional collaboration networks have low, bipartivity values. In some other cases, probably due to low average degree of the network, the bipartivity measures cannot distinguish between romantic and friendship oriented interaction.

Journal Article↗
PubMed2006

Maximum-entropy closures for kinetic theories of neuronal network dynamics.

We analyze (1 + 1)D kinetic equations for neuronal network dynamics, which are derived via an intuitive closure from a Boltzmann-like equation governing the evolution of a one-particle (i.e., one-neuron) probability density function. We demonstrate that this intuitive closure is a generalization of moment closures based on the maximum-entropy principle. By invoking maximum-entropy closures, we show how to systematically extend this kinetic theory to obtain higher-order, kinetic equations and to include coupled networks of both excitatory and inhibitory neurons.

Algorithms↗
PubMed2005

A molecular viewer for the analysis of TLS rigid-body motion in macromolecules.

TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement.

Algorithms↗
PubMed2004

DBMap: a space-conscious data visualization and knowledge discovery framework for biomedical data warehouse.

Advances in digital imaging modalities as well as other diagnosis and therapeutic techniques have generated a massive amount of diverse data for clinical research. The purpose of this study is to investigate and implement a new intuitive and space-conscious visualization framework, called DBMap, to facilitate efficient multidimensional data visualization and knowledge discovery against the large-scale data warehouses of integrated image and nonimage data. The DBMap framework is built upon the TreeMap concept. TreeMap is a space constrained graphical representation of large hierarchical data sets, mapped to a matrix of rectangles, whose size and color represent interested database fields. It allows the display of a large amount of numerical and categorical information in limited real estate of the computer screen with an intuitive user interface. DBMap has been implemented and integrated into a large brain research data warehouse to support neurologic and neuroradiologic research at the University of California, San Francisco Medical Center. For imaging specialists and clinical researchers, this novel DBMap framework facilitates another way to better explore and classify the hidden knowledge embedded in medical image data warehouses.

Algorithms↗
PubMed2002

Multiscale deformable model segmentation and statistical shape analysis using medial descriptions.

This paper presents a multiscale framework based on a medial representation for the segmentation and shape characterization of anatomical objects in medical imagery. The segmentation procedure is based on a Bayesian deformable templates methodology in which the prior information about the geometry and shape of anatomical objects is incorporated via the construction of exemplary templates. The anatomical variability is accommodated in the Bayesian framework by defining probabilistic transformations on these templates. The transformations, thus, defined are parameterized directly in terms of natural shape operations, such as growth and bending, and their locations. A preliminary validation study of the segmentation procedure is presented. We also present a novel statistical shape analysis approach based on the medial descriptions that examines shape via separate intuitive categories, such as global variability at the coarse scale and localized variability at the fine scale. We show that the method can be used to statistically describe shape variability in intuitive terms such as growing and bending.

Algorithms↗