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PubMed1994

Kinlsq: a program for fitting kinetics data with numerically integrated rate equations and its application to the analysis of slow, tight-binding inhibition data.

Kinlsq, a Matlab-based computer program for the least-squares fitting of parameters to kinetics data described by numerically integrated rate equations, is described, and three applications to the analysis of enzyme kinetics data are given. The first application was to the analysis of a simple bimolecular enzyme plus inhibitor binding curve. The kinlsq fit to these data was essentially identical to that obtained with the corresponding analytically integrated rate equation, validating kinlsq. The second application was to the fit of a numerically integrated Michaelis-Menten model to the progress curve for dipeptidyl peptidase IV-catalyzed hydrolysis of Ala-Pro-p-nitroanilide as a demonstration of the analysis of steady-state enzyme kinetics data. The results obtained with kinlsq were compared with the results obtained by fitting this time course with the integrated Michaelis-Menten equation, and with the results obtained by fitting the (S,dP/dt) transform of the data with the Michaelis-Menten equation. The third application was to the analysis of the inhibition of chymotrypsin by the slow, tight-binding inhibitor MeOSuc-Ala-Ala-Pro-boroPhe, data not readily amenable to other methods of analysis. These applications demonstrate how kinlsq can be used to fit rate constants, equilibrium constants, steady-state constants, and the stoichiometric relationships between components.

Amino Acid Sequence↗

PubMed2006

Computational approaches for predicting protein-protein interactions: a survey.

Discovery of the protein interactions that take place within a cell can provide a starting point for understanding biological regulatory pathways. Global interaction patterns among proteins, for example, can suggest new drug targets and aid the design of new drugs by providing a clearer picture of the biological pathways in the neighborhoods of the drug targets. High-throughput experimental screens have been developed to detect protein-protein interactions, however, they show high rates of errors in terms of false positives and false negatives. Many computational approaches have been proposed to tackle the problem of protein-protein interaction prediction. They range from comparative genomics based methods to data integration based approaches. Challenging properties of protein-protein interaction data have to be addressed appropriately before a higher quality interaction map with better coverage can be achieved. This paper presents a survey of major works in computational prediction of protein-protein interactions, explaining their assumptions, main ideas, and limitations.

Humans↗

PubMed1996

Interactive and dynamic ECG analysis. Is it just an IDEA or a clinically relevant approach?

The idea that it is possible to increase the overall electrocardiographic (ECG) diagnostic performance is developed in this paper, provided that different programs or methods and various data sources are combined and that the dynamicity of the patients' record is considered. This dynamicity consists of the following three dimensions: beat-to-beat changes within continuous recordings, changes between serial records, and clinical events. Data integration should be time- or event-related, and multisources data should interact. Interactive and dynamic ECG analysis (IDEA), however, can only be achieved if powerful clinical workstations are developed that access the right information, when and where needed, a challenge that the IDEA workstation intends to accomplish.

Clinical Laboratory Information Systems↗

PubMed2001

Standardized terminological services enabling semantic interoperability between distributed and heterogeneous systems.

The interconnection of heterogeneous computer applications in medicine raises the issue of semantic interoperability, going beyond traditional approaches of terminological standardization in basically three aspects. First, the variety of medical vocabularies that currently coexist in different domains is a major barrier for the integration of autonomously developed applications. Fortunately, with the Unified Medical Language System (UMLS) there are machine-readable terminological sources that cover and integrate most of the existing medical vocabularies. Second, the exchanged data need to be processed by a machine for different purposes like patient data integration, access to literature and knowledge bases as well as clinical audit and research. Medical vocabularies provided as passive dictionaries are no longer sufficient. Software system developers should take advantage of terminological services for refining user queries, for mapping the user's terms to appropriate medical vocabularies etc. Third, the services should be accessible uniformly and transparently. In the CORBAmed initiative a proposal for a standardized interface for querying and accessing computerized medical terminology resources was created. Based on the mentioned principles the MUSTANG system (Medical UMLS based Terminology Server for Authoring, Navigating and Guiding the Retrieval to Heterogeneous Knowledge Sources) has been developed. It is implemented on a Windows NT platform using the ORACLE database management and development software. The terminological services are accessible via multiple interfaces. The MUSTANG-System and the experiences with using terminological services in practice are described. Opposed to other levels of standardization like syntactical message standards there is much more a hesitation in the use of standardized terminology.

Humans↗

PubMed2005

ArrayExpress--a public repository for microarray gene expression data at the EBI.

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by various parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

Animals↗

PubMed2001

History and trends in clinical information systems in the United States.

PURPOSE: To provide a synopsis of issues about clinical information systems for nurses not schooled in nursing informatics. ORGANIZING CONSTRUCT: The past, present, and future of clinical computing, including major factors resulting in the early hospital information systems (HIS) and decision support systems (DSS) in the United States, current advances and issues in managing clinical information, and future trends and issues. METHODS: Literature review and analysis. FINDINGS AND CONCLUSIONS: The first HIS and DSS were used in the late 1960s and were focused on applications for acute care. The change from fee-for-service to managed care required a change in the design of clinical information systems toward more patient-centered systems that span the care continuum, such as the computer-based patient record (CPR). Current difficulties with CPR systems include lack of systems integration, data standardization, and implementation. Increased advances in information and technology integration and increased use of the Internet for health information will shape the future of clinical information systems.

Decision Making, Computer-Assisted↗

PubMed2003

Autofocus algorithm for dispersion correction in optical coherence tomography.

Practical clinical optical coherence tomography (OCT) systems require automatic tools for identifying and correcting flaws in OCT images. One type of flaw is the loss of image detail owing to the dispersion of the medium, which in most cases is unknown. We present an autofocus algorithm for estimating the delay line and material dispersion from OCT reflectance data, integrating a previously presented dispersion compensation algorithm to correct the data. The algorithm is based on minimizing the Renyi entropy of the corrected axial-scan image, which is a contrast-enhancement criterion. This autofocus algorithm can be used in conjunction with a high-speed, digital-signal-processor-based OCT acquisition system for rapid image correction.

Algorithms↗

PubMed2004

Functionally and structurally integrated computational modeling of ventricular physiology.

Computational biology is integrative in several ways. Functionally, computational models are valuable for integrating the many interacting processes within biochemical networks and the many interacting physiological subsystems within the cell. Structurally detailed models provide a way of integrating across scales of biological organization from molecule to organism. Data integration across diverse laboratory and clinical measurements is another unique strength of computational biology. We describe examples of all three categories of integration by using recent advances in modeling cardiac excitation-contraction coupling and whole-heart electromechanics in health and disease.

Animals↗

PubMed2000

An infrastructure for comparative genomics to functionally characterize genes and proteins.

Current genome projects are resulting in a flood of sequence data. The interpretation of these sequences is lagging, and optimized data analysis strategies need to be developed. Much can be learned from comparing different genomes, as genomes of distant organisms may still encode proteins with high sequence similarity. The order of genes (co linearity) in genomes may also be conserved to some extend. We have employed both these observations to create a multi-functional, computational analysis system (genomeSCOUT) which allows for rapid identification and functional characterization of genes and proteins through genome comparison. With a number of independent algorithms, information about different levels of protein homology (concerning e.g. paralogs, orthologs and clusters of orthologous groups, COGs) and gene order is collected and stored in several value added databases. These databases are then used for interactive comparison of genomes and subsequent analysis. The application is based on the well established data integration system SRS. This ensures (1) fast handling of large genomic data sets, (2) straightforward access to a multitude of biological databases, (3) unique linking functions between these databases, (4) highly efficient collection of information on genes and proteins, and 5. fully integrated and user friendly graphical representations of search results. This application can be used for projects as diverse as the correct annotation of genomes, the optimization of (micro) organisms for industrial production, or the identification of drug targets.

Computational Biology↗

PubMed2003

Translating multiple assessment techniques into an intervention selection model for classrooms.

Translating current research to school-based clinical practice highlights issues not often encountered in laboratory settings. With the assistance of a consultant, teachers conducted functional analyses, brief multielement treatment comparisons, and controlled treatment evaluations under naturalistic conditions in the classroom. Teachers also provided input on treatment selection. Treatment integrity data collected throughout the study suggested that teachers implemented analyses and treatments with high integrity. The functional analysis outcomes combined with effectiveness and acceptability data led to the selection of interventions that reduced problem behavior in the classrooms for each of 3 children.

Behavior Therapy↗

PubMed2003

Integrating functional genomics data.

Functional annotation of fully sequenced genomes is still a major issue. High-throughput data sets could be used to provide more and better functional annotations. However differences in data quality need to be taken into account. For this purpose these high-throughput data sets need to be integrated so that the data quality can be assessed, hypotheses can be prioritized and existing annotations can be improved and extended.

Computational Biology↗

PubMed2006

Evaluation of in vivo P-glycoprotein function at the blood-brain barrier among MDR1 gene polymorphisms by using 11C-verapamil.

UNLABELLED: P-glycoprotein (P-gp) is a membrane protein that functions as an adenosine triphosphate-dependent efflux pump for xenobiotics at the blood-brain barrier (BBB). Polymorphisms of MDR1 gene have been reported to be associated with the expression level of P-gp. (11)C-Verapamil is considered to be one of the suitable radioligands for evaluating P-gp functions. However, the metabolites of verapamil might complicate the quantitative analysis because of their possible brain penetration. In the present study, we investigated the P-gp functional differences at the BBB between the haplotypes (1236TT, 2677TT, 3435TT vs. 1236CC, 2677GG, 3435CC) of the MDR1 gene with different quantitative analyses of (11)C-verapamil. METHODS: Thirty-three healthy male volunteers were enrolled in this study after identification of the haplotypes of the MDR1 gene. Brain PET scans with (11)C-verapamil were performed for 16 min. Integration plot analysis, which yields brain uptake clearance, was performed with the first 3-min data. Integration plot analysis was then compared with several other quantitative analyses with 16-min data (1-input, 1-tissue compartment model, and the area under the curve ratio (AUC(ratio)) between brain and plasma). RESULTS: In the integration plot, there was no difference in the absolute values of brain uptake clearance (CL(uptake)) between the haplotypes; CL(uptake) of (11)C-verapamil for the haplotypes (1236TT, 2677TT, 3435TT vs. 1236CC, 2677GG, 3435CC) were 0.053 +/- 0.011 and 0.051 +/- 0.011 mL/g/min, respectively. CL(uptake) of (11)C-verapamil in the integration plot was significantly correlated with K1 and DV(K1/k2) (DV is distribution volume; K1 and k2 are plasma and tissue rate constants) in the 1-input, 1-tissue compartment model and the AUC(ratio). CONCLUSION: On the basis of the several quantitative analyses of (11)C-verapamil, the assumption that the function of P-gp at the BBB is different between the haplotypes (3 single nucleotide polymorphisms: C1236T, G2677T, and C3435T) of MDR1 gene was not supported.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed1995

Integrated genetic map of human chromosome 2.

A framework genetic map of human chromosome 2 is described, integrating data from the Centre d'Etude du Polymorphisme Humain (CEPH) version 6 database, the CEPH chromosome 2 consortium database, the National Institute of Health (NIH)/CEPH Collaborative Mapping group and other laboratories. A comprehensive map is also presented, showing regional locations of a large number of additional loci. The framework map is used to identify an informative set of meiotic breakpoints within the CEPH families, and the utility of this information for mapping new markers is discussed. The degree of typing error within the data set is estimated, as are the sex-specific interference parameters. A location database for these genetic and additional cytogenetic data is constructed using algorithms which map genetic distances on to a physical scale, and the potential for this approach to aid the integration of genetic and physical data is examined.

Chromosome Mapping↗

PubMed1998

The unpackaging of routine in older women.

OBJECTIVE: A qualitative research design using grounded theory procedures and techniques was used to explore how routine changed in later adulthood for seven Caucasian, college-educated, middle-class women who were not employed and who were free of major functional impairments. METHOD: In-depth interviews, observations, an autobiography, and researcher-generated memos provided data. Data analysis involved concept formation, concept development, and conceptual modification and integration. Data collection and analysis were concurrent, iterative, reflective, and reflexive. RESULTS: Although the participants used routines to facilitate their well-being, they reported doing so to a lesser extent than when they had children living at home or when they worked. These participants unpackaged routines and molded them into increasingly flexible time-use strategies in response to age-related changes in their ecocultural niche, philosophy of life, and physical status. CONCLUSION: That the participants sought less obligation and more freedom as they aged may influence the way they respond to a health care practitioner's advocating for an increase in routine. Interventions with older women must be compatible with existing routines and family themes and directly linked to well-being.

Activities of Daily Living↗

PubMed1991

SESAM: a relational database for structure and sequence of macromolecules.

A system is described that provides ways of integrating data on protein structure, sequence, and survey results, with molecular graphics and molecular mechanics software. Its major component is the relational database SESAM, presently implemented under the commercial package SYBASE. By design, the database allows full integration--within the same data organization--of raw data on protein structure, sequence, ligands, and heterogroups, obtained from the Brookhaven Protein Databank, with pure sequence information available from other databanks such as SWISS-PROT. It contains in addition higher level descriptions of structural and topological properties, as well as survey results, obtained by executing specialized computer programs. Aside from the very useful attribute of closely combining structural and nonstructural information, other important features distinguish it from analogous systems developed elsewhere. It includes a molecular dictionary with complete description of geometric properties and energy parameters used in modeling and conformational energy calculations. Using this dictionary, structural data are validated by checking for localized inconsistencies in atomic coordinates, atomic symbols, chirality definitions, and flagging errors and incomplete entries. Because of both the dictionary and the validation procedures, SESAM can be readily interfaced with conventional molecular graphics and mechanics software packages, or with other specialized application programs. With the aid of appropriate interfaces, data access is sufficiently fast for SESAM to be interrogated interactively. Prototypes of user interfaces, as well as an interface with the molecular graphics package BRUGEL, are described and the power of the system is illustrated in applications such as homology-based protein modeling, computer-aided protein design, protein structure predictions, analysis of local structure motifs, and of relationships between protein sequence and structure.

Amino Acid Sequence↗

PubMed2003

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.

The flood of data acquired from the increasing number of publicly available genomes has led to new demands for bioinformatics software. With the growing amount of information resulting from high throughput experiments new questions arise that often focus on the comparison of genes, genomes, and their expression profiles. Inferring new knowledge by combining different kinds of "post-genomics" data obviously necessitates the development of new approaches that allow the integration of variable data sources into a flexible framework. In this paper, we describe our concept for the integration of heterogeneous data into a platform for systems biology. We have implemented a Bioinformatics Resource for the Integration of heterogeneous Data from Genomic Explorations (BRIDGE) and illustrate the usability of our approach as a platform for systems biology for two sample applications.

Algorithms↗

PubMed2003

The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system.

Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical modeling and information theory to provide a seamless approach to the modeling/data analysis endeavor. Thereby the rapidly growing mess of genomic, proteomic, metabolic, and cell physiological data can be automatically used to develop and calibrate a predictive cell model. The discussion focuses on the Karyote cell modeling system and an introduction to the CellX and VirusX models. The Karyote software system integrates three elements: (1) a model-building and data archiving module that allows one to define a cell type to be modeled through its reaction network, structure, and transport processes as well as to choose the surrounding medium and other parameters of the phenomenon to be modeled; (2) a genomic, proteomic, metabolic cell simulator that solves the equations of metabolic reaction, transcription/translation polymerization and the exchange of molecules between parts of the cell and with the surrounding medium; and (3) an information theory module (ITM) that automates model calibration and development, and integrates a variety of data types with the cell dynamic computations. In Karyote, reactions may be fast (equilibrated) or slow (finite rate), and the special effects of enzymes and other minority species yielding steady-state cycles of arbitrary complexities are accounted for. These features of the dynamics are handled via rigorous multiple scale analysis. A user interface allows for an automated generation and solution of the equations of multiple timescale, compartmented dynamics. Karyote is based on a fixed intracellular structure. However, cell response to changes in the host medium, damage, development or transformation to abnormality can involve dramatic changes in intracellular structure. As this changes the nature of the cellular dynamics, a new model, CellX, is being developed based on the spatial distribution of concentration and other variables. This allows CellX to capture the self-organizing character of cellular behavior. The self-assembly of organelles, viruses, and other subcellular bodies is being addressed in a second new model, VirusX, that integrates molecular mechanics and continuum theory. VirusX is designed to study the influence of a host medium on viral self-assembly, structural stability, infection of a single cell, and transmission of disease.

Animals↗

PubMed1996

Optimal normalization tests for shoulder muscle activation: an electromyographic study.

To accurately compare electromyographic data from different muscles and different subjects, it is necessary to normalize the integrated data obtained from each muscle. The purpose of this study was to identify the manual muscle testing positions that elicit maximal neural activation (integrated electromyography) of three rotator cuff muscles (supraspinatus, infraspinatus, and subscapularis) and five shoulder synergists (pectoralis major, latissimus dorsi, and anterior, middle, and posterior deltoids). The electromyographic activity of these eight muscles was examined in the nondominant shoulders of nine subjects. Indwelling wire electrodes (supraspinatus, infraspinatus, and subscapularis) and surface adhesive electrodes (pectoralis major, latissimus dorsi, and anterior, middle, and posterior deltoids) were placed. Each subject performed a series of 27 isometric contractions, and optimal tests (maximal neural activation) were identified for each muscle. Four tests were identified that resulted in the maximal neural activation of all eight shoulder muscles: 90 degrees of scapular elevation with -45 degrees of humeral rotation for the supraspinatus, anterior deltoid, and middle deltoid: external rotation at 90 degrees of scapular elevation and -45 degrees of humeral rotation for the infraspinatus and posterior deltoid: internal rotation at 90 degrees of scapular elevation and neutral humeral rotation for the subscapularis and latissimus dorsi: and internal rotation at 0 degree of elevation and neutral rotation for the pectoralis major. These results identify four standard testing positions that will provide reference values for normalization of maximal voluntary contraction for the eight muscles of the shoulder examined in this study. Standardization of these test positions offers normalization guidelines that can be used in future dynamic electromyography studies of the shoulder.

Adult↗