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PubMed2002

Preparation of name and address data for record linkage using hidden Markov models.

BACKGROUND: Record linkage refers to the process of joining records that relate to the same entity or event in one or more data collections. In the absence of a shared, unique key, record linkage involves the comparison of ensembles of partially-identifying, non-unique data items between pairs of records. Data items with variable formats, such as names and addresses, need to be transformed and normalised in order to validly carry out these comparisons. Traditionally, deterministic rule-based data processing systems have been used to carry out this pre-processing, which is commonly referred to as "standardisation". This paper describes an alternative approach to standardisation, using a combination of lexicon-based tokenisation and probabilistic hidden Markov models (HMMs). METHODS: HMMs were trained to standardise typical Australian name and address data drawn from a range of health data collections. The accuracy of the results was compared to that produced by rule-based systems. RESULTS: Training of HMMs was found to be quick and did not require any specialised skills. For addresses, HMMs produced equal or better standardisation accuracy than a widely-used rule-based system. However, accuracy was worse when used with simpler name data. Possible reasons for this poorer performance are discussed. CONCLUSION: Lexicon-based tokenisation and HMMs provide a viable and effort-effective alternative to rule-based systems for pre-processing more complex variably formatted data such as addresses. Further work is required to improve the performance of this approach with simpler data such as names. Software which implements the methods described in this paper is freely available under an open source license for other researchers to use and improve.

Data Collection↗
PubMed2003

A markup language for electrocardiogram data acquisition and analysis (ecgML).

BACKGROUND: The storage and distribution of electrocardiogram data is based on different formats. There is a need to promote the development of standards for their exchange and analysis. Such models should be platform-/ system- and application-independent, flexible and open to every member of the scientific community. METHODS: A minimum set of information for the representation and storage of electrocardiogram signals has been synthesised from existing recommendations. This specification is encoded into an XML-vocabulary. The model may aid in a flexible exchange and analysis of electrocardiogram information. RESULTS: Based on advantages of XML technologies, ecgML has the ability to present a system-, application- and format-independent solution for representation and exchange of electrocardiogram data. The distinction between the proposal developed by the U.S Food and Drug Administration and ecgML model is given. A series of tools, which aim to facilitate ecgML-based applications, are presented. CONCLUSIONS: The models proposed here can facilitate the generation of a data format, which opens ways for better and clearer interpretation by both humans and machines. Its structured and transparent organisation will allow researchers to expand and test its capabilities in different application domains. The specification and programs for this protocol are publicly available.

Decision Support Techniques↗
PubMed2003

Feasibility study of multidisciplinary oncology rounds by videoconference for surgeons in remote locales.

BACKGROUND: This study was undertaken to assess the feasibility of using videoconferencing to involve community-based surgeons in interactive, multidisciplinary oncology rounds so they may benefit from the type of community of practice that is usually only available in academic cancer centres. METHODS: An existing videoconference service provider with sites across Ontario was chosen and the series was accredited. Indirect needs assessment involved examining responses to a previously conducted survey of provincial surgeons; interviewing three cancer surgeons from different regions of Ontario; and by analyzing an online portfolio of self-directed learning projects. Direct needs assessment involved a survey of surgeons at videoconference-enabled sites. A surgical, medical and radiation oncologist plus a facilitator were scheduled to guide discussion for each session. A patient scenario developed by the discussants was distributed to participants one week prior to each session. RESULTS: Direct and indirect needs assessment confirmed that breast cancer and colorectal cancer topics were of greatest importance to community surgeons. Six one-hour sessions were offered (two breast, two colorectal, one gynecologic and one lung cancer). A median of 22 physicians and a median of eight sites participated in each session. The majority of respondents were satisfied with the videoconference format, presenters and content. Many noted that discussion prompted reflection on practice and that current practice would change. CONCLUSIONS: This pilot study demonstrated that it is possible to engage remote surgeons in multidisciplinary oncology rounds by videoconference. Continued assessment of videoconferencing is warranted but further research is required to develop frameworks by which to evaluate the benefits of telehealth initiatives.

Data Collection↗
PubMed2004

Some methods for blindfolded record linkage.

BACKGROUND: The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects - a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. METHODS: A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. RESULTS: The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. CONCLUSION: Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy.

Computer Communication Networks↗
PubMed2004

Translation research: from accurate diagnosis to appropriate treatment.

This review article focuses on the various aspects of translational research, where research on human subjects can ultimately enhance the diagnosis and treatment of future patients. While we will use specific examples relating to the asbestos related cancer mesothelioma, it should be stressed that the general approach outlined throughout this review is readily applicable to other diseases with an underlying molecular basis. Through the integration of molecular-based technologies, systematic tissue procurement and medical informatics, we now have the ability to identify clinically applicable "genotype"-"phenotype" associations across cohorts of patients that can rapidly be translated into useful diagnostic and treatment strategies. This review will touch on the various steps in the translational pipeline, and highlight some of the most essential elements as well as possible roadblocks that can impact success of the program. Critical issues with regard to Institutional Review Board (IRB) and Health Insurance Portability and Accountability Act (HIPAA) compliance, data standardization, sample procurement, quality control (QC), quality assurance (QA), data analysis, preclinical models and clinical trials are addressed. The various facets of the translational pipeline have been incorporated into a fully integrated computational system, appropriately named Dx2Tx. This system readily allows for the identification of new diagnostic tests, the discovery of biomarkers and drugable targets, and prediction of optimal treatments based upon the underlying molecular basis of the disease.

Journal Article↗
PubMed2000

Utilization of human tissue in breast cancer research.

The use of human tissue, and material derived from such tissue, for research purposes is currently the subject of much debate. This debate needs to address several issues, including: the principle of abandonment; the distinction between identified and unidentified specimens; general versus specific informed consent; and, with the improvement in biotechnology and medical informatics, the design and security of research databases. The outcome of this debate will shape the way in which research studies using human biological materials are designed and executed.

Breast Neoplasms↗
PubMedDate not supplied

Exploring issues of quality of service in a Next Generation Internet testbed: a case study using PathMaster.

This case study describes a project that explores issues of quality of service (QoS) relevant to the next-generation Internet (NGI), using the PathMaster application in a testbed environment. PathMaster is a prototype computer system that analyzes digitized cell images from cytology specimens and compares those images against an image database, returning a ranked set of "similar" cell images from the database. To perform NGI testbed evaluations, we used a cluster of nine parallel computation workstations configured as three subclusters using Cisco routers. This architecture provides a local "simulated Internet" in which we explored the following QoS strategies: (1) first-in-first-out queuing, (2) priority queuing, (3) weighted fair queuing, (4) weighted random early detection, and (5) traffic shaping. The study describes the results of using these strategies with a distributed version of the PathMaster system in the presence of different amounts of competing network traffic and discusses certain of the issues that arise. The goal of the study is to help introduce NGI QoS issues to the Medical Informatics community and to use the PathMaster NGI testbed to illustrate concretely certain of the QoS issues that arise.

Cell Biology↗
PubMedDate not supplied

Incentives and barriers that influence clinical computerization in Hong Kong: a population-based physician survey.

OBJECTIVE: Given the slow adoption of medical informatics in Hong Kong and Asia, we sought to understand the contributory barriers and potential incentives associated with information technology implementation. DESIGN AND MEASUREMENTS: A representative sample of 949 doctors (response rate = 77.0%) was asked through a postal survey to rank a list of nine barriers associated with clinical computerization according to self-perceived importance. They ranked seven incentives or catalysts that may influence computerization. We generated mean rank scores and used multidimensional preference analysis to explore key explanatory dimensions of these variables. A hierarchical cluster analysis was performed to identify homogenous subgroups of respondents. We further determined the relationships between the sets of barriers and incentives/catalysts collectively using canonical correlation. RESULTS: Time costs, lack of technical support and large capital investments were the biggest barriers to computerization, whereas improved office efficiency and better-quality care were ranked highest as potential incentives to computerize. Cost vs. noncost, physician-related vs. patient-related, and monetary vs. nonmonetary factors were the key dimensions explaining the barrier variables. Similarly, within-practice vs external and "push" vs "pull" factors accounted for the incentive variables. Four clusters were identified for barriers and three for incentives/catalysts. Canonical correlation revealed that respondents who were concerned with the costs of computerization also perceived financial incentives and government regulation to be important incentives/catalysts toward computerization. Those who found the potential interference with communication important also believed that the promise of improved care from computerization to be a significant incentive. CONCLUSION: This study provided evidence regarding common barriers associated with clinical computerization. Our findings also identified possible incentive strategies that may be employed to accelerate uptake of computer systems.

Attitude of Health Personnel↗
PubMed2004

A consensus action agenda for achieving the national health information infrastructure.

BACKGROUND: Improving the safety, quality, and efficiency of health care will require immediate and ubiquitous access to complete patient information and decision support provided through a National Health Information Infrastructure (NHII). METHODS: To help define the action steps needed to achieve an NHII, the U.S. Department of Health and Human Services sponsored a national consensus conference in July 2003. RESULTS: Attendees favored a public-private coordination group to guide NHII activities, provide education, share resources, and monitor relevant metrics to mark progress. They identified financial incentives, health information standards, and overcoming a few important legal obstacles as key NHII enablers. Community and regional implementation projects, including consumer access to a personal health record, were seen as necessary to demonstrate comprehensive functional systems that can serve as models for the entire nation. Finally, the participants identified the need for increased funding for research on the impact of health information technology on patient safety and quality of care. Individuals, organizations, and federal agencies are using these consensus recommendations to guide NHII efforts.

Health Policy↗
PubMed2006

Viewpoint: a pragmatic approach to constructing a minimum data set for care of patients with HIV in developing countries.

Providing quality health care requires access to continuous patient data that developing countries often lack. A panel of medical informatics specialists, clinical human immunodeficiency virus (HIV) specialists, and program managers suggests a minimum data set for supporting the management and monitoring of patients with HIV and their care programs in developing countries. The proposed minimum data set consists of data for registration and scheduling, monitoring and improving practice management, and describing clinical encounters and clinical care. Data should be numeric or coded using standard definitions and minimal free text. To enhance accuracy, efficiency, and availability, data should be recorded electronically by those generating them. Data elements must be sufficiently detailed to support clinical algorithms/guidelines and aggregation into broader categories for consumption by higher level users (e.g., national and international health care agencies). The proposed minimum data set will evolve over time as funding increases, care protocols change, and additional tests and treatments become available for HIV-infected patients in developing countries.

Databases, Factual↗
PubMed2006

Finding leading indicators for disease outbreaks: filtering, cross-correlation, and caveats.

Bioterrorism and emerging infectious diseases such as influenza have spurred research into rapid outbreak detection. One primary thrust of this research has been to identify data sources that provide early indication of a disease outbreak by being leading indicators relative to other established data sources. Researchers tend to rely on the sample cross-correlation function (CCF) to quantify the association between two data sources. There has been, however, little consideration by medical informatics researchers of the influence of methodological choices on the ability of the CCF to identify a lead-lag relationship between time series. We draw on experience from the econometric and environmental health communities, and we use simulation to demonstrate that the sample CCF is highly prone to bias. Specifically, long-scale phenomena tend to overwhelm the CCF, obscuring phenomena at shorter wave lengths. Researchers seeking lead-lag relationships in surveillance data must therefore stipulate the scale length of the features of interest (e.g., short-scale spikes versus long-scale seasonal fluctuations) and then filter the data appropriately--to diminish the influence of other features, which may mask the features of interest. Otherwise, conclusions drawn from the sample CCF of bi-variate time-series data will inevitably be ambiguous and often altogether misleading.

Bioterrorism↗
PubMed2007

Proposal for fulfilling strategic objectives of the U.S. Roadmap for national action on clinical decision support through a service-oriented architecture leveraging HL7 services.

Despite their demonstrated effectiveness, clinical decision support (CDS) systems are not widely used within the U.S. The Roadmap for National Action on Clinical Decision Support, published in June 2006 by the American Medical Informatics Association, identifies six strategic objectives for achieving widespread adoption of effective CDS capabilities. In this manuscript, we propose a Service-Oriented Architecture (SOA) for CDS that facilitates achievement of these six objectives. Within the proposed framework, CDS capabilities are implemented through the orchestration of independent software services whose interfaces are being standardized by Health Level 7 and the Object Management Group through their joint Healthcare Services Specification Project (HSSP). Core services within this framework include the HSSP Decision Support Service, the HSSP Common Terminology Service, and the HSSP Retrieve, Locate, and Update Service. Our experiences, and those of others, indicate that the proposed SOA approach to CDS could enable the widespread adoption of effective CDS within the U.S. health care system.

Computer Systems↗
PubMed2003

Validity of family history data on PD: evidence for a family information bias.

OBJECTIVE: To study the validity of information provided by case and control subjects (or their proxies) about PD among their first-degree relatives. METHODS: Secondary cases of PD were assessed both through a single informant (family history method) and through the study of each relative (family study method). The family study method was considered as the standard for comparison, and the sensitivity and specificity of the family history method were studied. RESULTS: A total of 133 population-based case subjects and their 655 relatives were recruited, and 119 population-based control subjects and their 511 relatives. Sensitivity was 68% (95% CI = 47 to 85) for cases and 45% (95% CI = 17 to 77) for controls. Specificity was 99% (95% CI = 98 to 99) for cases and 100% (95% CI = 99 to 100) for controls. The odds ratio (OR) for family history of PD was 4.34 (95% CI = 1.63 to 11.58, p = 0.003) using the family history method and 1.86 (95% CI = 0.78 to 4.44, p = 0.16) using the family study method. The former significant OR more than doubled the latter not significant OR (relative bias = 133%). Bias was more pronounced for proxy interviews and for women informants, and when the relatives were siblings, were living, and were examined or had medical record documentation. CONCLUSIONS: Case subjects with PD (or their proxies) are more aware of PD among their first-degree relatives than control subjects (or their proxies); however, they overreport PD in relatives who are not affected. This causes a substantial family information bias.

Adult↗
PubMed2006

Quality of health information on the Internet in pediatric neuro-oncology.

The Internet is now the single largest source of health information and is used by many patients and their families who are affected by childhood brain tumors. To assess the quality of pediatric neuro-oncology information on the Internet, we used search engines to look for information on five common tumor types (brain stem glioma, craniopharyngioma, ependymoma, low-grade glioma, and medulloblastoma). The Web sites were evaluated for content quality by using the validated DISCERN rating instrument. Breadth of content and its accuracy were also scored by a checklist tool. Readability statistics were computed on the highest-rated sites. Of 114 evaluated Web sites, the sources were as follows: institutional, 46%; commercial, 35%; charitable, 15%; support group, 2%; and alternative medicine, 2%. Good interobserver correlation was found for both ratings instruments. The DISCERN tool rated Web sites as excellent (4%), good (7%), fair (29%), poor (39%), or very poor (21%). Only 5% of the Web sites provided one or more inaccurate pieces of information. Web sites were found deficient in topics covering etiology, late effects, prognosis, and treatment choices. Few sites offered information in languages other than English, and readability statistics showed an average required reading level of U.S. grade 12+ (the suggested level being grades 6-8 for an adult audience). The Internet is increasingly being used as a source of oncology information for patients and their families. Health care professionals should be actively involved in developing high-quality information for use in the next generation of Web sites.

Brain Neoplasms↗
PubMed2003

Laying the foundations for good medical practice: a new educational resource.

Balancing service commitments with educational development is never easy. The European Working Time Directive and the Chief Medical Officer's report on senior house officer training bring new challenges. The Royal College of Physicians has developed 'Laying the Foundations for Good Medical Practice', a resource that enables tutors to teach generic skills to small groups of trainees in a fun and interactive way.

Education, Medical, Continuing↗