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PubMed2006

Design and development of a secure DICOM-Network Attached Server.

It is not easy to connect a web-based server with an existing DICOM server, and using a web-based server on the INTERNET has risks. In this study, we designed and developed the secure DICOM-Network Attached Server (DICOM-NAS) through which the DICOM server in a hospital-Local Area Network (LAN) was connected to the INTERNET. After receiving a Client's image export request, the DICOM-NAS sent it to the DICOM server with DICOM protocol. The server then provided DICOM images to the DICOM-NAS, which transferred them to the Client using HTTP. The DICOM-NAS plays an important role between DICOM protocol and HTTP, and only temporarily stores the requested images. The DICOM server keeps all of the original DICOM images. When unwanted outsiders attempt to get into the DICOM-NAS, they cannot access any medical images because these images are not stored in the DICOM-NAS. Therefore, the DICOM-NAS does not require large storage, but can greatly improve information security.

Computational Biology↗
PubMed2006

W3MAMCAT: a world wide web based tool for mammillary and catenary compartmental modeling and expert system distinguishability.

W(3)MAMCAT is a new web-based and interactive system for building and quantifying the parameters or parameter ranges of n-compartment mammillary and catenary model structures, with input and output in the first compartment, from unstructured multiexponential (sum-of-n-exponentials) models. It handles unidentifiable as well as identifiable models and, as such, provides finite parameter interval solutions for unidentifiable models, whereas direct parameter search programs typically do not. It also tutorially develops the theory of model distinguishability for same order mammillary versus catenary models, as did its desktop application predecessor MAMCAT+. This includes expert system analysis for distinguishing mammillary from catenary structures, given input and output in similarly numbered compartments. W(3)MAMCAT provides for universal deployment via the internet and enhanced application error checking. It uses supported Microsoft technologies to form an extensible application framework for maintaining a stable and easily updatable application. Most important, anybody, anywhere, is welcome to access it using Internet Explorer 6.0 over the internet for their teaching or research needs. It is available on the Biocybernetics Laboratory website at UCLA: www.biocyb.cs.ucla.edu.

Algorithms↗
PubMed2006

Development and applications of a software tool for diarthrodial joint analysis.

This paper describes a new software environment for advanced analysis of diarthrodial joints. The new tool provides a number of elaboration functions to investigate the joint kinematics, bone anatomy, and ligament and tendon properties. In particular, the shapes and the contact points of the articulating surfaces can be displayed and analysed through 2D user-defined sections and fittings (lines or conics). Ligament behaviour can be evaluated during joint movement, through the computation of elongations, orientations, and fiber strain. Motion trajectories can be also analysed through the calculation of helical axes, instantaneous rotations, and displacements in specific user-chosen coordinate reference frames. The software has an user-friendly graphical interface to display four-dimensional data (time-space data) obtained from medical images, navigation systems, spatial linkages or digitalizers, and can also generate printable reports and multiple graphs as well as ASCII files that can be imported to spreadsheet programs such as Microsoft Excel.

Algorithms↗
PubMed2006

Creating non-parametric bootstrap samples using Poisson frequencies.

This article describes how, in the high-level software packages used by non-statisticians, approximate non-parametric bootstrap samples can be created and analyzed without physically creating new data sets, or resorting to complex programming. The comparable performance of this shortcut method, which uses Poisson rather than multinomial frequencies for the numbers of copies of each observation, is demonstrated theoretically by evaluating the bootstrap variance in an example where the classic estimator of the sampling variance of the statistic of interest has a known closed form. For sample sizes of 50 or more, bootstrap standard errors obtained by this shortcut method exceeded those obtained by the standard version by less than 1%. The proposed method is also evaluated in two worked examples, involving statistics whose sampling distribution is more complex. The second of these is also used to illustrate when one can and cannot use non-parametric bootstrap samples.

Computational Biology↗
PubMed2006

SCEW: a Microsoft Excel add-in for easy creation of survival curves.

Survival curves are frequently used for reporting survival or mortality outcomes of experimental pharmacological/toxicological studies and of clinical trials. Microsoft Excel is a simple and widely used tool for creation of numerous types of graphic presentations however it is difficult to create step-wise survival curves in Excel. Considering the familiarity of clinicians and biomedical scientists with Excel, an algorithm survival curves in Excel worksheet (SCEW) has been developed for easy creation of survival curves directly in Excel worksheets. The algorithm has been integrated in the form of Excel add-in for easy installation and usage. The program is based on modification of frequency data for binary break-up using the spreadsheet formula functions whereas a macro subroutine automates the creation of survival curves. The advantages of this program are simple data input, minimal procedural steps and the creation of survival curves in the familiar confines of Excel.

Algorithms↗
PubMed2006

CASANDRA: a prototype implementation of a system of network progressive transmission of medical digital images.

In this paper, a prototype for progressive transmission of medical digital 2D images through the network, called CASANDRA, is presented. The prototype consists of the server part and the client part. In the server part, the images are acquired, stored, computed their wavelet transform and the wavelet coefficients stored, then transmitted progressively, when required, via TCP to the client. In the client part, with the inverse wavelet transform, the received wavelet coefficients are used to build successive improved reconstructions of the image. This prototype has been implemented and is being tested in the Radiotherapy Service of the Valencia University Hospital (Valencia, Spain).

Medical Informatics Applications↗
PubMed2006

Development of a personal digital assistant-based wireless application in clinical practice.

PURPOSE: Our study aims to develop a personal digital assistant (PDA)-based wireless application in medical information processing by using Bluetooth and IEEE 802.11b wireless standards and SyncML codes. METHODS: In this study, an "integrated database access module" is used to provide a unified integrated access interface while consistency of wireless data transmission is achieved by using the standardized SyncML protocol. A prototype of the system has been developed, implemented, and tested for its mobility, usability, stability, and performance with questionnaire survey. RESULTS: Response time for browsing/searching was usually less than 3s. The average time intervals needed for data transmissions were 68.6+/-8.5s for Bluetooth and 47.0+/-4.8s for 802.11b. The five-point Likert scale (from 1=least to 5=most) questionnaire survey of 30 medical professionals yielded a high degree of satisfaction with the system's mobility (4.18+/-0.89), usability (4.69+/-0.90), stability (3.81+/-0.94), and performance (3.97+/-0.88). CONCLUSION: The results of our study suggested that PDA applications which exploit wireless communication are convenient and feasible in clinical practice.

Computers, Handheld↗
PubMed2006

Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection.

In recent years, the study of immune response behaviour through mathematical and computational models has attracted considerable efforts. The dynamics of key cell types, and their interactions, has been a primary focus in terms of building a picture of how the immune system responds to a threat. Discrete methods, based on lattice Monte-Carlo (MC) models, with their flexibility and relative simplicity have previously been used to model the immune system behaviour. However, due to speed and memory constraints, large-scale simulations cannot be done on a single computer. Key issues in the reduction of simulation time are code optimisation and code parallelisation. In this paper, optimisation and parallelisation solutions are discussed, with reference to existing MC simulation code for dynamics of HIV infection.

Antibodies, Viral↗
PubMed2006

Nonlinear analysis of wheezes using wavelet bicoherence.

Wheezes, as being abnormal breath sounds, are observed in patients with obstructive pulmonary diseases, such as asthma. The aim of this study was to capture and analyze the nonlinear characteristics of asthmatic wheezes, reflected in the quadrature phase coupling of their harmonics, as they evolve over time within the breathing cycle. To achieve this, the continuous wavelet transform (CWT) was combined with third-order statistics/spectra. Wheezes from patients with diagnosed asthma were drawn from a lung sound database and analyzed in the time-bi-frequency domain. The analysis results justified the efficient performance of this combinatory approach to reveal and quantify the evolution of the nonlinearities of wheezes with time.

Algorithms↗
PubMed2006

O3-DPACS Open-Source Image-Data Manager/Archiver and HDW2 Image-Data Display: an IHE-compliant project pushing the e-health integration in the world.

After many years of study, development and experimentation of open PACS and Image workstation solutions including management of medical data and signals (DPACS project), the research and development at the University of Trieste have recently been directed towards Java-based, IHE compliant and multi-purpose servers and clients. In this paper an original Image-Data Manager/Archiver (O3-DPACS) and a universal Image-Data Display (HDW2) are described. O3-DPACS is also part of a new project called Open Three (O3) Consortium, promoting Open Source adoption in e-health at European and world-wide levels. This project aims to give a contribution to the development of e-health through the study of Healthcare Information Systems and the contemporary proposal of new concepts, designs and solutions for the management of health data in an integrated environment: hospitals, Regional Health Information Organizations and citizens (home-care, mobile-care and ambient assisted living).

Data Display↗
PubMed2005

The JAVA-based DICOM query interface DicoSE.

DICOM 3 is a very elaborate standard for the communication between medical image devices. It is published in several parts by the National Electrical Manufacturers Association (NEMA). To adequately visualize the data structure defined in parts 3, 5 and 6 of the DICOM standard, we implemented the web based Dicom Search Engine (DicoSE). It allows for querying the DICOM standard data dictionary for defined data fields and visualizes the topology of the data which is inherently present in DICOM datasets. For the administration of the underlying data a web based administration interface is provided. The service is entirely based on freely available software.

Information Storage and Retrieval↗
PubMed2005

Implementing health care systems using XML standards.

Most healthcare data is narrative text and often not accessible and easy to find at the clinical workstation. XML related standards (XML schema, XForms, XSL, Topic Maps, etc.) provide an infrastructure that might change the situation. Yet, it is up to the application developers to combine the given standards and tools into a running system. The cost of development is often underestimated and may explain the absence of comprehensive XML applications. Our goal is the clinical application of these standards. We have, therefore, implemented the idea of "plug-and-play XML", i.e. the development of new applications by means of XML standards. This paper will communicate our experience using such an approach at the example of a clinical drug information system.

Drug Information Services↗
PubMed2005

Extending the GEM model to support knowledge extraction from textual guidelines.

Clinical Practice Guidelines (CPGs) are being developed as a tool to promote best practice in medicine. However, the diffusion of paper guidelines has been shown to only have a limited impact. This is why computerization of CPGs has recently been suggested as a means to improve their dissemination as well as physicians' compliance. The Guideline Elements Model (GEM) has been proposed to facilitate the encoding of CPGs and support the automatic processing of marked-up documents. In this paper, we explore the automatic generation of a rule base from a textual guideline using GEM. In this study, we propose an extension of the GEM model that introduces additional levels of structuring centered on decision variables. This allows a more efficient representation of the decision processes, which supports the automatic generation of decision rules from textual guidelines. The 1999 Canadian recommendations for the management of hypertension have been marked-up as a GEM-encoded instance of our extended DTD. We derived a rule base using an XML parser to extract the relevant elements to instantiate the IF and THEN clauses of decision rules. The rule base automatically generated compares favourably with the manual generation of decision rules in the ASTI project. This approach is an interesting case study in the computerization of CPGs, as it illustrates processing steps that are relevant to the various aspects of CPGs life-cycle, from production to consultation and use.

Canada↗
PubMed2004

A multi-layered application for the gross description using Semantic Web technology.

OBJECTIVE: Development of a Semantic Web technology based system for the formalization of the gross description. METHOD: A system is developed using the Java-2 platform. It is based on a light-weight version of the Galen top level ontology. Web technologies like XML, SAX en DOM have been used. RESULT: Three system components have been developed to support the semantic, the object and the syntax layers of the PathOnt architecture. CONCLUSION: The PathOnt approach provides a tool for the communication among clinicians and technicians involved in pathology examinations. This tool also provides a foundation for linking the specimen-specific data with the controlled medical ontology so that the stored information can be used in different circumstances.

Internet↗
PubMed2006

The life and death of URLs in five biomedical informatics journals.

OBJECTIVE: To determine the decay rate of Uniform Record Locators (URLs) in the reference section of biomedical informatics journals. METHODS: URL references were collected from printed journal articles of the first and middle issues of 1999-2004 and electronically available in-press articles in January 2005. We limited this set to five biomedical informatics journals: Artificial Intelligence in Medicine, International Journal of Medical Informatics, Journal of the American Medical Informatics Association: JAMIA, Methods of Information in Medicine, and Journal of Biomedical Informatics. During a 1-month period, URL access attempts were performed eight times a day at regular intervals. RESULTS: Of the 19,108 references extracted from 606 printed and 86 in-press articles, 1112 (5.8%) references contained a URL. Of the 1049 unique URLs, 726 (69.2%) were alive, 230 (21.9%) were dead, and 93 (8.9%) were comatose. URLs from in-press articles included 212 URLs, of which 169 (79.7%) were alive, 21 (9.9%) were dead, and 22 (10.4%) were comatose. The average annual decay, or link rot, rate was 5.4%. CONCLUSION: The URL decay rate in biomedical informatics journals is high. A commonly accepted strategy for the permanent archival of digital information referenced in scholarly publications is urgently needed.

Bibliometrics↗
PubMed2006

Implementing a new ADT based on the HL7 version 3 RIM.

The University Hospitals of Geneva (HUG) are the result of the merge of six hospitals into one single organization. While a true fusion of the management has been effectively done, it was not the case 5 years after for several databases, and in particular the ADT (admission, discharge, transfer). In order to truly realize the fusion, a new ADT service has been built using state of the art technology and standards in order to replace the existing seven services. This paper presents the results of the redesign and development of the new ADT service. The data model, based on HL7 RIM, is described and the technologies selected are presented. Finally, a status after 1 year of production is presented.

Hospital Information Systems↗
PubMed2005

Strategies for referent tracking in electronic health records.

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems are used in what is called "clinical coding." In this paper, we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor--though nevertheless ontologically important--technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto.

Computational Biology↗