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PubMedDate not supplied

Potential added value of three-dimensional reconstruction and display of single photon emission computed tomographic gated blood pool images.

BACKGROUND: Single photon emission computed tomographic (SPECT) acquisition provides potential advantages for blood pool imaging. However, the method has been little applied. METHODS: An improved method of three-dimensional (3-D) reconstruction and display of SPECT equilibrium blood pool scintigrams and related phase data was developed. Dynamic slices and volume-rendered dynamic 3-D images were displayed. Images were viewed from each of 34 solid angles referenced to a sphere surrounding the reconstruction field. Each image pixel was "painted" with intensity-coded regional amplitude and color-coded for its phase angle. The method was applied to evaluate the cardiac anatomy, regional contraction, and related conduction sequence at rest in 17 patients. Twelve had normal left ventricular function including 7 patients with minimal septal preexcitation. Five patients had abnormal left ventricular function, including 2 with left bundle branch block. RESULTS: Slices contained all of the functional information, but necessary data integration was time-consuming and evaluation of chamber size and anatomy was difficult. Three-dimensional projection images condensed and integrated the data, presenting new vantage points on anatomy, contraction, and conduction not otherwise available in the clinically limited angulations of planar images. This provided excellent visual separation of cardiac chambers with full and increased visualization of right and left ventricular wall motion in all segments compared with the conventional projections acquired clinically (p < 0.05). Atria and great vessels were well separated with evident size and function. Phase-angle progression paralleled the electrocardiogram, permitting bypass pathway localization and the direct noninvasive localization of posteroseptal pathways. CONCLUSIONS: The 3-D method permits greater access to and utilization of SPECT blood pool image data. It suggests specific advantages for clinical use.

Adult↗
PubMed2006

Create and assess protein networks through molecular characteristics of individual proteins.

MOTIVATION: The study of biological systems, pathways and processes relies increasingly on analyses of networks. Most often, such analyses focus on network topology, thereby treating all proteins or genes as identical, featureless nodes. Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes. RESULTS: Here, we introduce a novel platform for data integration that generates networks on the macro system-level, analyzes the molecular characteristics of each protein on the micro level, and then combines the two levels by using the molecular characteristics to assess networks. It also annotates the function and subcellular localization of each protein and displays the process on an image of a cell, rendering each protein in its respective cellular compartment. By thus visualizing the network in a cellular context we are able to analyze pathways and processes in a novel way. As an example, we use the system to analyze proteins implicated with Alzheimers disease and show how the integrated view corroborates previous observations and how it helps in the formulation of new hypotheses regarding the molecular underpinnings of the disease. AVAILABILITY: http://www.rostlab.org/services/pinat.

Cell Physiological Phenomena↗
PubMed2005

Surgical management of colorectal cancer in south-western Sydney 1997-2001: a prospective series of 1293 unselected cases from six public hospitals.

BACKGROUND: The aim of the present study is to provide local data for the management of colorectal cancers in the south-western Sydney health area from 1997 to 2001. METHODS: The data were collected prospectively. Follow up was conducted in late 2001 and early 2002. Data were cross-validated with hospital and area databases and with data from the New South Wales Registry of Births, Deaths and Marriages. RESULTS: This was an unselected series of 1293 patients from 36 surgeons; 16.5% of patients presented as emergencies. Only 3% presented as a result of bowel cancer screening. Of the 1293 patients, 1270 received an operation. There were 598 elective colonic resections with the mortality rate of 1.2%, reoperation rate of 2.7% and anastomotic leak rate of 0.8%. For the 410 elective rectal resections, the rates were 2.9%, 2.7% and 1.2%, respectively. For the 290 emergency operations, the rates were much worse at 7.7%, 6.6% and 4.8%, respectively. The corrected overall 3-year survival rate was 64%. For Dukes' A, B, C and D, the figures were 94%, 87%, 61% and 7%, respectively. CONCLUSIONS: Colorectal cancer is a major cause of mortality and morbidity in our community. Very few bowel cancers were discovered at the asymptomatic stage. This paper strongly supports community bowel cancer screening and early diagnosis. The local database has provided a rich source of information to benchmark management and outcomes of bowel cancer patients treated in the South Western Sydney Area Health Service. An area-wide computer network with online data input facilities at individual workplaces will improve data integrity and data collection efficiency.

Adult↗
PubMed1993

Teaching biopsychosocial integration and formulation.

This paper describes the mental processes by which the psychiatrist organizes and integrates data to produce a case formulation. The biopsychosocial formulation uses three perspectives (biological, psychological and social) to view the data and integrates these viewpoints into one broad, complex and dynamic appreciation of the patient. Guidelines for creating and communicating a case formulation are proposed.

Curriculum↗
PubMed2004

MuTrack: a genome analysis system for large-scale mutagenesis in the mouse.

BACKGROUND: Modern biological research makes possible the comprehensive study and development of heritable mutations in the mouse model at high-throughput. Using techniques spanning genetics, molecular biology, histology, and behavioral science, researchers may examine, with varying degrees of granularity, numerous phenotypic aspects of mutant mouse strains directly pertinent to human disease states. Success of these and other genome-wide endeavors relies on a well-structured bioinformatics core that brings together investigators from widely dispersed institutions and enables them to seamlessly integrate data, observations and discussions. DESCRIPTION: MuTrack was developed as the bioinformatics core for a large mouse phenotype screening effort. It is a comprehensive collection of on-line computational tools and tracks thousands of mutagenized mice from birth through senescence and death. It identifies the physical location of mice during an intensive phenotype screening process at several locations throughout the state of Tennessee and collects raw and processed experimental data from each domain. MuTrack's statistical package allows researchers to access a real-time analysis of mouse pedigrees for aberrant behavior, and subsequent recirculation and retesting. The end result is the classification of potential and actual heritable mutant mouse strains that become immediately available to outside researchers who have expressed interest in the mutant phenotype. CONCLUSION: MuTrack demonstrates the effectiveness of using bioinformatics techniques in data collection, integration and analysis to identify unique result sets that are beyond the capacity of a solitary laboratory. By employing the research expertise of investigators at several institutions for a broad-ranging study, the TMGC has amplified the effectiveness of any one consortium member. The bioinformatics strategy presented here lends future collaborative efforts a template for a comprehensive approach to large-scale analysis.

Animals↗
PubMed2003

Growth stage-based phenotypic profiling of plants.

Recent high-throughput methods for the analysis of biological samples are raising the possibility of data integration between investigators and even across technology platforms. In plant biology, integration of data can be problematic, since heterogeneity of plant growth conditions and phenotypes result in data sets that are not consistent or easily comparable. In this chapter, we describe the development of a plant phenotyping platform based on a growth stage scale that will aid in the generation of coherent data. While the emphasis is on the development of a phenotyping platform for Arabidopsis, the aim of this chapter is to describe principles that can be applied to other plant systems as well. Additionally, we discuss approaches for data analysis and quality control.

Animals↗
PubMed2006

Bridging information gaps between primary and secondary healthcare.

Medication errors are harmful and costly for healthcare systems. Recent studies show that a major part of these errors are due to the problems in transferring the patient current medication-data between primary and secondary healthcare. Recent ICT development promises to improve the communication between primary and secondary healthcare. In order to find out the constraints that may hamper a communication project's productivity, an IT configuration for building a medication-data communication network between primary and secondary healthcare in the Netherlands was followed applying qualitative methods. We analysed some important problems that project faced and conclude that problems with the data integration and saving the data integrity are important challenges for the project to maintain its objectives.

Communication↗
PubMed1991

[Experiences with a Token Ring Network in blood bank administration of the Hannover medical university].

The Token Ring Network is a Local Area Network of IBM. It is a very helpful tool for modulating working processes by personal computers. The Token Ring is a network of the third generation and constructed like a star net. The blood bank of the Medical University of Hannover (MHH) is using the Token Ring for the administration of blood storage and donors. Medical data of foreign laboratories are transmitted into the blood bank computer. During the last year, we had no difficulties working with this software tool in response time and data security and it seemed to us a very cheap opportunity for data integration and data collection on decentralized systems.

Blood Banks↗
PubMed1998

The GAIA software framework for genome annotation.

We describe a software framework, GAIA, that supports semi-automated annotation of uncharacterized sequence data. The annotation framework incorporates annotation by data source integration, data analysis, and manual data entry. Components of the system include a configurable, open data analysis pipeline, a relational information storage manager, and Java-based graphical user interfaces. We discuss design decisions and tradeoffs in building such a system, and policies and strategies for producing consistent, uniform, high quality annotation.

Base Sequence↗
PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗
PubMed1996

Integrating assessment data from multiple informants.

OBJECTIVE: To examine the consequences for measurement of child psychiatric disorder (conduct and oppositional disorders) of not integrating the data on the same individual from different informants compared with integrating the information from parents and teachers, using three different strategies. METHOD: Data for the study came from problem checklist assessments done by parents and teachers of children aged 6 to 16 years (N = 1,134) selected with known probability from a general population sample and from structured interviews obtained in a stratified random subsample (n = 251). RESULTS: As expected, parent-teacher agreement was low. The pattern of associated features of disorder was found to vary markedly in parent-identified compared with teacher-identified disorder. Furthermore, combining informants had the disadvantage of masking the distinctive patterns of associated features noted in informant-specific disorders. Finally, by treating disorder as informant-specific, the internal properties of the measure are not generally inferior to those obtained by combining informants in various ways. CONCLUSION: Child psychiatric disorders should be conceptualized as informant-specific phenomena.

Adolescent↗
PubMed1994

Implications of graphics enhancements for the visualization of scientific data: dimensional integrality, stereopsis, motion, and mesh.

This study examines the effectiveness of four techniques to assist scientists in evaluating multidimensional data. Subjects viewed a series of complex 3D data sets, each representing an underlying complex surface, from which a set of discrete points or observations were sampled. From each sample they answered questions that required focus of attention on certain data points or integration across varying numbers of data points and dimensions. After a number of samples were viewed from each surface, subjects were tested for their retention of the surface characteristics. In Experiment 1, 3D (perspective) representations were found to support superior performance to 2D (planar) representations, but only for more integrative questions. Animated motion provided no benefits. In Experiment 2, stereoptic views of a 3D display were also found to support performance, particularly for integrative questions, but the ability to rotate the data space (motion parallax) and the presence of a mesh surface connecting the points did not. The posttests revealed some evidence that 3D representations improved the ability to visualize the surface, but neither 3D renderings nor stereopsis led to a better abstract representation of the data.

Adult↗
PubMed2002

TAIR: a resource for integrated Arabidopsis data.

The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana. The information is obtained from a battery of sources, including the Arabidopsis user community, the literature, and the major genome centers. Currently TAIR provides information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. In addition, users can find Arabidopsis publications and information about Arabidopsis researchers. Our emphasis is now on incorporating functional annotations of genes and gene products, genome-wide expression, and biochemical pathway data. Among the tools developed at TAIR, the most notable is the Sequence Viewer, which displays gene annotation, clones, transcripts, markers and polymorphisms on the Arabidopsis genome, and allows zooming in to the nucleotide level. A tool recently released is AraCyc, which is designed for visualization of biochemical pathways. We are also developing tools to extract information from the literature in a systematic way, and building controlled vocabularies to describe biological concepts in collaboration with other database groups. A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.

Arabidopsis↗
PubMed2006

Database integration for predisposition genes discovery.

Lightweight and flexible data integration is nowadays a great challenge in biology. Databases size increased exponentially, and biologists need tools to extract and merge interesting data coming from several heterogeneous and distributed sources over the Internet. Furthermore, there is a great need for data mediation on grid computing architectures. This paper is about a demonstration which goal is to show how Mediation, a data integration technique, can help in building such bioinformatics tools. We focused on research of genes functions, especially those involved in the resistance to malaria or those that may be considered as predisposition genes.

Computational Biology↗
PubMed1997

An integrated graphic data display improves detection and identification of critical events during anesthesia.

OBJECTIVE: To show that an integrated graphic data display can shorten the time taken to detect and correctly identify critical events during anesthesia. METHODS: We developed a graphic display which presents 30 anesthesia-related physiologic variables as shapes and colors, rather than traditional digits and waveforms. To evaluate the new display, we produced four critical events on a computer-based anesthesia simulator and asked two groups of five anesthesiologists to identify the events as quickly as possible. One group observed the new display while the other group viewed a traditional cardiovascular monitor with digital and waveform displays. RESULTS: The group which observed the integrated graphic display saw changes caused by inadequate paralysis 2.4 min sooner, and changes caused by a cuff leak 3.1 min sooner than those observing the traditional display. The integrated display group correctly identified the reason for the change 2.8 min sooner for inadequate paralysis, 3.1 min sooner for cuff leak and 3.1 min sooner for bleeding. These differences were all statistically significant. CONCLUSIONS: The results show that some simulated critical events are detected and correctly identified sooner, when an anesthesiologist views an integrated graphic display, rather than a traditional digital/waveform monitor.

Adult↗
PubMed2003

Towards an integrated approach to natural hazards risk assessment using GIS: with reference to bushfires.

This paper develops a GIS-based integrated approach to risk assessment in natural hazards, with reference to bushfires. The challenges for undertaking this approach have three components: data integration, risk assessment tasks, and risk decision-making. First, data integration in GIS is a fundamental step for subsequent risk assessment tasks and risk decision-making. A series of spatial data integration issues within GIS such as geographical scales and data models are addressed. Particularly, the integration of both physical environmental data and socioeconomic data is examined with an example linking remotely sensed data and areal census data in GIS. Second, specific risk assessment tasks, such as hazard behavior simulation and vulnerability assessment, should be undertaken in order to understand complex hazard risks and provide support for risk decision-making. For risk assessment tasks involving heterogeneous data sources, the selection of spatial analysis units is important. Third, risk decision-making concerns spatial preferences and/or patterns, and a multicriteria evaluation (MCE)-GIS typology for risk decision-making is presented that incorporates three perspectives: spatial data types, data models, and methods development. Both conventional MCE methods and artificial intelligence-based methods with GIS are identified to facilitate spatial risk decision-making in a rational and interpretable way. Finally, the paper concludes that the integrated approach can be used to assist risk management of natural hazards, in theory and in practice.

Conservation of Natural Resources↗
PubMed1999

"Conventional" Signals in Avian Agonistic Displays: Integrating Theory, Data and Different Levels of Analysis.

We present an integration of communication theory and data, drawing on examples from titmice (Aves: Paridae). We suggest how display actions such as lifting the head, raising the nape feathers, crest erecting and spreading the wings, act in agonistic communication when physical contact between opponents is rare. We propose that such displays largely act as strategic choice handicap signals. By giving these displays the signaller is believed to incur costs which underwrite the reliability of the signals; it may strategically increase these costs (for example by display repetition or adding additional elements) to signal its condition, motivation and hence the subjective value of a resource. It is shown that linking these ideas with earlier theories on the causation of display components, leads to an explanation of why birds have a greater repertoire of signals associated with aggression/winning, than with submission/losing. It is suggested that modellers of communication systems and those interested in the theory of signal design should pay more attention to the evolutionary constraints imposed by signal origin. Copyright 1999 Academic Press.

Journal Article↗
PubMed2003

Bioinformatics data distribution and integration via Web Services and XML.

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

Computational Biology↗