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At least 271 records · Page 15Linked to original sources
PubMed2006

Graph-based analysis and visualization of experimental results with ONDEX.

MOTIVATION: Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise. RESULTS: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function.

Algorithms↗
PubMed1990

Coccidioidomycosis in human immunodeficiency virus-infected patients.

Coccidioidomycosis is at best a complicated fungal infection; often it is life-threatening. Coccidioidomycosis is confined epidemiologically to the southwestern region of the USA, and most cases have occurred in that area, particularly in Arizona. However, we have seen several cases in San Francisco in patients with only a history of travel to endemic areas. In part because of its regional distribution, information about the clinical presentation, diagnosis, and treatment of patients with coccidioidomycosis has lagged behind information about other, more commonly encountered AIDS-associated opportunistic infections. Drs. Galgiani and Ampel have probably had the largest single experience with coccidioidomycosis in individuals infected with the human immunodeficiency virus. These specialists share their experience and make recommendations as to how these complicated conditions should be approached.

Acquired Immunodeficiency Syndrome↗
PubMed2003

tmRDB (tmRNA database).

Maintained at the University of Texas Health Science Center at Tyler, Texas, the tmRNA database (tmRDB) is accessible at the URL http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html with mirror sites located at Auburn University, Auburn, Alabama (http://www.ag.auburn.edu/mirror/tmRDB/) and the Bioinformatics Research Center, Aarhus, Denmark (http://www.bioinf.au.dk/tmRDB/). The tmRDB collects and distributes information relevant to the study of tmRNA. In trans-translation, this molecule combines properties of tRNA and mRNA and binds several proteins to form the tmRNP. Related RNPs are likely to be functional in all bacteria. In this release of tmRDB, 186 new entries from 10 bacterial groups for a total of 274 tmRNA sequences have been added. Lists of the tmRNAs and the corresponding tmRNA-encoded tag-peptides are presented in alphabetical and phylogenetic order. The tmRNA sequences are aligned manually, assisted by computational tools, to determine base pairs supported by comparative sequence analysis. The tmRNA alignment, available in a variety of formats, provides the basis for the secondary and tertiary structure of each tmRNA molecule. Three-dimensional models of the tmRNAs and their associated proteins in PDB format give evidence for the recent progress that has been made in the understanding of tmRNP structure and function.

Bacteria↗
PubMed2005

GeneNet in 2005.

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/.

Computer Graphics↗
PubMed2002

Dose-response modeling of continuous endpoints.

A family of (nested) dose-response models is introduced herein that can be used for describing the change in any continuous endpoint as a function of dose. A member from this family of models may be selected using the likelihood ratio test as a criterion, to prevent overparameterization. The proposed methodology provides for a formal approach of model selection, and a transparent way of assessing the benchmark dose. Apart from a number of natural constraints, the model expressions follow from an obvious way of quantifying differences in sensitivity between populations. As a consequence, dose-response data that relate to both sexes can be efficiently analyzed by incorporating the data from both sexes in the same analysis, even if the sexes are not equally sensitive to the compound studied. The idea of differences in sensitivity is closely related to the assessment factors used in risk assessment. Thus, the models are directly applicable to estimating such factors, if data concerning populations to be compared are available. Such information is valuable for further validation or adjustment of default assessment factors, as well as for informing distributional assessment factors in a probabilistic risk assessment. The various applications of the proposed methodology are illustrated by real data sets.

Animals↗
PubMedDate not supplied

Agency nurse assessment for competency.

The goal of this study is to make the agency nurse's performance standards equivalent to that of hospital nurse levels of performance based in hospital staff observation to provide continuity of safe, quality patient care. To attain this goal, the following should be done: (1) develop orientation process that includes module for general orientation; (2) agencies pay for nurse orientation to include 8-hour session and a 4-hour skills assessment; (3) develop flip cards for agency nurses as a resource tool; (4) annual general assessment for hospital employees to be completed by agency nurses; and (5) develop process to document and distribute information to charge nurses about agency nurse competency. Leaders should ensure that the process for identifying and managing are defined and implemented. The intent of this standard is to hold leaders within the healthcare organizations accountable.

Clinical Competence↗
PubMed2004

Coherence and discontinuity in the scaling of species' distribution patterns.

The spatial distribution of a species can be characterized at many different spatial scales, from fine-scale measures of local population density to coarse-scale geographical-range structure. Previous studies have shown a degree of correlation in species' distribution patterns across narrow ranges of scales, making it possible to predict fine-scale properties from coarser-scale distributions. To test the limits of such extrapolation, we have compiled distributional information on 16 species of British plants, at scales ranging across six orders of magnitude in linear resolution (1 m to 100 km). As expected, the correlation between patterns at different spatial scales tends to degrade as the scales become more widely separated. There is, however, an abrupt breakdown in cross-scale correlations across intermediate (ca. 0.5 km) scales, suggesting that local and regional patterns are influenced by essentially non-overlapping sets of processes. The scaling discontinuity may also reflect characteristic scales of human land use in Britain, suggesting a novel method for analysing the 'footprint' of humanity on a landscape.

Demography↗
PubMed2003

Vlasov model using kinetic phase point trajectories.

A method of solution of the collisionless Vlasov equation by following fixed collisionless phase point ("particle") trajectories (characteristics) in phase space is presented. It solves the coupled Vlasov Maxwell system self-consistently and employs the Leapfrog-Trapezoidal scheme to solve for the characteristics explicitly. It then uses the bilinear finite element interpolation scheme in phase space and maps vital instantaneous phase point information (distribution function) to a fixed background phase space mesh while retaining it at the phase point. The scheme is an enhanced second order one in time and fourth order in space. The code is then used to model a thermal plasma as well as two stream instability using mobile electrons and fixed background ions: the scheme being a momentum conserving one by construction allows energy conservation without assignment of particle shape functions; Langmuir waves are obtained with very good agreement with the Bohm-Gross dispersion relation; the two stream results do not show any numerically induced oscillations attributed to the initial well-ordered velocity distributions. Retention of the characteristics also minimized diffusion. Extensive numerical stability analysis deriving Courant condition for the scheme as well as behavior of computational modes are done in Appendix A, as well as estimating the impact of numerical diffusion in Appendix B. Two to five dimensional versions in phase space exist.

Journal Article↗
PubMed1998

The Nucleic Acid Database: A resource for nucleic acid science.

The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.

Database Management Systems↗
PubMed1989

The theoretical development of a multichannel time-series myoprocessor for simultaneous limb function detection and muscle force estimation.

This paper details the theoretical development and simulation of a complete time-series myoprocessor which provides reliable and economical predictions of both the magnitude and direction of limb motion from the spectral content of the surface EMG. Treating multiple channels of surface EMG as a vector-valued autoregressive process incorporates spatially distributed information which extends the operating range of parallel filtering limb function classifiers and reduces their sensitivity to modeling conditions. Active joint moment is estimated simultaneously from the pooled variance of the prewhitened EMG generated during the classification procedure. Estimation from the prewhitened sequence imposes no additional computational requirements and extends optimal myoprocessors to include multiple channels of serially dependent data. Such a system may be applied to the control of actively powered prostheses or orthoses.

Artificial Limbs↗
PubMed1989

The experimental demonstration of a multichannel time-series myoprocessor: system testing and evaluation.

A multichannel time-series myoprocessor which combines the advantages of the parallel filtering limb function classifiers of Doerschuk et al. and the "optimal myoprocessor" muscle force estimators described by Hogan et al. have been developed and evaluated experimentally. Magnitudes and directions of knee movements were identified accurately and robustly from EMG sites intermediate to the major thigh muscles of intact individuals. Electrode placement criteria were tested, and system performance and sensitivity to contraction level as functions of channel number were computed. By including spatially distributed information into the structure of the processor, gains in accuracy and reliability over systems with fewer channels were demonstrated. Operating range increased with the number of channels included in the processor. Joint moment was estimated from multiple channels of temporally correlated data, extending and generalizing previously reported techniques. Identifying the parameters of AR models of the EMG at low levels of contraction resulted in more robust classification and joint moment estimation. Optimal electrode position could not be predicted a priori. The system may be applicable to the proportional control of myoelectric prostheses.

Adult↗
PubMed1998

Detection of atrial activity from high-voltage leads of implantable ventricular defibrillators using a cancellation technique.

The inability to detect atrial activity limits implantable ventricular cardioverter defibrillators (ICD) in discriminating tachycardias and can result in inappropriate therapy. This study attempted to detect atrial activity on the wide-spaced bipole signals formed by the high-voltage (HV) leads of the ICD during device implantation and to develop an algorithm for the detection of atrial fibrillation (AFib) from these signals. We used a method that canceled ventricular and correlated atrial activity from the HV lead signals and measured frequency and amplitude distribution information to discriminate sinus rhythm (SR) and AFib segments. We analyzed 186 data segments from 21 patients (six AFib, 14 SR, one AFib and SR). For individual segments in this data set, the sensitivity of the algorithm was 78%, specificity 92.65%, positive and negative predictive values 79.59 and 91.97%, respectively. These results demonstrate that atrial activity is present in the HV lead signals, and AFib detection can be achieved in many, but not all cases, using information currently available to ICD's. Prior work from surface electrocardiograms suggests that this algorithm can function during ventricular tachycardias. However, specificity of the algorithm is not high enough for clinical use.

Aged↗
PubMed1997

An open medical imaging workstation architecture for platform-independent 3-D medical image processing and visualization.

A need for an entirely new medical workstation design was identified to increase the deployment of 3-D medical imaging and multimedia communication. Recent wide acceptance of the Word Wide Web (WWW) as a general communication service within the global network has shown how big the impact of standards and open systems can be. Information is shared among heterogeneous systems and diverse applications on various hardware platforms only by agreeing on a common format for information distribution. For medical image communications, the Digital Imaging and Communication in Medicine (DICOM) standard is possibly anticipating such a role. Logically, the next step is open software: platform-independent tools, which can as easily be transferred and used on multiple platforms. Application of the platform-independent programming language Java enables creation of plug-in tools, which can easily extend the basic system. Performance problems inherent to all interpreter systems can be circumvented by using a hybrid approach. Computationally intensive functions like image processing functions can be integrated into a natively implemented optimized image processing kernel. Plug-in tools implemented in Java can utilize the kernel functions via a Java-wrapper library. This approach is comparable to the implementation of computationally intensive operations in hardware.

Computer Communication Networks↗
PubMed1996

Creating a virtual materials and resources index for health education using the World Wide Web.

The Internet represents the principal system for distributing information worldwide, offering health educators a powerful communications medium. This article describes an assignment that teaches students how to use the World Wide Web (WWW). The first part provides an overview of the Internet, its principal services. browser software, and Netscape Navigator. The second part describes the assignment, complete with instructional objectives, computer facilities used to implement the strategy, and a summary of classroom and laboratory activities. The third part describes procedures for teaching students how to use the WWW. Students learn how to explore the WWW and to develop a customized virtual directory of health materials and resources using Netscape Navigator Bookmark tools. Recommendations on how the approach can be modified are offered.

Abstracting and Indexing↗
PubMedDate not supplied

A technique for computing dose volume histograms for structure combinations.

Graphical displays of three-dimensional dose distribution data are often too complex to be easily assimilated and interpreted for the evaluation of radiation treatment plans. Histograms showing dose versus volume are convenient and useful tools for summarizing dose distribution information throughout the entire volume of a given anatomic structure. They can quickly highlight characteristics such as dose uniformity and hot and cold spots, and can be used to produce statistics including tumor control and normal tissue complication probabilities. To obtain a dose volume histogram for a given structure, it may be necessary to examine its spatial relationships with neighboring structures. They may overlap, be completely disjoint, or one may be contained within another. To resolve potential ambiguities, a procedure has been developed that assigns hierarchies to anatomical structures for the purpose of histogram calculation. The hierarchy assigned to each structure is used to determine the structure within which a given dose matrix point is considered to lie. In this manner, regions of structure intersection are assigned to one object or another, and dose volume histograms can be calculated for each structure separately. From this framework, addition and subtraction of histograms can also be performed. Details of the algorithm are presented along with an example using patient data.

Algorithms↗
PubMed1980

Identification of vowels spoken in isolation versus vowels spoken in consonantal context.

Strange et al. [J. Acoust. Soc. Am. 60, 213--224 (1976)] report that naive listeners misidentified approximately three times as many tokens of vowels spoken in isolation as the corresponding vowels spoken in consonantal context. On the basis of these findings, they argue that the superior intelligibility of vowels in consonantal context is due to coarticulatory effects: "acoustic information distributed over the temporal course of the syllable is utilized regularly by the listener to identify vowels" (p. 213). The present study tested naive listeners' identification of eleven American English vowels spoken in isolation and in consonantal context with an experimental design comparable to that used by Strange et al. Here, however, listening tests were administered under high quality listening conditions, speakers and listeners were closely matched for regional dialect, and problems with the response alternatives for the vowels were minimized by having listeners identify the isolated vowels and /tVt/ syllables by rhyming them with English words. The results of the tests indicated that isolated vowels could be identified quite well; listeners misidentified only 2% of the vowels when tokens were blocked by speaker and only 8% when tokens were randomized across speakers. Further the tests did not reveal any overall difference in identifiability between the isolated vowels and vowels in consonantal context.

Adolescent↗
PubMed1999

Solution of the inverse problem for a linear cochlear model: a tonotopic cochlear amplifier.

The extraordinary fine-tuning characteristic of normal mammalian hearing is attributed to physiological mechanisms collectively known as the cochlear amplifier (CA), which amplifies and sharpens the basilar membrane (BM) vibration response to incoming acoustic pressure oscillations. Electromechanical properties of outer hair cells (OHCs) are believed to be the critical component of the CA, but its "circuitry" as yet remains unknown. Here, the required frequency-space response characteristics of the CA are computationally determined when typical in vivo tuning data are introduced as input to a linear hydroelastic cochlear model whose cross-sectional dynamics are represented by two coupled vibrational degrees of freedom. It is assumed that the CA senses motion at the tectorial membrane (TM) reticular lamina (RL) and applies proportional, equal, and opposite forces to the BM and the RL. The results show the CA to be tonotopically tuned, meaning it conforms to a space-frequency similarity principle like other cochlear dynamical responses. This requires that the active mechanism use information distributed along the cochlear partition. The physiological mechanism responsible for such behavior remains unknown, but here the computed CA characteristics can be qualitatively reproduced by a circuit spanning the length of the cochlea. This does not preclude other mechanisms, but is intended to motivate closer experimental investigation of extracellular and intercellular ionic flow pathways.

Animals↗