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At least 487 records · Page 27Linked to original sources

PubMed2004

Design, implementation and management of a web-based data entry system for ClinicalTrials.gov.

We describe the development and deployment of a web-based authoring capability, the first implementation of which is used for data entry and management in support of the ClinicalTrials.gov web site. The system facilitates efficient collection of summary protocol information from multiple geographically-dispersed organizations. We explain the motivation for developing this capability, and cite critical design goals. We then describe system design, implementation and operation, focusing on essential aspects of each. We conclude with a summary of the extent to which we met our stated objectives.

Clinical Trials as Topic↗

PubMed2004

Design and implementation of a web-enabled haematological system.

This paper describes the design and the implementation of a web-enabled integrated haematological system, named e-HS. The proposed system runs on a set of distributed network nodes providing useful haematological services. These services include patient-oriented data management, digitized histopathological slides (DHS) acquisition, teleconsulting facilities, etc. The objective of e-HS is to supply web-enabled services according to haematological requirements, implement a distributed storage scheme for DHS, and provide a common database containing all haematological laboratory results by using eXtensible Markup Language (XML) and web technologies. Our implementation can be accessible to every authorized physician at the distributed nodes without any additional software. The only software required for the user is the widely used browser (e.g. MS Internet Explorer v 3.02 or higher). Besides, by using a self-explaining user interfaces and HTML-techniques, such as hyperlinks, the necessary amount of training at the physicians-side is reduced to a minimum. A first implementation of the e-HS, has been established at the Medical Physics Department of the University of Patras (master node of the system), and has been tested with success by the medical staff of the Hospital Departments of the University of Patras and Thessalonica that served as distributed nodes of the system.

Clinical Laboratory Information Systems↗

PubMed2006

Addressing the problems with life-science databases for traditional uses and systems biology.

A prerequisite to systems biology is the integration of heterogeneous experimental data, which are stored in numerous life-science databases. However, a wide range of obstacles that relate to access, handling and integration impede the efficient use of the contents of these databases. Addressing these issues will not only be essential for progress in systems biology, it will also be crucial for sustaining the more traditional uses of life-science databases.

Animals↗

PubMed2003

Simulation and management games for training command and control in emergencies.

The aim of our project was to introduce and implement simulation techniques in a problematic field of increasing health care system preparedness for disasters. This field was chosen as knowledge is gained by few experienced staff members who need to disperse it to others during the busy routine work of the system personnel. Knowledge management techniques ranging from classifying the current data, centralized organizational knowledge storage and using it for decision making and dispersing it through the organization--were used in this project. In the first stage we analyzed the current system of building a preparedness protocol (set of orders). We identified the pitfalls of changing personnel and loosing knowledge gained through lessons from local and national experience. For this stage we developed a database of resources and objects (casualties) to be used in the simulation in different possibilities. One of those was the differentiation between drills with trainer and those in front of computers enable to set the needed solution. The model rules for different scenarios of multi-casualty incidents from conventional warfare trauma to combined chemical/toxicological as well as, levels of care pre and inside hospitals--were incorporated to the database management system (we used Microsoft Access' DBMS). The hardware for management game was comprised of serial computers with network and possibility of projection of scenes. For prehospital phase the possibility of portable PC's and connections to central server was used to assess bidirectional flow of information. Simulation software (ARENA) and graphical interfase (Visual Basic, GUI) as shown in the attached figure. We hereby conclude that our system provides solutions which are in use in different levels of healthcare system to assess and improve management command and control for different scenarios of multi-casualty incidents.

Computer Simulation↗

PubMed2006

Combination of text-mining algorithms increases the performance.

MOTIVATION: Recently, several information extraction systems have been developed to retrieve relevant information out of biomedical text. However, these methods represent individual efforts. In this paper, we show that by combining different algorithms and their outcome, the results improve significantly. For this reason, CONAN has been created, a system which combines different programs and their outcome. Its methods include tagging of gene/protein names, finding interaction and mutation data, tagging of biological concepts and linking to MeSH and Gene Ontology terms. RESULTS: In this paper, we will present data that show that combining different text-mining algorithms significantly improves the results. Not only is CONAN a full-scale approach that will ultimately cover all of PubMed/MEDLINE, we also show that this universality has no effect on quality: our system performs as well as or better than existing systems. AVAILABILITY: The LDD corpus presented is available by request to the author. The system will be available shortly. For information and updates on CONAN please visit http://www.cs.uu.nl/people/rainer/conan.html.

Abstracting and Indexing↗

PubMedDate not supplied

Scalable data servers for large multivariate volume visualization.

Volumetric datasets with multiple variables on each voxel over multiple time steps are often complex, especially when considering the exponentially large attribute space formed by the variables in combination with the spatial and temporal dimensions. It is intuitive, practical, and thus often desirable, to interactively select a subset of the data from within that high-dimensional value space for efficient visualization. This approach is straightforward to implement if the dataset is small enough to be stored entirely in-core. However, to handle datasets sized at hundreds of gigabytes and beyond, this simplistic approach becomes infeasible and thus, more sophisticated solutions are needed. In this work, we developed a system that supports efficient visualization of an arbitrary subset, selected by range-queries, of a large multivariate time-varying dataset. By employing specialized data structures and schemes of data distribution, our system can leverage a large number of networked computers as parallel data servers, and guarantees a near optimal load-balance. We demonstrate our system of scalable data servers using two large time-varying simulation datasets.

Computer Graphics↗

PubMed2006

Adverse outcomes in surgical patients: implementation of a nationwide reporting system.

PROBLEM: Lack of comparable data on adverse outcomes in hospitalised surgical patients. DESIGN: A Plan-Do-Study-Act (PDSA) cycle to implement and evaluate nationwide uniform reporting of adverse outcomes in surgical patients. Evaluation was done within the Reach Efficacy-Adoption Implementation Maintenance (RE-AIM) framework. SETTING: All 109 surgical departments in The Netherlands. KEY MEASURES FOR IMPROVEMENT: Increase in the number of departments implementing the reporting system and exporting data to the national database. STRATEGIES FOR CHANGE: The intervention included (1) a coordinator who could mediate in case of problems; (2) participation of an opinion leader; (3) a predefined plan of action communicated to all departments (including feedback of results during implementation); (4) connection with existing hospital databases; (5) provision of software and a helpdesk; and (6) an instrument based on nationwide standards. EFFECTS OF CHANGE: Implementation increased from 18% to 34% in 1.5 years. The main reason for not implementing the system was that the Information Computer Technology (ICT) department did not link data with the hospital information system (lack of time, finances, low priority). Only 5% of the departments exported data to the national database. Export of data was hindered mainly by slow implementation of the reporting system (so that departments did not have data to export) and by concerns regarding data quality and public availability of data from individual hospitals. LESSONS LEARNED: Hospitals need incentives to realise implementation. Important factors are financial support, sufficient manpower, adequate ICT linkage of data, and clarity with respect to public availability of data.

Benchmarking↗

PubMedDate not supplied

Retrospective data collection and analytical techniques for patient safety studies.

To enhance patient safety, data about actual clinical events must be collected and scrutinized. This paper has two purposes. First, it provides an overview of some of the methods available to collect and analyze retrospective data about medical errors, near misses, and other relevant patient safety events. Second, it introduces a methodological approach that focuses on non-routine events (NRE), defined as all events that deviate from optimal clinical care. In intermittent in-person surveys of anesthesia providers, 75 of 277 (27%) recently completed anesthetic cases contained a non-routine event (98 total NRE). Forty-six of the cases (17%) had patient impact while only 20 (7%) led to patient injury. In contrast, in the same hospitals over a two-year period, we collected event data on 135 cases identified with traditional quality improvement processes (event incidence of 0.7-2.7%). In these quality improvement cases, 120 (89%) had patient impact and 74 (55%) led to patient injury. Preliminary analyses not only illustrate some of the analytical methods applicable to safety data but also provide insight into the potential value of the non-routine event approach for the early detection of risks to patient safety before serious patient harm occurs.

Anesthesiology↗

PubMed2004

Development of a GIS-based spill management information system.

Spill Management Information System (SMIS) is a geographic information system (GIS)-based decision support system designed to effectively manage the risks associated with accidental or intentional releases of a hazardous material into an inland waterway. SMIS provides critical planning and impact information to emergency responders in anticipation of, or following such an incident. SMIS couples GIS and database management systems (DBMS) with the 2-D surface water model CE-QUAL-W2 Version 3.1 and the air contaminant model Computer-Aided Management of Emergency Operations (CAMEO) while retaining full GIS risk analysis and interpretive capabilities. Live 'real-time' data links are established within the spill management software to utilize current meteorological information and flowrates within the waterway. Capabilities include rapid modification of modeling conditions to allow for immediate scenario analysis and evaluation of 'what-if' scenarios. The functionality of the model is illustrated through a case study of the Cheatham Reach of the Cumberland River near Nashville, TN.

Air Pollution↗

PubMed2003

Quantitative image analysis: software systems in drug development trials.

Multi-dimensional image analysis is being used increasingly to arrive at surrogate end-points for drug development trials. Various imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET) and ultrasound are used to analyze treatments for diseases such as cancer, multiple sclerosis, osteoarthritis, and Alzheimer's disease. However, extracting information from images can be tedious and is prone to high user variability. The medical image analysis community is moving towards advanced software systems specifically designed for drug development trials. These systems can automatically identify the anatomy of interest in medical images (segmentation methods), can compare the anatomy over time or between patients (registration methods) and allow the quantitative extraction of anatomical features and the integration of the data and results into a database management system, automatically tracking the changes made to the data (audit trail generation). In this article, we present a case study using a prototype system that is used for quantifying multiple sclerosis lesions from multivariate MRI.

Clinical Trials as Topic↗

PubMed2005

Query3d: a new method for high-throughput analysis of functional residues in protein structures.

BACKGROUND: The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. RESULTS: Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. CONCLUSION: With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.

Algorithms↗

PubMed2003

[Clinical safety data management in company non-sponsored trials].

There is currently no harmonized way in Japan to manage safety data which are obtained during clinical trials supported by Government funds. There are two types of clinical trials, 'sponsored trials(sponsored by industrial companies)' and 'non-sponsored trials(funded by the Government, etc.)'. The Japanese Ministry of Health and Welfare has issued many of pharmaceutical laws(GCP, GPMSP etc.) for the regulation of sponsored trials, while none has ever established for non-sponsored trials, thus leaving the most important quality control/assurance unregulated. In this manuscript we discuss that the simple application of pharmaceutical laws to government-sponsored trials can not be a proper answer because of the different nature of the two types of trials.

Aged↗

PubMed1993

Operational departmentwide picture archiving communication system analysis using discrete event-driven block-oriented network simulation.

The accurate prediction of image throughput is a critical issue in planning for and acquisition of any successful picture archiving and communication system (PACS). Simulation plays an important role in this effort. The PACS image management chain is decomposed into eight subsystems. These subsystems include network transfers over three different networks and five software programs and/or queueing structures. This decomposition is used to create a simulation model that was effectuated using commercially available block-oriented network simulation software. From the PACS database, the traffic generation patterns of the imaging modality devices are used to drive the simulation. The simulation models the image file flow through the PACS for a 24-hour period. The behavior of the simulated traffic generators agreed well with the values derived from the PACS database. The mean delay for the simulated PACS is found to be 225 +/- 59 seconds. The delay time was found to vary during the simulated 24-hour cycle in a consistent manner with observations. This simulation provides estimates on what a radiological department can expect from a PACS in terms of throughput, utilization, and delay. The block-oriented network simulator (BONeS, Comdisco Systems Inc, Foster City, CA) simulation model of the modeled PACS is highly accurate. The models for the imaging modality traffic sources are validated with a high degree of accuracy. The simulation model allows for the study of what happens to the delay time under various loads. In this simulation, the reformatting process was determined to be the bottleneck causing a large increase in delay time under heavy loads.

Computer Communication Networks↗

PubMed2005

[Possibilities for workflow optimization in radiology departments beyond RIS and PACS].

Technological progress and the rising cost pressure on the healthcare system have led to a drastic change in the work environment of radiologists today. The pervasive demand for workflow optimization and increased efficiency of its activities raises the question of whether by employment of electronic systems, such as RIS and PACS, the potentials of digital technology are sufficiently used to fulfil this demand. This report describes the tasks and structures in radiology departments, which so far are only insufficiently supported by commercially available electronic systems but are nevertheless substantial. We developed and employed a web-based, integrated workplace system, which simplifies many daily tasks of departmental organization and administration apart from well-established tasks of documentation. Furthermore, we analyzed the effects exerted on departmental workflow by employment of this system for 3 years.

Database Management Systems↗

PubMed2002

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.

SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).

Algorithms↗

PubMed2004

In silico gene function prediction using ontology-based pattern identification.

MOTIVATION: With the emergence of genome-wide expression profiling data sets, the guilt by association (GBA) principle has been a cornerstone for deriving gene functional interpretations in silico. Given the limited success of traditional methods for producing clusters of genes with great amounts of functional similarity, new data-mining algorithms are required to fully exploit the potential of high-throughput genomic approaches. RESULTS: Ontology-based pattern identification (OPI) is a novel data-mining algorithm that systematically identifies expression patterns that best represent existing knowledge of gene function. Instead of relying on a universal threshold of expression similarity to define functionally related groups of genes, OPI finds the optimal analysis settings that yield gene expression patterns and gene lists that best predict gene function using the principle of GBA. We applied OPI to a publicly available gene expression data set on the life cycle of the malarial parasite Plasmodium falciparum and systematically annotated genes for 320 functional categories based on current Gene Ontology annotations. An ontology-based hierarchical tree of the 320 categories provided a systems-wide biological view of this important malarial parasite.

Algorithms↗

PubMed2005

GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.

SUMMARY: GenColors is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes, considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. The genome comparison tools determine, for example, best-bidirectional hits, gene conservation, syntenies and gene core sets. Swiss-Prot/TrEMBL hits allow annotations in an effective manner. To further support the annotation base-specific quality data can also be displayed if available. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and maintained. It has been efficiently used for Borrelia garinii and is currently applied to various ongoing genome projects. AVAILABILITY: Detailed information on GenColors is available at http://gencolors.imb-jena.de. Online usage of GenColors-based genome browsers is the preferred application mode. The system is also available upon request for local installation.

Borrelia↗

PubMed2005

Discovery and integrative neuroscience.

Hypothesis driven research has been shown to be an excellent model for pursuing investigations in neuroscience. The Human Genome Project demonstrated the added value of discovery research, especially in areas where large amounts of data are produced. Neuroscience has become a data rich field, and one that would be enhanced by incorporating the discovery approach. Databases, as well as analytical, modeling and simulation tools, will have to be developed, and they will need to be interoperable and federated. This paper presents an overview of the development of the field of neuroscience databases and associate tools: Neuroinformatics. The primary focus is on the impact of NIH funding of this process. The important issues of data sharing, as viewed from the perspective of the scientist and private and public funding organizations, are discussed. Neuroinformatics will provide more than just a sophisticated array of information technologies to help scientists understand and integrate nervous system data. It will make available powerful models of neural functions and facilitate discovery, hypothesis formulation and electronic collaboration.

Animals↗