Molecules to maps: tools for visualization and interaction in support of computational biology

The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding, and exchanging this data. At the 1998 Pacific Symposium on Biocomputing, a track entitled 'Molecules to Maps: Tools for Visualization and Interaction in Computational Biology' provided tool developers and users with the opportunity to discuss advances in tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. In this paper we present these advances and discuss some of the challenges that remain to be solved.     

An array of qualitative data analysis tools: A call for data analysis triangulation.

One of the most important steps in the qualitative research process is analysis of data. The purpose of this article is to provide elements for understanding multiple types of qualitative data analysis techniques available and the importance of utilizing more than one type of analysis, thus utilizing data analysis triangulation, in order to understand phenomenon more fully for school psychology research and beyond. The authors describe seven qualitative analysis tools: methods of constant comparison, keywords-in-context, word count, classical content analysis, domain analysis, taxonomic analysis, and componential analysis. Then, the authors outline when to use each type of analysis. In so doing, the authors use real qualitative data to help distinguish the various types of analyses. Furthermore, flowcharts and tables are provided to help delineate when to choose each type of analysis. Finally, the role of computer-assisted software in the qualitative data-analytic process is discussed. As such, use of the analyses outlined in this article should help to promote rigor in qualitative research. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Comparison of genomic methods for differentiating strains of Enterococcus faecium: assessment using clinical epidemiologic data

Genomic DNA extracted from 45 vancomycin-resistant Enterococcus faecium (VRE) isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis. The ability of this method (restriction endonuclease analysis [REA]) to distinguish strains at the subspecies level was compared with results previously determined by pulsed-field gel electrophoresis (PFGE). Chart reviews were performed to provide a clinical correlation of possible epidemiologic relatedness. A likely clinical association was found for 29 patients as part of two outbreaks. REA found 21 of 21 isolates were the same type in the first outbreak, with PFGE calling 19 strains the same type. In the second outbreak with eight patient isolates, HindIII found six were the same type and two were unique types. HaeIII found three strains were the same type, two strains were a separate type, and three more strains were unique types, while PFGE found three were the same type and five were unique types. No single "ideal" method can be used without clinical epidemiologic investigation, but any of these techniques is helpful in providing focus to infection control practitioners assessing possible outbreaks of nosocomial infection.     

Morphologic image processing operators: reduction of partial volume effects for improved 3D visualization of CT data

AIM: The quality of segmentation and three-dimensional reconstruction of anatomical structures in tomographic slices is often impaired by disturbances due to partial volume effects (PVE). The potential for artefact reduction by use of the morphological image processing operators (MO) erosion and dilation is investigated. DESIGN: The CT examinations of 31 patients with pathological alterations in lung or brain were segmented using automatic region growing and the MO were applied in a different number of iterations. The processed regions were 3D-reconstructed (shaded surface display, MIP, volume rendering) and the occurrence of PVE-related artefacts using the signal-to-background ratio (SBR) prior to and after MO application was compared. RESULTS: For all patients under review, the artefacts caused by PVE were significantly reduced by erosion (lung: mean SBRpre = 1.67, SBRpost = 4.83; brain: SBRpre = 1.06, SBRpost = 1.29) even with only a small number of iterations. Region dilation was applied to integrate further structures (e.g. at tumor borders) into a configurable neighbourhood for segmentation and quantitative analysis. CONCLUSIONS: The MO represent an efficient approach for the reduction of PVE artefacts in 3D-CT reconstructions and allow optimized visualization of individual objects.     

Evaluation of data in cardiology by new software tools

We describe an analysis of cardiology data using new software tools. First we use data of 1417 men aged 40 to 50 years living in the center of Prague gathered in the twenty years lasting longitudinal study. We show some results of application of the programs E.T. (Epidemiology Tools) and CORE (COnstitution and REduction of data). Second we show the way of application of the program HYPERTENSION, that supports decision making in therapy of arterial hypertension.     

Prediction of compressive strength based on visualization of pellet microstructure data

In recent years, with the wide application of image data visual extraction technology in the field of industrial engineering, the development of industrial econ...     

Anti-cytokines: promising tools for diagnosis and immunotherapy

Anti-cytokines belong to a new family of biological response modifiers which interfere with the biological functions of cytokines. An imbalance between cytokines and natural anti-cytokines may represent an important factor to explain the pathogenesis of some human diseases. Indeed, dysregulation of anti-cytokine serum levels was observed in cancers and auto-immune and infectious diseases. It was sometimes associated with disease activity and in some circumstances they may help to predict clinical response to treatment. Control of disease activity in septic shock and auto-immune diseases was demonstrated after administration of anti-cytokines such as soluble TNF receptors and IL1ra inhibitors. Therefore these agents are promising tools for diagnosis and immunotherapy.     

Scorpion toxins: tools for studying K+ channels

Over the last period of time, a large number of scorpion toxins have been characterized. These peptidyl inhibitors of K+ channels have been very useful as probes for determining the molecular architecture of these channels, for purifying channels from native tissue and determining their subunit composition, for developing the pharmacology of K+ channels, and for determining the physiologic role that K+ channels play in target tissues. The large knowledge that we have developed regarding K+ channel function would not have been possible without the discovery of these peptidyl inhibitors. It is expected that as more novel peptides are discovered, our understanding of K+ channel structure and function will be further enhanced.     

Libraries for genomic SELEX

An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX.     

Proteasome inhibitors: valuable new tools for cell biologists

Proteasomes are major sites for protein degradation in eukaryotic cells. The recent identification of selective proteasome inhibitors has allowed a definition of the roles of the ubiquitin-proteasome pathway in various cellular processes, such as antigen presentation and the degradation of regulatory or membrane proteins. This review describes the actions of these inhibitors, how they can be used to investigate cellular responses, the functions of the proteasome demonstrated by such studies and their potential applications in the future.     

Posters: innovative and cost-effective tools for staff development

A correlation between localization of morphological lesions and the presence of viral antigen in the CNS was established. Dissemination of the infectious process in the CNS depended on both topography of the inoculated areas and more so on traumatic injury of the ventricular system. Viral antigen could be detected in the reticuloendothelial system and epithelial cells of the respiratory tract without inducing specific cytopathic changes. Simultaneous morphological and immunofluorescent examination allowed the safety of live measles vaccine to be established more accurately.     

Structured care methodologies: tools for standardization and outcomes measurement

In today's healthcare environment, institutions are striving to streamline processes, reduce costs of healthcare, and establish best practice patterns while maintaining and improving the quality of care provided. Various healthcare delivery models are in use including case management and outcomes management. Various tools or structured-care methodologies (SCMs) are incorporated into these different models to support cost reduction and streamline processes while enhancing quality of care. This article discusses the tools frequently used, such as critical pathways, algorithms, and guidelines, as well as how these tools can be used in combination to support each other. This article also addresses the benefits of SCMs, how these tools are developed, and how the data obtained can be used in quality enhancement programs.     

Transcervical sonography: an investigational technique for visualization of the embryo

Due to the narrow therapeutic range of theophylline, plasma concentrations of this drug are monitored in patients undergoing chronic therapy. Slow-release preparations avoid the fluctuations in plasma levels and improve patient compliance. In this study, we have compared the pharmacokinetic profiles of a theophylline slow-release tablet and a syrup form, when administered in multiple doses to healthy adult volunteers. The classification based upon releasing patterns is confirmed.     

Bootstrapping for pharmacokinetic models: visualization of predictive and parameter uncertainty

PURPOSE: We explore use of "bootstrapping" methods to obtain a measure of reliability of predictions made in part from fits of individual drug level data with a pharmacokinetic (PK) model, and to help clarify parameter identifiability for such models. METHODS: Simulation studies use four sets (A-D) of drug concentration data obtained following a single oral dose. Each set is fit with a two compartment PK model, and the "bootstrap" is employed to examine the potential predictive variation in estimates of parameter sets. This yields an empirical distribution of plausible steady state (SS) drug concentration predictions that can be used to form a confidence interval for a prediction. RESULTS: A distinct, narrow confidence region in parameter space is identified for subjects A and B. The bootstrapped sets have a relatively large coefficient of variation (CV) (35-90% for A), yet the corresponding SS drug levels are tightly clustered (CVs only 2-9%). The results for C and D are dramatically different. The CVs for both the parameters and predicted drug levels are larger by a factor of 5 and more. The results reveal that the original data for C and D, but not A and B, can be represented by at least two different PK model manifestations, yet only one provides reliable predictions. CONCLUSIONS: The insights gained can facilitate making decisions about parameter identifiability. In particular, the results for C and D have important implications for the degree of implicit overparameterization that may exist in the PK model. In cases where the data support only a single model manifestation, the "bootstrap" method provides information needed to form a confidence interval for a prediction.