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Recent Articles in Journal of Medical Internet Research

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Cunningham JA, Humphreys K, Kypri K, van Mierlo T
Formative evaluation and three-month follow-up of an online personalized assessment feedback intervention for problem drinkers.
J Med Internet Res. 2006;8(2):e5.
BACKGROUND: In recent years, online services for problem drinkers have been developed. This paper describes ongoing efforts to improve one of these services, the Alcohol Help Center. OBJECTIVE: This report summarizes new modules added to the Check Your Drinking (CYD) screener, a component of the Alcohol Help Center, to make the CYD screener more useful to periodic heavy drinkers, as well as to regular alcohol consumers. Participants' initial reactions to the CYD screener and the changes in their drinking habits at a three-month follow-up are presented. METHODS: The CYD screener provides a free personalized Final Report that compares the user's drinking to that of others in the general population of the same age, gender, and country of origin. Current alcohol consumption and demographic characteristics are collected as part of the CYD screening process. After users were presented with a customized Final Report, they were hot-linked to a volunteer feedback survey. The voluntary feedback survey asked about impressions of the CYD Final Report. Respondents agreeing to participate were sent a follow-up survey after three months. RESULTS: We recruited 388 volunteers (69% female) who were registered users of another free-to-consumer online eHealth service. Of the 343 respondents agreeing to participate in the three-month follow-up, 138 accessed the survey, and 97 provided complete data (participation rate = 40%; completion rate = 70%). Compared to moderate drinkers, current problem drinkers judged the Final Report to be more useful (34% vs. 69%, chi2 (1) = 41.5, P < .001) and accurate (43% vs. 76%, chi2 (1) = 36.0, P < .001). Respondents who participated in the three-month follow-up displayed reductions in drinking compared to baseline (F(4,76) = 12.2, P = .001). CONCLUSIONS: Improvements can still be made to make the CYD screener more relevant to specific populations, particularly periodic heavy drinkers. There is a need to further tailor algorithms that can present questions only relevant to specific populations. There also appears to be a need to further customize the Final Report for respondents who identify themselves as infrequent heavy drinkers. These improvements will be made, and a randomized controlled trial is planned to conduct a rigorous evaluation of the CYD screener as an intervention to help problem drinkers. [Abstract/Link to Full Text]

Mayo-Wilson E
Health care interventions delivered over the Internet: how systematic was the review?
J Med Internet Res. 2006;8(2):e11; author reply e12. [Abstract/Link to Full Text]

Griffiths F, Lindenmeyer A, Powell J, Lowe P, Thorogood M
Why are health care interventions delivered over the internet? A systematic review of the published literature.
J Med Internet Res. 2006;8(2):e10.
BACKGROUND: As Internet use grows, health interventions are increasingly being delivered online. Pioneering researchers are using the networking potential of the Internet, and several of them have evaluated these interventions. OBJECTIVE: The objective was to review the reasons why health interventions have been delivered on the Internet and to reflect on the work of the pioneers in this field in order to inform future research. METHODS: We conducted a qualitative systematic review of peer-reviewed evaluations of health interventions delivered to a known client/patient group using networked features of the Internet. Papers were reviewed for the reasons given for using the Internet, and these reasons were categorized. RESULTS: We included studies evaluating 28 interventions plus 9 interventions that were evaluated in pilot studies. The interventions were aimed at a range of health conditions. Reasons for Internet delivery included low cost and resource implications due to the nature of the technology; reducing cost and increasing convenience for users; reduction of health service costs; overcoming isolation of users; the need for timely information; stigma reduction; and increased user and supplier control of the intervention. A small number of studies gave the existence of Internet interventions as the only reason for undertaking an evaluation of this mode of delivery. CONCLUSIONS: One must remain alert for the unintended effects of Internet delivery of health interventions due to the potential for reinforcing the problems that the intervention was designed to help. Internet delivery overcomes isolation of time, mobility, and geography, but it may not be a substitute for face-to-face contact. Future evaluations need to incorporate the evaluation of cost, not only to the health service but also to users and their social networks. When researchers report the outcomes of Internet-delivered health care interventions, it is important that they clearly state why they chose to use the Internet, preferably backing up their decision with theoretical models and exploratory work. Evaluation of the effectiveness of a health care intervention delivered by the Internet needs to include comparison with more traditional modes of delivery to answer the following question: What are the added benefits or disadvantages of Internet use that are particular to this mode of delivery? [Abstract/Link to Full Text]

Ahern DK, Kreslake JM, Phalen JM
What is eHealth (6): perspectives on the evolution of eHealth research.
J Med Internet Res. 2006;8(1):e4.
BACKGROUND: The field of eHealth holds promise for supporting and enabling health behavior change and the prevention and management of chronic disease. OBJECTIVE: In order to establish areas of congruence and controversy among contributors to the early development, evaluation, and dissemination of eHealth applications, as well as the desire to inform an evaluation research funding agenda, 38 semistructured, qualitative interviews were conducted among stakeholders in eHealth between May 2002 and September 2003. METHODS: Participants were asked about their perspectives on the credibility, value, and future potential of information technology for health behavior change and chronic disease management. Interviews were coded and analyzed for emergent themes using qualitative methods. RESULTS: Consistent themes were identified across stakeholder groups, with slight differences in emphasis. These topics included the following: (1) consensus and standardization-most stakeholders expressed a strong desire for a more coordinated, rigorous effort to define and integrate the field; (2) evaluation methods and challenges-demonstrating outcomes is required to establish eHealth quality and efficacy, but stakeholders were not satisfied with the sensitivity, validity, and reliability of existing outcome measures; (3) quality, value, and future potential-the intersection between eHealth's potential cost-effectiveness, efficiency, and improved clinical status among users generated a high degree of interest; and (4) health disparities-many stakeholders contended that traditionally underserved populations will particularly benefit from eHealth applications, although others argued that the underserved are also disadvantaged in terms of access to technology. CONCLUSIONS: Recommendations included the need for improvement and formalization of development and evaluation standards across private and public sectors, additional research on the technology needs and preferences of traditionally underserved populations, and long-term epidemiologic studies of the impact of eHealth on outcomes and cost-effectiveness. [Abstract/Link to Full Text]

Franklin PD, Rosenbaum PF, Carey MP, Roizen MF
Using sequential e-mail messages to promote health behaviors: evidence of feasibility and reach in a worksite sample.
J Med Internet Res. 2006;8(1):e3.
BACKGROUND: US adults report suboptimal physical activity and fruit and vegetable intake. Innovative strategies to promote healthy behaviors are needed. Employee health promotion programs have been associated with reductions in health risks but are labor-intensive and costly to implement. E-mail and Web-based worksite programs have the potential to reach a broad adult population and to provide a cost-effective approach to employee wellness programming. OBJECTIVE: To assess the feasibility of using sequential e-mail messages to promote physical activity and increase fruit and vegetable intake among employed adults. METHODS: Employees at one worksite of a large insurance company in New York State were invited to participate. Interested workers provided written consent. After completing a baseline survey, participants received daily e-mails, Monday through Friday, for 26 weeks. The e-mails provided (a) succinct strategies to encourage physical activity or increase fruit and vegetable intake and (b) links to detailed Web-based information and tools. Program reach was assessed by the number of e-mails opened, measures of sustained participation over 6 months, and the number of health-related Web-links clicked. RESULTS: Of 960 employees, 388 (40%) consented to participate; of these, 345 (89%) completed the baseline health survey. After 6 months, 70% of the 345 participants had opened 50% or more of the daily e-mails. In addition, 75% of participants continued to open at least one e-mail a week through week 26 of the study. E-mail opening rates did not vary by gender, age, income, education, ethnicity, or baseline health behavior. CONCLUSIONS: The rate of enrollment and sustained participation document the feasibility, broad reach, employee acceptance, and potential value of using electronic communications for health promotion in the workplace. [Abstract/Link to Full Text]

Brooks RG, Menachemi N
Physicians' use of email with patients: factors influencing electronic communication and adherence to best practices.
J Med Internet Res. 2006;8(1):e2.
BACKGROUND: With the public's increased use of the Internet, the use of email as a means of communication between patients and physicians will likely increase. Yet, despite evidence of increased interest by patients, e-mail use by physicians for clinical care has been slow. OBJECTIVE: To examine the factors associated with physician-patient e-mail, and report on the physicians' adherence to recognized guidelines for e-mail communication. METHODS: Cross-sectional survey (March-May, 2005) of all primary care physicians (n = 10253), and a 25% stratified, random sample of all ambulatory clinical specialists (n = 3954) in the state of Florida. Physicians were surveyed on email use with patients, adherence to recognized guidelines, and demographics. RESULTS: The 4203 physicians completed the questionnaire (a 28.2% participation rate). Of these, 689 (16.6%) had personally used e-mail to communicate with patients. Only 120 (2.9%) used e-mail with patients frequently. In univariate analysis, e-mail use correlated with physician age (decreased use: age > 61; P = .014), race (decreased use: Asian background; P < .001), medical training (increased use: family medicine, P = .001; or surgical specialty, P = .007; but not internal medicine, P = .112), practice size (> 50 physicians, P < .001), and geographic location (urban 17.2% vs. rural, 7.9%; P < .001). Multivariate modeling showed that only practice size greater than 50 (OR = 1.94; 95% CI = 1.01-3.79) and Asian-American race (OR = 0.26; 95% CI = 0.14-0.49) were related to e-mail use with patients. Remarkably, only 46 physicians (6.7%) adhered to at least half of the 13 selected guidelines for e-mail communication. CONCLUSIONS: This large survey of physicians, practicing in ambulatory settings, shows only modest advances in the adoption of e-mail communication, and little adherence to recognized guidelines for e-mail correspondence. Further efforts are required to educate both patients and physicians on the advantages and limitations of e-mail communication, and to remove fiscal and legal barriers to its adoption. [Abstract/Link to Full Text]

Séror AC
A case analysis of INFOMED: the Cuban national health care telecommunications network and portal.
J Med Internet Res. 2006;8(1):e1.
BACKGROUND: The Internet and telecommunications technologies contribute to national health care system infrastructures and extend global health care services markets. The Cuban national health care system offers a model to show how a national information portal can contribute to system integration, including research, education, and service delivery as well as international trade in products and services. OBJECTIVE: The objectives of this paper are (1) to present the context of the Cuban national health care system since the revolution in 1959, (2) to identify virtual institutional infrastructures of the system associated with the Cuban National Health Care Telecommunications Network and Portal (INFOMED), and (3) to show how they contribute to Cuban trade in international health care service markets. METHODS: Qualitative case research methods were used to identify the integrated virtual infrastructure of INFOMED and to show how it reflects socialist ideology. Virtual institutional infrastructures include electronic medical and information services and the structure of national networks linking such services. RESULTS: Analysis of INFOMED infrastructures shows integration of health care information, research, and education as well as the interface between Cuban national information networks and the global Internet. System control mechanisms include horizontal integration and coordination through virtual institutions linked through INFOMED, and vertical control through the Ministry of Public Health and the government hierarchy. Telecommunications technology serves as a foundation for a dual market structure differentiating domestic services from international trade. CONCLUSIONS: INFOMED is a model of interest for integrating health care information, research, education, and services. The virtual infrastructures linked through INFOMED support the diffusion of Cuban health care products and services in global markets. Transferability of this model is contingent upon ideology and interpretation of values such as individual intellectual property and confidentiality of individual health information. Future research should focus on examination of these issues and their consequences for global markets in health care. [Abstract/Link to Full Text]

Eysenbach G, Trudel M
Going, going, still there: using the WebCite service to permanently archive cited web pages.
J Med Internet Res. 2005;7(5):e60.
Scholars are increasingly citing electronic "web references" which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To "webcite" a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its "instructions for authors" accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) "prospectively" before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted "citing articles" (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. [Abstract/Link to Full Text]

Griffiths KM, Tang TT, Hawking D, Christensen H
Automated assessment of the quality of depression websites.
J Med Internet Res. 2005;7(5):e59.
BACKGROUND: Since health information on the World Wide Web is of variable quality, methods are needed to assist consumers to identify health websites containing evidence-based information. Manual assessment tools may assist consumers to evaluate the quality of sites. However, these tools are poorly validated and often impractical. There is a need to develop better consumer tools, and in particular to explore the potential of automated procedures for evaluating the quality of health information on the web. OBJECTIVE: This study (1) describes the development of an automated quality assessment procedure (AQA) designed to automatically rank depression websites according to their evidence-based quality; (2) evaluates the validity of the AQA relative to human rated evidence-based quality scores; and (3) compares the validity of Google PageRank and the AQA as indicators of evidence-based quality. METHOD: The AQA was developed using a quality feedback technique and a set of training websites previously rated manually according to their concordance with statements in the Oxford University Centre for Evidence-Based Mental Health's guidelines for treating depression. The validation phase involved 30 websites compiled from the DMOZ, Yahoo! and LookSmart Depression Directories by randomly selecting six sites from each of the Google PageRank bands of 0, 1-2, 3-4, 5-6 and 7-8. Evidence-based ratings from two independent raters (based on concordance with the Oxford guidelines) were then compared with scores derived from the automated AQA and Google algorithms. There was no overlap in the websites used in the training and validation phases of the study. RESULTS: The correlation between the AQA score and the evidence-based ratings was high and significant (r=0.85, P<.001). Addition of a quadratic component improved the fit, the combined linear and quadratic model explaining 82 percent of the variance. The correlation between Google PageRank and the evidence-based score was lower than that for the AQA. When sites with zero PageRanks were included the association was weak and non-significant (r=0.23, P=.22). When sites with zero PageRanks were excluded, the correlation was moderate (r=.61, P=.002). CONCLUSIONS: Depression websites of different evidence-based quality can be differentiated using an automated system. If replicable, generalizable to other health conditions and deployed in a consumer-friendly form, the automated procedure described here could represent an important advance for consumers of Internet medical information. [Abstract/Link to Full Text]

Tufano JT, Karras BT
Mobile eHealth interventions for obesity: a timely opportunity to leverage convergence trends.
J Med Internet Res. 2005;7(5):e58.
Obesity is often cited as the most prevalent chronic health condition and highest priority public health problem in the United States. There is a limited but growing body of evidence suggesting that mobile eHealth behavioral interventions, if properly designed, may be effective in promoting and sustaining successful weight loss and weight maintenance behavior changes. This paper reviews the current literature on the successes and failures of public health, provider-administered, and self-managed behavioral health interventions for weight loss. The prevailing theories of health behavior change are discussed from the perspective of how this knowledge can serve as an evidence base to inform the design of mobile eHealth weight loss interventions. Tailored informational interventions, which, in recent years, have proven to be the most effective form of conventional health behavior intervention for weight loss, are discussed. Lessons learned from the success of conventional tailored informational interventions and the early successes of desktop computer-assisted self-help weight management interventions are presented, as are design principles suggested by Social Cognitive Theory and the Social Marketing Model. Relevant computing and communications technology convergence trends are also discussed. The recent trends in rapid advancement, convergence, and public adoption of Web-enabled cellular telephone and wireless personal digital assistant (PDA) devices provide timely opportunities to deliver the mass customization capabilities, reach, and interactivity required for the development, administration, and adoption of effective population-level eHealth tailored informational interventions for obesity. [Abstract/Link to Full Text]

Gammon D, Arsand E, Walseth OA, Andersson N, Jenssen M, Taylor T
Parent-child interaction using a mobile and wireless system for blood glucose monitoring.
J Med Internet Res. 2005;7(5):e57.
BACKGROUND: Children with type 1 diabetes and their parents face rigorous procedures for blood glucose monitoring and regulation. Mobile telecommunication systems show potential as an aid for families' self-management of diabetes. OBJECTIVE: A prototype designed to automatically transfer readings from a child's blood glucose monitor to their parent's mobile phone was tested. In this formative stage of development, we sought insights into the appropriateness of the concept, feasibility of use, and ideas for further development and research. METHODS: During four months, a self-selected sample of 15 children (aged 9 to 15 years) with type 1 diabetes and their parents (n = 30) used the prototype approximately three times daily. Parent and child experiences were collected through questionnaires and through interviews with 9 of the parents. RESULTS: System use was easily integrated into everyday life, and parents valued the sense of reassurance offered by the system. Parents' ongoing struggle to balance control of their children with allowing independence was evident. For children who measured regularly, use appeared to reduce parental intrusions. For those who measured irregularly, however, parental reminders (eg, "nagging") appeared to increase. Although increased reminders could be considered a positive outcome, they can potentially increase parent-child conflict and thus also undermine proper metabolic control. Parents felt that system appropriateness tapered off with the onset of adolescence, partly due to a potential sense of surveillance from the child's perspective that could fuel oppositional behavior. Parental suggestions for further developments included similar alerts of irregular insulin dosages and automatically generated dietary and insulin dosage advice. CONCLUSIONS: User enthusiasm suggests that such systems might find a consumer market regardless of whether or not they ultimately improve health outcomes. Thus, more rigorous studies are warranted to inform guidelines for appropriate use. Potentially fruitful approaches include integrating such systems with theory-based parenting interventions and approaches that can aid in interpreting and responding to experiences of surveillance, virtual presence, and balances of power in e-mediated relationships. [Abstract/Link to Full Text]

Richardson CR, Brown BB, Foley S, Dial KS, Lowery JC
Feasibility of adding enhanced pedometer feedback to nutritional counseling for weight loss.
J Med Internet Res. 2005;7(5):e56.
BACKGROUND: Intensive interventions targeting diet and physical activity are effective for weight reduction but are costly. Tailored, computer-generated, step-count feedback may provide an intensive and affordable way to increase the physical activity of people at high risk for cardiovascular disease. OBJECTIVE: The objective was to test the feasibility of adding tailored, computer-generated, step-count feedback to a face-to-face nutritional counseling weight loss intervention. METHODS: We recruited 12 participants, 4 from each of three Department of Veterans Affairs medical centers. There were 11 male participants and 1 female participant. Each had a body mass index of 30 or greater and at least one of the following cardiovascular disease risk factors: diabetes, hypertension, hypercholesterolemia, obesity, or coronary artery disease. Participants attended one-on-one counseling sessions with a registered dietitian for four sessions over three weeks. At the initial session, each participant received an enhanced pedometer to record time-stamped, step-count data. Participants wore the device daily throughout the intervention. At the three follow-up sessions, the dietitian uploaded the computer data, reviewed a Web-based graphical display of step-count feedback, and helped set new walking goals. RESULTS: All 12 participants completed the program (100% attendance). Initial mean weight was 255 lbs (SD = 49 lbs), and weight loss was just over 4 lbs (n = 12, paired t test, P = .004). Mean daily step counts during the first week averaged 6019 steps per day, increasing to an average of 7358 per day after the third week (average increase of 1339 steps per day, or 0.6 miles, or 12 minutes of walking, n = 10, paired t test, P = .04). CONCLUSIONS: Enhanced pedometer feedback in conjunction with nutritional counseling is feasible and results in significant weight loss and increased walking among individuals at high risk for cardiovascular disease. [Abstract/Link to Full Text]

Griffiths KM, Christensen H
Website quality indicators for consumers.
J Med Internet Res. 2005;7(5):e55.
BACKGROUND: The rating tool DISCERN was designed for use by consumers without content expertise to evaluate the quality of health information. There is some evidence that DISCERN may be a valid indicator of evidence-based website quality when applied by health professionals. However, it is not known if the tool is a valid measure of evidence-based quality when used by consumers. Since it is a lengthy instrument requiring training in its use, DISCERN may prove impractical for use by the typical consumer. It is therefore important to explore the validity of other simpler potential indicators of site quality such as Google PageRank. OBJECTIVE: This study aimed to determine (1) whether the instrument DISCERN is a valid indicator of evidence-based Web content quality for consumers without specific mental health training, and (2) whether Google PageRank is an indicator of website content quality as measured by an evidence-based gold standard. METHODS: This was a cross-sectional survey of depression websites using consumer and health professional raters. The main outcome measures were (1) site characteristics, (2) evidence-based quality of content as measured by evidence-based depression guidelines, (3) DISCERN scores, (4) Google PageRank, and (5) user satisfaction. RESULTS: There was a significant association between evidence-based quality ratings and average DISCERN ratings both for consumers (r = 0.62, P = .001) and health professionals (r = 0.80, P < .001). Consumer and health professional DISCERN ratings were significantly correlated (r = 0.77, P < .001). The evidence-based quality score correlated with Google PageRank (r = 0.59, P = .002). However, the correlation between DISCERN scores and user satisfaction was higher than the correlation between Google PageRank and user satisfaction. CONCLUSIONS: DISCERN has potential as an indicator of content quality when used either by experts or by consumers. Google PageRank shows some promise as an automatic indicator of quality. [Abstract/Link to Full Text]

Jones R, Rogers R, Roberts J, Callaghan L, Lindsey L, Campbell J, Thorogood M, Wright G, Gaunt N, Hanks C, Williamson GR
What is eHealth (5): a research agenda for eHealth through stakeholder consultation and policy context review.
J Med Internet Res. 2005;7(5):e54.
BACKGROUND: In 2003, the National Health Service in England and Wales, despite its large investment in information and communication technology, had not set a national research agenda. The National Health Service has three main research and development programs: one is the Service Delivery and Organisation program, commissioned in 2003, and the others are two parallel "scoping exercises" to help set a research agenda. This paper reports on one of those projects. A parallel literature review was carried out by others and has been reported elsewhere. OBJECTIVE: The objective was to explore the concerns of stakeholders and to review relevant policy in order to produce recommendations and a conceptual map of eHealth research. METHODS: There were two parallel strands. For the stakeholder consultation, 37 professionals representing 12 "stakeholder" groups participated in focus groups or interviews. Discussion was prompted by eHealth "scenarios" and analyzed using thematic content analysis. Subsequently, 17 lay participants, in three focus groups, discussed and prioritized these themes. For the policy review, 26 policy makers were interviewed, and 95 policy documents were reviewed. Recommendations were subsequently reviewed in a conference workshop. Recommendations for research from both strands were combined into a conceptual map. RESULTS: Themes from stakeholder consultation and policy review were combined as 43 recommendations under six headings. Four of these headings (using, processing, sharing, and controlling information) describe the scope of eHealth research. The other two relate to how research should be carried out (ensuring best practice is first identified and disseminated) and to the values considered important by stakeholders (in particular, measuring improvement in health). CONCLUSIONS: The scope of eHealth research (using, processing, sharing, controlling information) derived empirically from this study corresponds with "textbook" descriptions of informatics. Stakeholders would like eHealth research to include outcomes such as improved health or quality of life, but such research may be long term while changes in information technology are rapid. Longer-term research questions need to be concerned with human behavior and our use of information, rather than particular technologies. In some cases, "modelling" longer-term costs and benefits (in terms of health) may be desirable. [Abstract/Link to Full Text]

Schleyer TK, Teasley SD, Bhatnagar R
Comparative case study of two biomedical research collaboratories.
J Med Internet Res. 2005;7(5):e53.
BACKGROUND: Working together efficiently and effectively presents a significant challenge in large-scale, complex, interdisciplinary research projects. Collaboratories are a nascent method to help meet this challenge. However, formal collaboratories in biomedical research centers are the exception rather than the rule. OBJECTIVE: The main purpose of this paper is to compare and describe two collaboratories that used off-the-shelf tools and relatively modest resources to support the scientific activity of two biomedical research centers. The two centers were the Great Lakes Regional Center for AIDS Research (HIV/AIDS Center) and the New York University Oral Cancer Research for Adolescent and Adult Health Promotion Center (Oral Cancer Center). METHODS: In each collaboratory, we used semistructured interviews, surveys, and contextual inquiry to assess user needs and define the technology requirements. We evaluated and selected commercial software applications by comparing their feature sets with requirements and then pilot-testing the applications. Local and remote support staff cooperated in the implementation and end user training for the collaborative tools. Collaboratory staff evaluated each implementation by analyzing utilization data, administering user surveys, and functioning as participant observers. RESULTS: The HIV/AIDS Center primarily required real-time interaction for developing projects and attracting new participants to the center; the Oral Cancer Center, on the other hand, mainly needed tools to support distributed and asynchronous work in small research groups. The HIV/AIDS Center's collaboratory included a center-wide website that also served as the launch point for collaboratory applications, such as NetMeeting, Timbuktu Conference, PlaceWare Auditorium, and iVisit. The collaboratory of the Oral Cancer Center used Groove and Genesys Web conferencing. The HIV/AIDS Center was successful in attracting new scientists to HIV/AIDS research, and members used the collaboratory for developing and implementing new research studies. The Oral Cancer Center successfully supported highly distributed and asynchronous research, and the collaboratory facilitated real-time interaction for analyzing data and preparing publications. CONCLUSIONS: The two collaboratory implementations demonstrated the feasibility of supporting biomedical research centers using off-the-shelf commercial tools, but they also identified several barriers to successful collaboration. These barriers included computing platform incompatibilities, network infrastructure complexity, variable availability of local versus remote IT support, low computer and collaborative software literacy, and insufficient maturity of available collaborative software. Factors enabling collaboratory use included collaboration incentives through funding mechanism, a collaborative versus competitive relationship of researchers, leadership by example, and tools well matched to tasks and technical progress. Integrating electronic collaborative tools into routine scientific practice can be successful but requires further research on the technical, social, and behavioral factors influencing the adoption and use of collaboratories. [Abstract/Link to Full Text]

Coiera E, Walther M, Nguyen K, Lovell NH
Architecture for knowledge-based and federated search of online clinical evidence.
J Med Internet Res. 2005;7(5):e52.
BACKGROUND: It is increasingly difficult for clinicians to keep up-to-date with the rapidly growing biomedical literature. Online evidence retrieval methods are now seen as a core tool to support evidence-based health practice. However, standard search engine technology is not designed to manage the many different types of evidence sources that are available or to handle the very different information needs of various clinical groups, who often work in widely different settings. OBJECTIVES: The objectives of this paper are (1) to describe the design considerations and system architecture of a wrapper-mediator approach to federate search system design, including the use of knowledge-based, meta-search filters, and (2) to analyze the implications of system design choices on performance measurements. METHODS: A trial was performed to evaluate the technical performance of a federated evidence retrieval system, which provided access to eight distinct online resources, including e-journals, PubMed, and electronic guidelines. The Quick Clinical system architecture utilized a universal query language to reformulate queries internally and utilized meta-search filters to optimize search strategies across resources. We recruited 227 family physicians from across Australia who used the system to retrieve evidence in a routine clinical setting over a 4-week period. The total search time for a query was recorded, along with the duration of individual queries sent to different online resources. RESULTS: Clinicians performed 1662 searches over the trial. The average search duration was 4.9 +/- 3.2 s (N = 1662 searches). Mean search duration to the individual sources was between 0.05 s and 4.55 s. Average system time (ie, system overhead) was 0.12 s. CONCLUSIONS: The relatively small system overhead compared to the average time it takes to perform a search for an individual source shows that the system achieves a good trade-off between performance and reliability. Furthermore, despite the additional effort required to incorporate the capabilities of each individual source (to improve the quality of search results), system maintenance requires only a small additional overhead. [Abstract/Link to Full Text]

Valaitis RK
Computers and the internet: tools for youth empowerment.
J Med Internet Res. 2005;7(5):e51.
BACKGROUND: Youth are often disenfranchised in their communities and may feel they have little voice. Since computers are an important aspect of youth culture, they may offer solutions to increasing youth participation in communities. OBJECTIVE: This qualitative case study investigated the perceptions of 19 (predominantly female) inner-city school youth about their use of computers and the Internet in a school-based community development project. METHODS: Youth working with public health nurses in a school-based community development project communicated with local community members using computer-mediated communication, surveyed peers online, built websites, searched for information online, and prepared project materials using computers and the Internet. Participant observation, semistructured interviews, analysis of online messages, and online- and paper-based surveys were used to gather data about youth's and adults' perceptions and use of the technologies. Constant comparison method and between-method triangulation were used in the analysis to satisfy the existence of themes. RESULTS: Not all youth were interested in working with computers. Some electronic messages from adults were perceived to be critical, and writing to adults was intimidating for some youth. In addition, technical problems were experienced. Despite these barriers, most youth perceived that using computers and the Internet reduced their anxiety concerning communication with adults, increased their control when dealing with adults, raised their perception of their social status, increased participation within the community, supported reflective thought, increased efficiency, and improved their access to resources. CONCLUSIONS: Overall, youth perceived computers and the Internet to be empowering tools, and they should be encouraged to use such technology to support them in community initiatives. [Abstract/Link to Full Text]

Gibbons MC
A historical overview of health disparities and the potential of eHealth solutions.
J Med Internet Res. 2005;7(5):e50.
Over the past decade, a rapidly expanding body of literature has demonstrated the existence of disparities in health and health care. While consensus has not emerged regarding the causes of disparities, they are generally thought to be related to sociocultural, behavioral, economic, environmental, biologic, or societal factors. To effectively address disparities, several authorities have suggested the need for greater information technology research and investments. eHealth researchers may be able to make significant contributions in this area through research and its applications. This paper begins with a historical overview of health disparities in the United States and Europe. It then discusses the role that the Internet, and access to the Internet, may play in the genesis of health disparities. Finally, this paper closes with a discussion of the potential benefits of eHealth applications and the possible contributions of the field to overcoming disparities in health and health care. [Abstract/Link to Full Text]

Danaher BG, Jazdzewski SA, McKay HG, Hudson CR
Bandwidth constraints to using video and other rich media in behavior change websites.
J Med Internet Res. 2005;7(4):e49.
BACKGROUND: Web-based behavior change interventions often include rich media (eg, video, audio, and large graphics). The rationale for using rich media includes the need to reach users who are not inclined or able to use text-based website content, encouragement of program engagement, and following the precedent set by news and sports websites. OBJECTIVES: We describe the development of a bandwidth usage index, which seeks to provide a practical method to gauge the extent to which websites can successfully be used within different Internet access scenarios (eg, dial-up and broadband). METHODS: We conducted three studies to measure bandwidth consumption. In Study 1, we measured the bandwidth usage index for three video-rich websites (for smoking cessation, for caregivers, and for improving eldercare by family members). We then estimated the number of concurrent users that could be accommodated by each website under various Internet access scenarios. In Study 2, we sought to validate our estimated threshold number of concurrent users by testing the video-rich smoking cessation website with different numbers of concurrent users. In Study 3, we calculated the bandwidth usage index and threshold number of concurrent users for three versions of the smoking cessation website: the video-rich version (tested in Study 1), an audio-rich version, and a Web-enabled CD-ROM version in which all media-rich content was placed on a CD-ROM on the client computer. RESULTS: In Study 1, we found that the bandwidth usage index of the video-rich websites ranged from 144 Kbps to 93 Kbps. These results indicated that dial-up modem users would not achieve a "good user experience" with any of the three rich media websites. Results for Study 2 confirmed that usability was compromised when the estimated threshold number of concurrent users was exceeded. Results for Study 3 indicated that changing a website from video- to audio-rich content reduced the bandwidth requirement by almost 50%, but it remained too large to allow satisfactory use in dial-up modem scenarios. The Web-enabled CD-ROM reduced bandwidth requirements such that even a dial-up modem user could have a good user experience with the rich media content. CONCLUSIONS: We conclude that the bandwidth usage index represents a practical tool that can help developers and researchers to measure the bandwidth requirements of their websites as well as to evaluate the feasibility of certain website designs in terms of specific use cases. These findings are discussed in terms of reaching different groups of users as well accommodating the intended number of concurrent users. We also discuss the promising option of using Web-enabled CD-ROMs to deliver rich media content to users with dial-up Internet access. We introduce a number of researchable themes for improving our ability to develop Web-based behavior change interventions that can better deliver what they promise. [Abstract/Link to Full Text]

Wall TC, Mian MA, Ray MN, Casebeer L, Collins BC, Kiefe CI, Weissman N, Allison JJ
Improving physician performance through Internet-based interventions: who will participate?
J Med Internet Res. 2005;7(4):e48.
BACKGROUND: The availability of Internet-based continuing medical education is rapidly increasing, but little is known about recruitment of physicians to these interventions. OBJECTIVE: The purpose of this study was to examine predictors of physician participation in an Internet intervention designed to increase screening of young women at risk for chlamydiosis. METHODS: Eligibility was based on administrative claims data, and eligible physicians received recruitment letters via fax and/or courier. Recruited offices had at least one physician who agreed to participate in the study by providing an email address. After one physician from an office was recruited, intensive recruitment of that office ceased. Email messages reminded individual physicians to participate by logging on to the Internet site. RESULTS: Of the eligible offices, 325 (33.2%) were recruited, from which 207 physicians (52.8%) participated. Recruited versus nonrecruited offices had more eligible patients (mean number of eligible patients per office: 44.1 vs 33.6; P < .001), more eligible physicians (mean number of eligible physicians per office: 6.2 vs 4.1; P < .001), and fewer doctors of osteopathy (mean percent of eligible physicians per office who were doctors of osteopathy: 20.5% vs 26.4%; P = .02). Multivariable analysis revealed that the odds of recruiting at least one physician from an office were greater if the office had more eligible patients and more eligible physicians. More participating versus nonparticipating physicians were female (mean percent of female recruited physicians: 39.1% vs 27.0%; P = .01); fewer participating physicians were doctors of osteopathy (mean percent of recruited physicians who were doctors of osteopathy: 15.5% vs 23.9%; P = .04) or international medical graduates (mean percent of recruited physicians who were international graduates: 12.3% vs 23.8%; P = .003). Multivariable analysis revealed that the odds of a physician participating were greater if the physician was older than 55 years (OR = 2.31; 95% CI = 1.09-4.93) and was from an office with a higher Chlamydia screening rate in the upper tertile (OR = 2.26; 95% CI = 1.23-4.16). CONCLUSIONS: Physician participation in an Internet continuing medical education intervention varied significantly by physician and office characteristics. [Abstract/Link to Full Text]

Lin CT, Wittevrongel L, Moore L, Beaty BL, Ross SE
An Internet-based patient-provider communication system: randomized controlled trial.
J Med Internet Res. 2005;7(4):e47.
BACKGROUND: Internet-based interactive websites for patient communication (patient portals) may improve communication between patients and their clinics and physicians. OBJECTIVE: The aim of the study was to assess the impact of a patient portal on patients' satisfaction with access to their clinic and clinical care. Another aim was to analyze the content and volume of email messages and telephone calls from patients to their clinic. METHODS: This was a randomized controlled trial with 606 patients from an academic internal medicine practice. The intervention "portal" group used a patient portal to send secure messages directly to their physicians and to request appointments, prescription refills, and referrals. The control group received usual care. We assessed patient satisfaction at the end of the 6-month trial period and compared the content of telephone and portal communications. RESULTS: Portal group patients reported improved communication with the clinic (portal: 77/174 [44%] "a little better" or "a lot better;" control: 18/146 [12%]; chi2 = 38.8, df = 1, P < .001) and higher satisfaction with overall care (portal: 103/174 [59%] "very good" or "excellent;" control: 78/162 [48%]; chi2 = 4.1, df = 1, P = .04). Portal group patients also reported higher satisfaction with each of the portal's services. Physicians received 1 portal message per day for every 250 portal patients. Total telephone call volume was not affected. Patients were more likely to send informational and psychosocial messages by portal than by phone. Of all surveyed patients, 162/341 (48%) were willing to pay for online correspondence with their physician. Of those willing to pay, the median amount cited was 2 USD per message. CONCLUSIONS: Portal group patients demonstrated increased satisfaction with communication and overall care. Patients in the portal group particularly valued the portal's convenience, reduced communication barriers, and direct physician responses. More online messages from patients contained informational and psychosocial content compared to telephone calls, which may enhance the patient-physician relationship. [Abstract/Link to Full Text]

Rizo CA, Lupea D, Baybourdy H, Anderson M, Closson T, Jadad AR
What Internet services would patients like from hospitals during an epidemic? Lessons from the SARS outbreak in Toronto.
J Med Internet Res. 2005;7(4):e46.
BACKGROUND: International health organizations and officials are bracing for a pandemic. Although the 2003 severe acute respiratory syndrome (SARS) outbreak in Toronto did not reach such a level, it created a unique opportunity to identify the optimal use of the Internet to promote communication with the public and to preserve health services during an epidemic. OBJECTIVE: The aim of the study was to explore patients' attitudes regarding the health services that might be provided through the Internet to supplement those traditionally available in the event of a future mass emergency situation. METHODS: We conducted "mask-to-mask" surveys of patients at three major teaching hospitals in Toronto during the second outbreak of SARS. Patients were surveyed at the hospital entrances and selected clinics. Descriptive statistics and logistic regression models were used for the analysis. RESULTS: In total, 1019 of 1130 patients responded to the survey (90% overall response rate). With respect to Internet use, 70% (711/1019) used the Internet by themselves and 57% (578/1019) with the help of a friend or family member. Of the Internet users, 68% (485/711) had already searched the World Wide Web for health information, and 75% (533/711) were interested in communicating with health professionals using the Internet as part of their ongoing care. Internet users expressed interest in using the Web for the following reasons: to learn about their health condition through patient education materials (84%), to obtain information about the status of their clinic appointments (83%), to send feedback to the hospital about how to improve its services (77%), to access screening tools to help determine if they were potentially affected by the infectious agent responsible for the outbreak (77%), to renew prescriptions (75%), to consult with their health professional about nonurgent matters (75%), and to access laboratory test results (75%). Regression results showed that younger age, higher education, and English as a first language were predictors of patients' interest in using Internet services in the event of an epidemic. CONCLUSION: Most patients are willing and able to use the Internet as a means to maintain communication with the hospital during an outbreak of an infectious disease such as SARS. Hospitals should explore new ways to interact with the public, to provide relevant health information, and to ensure continuity of care when they are forced to restrict their services. [Abstract/Link to Full Text]

Finer D
"Is cybermedicine killing you?"--codes of ethics for journalists.
J Med Internet Res. 2005;7(4):e45. [Abstract/Link to Full Text]

Rada R
A case study of a retracted systematic review on interactive health communication applications: impact on media, scientists, and patients.
J Med Internet Res. 2005;7(2):e18.
BACKGROUND: In October 2004, a flawed systematic review entitled "Interactive Health Communication Applications for People with Chronic Disease" was published in the Cochrane Library, accompanied by several press releases in which authors warned the public of the negative health consequences of interactive health communication applications, including the Internet. Within days of the review's publication, scientists identified major coding errors and other methodological problems that invalidated the principal conclusions of the study and led to a retraction. While the original study results and their negative conclusions were widely publicized in the media, the retraction seemed to go unnoticed. OBJECTIVE: This paper aims to document an unprecedented case of misinformation from a Cochrane review and its impact on media, scientists, and patients. As well, it aims to identify the generic factors leading to the incident and suggest remedies. METHODS: This was a qualitative study of the events leading to the retraction of the publication and of the reactions from media, scientists, and patients. This includes a review and content analysis of academic and mass media articles responding to the publication and retraction. Mass media articles were retrieved in May 2005 from LexisNexis Academic and Google and were classified and tallied. The extended case method is employed, and the analysis is also applied to comparable publishing events. RESULTS: A search on LexisNexis Academic database with the query "Elizabeth Murray AND health" for the period of June 2004 to May 2005 revealed a total of 15 press reports, of which only 1 addressed the retraction. Google was searched for references to the review, and the first 200 retrieved hits were analyzed. Of these, 170 pages were not related to the review. Of the remaining 30 pages, 23 (77%) were reports about the original publication that did not mention the retraction, 1 (3%) was a bibliography not mentioning the retraction, and 6 (20%) addressed the retraction, of which only 1 was a non-Cochrane-related source. CONCLUSIONS: Analyzed retrievals showed that the mass media gave more coverage to the Cochrane review than to the retraction or to a related systematic review with a similar scope but a different conclusion. Questionable results were prematurely disseminated, oversimplified, and sensationalized, while the retraction was hardly noticed by the public. Open commentary by scientists and patients helped to rapidly identify the errors but did not prevent or correct the dissemination of misinformation. [Abstract/Link to Full Text]

Eysenbach G, Kummervold PE
"Is Cybermedicine Killing You?"--The story of a Cochrane disaster.
J Med Internet Res. 2005;7(2):e21.
This editorial briefly reviews the series of unfortunate events that led to the publication, dissemination, and eventual retraction of a flawed Cochrane systematic review on interactive health communication applications (IHCAs), which was widely reported in the media with headlines such as "Internet Makes Us Sick," "Knowledge May Be Hazardous to Web Consumers' Health," "Too Much Advice Can Be Bad for Your Health," "Click to Get Sick?," and even "Is Cybermedicine Killing You?". While the media attention helped to speed up the identification of errors, leading to a retraction of the review after only 13 days, a paper published in this issue of JMIR by Rada shows that the retraction, in contrast to the original review, remained largely unnoticed by the public. We discuss the three flaws of the review, which include (1) data extraction and coding errors, (2) the pooling of heterogeneous studies, and (3) a problematic and ambiguous scope and, possibly, some overlooked studies. We then discuss "retraction ethics" for researchers, editors/publishers, and journalists. Researchers and editors should, in the case of retractions, match the aggressiveness of the original dissemination campaign if errors are detected. It is argued that researchers and their organizations may have an ethical obligation to track down journalists who reported stories on the basis of a flawed study and to specifically ask them to publish an article indicating the error. Journalists should respond to errors or retractions with reports that have the same prominence as the original story. Finally, we look at some of the lessons for the Cochrane Collaboration, which include (1) improving the peer-review system by routinely sending out pre-prints to authors of the original studies, (2) avoiding downplay of the magnitude of errors if they occur, (3) addressing the usability issues of RevMan, and (4) making critical articles such as retraction notices open access. [Abstract/Link to Full Text]

Fourniol D
"Is cybermedicine killing you?"--University College London (UCL) media strategy explained.
J Med Internet Res. 2005;7(4):e43; author reply e44. [Abstract/Link to Full Text]

Murray E, Burns J, Tai SS, Nazareth I
"Is cybermedicine killing you?"--a response from the authors of the Cochrane Review.
J Med Internet Res. 2005;7(4):e40; author reply e41-2. [Abstract/Link to Full Text]

Fogel J
"Is cybermedicine killing you?"--peer review and evidence-based medicine.
J Med Internet Res. 2005;7(4):e38; author reply e39. [Abstract/Link to Full Text]

Pulier ML
"Is cybermedicine killing you?"--Cochrane Collaboration needs to restore confidence.
J Med Internet Res. 2005;7(4):e37. [Abstract/Link to Full Text]

Cooper CP, Mallon KP, Leadbetter S, Pollack LA, Peipins LA
Cancer Internet search activity on a major search engine, United States 2001-2003.
J Med Internet Res. 2005 Jul 1;7(3):e36.
BACKGROUND: To locate online health information, Internet users typically use a search engine, such as Yahoo! or Google. We studied Yahoo! search activity related to the 23 most common cancers in the United States. OBJECTIVE: The objective was to test three potential correlates of Yahoo! cancer search activity--estimated cancer incidence, estimated cancer mortality, and the volume of cancer news coverage--and to study the periodicity of and peaks in Yahoo! cancer search activity. METHODS: Yahoo! cancer search activity was obtained from a proprietary database called the Yahoo! Buzz Index. The American Cancer Society's estimates of cancer incidence and mortality were used. News reports associated with specific cancer types were identified using the LexisNexis "US News" database, which includes more than 400 national and regional newspapers and a variety of newswire services. RESULTS: The Yahoo! search activity associated with specific cancers correlated with their estimated incidence (Spearman rank correlation, rho = 0.50, P = .015), estimated mortality (rho = 0.66, P = .001), and volume of related news coverage (rho = 0.88, P < .001). Yahoo! cancer search activity tended to be higher on weekdays and during national cancer awareness months but lower during summer months; cancer news coverage also tended to follow these trends. Sharp increases in Yahoo! search activity scores from one day to the next appeared to be associated with increases in relevant news coverage. CONCLUSIONS: Media coverage appears to play a powerful role in prompting online searches for cancer information. Internet search activity offers an innovative tool for passive surveillance of health information-seeking behavior. [Abstract/Link to Full Text]

Doolittle GC, Spaulding A
Online cancer services: types of services offered and associated health outcomes.
J Med Internet Res. 2005 Jul 1;7(3):e35.
There are advantages and disadvantages associated with utilization of online health services among individuals living with cancer. Accessing accurate, reliable health-related information online gives patients the power to enhance their understanding of information they obtain from their health care providers. However, online health information can often be confusing for patients to interpret, and it can sometimes be conflicting or incorrect. Based on a framework by Eysenbach, the following paper discusses various types of cancer services that are available online, and it addresses both positive and negative health outcomes that have been linked to utilizing such services. [Abstract/Link to Full Text]

Whitten P, Kreps GL, Eastin MS
Creating a framework for online cancer services research to facilitate timely and interdisciplinary applications.
J Med Internet Res. 2005 Jul 1;7(3):e34.
Researchers from a wide array of disciplines have conducted engaging and informative studies in recent years concerning the use of the Internet for cancer-related services. Typically, these publications provide key data related to utilization statistics, how online information can be used, what users want or expect from the Internet, outcomes or impacts, and quality and credibility of websites. These are important themes for understanding online cancer issues. However, this special issue of the Journal of Medical Internet Research seeks to recast these themes in a way that will facilitate pragmatic and applied means of employing data in prescriptive and interdisciplinary ways. This issue includes 14 papers that exemplify applications for the research framework recommended in this paper. This framework includes an expanded focus on the development and design of online cancer services, online consumer behavior/communication, behavior change, and living with cancer. [Abstract/Link to Full Text]

Walther JB, Pingree S, Hawkins RP, Buller DB
Attributes of interactive online health information systems.
J Med Internet Res. 2005 Jul 1;7(3):e33.
The development of online communication systems related to prevention, decision making, and coping with cancer has outpaced theoretical attention to the attributes that appeal to system users and that create effective interactions. This essay reviews a number of sociotechnical attributes related to online discussion systems and tutorials, including interactivity, presence, homophily, social distance, anonymity/privacy, and interaction management. These attributes are derived from different theoretical perspectives which have led to clinical trials and other empirical studies demonstrating effectiveness or attraction to end users. The effects of a subset of these attributes are connected to learning, social influence, and coping, as illustrated in evaluations of an interactive smoking prevention site and a cancer advice/support discussion system. [Abstract/Link to Full Text]

Rimer BK, Lyons EJ, Ribisl KM, Bowling JM, Golin CE, Forlenza MJ, Meier A
How new subscribers use cancer-related online mailing lists.
J Med Internet Res. 2005 Jul 1;7(3):e32.
BACKGROUND: Online cancer-related support is an under-studied resource that may serve an important function in the information seeking, care, and support of cancer patients and their families. With over 9.8 million cancer survivors (defined as anyone living with cancer) in the United States alone and the number growing worldwide, it is important to understand how they seek and use online resources to obtain the information they need, when they need it, and in a form and manner appropriate to them. These are stated cancer communication goals of the US National Cancer Institute. OBJECTIVES: Our purposes are to (1) present background information about online mailing lists and electronic support groups, (2) describe the rationale and methodology for the Health eCommunities (HeC) study, and (3) present preliminary baseline data on new subscribers to cancer-related mailing lists. In particular, we describe subscribers' use of mailing lists, their reasons for using them, and their reactions to participating shortly after joining the lists. METHODS: From April to August 2004, we invited all new subscribers to 10 Association of Cancer Online Resources mailing lists to complete Web-based surveys. We analyzed baseline data from the respondents to examine their perceptions about cancer-related mailing lists and to describe how cancer patients and survivors used these lists in the period shortly after joining them. RESULTS: Cumulative email invitations were sent to 1368 new mailing list subscribers; 293 Web surveys were completed within the allotted time frame (21.4% response rate). Most respondents were over age 50 (n = 203, 72%), white (n = 286, 98%), college graduates (n = 161, 55%), and had health insurance (n = 283, 97%). About 41% (n = 116) of new subscribers reported spending 1 to 3 hours per day reading and responding to list messages. They used the mailing lists for several reasons. Among the most frequently reported, 62% (n = 179) strongly agreed they used mailing lists to obtain information on how to deal with cancer, 42% (n = 121) strongly agreed they used mailing lists for support, and 37% (n = 109) strongly agreed that they were on the mailing lists to help others. Smaller proportions of new subscribers strongly agreed that others on the mailing lists had similar cancer experiences (n = 23, 9%), that they could relate to the experiences of others on the lists (n = 66, 27%), and that others on the list gave them good ideas about how to cope with cancer (n = 66, 27%). CONCLUSIONS: Cancer-related online mailing lists appear to be an important resource, especially for information seeking but also for support of cancer survivors. These were the primary motivators most members reported for joining mailing lists. The modest proportion of subscribers who strongly agreed that they could relate to others' cancer experiences (as well as similar responses to other process questions) is undoubtedly due at least in part to the short duration that these subscribers were involved with the mailing lists. Emerging data, including our own, suggest that mailing lists are perhaps under-used by minority patients/survivors. These preliminary data add to a growing body of research on health-related online communities, of which online mailing lists are one variant. [Abstract/Link to Full Text]

Wood FB, Benson D, LaCroix EM, Siegel ER, Fariss S
Use of Internet audience measurement data to gauge market share for online health information services.
J Med Internet Res. 2005 Jul 1;7(3):e31.
BACKGROUND: The transition to a largely Internet and Web-based environment for dissemination of health information has changed the health information landscape and the framework for evaluation of such activities. A multidimensional evaluative approach is needed. OBJECTIVE: This paper discusses one important dimension of Web evaluation-usage data. In particular, we discuss the collection and analysis of external data on website usage in order to develop a better understanding of the health information (and related US government information) market space, and to estimate the market share or relative levels of usage for National Library of Medicine (NLM) and National Institutes of Health (NIH) websites compared to other health information providers. METHODS: The primary method presented is Internet audience measurement based on Web usage by external panels of users and assembled by private vendors-in this case, comScore. A secondary method discussed is Web usage based on Web log software data. The principle metrics for both methods are unique visitors and total pages downloaded per month. RESULTS: NLM websites (primarily MedlinePlus and PubMed) account for 55% to 80% of total NIH website usage depending on the metric used. In turn, NIH.gov top-level domain usage (inclusive of NLM) ranks second only behind WebMD in the US domestic home health information market and ranks first on a global basis. NIH.gov consistently ranks among the top three or four US government top-level domains based on global Web usage. On a site-specific basis, the top health information websites in terms of global usage appear to be WebMD, MSN Health, PubMed, Yahoo! Health, AOL Health, and MedlinePlus. Based on MedlinePlus Web log data and external Internet audience measurement data, the three most heavily used cancer-centric websites appear to be www.cancer.gov (National Cancer Institute), www.cancer.org (American Cancer Society), and www.breastcancer.org (non-profit organization). CONCLUSIONS: Internet audience measurement has proven useful to NLM, with significant advantages compared to sole reliance on usage data from Web log software. Internet audience data has helped NLM better understand the relative usage of NLM and NIH websites in the intersection of the health information and US government information market sectors, which is the primary market intersector for NLM and NIH. However important, Web usage is only one dimension of a complete Web evaluation framework, and other primary research methods, such as online user surveys, usability tests, and focus groups, are also important for comprehensive evaluation that includes qualitative elements, such as user satisfaction and user friendliness, as well as quantitative indicators of website usage. [Abstract/Link to Full Text]

Eng TR
Emerging technologies for cancer prevention and other population health challenges.
J Med Internet Res. 2005 Jul 1;7(3):e30.
Emerging technologies, such as information and communication technologies (including future versions of the Internet), microelectromechanical systems, nanotechnologies, genomics, robotics, artificial intelligence, and sensors, provide enormous opportunities for enhancing health and quality of life. Population health technologies (PHTs) encompass the various applications of emerging technologies to improve the health of populations and communities. These technologies may change many population health paradigms, including those related to cancer prevention and control. In the future, emerging technologies will allow true customization of health communication to individuals, and existing tailoring approaches will be considered very crude. Environmental monitoring systems based on emerging technologies could also provide real-time information that health officials and community residents could use immediately to ameliorate potential carcinogenic or unhealthy exposures. Accelerating the application and diffusion of emerging technologies to population health challenges will require a multipronged approach, including new transdisciplinary programs, increased funding, supportive infrastructure, and policy changes. [Abstract/Link to Full Text]

Bradley CJ
The need for online information on the economic consequences of cancer diagnosis, treatment, and survivorship.
J Med Internet Res. 2005 Jul 1;7(3):e29.
The Internet is commonly used to provide treatment information to patients diagnosed with cancer. Notably missing from the existing websites is information on the cost of cancer care in terms of medical costs to the patient and work-related consequences. The purpose of this paper is to describe what is known about the economic cost of cancer and to describe how this information can be structured so that it is of more benefit to patients. This paper first provides an overview of the information available regarding medical expenses and productivity costs associated with cancer survivorship, particularly with respect to cancer and employment. Second, it draws attention to the sparse economic information available online to cancer survivors. Patients can find information on sources of financial assistance, but they cannot estimate from the available information the cost of their care or anticipate the impact that cancer and its treatment may have on their jobs. Finally, a strategy for filling the void in online economic cancer information is described. Substantial opportunity exists to provide economic information to cancer patients and their families. The Internet is a natural forum for gathering and disseminating economic information. A unique advantage of the Internet is its ability to put information immediately in the hands of cancer patients and their families--assisting them to become informed consumers and skilled negotiators. [Abstract/Link to Full Text]

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Recent Articles in BMC Bioinformatics

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Archer KJ, Dumur CI, Taylor GS, Chaplin MD, Guiseppi-Elie A, Grant G, Ferreira-Gonzalez A, Garrett CT
Application of a correlation correction factor in a microarray cross-platform reproducibility study.
BMC Bioinformatics. 2007 Nov 15;8(1):447.
ABSTRACT: BACKGROUND: Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. RESULTS: In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson's correlation. Additionally, we previously developed a correction factor for Pearson's correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the "disattenuated" correlation substantially improves cross-platform correlations. CONCLUSIONS: When estimating cross-platform correlation, it is essential to thoroughly evaluate intra-platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates. [Abstract/Link to Full Text]

Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S
Novel definition files for human GeneChips based on GeneAnnot.
BMC Bioinformatics. 2007 Nov 15;8(1):446.
ABSTRACT: BACKGROUND: Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence. RESULTS: We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene. CONCLUSIONS: GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from www.xlab.unimo.it/GA_CDF, along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results). [Abstract/Link to Full Text]

Morgan XC, Ni S, Miranker DP, Iyer VR
Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining.
BMC Bioinformatics. 2007 Nov 15;8(1):445.
ABSTRACT: BACKGROUND: Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cis-regulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset, thus identifying frequently occurring pairs of distinct motifs within a segment. RESULTS: Support for most pairs of transcription factor binding motifs was highly correlated across different chromosomes although pair significance varied. Known true positive motif pairs showed higher association rule support, confidence, and significance than background. Our subsets of high-confidence, high-significance mined pairs of transcription factors showed enrichment for co-citation in PubMed abstracts relative to all pairs, and the predicted associations were often readily verifiable in the literature. CONCLUSIONS: Functional elements in the genome where transcription factors bind to regulate expression in a combinatorial manner are more likely to be predicted by identifying statistically and biologically significant combinations of transcription factor binding motifs than by simply scanning the genome for the occurrence of binding sites for a single transcription factor. [Abstract/Link to Full Text]

Jiang H, Blouin C
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions.
BMC Bioinformatics. 2007 Nov 15;8(1):444.
ABSTRACT: BACKGROUND: In protein evolution, the mechanism of the emergence of novel protein domain is still an open question. The incremental growth of protein variable regions, which was produced by stochastic insertions, has the potential to generate large and complex sub-structures. In this study, a deterministic methodology is proposed to reconstruct phylogenies from protein structures, and to infer insertion events in protein evolution. The analysis was performed on a broad range of SCOP domain families. RESULTS: Phylogenies were reconstructed from protein 3D structural data. The phylogenetic trees were used to infer ancestral structures with a consensus method. From these ancestral reconstructions, 42.7% of the observed insertions are nested insertions, which locate in previous insert regions. The average size of inserts tends to increase with the insert rank or total number of insertions in the variable regions. We found that the structures of some nested inserts show complex or even domain-like fold patterns with helices, strands and loops. Furthermore, a basal level of structural innovation was found in inserts which displayed a significant structural similarity exclusively to themselves. The beta-Lactamase/D-ala carboxypeptidase domain family is provided as an example to illustrate the inference of insertion events, and how the incremental growth of a variable region is capable to generate novel structural patterns. CONCLUSIONS: Using 3D data, we proposed a method to reconstruct phylogenies. We applied the method to reconstruct the sequences of insertion events leading to the emergence of potentially novel structural elements within existing protein domains. The results suggest that structural innovation is possible via the stochastic process of insertions and rapid evolution within variable regions where inserts tend to be nested. We also demonstrate that the structure-based phylogeny enables the study of new questions relating to the evolution of protein domain and biological function. [Abstract/Link to Full Text]

Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W
Correction: Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts.
BMC Bioinformatics. 2007 Nov 15;8(1):443.
ABSTRACT: Correction Following the publication of the article "Ringo - an R/Bioconductor package for analyzing ChIP-chip readouts - BMC Bioinformatics 2007, 8:221", the submitting author became aware that co-authors had been omitted from the publication. Therefore, this article has been submitted as a correction to the original text, and highlights the contributions that these authors made to the original article. The author would like to apologise for any inconvenience this may have caused. Corrected author list Joern Toedling, Oleg Skylar, Tammo Krueger, Jenny J. Fischer, Silke Sperling and Wolfgang Huber. Corrected authors' contributions JT, OS and TK developed the software. JT wrote the manuscript. JJF and SS provided example data. All authors contributed to design of analytical algorithms. All authors read and approved the final manuscript. [Abstract/Link to Full Text]

Marco A, Marin I
A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification.
BMC Bioinformatics. 2007 Nov 15;8(1):442.
ABSTRACT: BACKGROUND: Classification procedures are widely used in phylogenetic inference, the analysis of expression profiles, the study of biological networks, etc. Many algorithms have been proposed to establish the similarity between two different classifications of the same elements. However, methods to determine significant coincidences between hierarchical and non-hierarchical partitions are still poorly developed, in spite of the fact that the search for such coincidences is implicit in many analyses of massive data. RESULTS: We describe a novel strategy for comparing a hierarchical and a dichotomic non-hierarchical classification of elements, in order to find clusters in a hierarchical tree in which elements of a given "flat" partition are overrepresented. The key improvement of our strategy respect to previous methods is using permutation analyses of ranked clusters to determine whether regions of the dendrograms present a significant enrichment. We show that this method is more sensitive than previously developed strategies and how it can be applied to several real cases, including microarray and interactome data. Particularly, we use it to compare a hierarchical representation of the yeast mitochondrial interactome and a catalogue of known mitochondrial protein complexes, demonstrating a high level of congruence between those two classifications. We also discuss extensions of this method to other cases which are conceptually related. CONCLUSIONS: Our method is highly sensitive and outperforms previously described strategies. A PERL script that implements it is available at http://www.uv.es/~genomica/treetest. [Abstract/Link to Full Text]

Popadin KY, Mamirova LA, Kondrashov FA
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
BMC Bioinformatics. 2007 Nov 14;8(1):441.
ABSTRACT: BACKGROUND: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. CONCLUSIONS: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation. [Abstract/Link to Full Text]

Besnier F, Carlborg O
A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL.
BMC Bioinformatics. 2007 Nov 13;8(1):440.
ABSTRACT: BACKGROUND: Identity by descent (IBD) matrix estimation is a central component in mapping of Quantitative Trait Loci (QTL) using variance component models. A large number of algorithms have been developed for estimation of IBD between individuals in populations at discrete locations in the genome for use in genome scans to detect QTL affecting various traits of interest in experimental animal, human and agricultural pedigrees. Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values. RESULTS: Estimation of IBD functions improved the computational efficiency and memory usage in genome scanning for QTL. We have explored two approaches to obtain continuous marker-bracket IBD-functions. By re-implementing an existing and fast deterministic IBD-estimation method, we show that this approach results in IBD functions that produces the exact same IBD as the original algorithm, but with a greater than 2-fold improvement of the computational efficiency and a considerably lower memory requirement for storing the resulting genome-wide IBD. By developing a general IBD function approximation algorithm, we show that it is possible to estimate marker-bracket IBD functions from IBD matrices estimated at marker locations by any existing IBD estimation algorithm. The general algorithm provides approximations that lead to QTL variance component estimates that even in worst-case scenarios are very similar to the true values. The approach of storing IBD as polynomial IBD-function was also shown to reduce the amount of memory required in genome scans for QTL. CONCLUSIONS: In addition to direct improvements in computational and memory efficiency, estimation of IBD-functions is a fundamental step needed to develop and implement new efficient optimization algorithms for high precision localization of QTL. Here, we discuss and test two approaches for estimating IBD functions based on existing IBD estimation algorithms. Our approaches provide immediately useful techniques for use in single QTL analyses in the variance component QTL mapping framework. They will, however, be particularly useful in genome scans for multiple interacting QTL, where the improvements in both computational and memory efficiency are the key for successful development of efficient optimization algorithms to allow widespread use of this methodology. [Abstract/Link to Full Text]

Bernardes JS, Davila AM, Costa VS, Zaverucha G
Improving model construction of profile HMMs for remote homology detection through structural alignment.
BMC Bioinformatics. 2007 Nov 9;8(1):435.
ABSTRACT: BACKGROUND: Remote homology detection is a challenging problem in Bioinformatics. Arguably, profle Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. RESULTS: We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. CONCLUSIONS: We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area. [Abstract/Link to Full Text]

Turro E, Bochkina N, Hein AM, Richardson S
BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.
BMC Bioinformatics. 2007 Nov 12;8(1):439.
ABSTRACT: BACKGROUND: Affymetrix 3' GeneChip microarrays are widely used to profile the expression of thousands of genes simultaneously. They differ from many other microarray types in that GeneChips are hybridised using a single labelled extract and because they contain multiple 'match' and 'mismatch' sequences for each transcript. Most algorithms extract the signal from GeneChip experiments in a sequence of separate steps, including background correction and normalisation, which inhibits the simultaneous use of all available information. They principally provide a point estimate of gene expression and, in contrast to BGX, do not fully integrate the uncertainty arising from potentially heterogeneous responses of the probes. RESULTS: BGX is a new Bioconductor R package that implements an integrated Bayesian approach to the analysis of 3' GeneChip data. The software takes into account additive and multiplicative error, non-specific hybridisation and replicate summarisation in the spirit of the model outlined in [1]. It also provides a posterior distribution for the expression of each gene. Moreover, BGX can take into account probe affinity effects from probe sequence information where available. The package employs a novel adaptive Markov chain Monte Carlo (MCMC) algorithm that raises considerably the efficiency with which the posterior distributions are sampled from. Finally, BGX incorporates various ways to analyse the results, such as ranking genes by expression level as well as statistically based methods for estimating the amount of up and down regulated genes between two conditions. CONCLUSIONS: BGX performs well relative to other widely used methods at estimating expression levels and fold changes. It has the advantage that it provides a measure of uncertainty for its estimates. BGX includes various analysis functions to visualise and exploit the rich output that is produced by the Bayesian model. [Abstract/Link to Full Text]

Caragea C, Sinapov J, Silvescu A, Dobbs D, Honavar V
Glycosylation site prediction using ensembles of Support Vector Machine classifiers.
BMC Bioinformatics. 2007 Nov 9;8(1):438.
ABSTRACT: BACKGROUND: Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and subcellular localization, to ligand recognition and cell-cell interactions. Experimental identification of glycosylation sites is expensive and laborious. Hence, there is significant interest in the development of computational methods for reliable prediction of glycosylation sites from amino acid sequences. RESULTS: We explore machine learning methods for training classifiers to predict the amino acid residues that are likely to be glycosylated using information derived from the target amino acid residue and its sequence neighbors. We compare the peformance of Support Vector Machine classifiers and ensembles of Support Vector Machine classifers trained on a dataset of experimentally determined N-linked, O-linked, and C-linked glycosylation sites extracted from O-GlycBase version 6.00, a database of 242 proteins from several different species. The results of our experiments show that the ensembles of Support Vector Machine classifiers outperform single Support Vector Machine classifiers on the problem of predicting glycosylation sites in terms of a range of standard measures for comparing the performance of classifiers. The resulting methods have been implemented in EnsembleGly, a web server for glycosylation site prediction. CONCLUSIONS: Ensembles of Support Vector Machine classifiers offer an accurate and reliable approach to automated identification of putative glycosylation sites in glycoprotein sequences. [Abstract/Link to Full Text]

Yu X, Lin J, Zack DJ, Qian J
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.
BMC Bioinformatics. 2007 Nov 9;8(1):437.
ABSTRACT: Background Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation. Results The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding sites of these interacting TFs. We applied this approach to 30 human tissues and identified 6232 putative cis-regulatory modules (CRMs) regulating 2130 tissue-specific genes. Interestingly, some genes appear to be regulated by different CRMs in different tissues. Known regulatory regions are highly enriched in our predicted CRMs. In addition, DNase I hypersensitive sites, which tend to be associated with active regulatory regions, significantly overlap with the predicted CRMs, but not with more conserved regions. We also find that conserved and non-conserved CRMs regulate distinct gene groups. Conserved CRMs control more essential genes and genes involved in fundamental cellular activities such as transcription. In contrast, non-conserved CRMs, in general, regulate more non-essential genes, such as genes related to neural activity. Conclusions These results demonstrate that identifying relevant sets of binding motifs can help in the mapping of DNA regulatory regions, and suggest that non-conserved CRMs play an important role in gene regulation. [Abstract/Link to Full Text]

Yu W, Yesupriya A, Wulf A, Qu J, Khoury MJ, Gwinn M
An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.
BMC Bioinformatics. 2007 Nov 9;8(1):436.
ABSTRACT: BACKGROUND: Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications--Literature Finder and Investigator Browser--as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. RESULTS: Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. CONCLUSIONS: The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field. [Abstract/Link to Full Text]

Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.
BMC Bioinformatics. 2007 Nov 9;8(1):434.
ABSTRACT: BACKGROUND: Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-numbers are today routinely derived from SNP array data, but the proposed algorithms for this task most often disregard the genotype information available from germline cells in paired germline-tumour samples. Including this information may deepen our understanding of the 'true' biological situation e.g. by enabling analysis of allele specific copy numbers. Here we rely on matched germline-tumour samples and have developed a Hidden Markov Model (HMM) to estimate allelic copy-number changes in tumour cells. Further with this approach we are able to estimate the proportion of normal cells in the tumour (mixture proportion). RESULTS: We show that our method is able to recover the underlying copy-number changes in simulated data sets with high accuracy (above 97.71%). Moreover, although the known copy-numbers could be well recovered in simulated cancer samples with more than 70% cancer cells (and less than 30% normal cells), we demonstrate that including the mixture proportion in the HMM increases the accuracy of the method. Finally, the method is tested on HapMap samples and on bladder and prostate cancer samples. CONCLUSIONS: The HMM method developed here uses the genotype calls of germline DNA and the allelic SNP intensities from the tumour DNA to estimate allelic copy-numbers (including changes) in the tumour. It differentiates between different events like uniparental disomy and allelic imbalances. Moreover, the HMM can estimate the mixture proportion, and thus inform about the purity of the tumour sample. [Abstract/Link to Full Text]

Yartseva A, Klaudel H, Devillers R, Kepes F
Incremental and unifying modelling formalism for biological interaction networks.
BMC Bioinformatics. 2007 Nov 8;8(1):433.
ABSTRACT: BACKGROUND: An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems. RESULTS: We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the lambda phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system. CONCLUSIONS: This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way. [Abstract/Link to Full Text]

Gu J, Fu H, Zhang X, Li Y
Identifications of conserved 7-mers in 3-UTRs and microRNAs in Drosophila.
BMC Bioinformatics. 2007 Nov 8;8(1):432.
ABSTRACT: BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5-end of miRNA and the target mRNA 3-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3-UTRs, which are fully complementary to miRNA 5-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the de novo identification of miRNAs by requiring the complete base-pairing between the 5-end of miRNA candidates and the potential seed matches in 3-UTRs. RESULTS: We presented a new method, which combined multiple pairwise conservation information, to identify the frequently-occurred and conserved 7-mers in 3-UTRs. A pairwise conservation score (PCS) was introduced to describe the conservation of all 7-mers in 3-UTRs between any two Drosophila species. Using PCSs computed from 6 pairs of flies, we developed a support vector machine (SVM) classifier ensemble, named Cons-SVM and identified 689 conserved 7-mers including 63 seed matches covering 32 out of 38 known miRNA families in the reference dataset. In the second stage, we searched for 90nt conserved stem-loop regions containing the complementary sequences to the identified 7-mers and used the previously published miRNA prediction software to analyze these stem-loops. We predicted 47 miRNA candidates in the genome-wide screen. CONCLUSIONS: Cons-SVM takes advantage of the independent evolutionary information from the 6 pairs of flies and shows high sensitivity in identifying seed matches in 3-UTRs. Combining the conservation information by the machine learning approach, we finally identified 47 miRNA candidates in D. melanogaster. [Abstract/Link to Full Text]

Liu Q, Dinu I, Adewale AJ, Potter JD, Yasui Y
Comparative evaluation of gene-set analysis methods.
BMC Bioinformatics. 2007 Nov 7;8(1):431.
ABSTRACT: BACKGROUND: Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Buhlmann's recent review, we compared statistical performance of three methods, namely, Global Test, ANCOVA Global Test, and SAM-GS, that test "self-contained null hypotheses" via. subject sampling. The three methods were compared based on a simulation experiment and analyses of three real-world microarray datasets. RESULTS: In the simulation experiment, we found that the use of the asymptotic distribution in the two Global Tests leads to a statistical test with an incorrect size. Specifically, p-values calculated by the scaled chi-square distribution of Global Test and the asymptotic distribution of ANCOVA Global Test are too liberal, while the asymptotic distribution with a quadratic form of the Global Test results in p-values that are too conservative. The two Global Tests with permutation-based inference, however, gave a correct size. While the three methods showed similar power using permutation inference after a proper standardization of gene expression data, SAM-GS showed slightly higher power than the Global Tests. In the analysis of a real-world microarray dataset, the two Global Tests gave markedly different results, compared to SAM-GS, in identifying pathways whose gene expressions are associated with p53 mutation in cancer cell lines. A proper standardization of gene expression variances is necessary for the two Global Tests in order to produce biologically sensible results. After the standardization, the three methods gave very similar biologically-sensible results, with slightly higher statistical significance given by SAM-GS. The three methods gave similar patterns of results in the analysis of the other two microarray datasets. CONCLUSIONS: An appropriate standardization makes the performance of all three methods similar, given the use of permutation-based inference. SAM-GS tends to have slightly higher power in the lower alpha-level region (i.e. gene sets that are of the greatest interest). Global Test and ANCOVA Global Test have the important advantage of being able to analyze continuous and survival phenotypes and to adjust for covariates. A free Microsoft Excel Add-In to perform SAM-GS is available from http://www.ualberta.ca/~yyasui/homepage.html. [Abstract/Link to Full Text]

Kwon YK, Cho KH
Analysis of feedback loops and robustness in network evolution based on boolean models.
BMC Bioinformatics. 2007 Nov 7;8(1):430.
ABSTRACT: BACKGROUND: Many biological networks such as protein-protein interaction networks, signaling networks, and metabolic networks have topological characteristics of a scale-free degree distribution. Preferential attachment has been considered as the most plausible evolutionary growth model to explain this topological property. Although various studies have been undertaken to investigate the structural characteristics of a network obtained using this growth model, its dynamical characteristics have received relatively less attention. RESULTS: In this paper, we focus on the robustness of a network that is acquired during its evolutionary process. Through simulations using Boolean network models, we found that preferential attachment increases the number of coupled feedback loops in the course of network evolution. Whereas, if networks evolve to have more coupled feedback loops rather than following preferential attachment, the resulting networks are more robust than those obtained through preferential attachment, although both of them have similar degree distributions. CONCLUSIONS: The presented analysis demonstrates that coupled feedback loops may play an important role in network evolution to acquire robustness. The result also provides a hint as to why various biological networks have evolved to contain a number of coupled feedback loops. [Abstract/Link to Full Text]

Baumbach J
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
BMC Bioinformatics. 2007 Nov 6;8(1):429.
ABSTRACT: BACKGROUND: Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. RESULTS: Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. CONCLUSIONS: The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at http://www.CoryneRegNet.DE. [Abstract/Link to Full Text]

Gaunt TR, Rodriguez S, Day IN
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'
BMC Bioinformatics. 2007 Nov 2;8(1):428.
ABSTRACT: BACKGROUND: The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequilibrium analysis programs use iteration-based algorithms which substitute an estimate of haplotype frequency into the equation, producing a new estimate which is repeatedly fed back into the equation until the values converge to a maximum likelihood estimate (expectation-maximisation). RESULTS: We present a program, "CubeX", which calculates the biologically possible exact solution(s) and provides estimated haplotype frequencies, D', r;2 and X;2 values for each. CubeX provides a "complete" analysis of haplotype frequencies and linkage disequilibrium for a pair of biallelic markers under situations where sampling variation and genotyping errors distort sample Hardy-Weinberg equilibrium, potentially causing more than one biologically possible solution. We also present an analysis of simulations and real data using the algebraically exact solution, which indicates that under perfect sample Hardy-Weinberg equilibrium there is only one biologically possible solution, but that under other conditions there may be more. CONCLUSIONS: Our analyses demonstrate that lower allele frequencies, lower sample numbers, population stratification and a possible |D'| value of 1 are particularly susceptible to distortion of sample Hardy-Weinberg equilibrium, which has significant implications for calculation of linkage disequilibrium in small sample sizes (eg HapMap) and rarer alleles (eg paucimorphisms, q<0.05) that may have particular disease relevance and require improved approaches for meaningful evaluation. "CubeX" is available online at http://www.oege.org/software/cubex. [Abstract/Link to Full Text]

Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR
Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes.
BMC Bioinformatics. 2007 Nov 2;8(1):427.
ABSTRACT: BACKGROUND: A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. RESULTS: Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV) or ionizing radiation (IR)-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying biological processes affected by IR- and/or UV- induced DNA damage. CONCLUSIONS: EPIG competed with CLICK and performed better than CAST in extracting patterns from simulated data. EPIG extracted more biological informative patterns and co-expressed genes from both C. elegans and IR/UV-treated human fibroblasts. Using Gene Ontology analysis of the genes in the patterns extracted by EPIG, several key biological categories related to p53-dependent cell cycle control were revealed from the IR/UV data. Among them were mitotic cell cycle, DNA replication, DNA repair, cell cycle checkpoint, and G0-like status transition. EPIG can be applied to data sets from a variety of experimental designs. [Abstract/Link to Full Text]

Sherman BT, Huang DW, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.
BMC Bioinformatics. 2007 Nov 2;8(1):426.
ABSTRACT: BACKGROUND: Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. CONCLUSION: The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/ [Abstract/Link to Full Text]

Teichert F, Bastolla U, Porto M
SABERTOOTH: protein structural alignment based on a vectorial structure representation.
BMC Bioinformatics. 2007 Oct 31;8(1):425.
ABSTRACT: BACKGROUND: The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of protein structures. Therefore, instead of manipulating coordinates directly, matrices of inter-atomic distances, sets of vectors between protein backbone atoms, and other reduced representations are used. These decrease the effort of comparing large sets of coordinates, but protein structural alignment still remains computationally expensive. RESULTS: We represent the topology of a protein structure through a structural profile that expresses the global effective connectivity of each residue. We have shown recently that this representation allows explicitly expressing the relationship between protein structure and protein sequence. Based on this very condensed vectorial representation, we develop a structural alignment framework that recognizes structural similarities with accuracy comparable to established alignment tools. Furthermore, our algorithm has favourable scaling of computation time with chain length. Since the algorithm is independent of the details of the structural representation, our framework can be applied to sequence-to-sequence and sequence-to-structure comparison within the same setup, and it is therefore more general than other existing tools. CONCLUSIONS: We show that protein comparison based on a vectorial representation of protein structure performs comparably to established algorithms based on coordinates. The conceptually new approach presented in this publication might assist to unify the view on protein comparison by unifying structure and sequence descriptions in this context. The framework discussed here is implemented in the ;SABERTOOTH' alignment server, freely accessible at http://www.fkp.tu-darmstadt.de/sabertooth/ . [Abstract/Link to Full Text]

Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M
Large-Scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
BMC Bioinformatics. 2007 Oct 31;8(1):424.
ABSTRACT: BACKGROUND: Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web-based tool designed for predicting human CTL epitopes in any given protein. It does so by integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity. At least four other methods have been developed recently that likewise attempt to predict CTL epitopes: EpiJen, MAPPP, MHC-pathway, and WAPP. In order to compare the performance of the methods, objective benchmarks and standardized performance measures are needed. Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods. RESULTS: We define a number of performance measures that can handle the different types of output data from the five methods. We use two evaluation datasets consisting of known HIV CTL epitopes and their source proteins. The source proteins are split into all possible 9mers and except for annotated epitopes; all other 9mers are considered non-epitopes. In the RANK measure, we compare two methods at a time and count how often each of the methods rank the epitope highest. In another measure we find the specificity of the methods at three predefined sensitivities. Lastly, for each method, we calculate the percentage of known epitopes that rank within the 5% peptides with the highest predicted score. CONCLUSIONS: NetCTL-1.2 is demonstrated to have a higher predictive performance than EpiJen, MAPPP, MHC-pathway, and WAPP on all performance measures. The higher performance of NetCTL-1.2 as compared to EpiJen and MHC-pathway is, however, not statistically significant on all measures. In the large-scale benchmark calculation consisting of 216 known HIV epitopes covering all 12 recognized HLA supertypes, the NetCTL-1.2 method was shown to have a sensitivity among the 5% top-scoring peptides above 0.72. On this dataset, the best of the other methods achieved a sensitivity of 0.64. The NetCTL-1.2 method is available at http://www.cbs.dtu.dk/services/NetCTL. All used datasets are available at http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php. [Abstract/Link to Full Text]

Lin J, Wilbur WJ
PubMed related articles: a probabilistic topic-based model for content similarity.
BMC Bioinformatics. 2007 Oct 30;8(1):423.
ABSTRACT: BACKGROUND: We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from term frequencies, modeled as Poisson distributions. Unlike previous probabilistic retrieval models, we do not attempt to estimate relevance---but rather our focus is "relatedness", the probability that a user would want to examine a particular document given known interest in another. We also describe a novel technique for estimating parameters that does not require human relevance judgments; instead, the process is based on the existence of MeSH in MEDLINE. RESULTS: The pmra retrieval model was compared against bm25, a competitive probabilistic model that shares theoretical similarities. Experiments using the test collection from the TREC 2005 genomics track shows a small but statistically significant improvement of pmra over bm25 in terms of precision. CONCLUSIONS: Our experiments suggest that the pmra model provides an effective ranking algorithm for related article search. [Abstract/Link to Full Text]

Lai C, Horlings HH, van de Vijver MM, van Beers EH, Nederlof PM, Wessels LF, Reinders MJ
SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets.
BMC Bioinformatics. 2007 Oct 30;8(1):422.
ABSTRACT: BACKGROUND: Array comparative genome hybridization (aCGH) provides information about genomic aberrations. Alterations in the DNA copy number may cause the cell to malfunction, leading to cancer. Therefore, the identification of DNA amplifications or deletions across tumors may reveal key genes involved in cancer and improve our understanding of the underlying biological processes associated with the disease. RESULTS: We propose a supervised algorithm for the analysis of aCGH data and the identification of regions of chromosomal alteration (SIRAC). We first determine the DNA-probes that are important to distinguish the classes of interest, and then evaluate in a systematic and robust scheme if these relevant DNA-probes are closely located, i.e. form a region of amplification/deletion. SIRAC does not need any preprocessing of the aCGH datasets, and requires only few, intuitive parameters. CONCLUSIONS: We illustrate the features of the algorithm with the use of a simple artificial dataset. The results on two breast cancer datasets show promising outcomes that are in agreement with previous findings, but SIRAC better pinpoints the dissimilarities between the classes of interest. [Abstract/Link to Full Text]

Llaneras F, Pico J
A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient.
BMC Bioinformatics. 2007 Oct 30;8(1):421.
ABSTRACT: BACKGROUND: An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry). Typically this estimation is done under a static point of view. Therefore, the fluxes so obtained are only valid while the environmental conditions and the cell state remain stable. However, estimating the evolution over time of the metabolic fluxes is valuable to investigate the dynamic behaviour of an organism and also to monitor industrial processes. Although Metabolic Flux Analysis can be successively applied with this aim, this approach has two drawbacks: i) sometimes it cannot be used because there is a lack of measurable fluxes, and ii) the uncertainty of experimental measurements cannot be considered. The Flux Balance Analysis could be used instead, but the assumption of optimal behaviour of the organism brings other difficulties. RESULTS: We propose a procedure to estimate the evolution of the metabolic fluxes that is structured as follows: 1) measure the concentrations of extracellular species and biomass, 2) convert this data to measured fluxes and 3) estimate the non-measured fluxes using the Flux Spectrum Approach, a variant of Metabolic Flux Analysis that overcomes the difficulties mentioned above without assuming optimal behaviour. We apply the procedure to a real problem taken from the literature: estimate the metabolic fluxes during a cultivation of CHO cells in batch mode. We show that it provides a reliable and rich estimation of the non-measured fluxes, thanks to considering measurements uncertainty and reversibility constraints. We also demonstrate that this procedure can estimate the non-measured fluxes even when there is a lack of measurable species. In addition, it offers a new method to deal with inconsistency. CONCLUSIONS: This work introduces a procedure to estimate time-varying metabolic fluxes that copes with the insufficiency of measured species and with its intrinsic uncertainty. The procedure can be used as an off-line analysis of previously collected data, providing an insight into the dynamic behaviour of the organism. It can be also profitable to the on-line monitoring of a running process, mitigating the traditional lack of reliable on-line sensors in industrial environments. [Abstract/Link to Full Text]

Shen YQ, Burger G
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools.
BMC Bioinformatics. 2007 Oct 29;8(1):420.
ABSTRACT: BACKGROUND: Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for a given protein. Since the individual tools each have particular strengths, we set out to integrate them in a way that optimally exploits their potential. The method we present here is applicable to various subcellular locations, but tailored for predicting whether or not a protein is localized in mitochondria. Knowledge of the mitochondrial proteome is relevant to understanding the role of this organelle in global cellular processes. RESULTS: In order to develop a method for enhanced prediction of subcellular localization, we integrated the outputs of available localization prediction tools by several strategies, and tested the performance of each strategy with known mitochondrial proteins. The accuracy obtained (up to 92%) surpasses by far the individual tools. The method of integration proved crucial to the performance. For the prediction of mitochondrion-located proteins, integration via a two-layer decision tree clearly outperforms simpler methods, as it allows emphasis of biologically relevant features such as the mitochondrial targeting peptide and transmembrane domains. CONCLUSIONS: We developed an approach that enhances the prediction accuracy of mitochondrial proteins by uniting the strength of specialized tools. The combination of machine-learning based integration with biological expert knowledge leads to improved performance. This approach also alleviates the conundrum of how to choose between conflicting predictions. Our approach is easy to implement, and applicable to predicting subcellular locations other than mitochondria, as well as other biological features. For a trial of our approach, we provide a webservice for mitochondrial protein prediction (named YimLOC), which can be accessed through the AnaBench suite at http://anabench.bcm.umontreal.ca/anabench/. The source code is provided in the additional file 2. [Abstract/Link to Full Text]

Robinson MD, De Souza DP, Wai Keen W, Saunders EC, McConville MJ, Speed TP, Likic VA
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.
BMC Bioinformatics. 2007 Oct 29;8(1):419.
ABSTRACT: BACKGROUND: Gas chromatography-mass spectrometry (GC-MS) is a robust platform for profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. RESULTS: A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. CONCLUSIONS: We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed. [Abstract/Link to Full Text]

Larsson E, Lindahl P, Mostad P
HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing.
BMC Bioinformatics. 2007 Oct 28;8(1):418.
ABSTRACT: BACKGROUND: Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence, cis-regulatory elements often colocalize in clusters termed cis-regulatory modules. These may have requirements on organizational features such as spacing, order and helical phasing (periodic spacing) between binding sites. Due to the turning of the DNA helix, a small modification of the distance between a pair of sites may sometimes drastically disrupt function, while insertion of a full helical turn of DNA (10-11 bp) between cis elements may cause functionality to be restored. Recently, de novo motif discovery methods which incorporate organizational properties such as colocalization and order preferences have been developed, but there are no tools which incorporate periodic spacing into the model. RESULTS: We have developed a web based motif discovery tool, HeliCis, which features a flexible model that allows de novo detection of motifs with periodic spacing. Depending on the parameter settings it may also be used for discovering colocalized motifs without periodicity or motifs separated by a fixed gap of known or unknown length. We show on simulated data that it can efficiently capture the synergistic effects of colocalization and periodic spacing to improve detection of weak DNA motifs. It provides a simple to use web interface which interactively visualizes the current settings and thereby makes it easy to understand the parameters and the model structure. CONCLUSIONS: HeliCis provides simple and efficient de novo discovery of colocalized DNA motif pairs, with or without periodic spacing. Our evaluations show that it can detect weak periodic patterns which are not easily discovered using a sequential approach, i.e. first finding the binding sites and second analyzing the properties of their pairwise distances. [Abstract/Link to Full Text]

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Recent Articles in Biomedical Digital Libraries

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No recent articles are currently available.

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Recent Articles in Cell Biology Education

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Watters C
Video views and reviews: mitosis, microfibers, and motility.
Cell Biol Educ. 2004;3(2):81-4. [Abstract/Link to Full Text]

Alberts B, Labov JB
From the National Academies: teaching the science of evolution.
Cell Biol Educ. 2004;3(2):75-80. [Abstract/Link to Full Text]

Tanner K, Allen D
Approaches to biology teaching and learning: from assays to assessments--on collecting evidence in science teaching.
Cell Biol Educ. 2004;3(2):69-74. [Abstract/Link to Full Text]

DiBartolomeis SM, Moné JP
Apoptosis: a four-week laboratory investigation for advanced molecular and cellular biology students.
Cell Biol Educ. 2003;2(4):275-95.
Over the past decade, apoptosis has emerged as an important field of study central to ongoing research in many diverse fields, from developmental biology to cancer research. Apoptosis proceeds by a highly coordinated series of events that includes enzyme activation, DNA fragmentation, and alterations in plasma membrane permeability. The detection of each of these phenotypic changes is accessible to advanced undergraduate cell and molecular biology students. We describe a 4-week laboratory sequence that integrates cell culture, fluorescence microscopy, DNA isolation and analysis, and western blotting (immunoblotting) to follow apoptosis in cultured human cells. Students working in teams chemically induce apoptosis, and harvest, process, and analyze cells, using their data to determine the order of events during apoptosis. We, as instructors, expose the students to an environment closely simulating what they would encounter in an active cell or molecular biology research laboratory by having students coordinate and perform multiple tasks simultaneously and by having them experience experimental design using current literature, data interpretation, and analysis to answer a single question. Students are assessed by examination of laboratory notebooks for completeness of experimental protocols and analysis of results and for completion of an assignment that includes questions pertaining to data interpretation and apoptosis. [Abstract/Link to Full Text]

Brill G, Yarden A
Learning biology through research papers: a stimulus for question-asking by high-school students.
Cell Biol Educ. 2003;2(4):266-74.
Question-asking is a basic skill, required for the development of scientific thinking. However, the way in which science lessons are conducted does not usually stimulate question-asking by students. To make students more familiar with the scientific inquiry process, we developed a curriculum in developmental biology based on research papers suitable for high-school students. Since a scientific paper poses a research question, demonstrates the events that led to the answer, and poses new questions, we attempted to examine the effect of studying through research papers on students' ability to pose questions. Students were asked before, during, and after instruction what they found interesting to know about embryonic development. In addition, we monitored students' questions, which were asked orally during the lessons. Questions were scored according to three categories: properties, comparisons, and causal relationships. We found that before learning through research papers, students tend to ask only questions of the properties category. In contrast, students tend to pose questions that reveal a higher level of thinking and uniqueness during or following instruction with research papers. This change was not observed during or following instruction with a textbook. We suggest that learning through research papers may be one way to provide a stimulus for question-asking by high-school students and results in higher thinking levels and uniqueness. [Abstract/Link to Full Text]

Sander U, Kerlen G, Steinke M, Huk T, Floto C
Evaluation of two CD-ROMs from a series on cell biology.
Cell Biol Educ. 2003;2(4):256-65.
Two CD-ROMs from a series dealing with various major aspects of cell biology are evaluated in this paper using quantitative and qualitative approaches. The findings delimit similarities and differences of the two CD-ROMs and shed light on how the programs could be used in the learning process and how they should not be. The overall impression, as well as the graphical and technical features, received a predominantly good rating. The defined target groups were reached (e.g., students in secondary schools), different learning approaches were supported (e.g., discovery and autonomous learning), the CD-ROMs' usability was assessed as being easy and intuitive, and the majority of the evaluators were satisfied with the level of interactivity. Navigational problems encountered in CD-ROM 1 were overcome by a successful implementation of new navigational functions in CD-ROM 2. Most students found the CD-ROM to be a suitable complement to, or an extension of, their lessons. We conclude that many, but not all of the requirements for the various stages of the learning process could be satisfied with the existing CD-ROMs. The requirements not met are discussed to obtain insights that could help to improve the production of multimedia learning material. The use of quantitative and qualitative approaches in the evaluation of learning modules is discussed, as the study began by collecting and analyzing anecdotal reviews and was then extended to include a qualitative evaluation. [Abstract/Link to Full Text]

Mulnix AB
Investigations of protein structure and function using the scientific literature: an assignment for an undergraduate cell physiology course.
Cell Biol Educ. 2003;2(4):248-55.
Undergraduate biology curricula are being modified to model and teach the activities of scientists better. The assignment described here, one that investigates protein structure and function, was designed for use in a sophomore-level cell physiology course at Earlham College. Students work in small groups to read and present in poster format on the content of a single research article reporting on the structure and/or function of a protein. Goals of the assignment include highlighting the interdependence of protein structure and function; asking students to review, integrate, and apply previously acquired knowledge; and helping students see protein structure/function in a context larger than cell physiology. The assignment also is designed to build skills in reading scientific literature, oral and written communication, and collaboration among peers. Assessment of student perceptions of the assignment in two separate offerings indicates that the project successfully achieves these goals. Data specifically show that students relied heavily on their peers to understand their article. The assignment was also shown to require students to read articles more carefully than previously. In addition, the data suggest that the assignment could be modified and used successfully in other courses and at other institutions. [Abstract/Link to Full Text]

Honts JE
Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculum.
Cell Biol Educ. 2003;2(4):233-47.
Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. [Abstract/Link to Full Text]

Wolyniak MJ
Balancing teaching and research experiences in doctoral training programs: lessons for the future educator.
Cell Biol Educ. 2003;2(4):228-32.
While a variety of alternative careers has emerged for Ph.D. life scientists in industry, business, law, and education in the past two decades, the structure of doctoral training programs in many cases does not provide the flexibility necessary to pursue career experiences not directly related to a research emphasis. Here I describe my efforts to supplement my traditional doctoral research training with independent teaching experiences that have allowed me to prepare myself for a career that combines both into a combined educational program. I describe the issues I have come across in finding and taking part in these endeavors, how these issues have affected my work in pursuing my Ph.D., and how my experiences translate into my hopes for a future education-based career in molecular and cell biology. [Abstract/Link to Full Text]

Kennedy D
Is bio2010 the right blueprint for the biology of the future?
Cell Biol Educ. 2003;2(4):224-7. [Abstract/Link to Full Text]

Gentile J
Is bio2010 the right blueprint for the biology of the future?
Cell Biol Educ. 2003;2(4):224-7. [Abstract/Link to Full Text]

Watters C
Video views and reviews.
Cell Biol Educ. 2003;2(4):210-3. [Abstract/Link to Full Text]

Wood W, Gentile J
Meeting report: the first National Academies Summer Institute for Undergraduate Education in Biology.
Cell Biol Educ. 2003;2(4):207-9. [Abstract/Link to Full Text]

Suitts S
Fueling education reform: historically black colleges are meeting a national science imperative.
Cell Biol Educ. 2003;2(4):205-6. [Abstract/Link to Full Text]

Labov JB
From the National Academies.
Cell Biol Educ. 2003;2(4):202-4. [Abstract/Link to Full Text]

Tanner KD, Chatman L, Allen D
Approaches to biology teaching and learning: science teaching and learning across the school--university divide--cultivating conversations through scientist-teacher partnerships.
Cell Biol Educ. 2003;2(4):195-201. [Abstract/Link to Full Text]

Blystone R
WWW.Cell Biology Education.
Cell Biol Educ. 2003;2(1):14-5. [Abstract/Link to Full Text]

Watters CD
Video views and reviews.
Cell Biol Educ. 2003;2(1):9-13. [Abstract/Link to Full Text]

Kitchen E, Bell JD, Reeve S, Sudweeks RR, Bradshaw WS
Teaching cell biology in the large-enrollment classroom: methods to promote analytical thinking and assessment of their effectiveness.
Cell Biol Educ. 2003;2(3):180-94.
A large-enrollment, undergraduate cellular biology lecture course is described whose primary goal is to help students acquire skill in the interpretation of experimental data. The premise is that this kind of analytical reasoning is not intuitive for most people and, in the absence of hands-on laboratory experience, will not readily develop unless instructional methods and examinations specifically designed to foster it are employed. Promoting scientific thinking forces changes in the roles of both teacher and student. We describe didactic strategies that include directed practice of data analysis in a workshop format, active learning through verbal and written communication, visualization of abstractions diagrammatically, and the use of ancillary small-group mentoring sessions with faculty. The implications for a teacher in reducing the breadth and depth of coverage, becoming coach instead of lecturer, and helping students to diagnose cognitive weaknesses are discussed. In order to determine the efficacy of these strategies, we have carefully monitored student performance and have demonstrated a large gain in a pre- and posttest comparison of scores on identical problems, improved test scores on several successive midterm examinations when the statistical analysis accounts for the relative difficulty of the problems, and higher scores in comparison to students in a control course whose objective was information transfer, not acquisition of reasoning skills. A novel analytical index (student mobility profile) is described that demonstrates that this improvement was not random, but a systematic outcome of the teaching/learning strategies employed. An assessment of attitudes showed that, in spite of finding it difficult, students endorse this approach to learning, but also favor curricular changes that would introduce an analytical emphasis earlier in their training. [Abstract/Link to Full Text]

Stevens R, Palacio-Cayetano J
Design and performance frameworks for constructing problem-solving simulations.
Cell Biol Educ. 2003;2(3):162-79.
Rapid advancements in hardware, software, and connectivity are helping to shorten the times needed to develop computer simulations for science education. These advancements, however, have not been accompanied by corresponding theories of how best to design and use these technologies for teaching, learning, and testing. Such design frameworks ideally would be guided less by the strengths/limitations of the presentation media and more by cognitive analyses detailing the goals of the tasks, the needs and abilities of students, and the resulting decision outcomes needed by different audiences. This article describes a problem-solving environment and associated theoretical framework for investigating how students select and use strategies as they solve complex science problems. A framework is first described for designing on-line problem spaces that highlights issues of content, scale, cognitive complexity, and constraints. While this framework was originally designed for medical education, it has proven robust and has been successfully applied to learning environments from elementary school through medical school. Next, a similar framework is detailed for collecting student performance and progress data that can provide evidence of students' strategic thinking and that could potentially be used to accelerate student progress. Finally, experimental validation data are presented that link strategy selection and use with other metrics of scientific reasoning and student achievement. [Abstract/Link to Full Text]

Klymkowsky MW, Garvin-Doxas K, Zeilik M
Bioliteracy and teaching efficacy: what biologists can learn from physicists.
Cell Biol Educ. 2003;2(3):155-61.
The introduction of the Force Concept Inventory (FCI) by David Hestenes and colleagues in 1992 produced a remarkable impact within the community of physics teachers. An instrument to measure student comprehension of the Newtonian concept of force, the FCI demonstrates that active learning leads to far superior student conceptual learning than didactic lectures. Compared to a working knowledge of physics, biological literacy and illiteracy have an even more direct, dramatic, and personal impact. They shape public research and reproductive health policies, the acceptance or rejection of technological advances, such as vaccinations, genetically modified foods and gene therapies, and, on the personal front, the reasoned evaluation of product claims and lifestyle choices. While many students take biology courses at both the secondary and the college levels, there is little in the way of reliable and valid assessment of the effectiveness of biological education. This lack has important consequences in terms of general bioliteracy and, in turn, for our society. Here we describe the beginning of a community effort to define what a bioliterate person needs to know and to develop, validate, and disseminate a tiered series of instruments collectively known as the Biology Concept Inventory (BCI), which accurately measures student comprehension of concepts in introductory, genetic, molecular, cell, and developmental biology. The BCI should serve as a lever for moving our current educational system in a direction that delivers a deeper conceptual understanding of the fundamental ideas upon which biology and biomedical sciences are based. [Abstract/Link to Full Text]

Labov JB
Education at the National Academies.
Cell Biol Educ. 2003;2(3):144-7. [Abstract/Link to Full Text]

Blystone R
WWW.Cell Biology Education.
Cell Biol Educ. 2003;2(3):141-3. [Abstract/Link to Full Text]

Watters C
Video views and reviews.
Cell Biol Educ. 2003;2(3):137-40. [Abstract/Link to Full Text]

Allen D, Tanner K
Approaches to cell biology teaching: mapping the journey-concept maps as signposts of developing knowledge structures.
Cell Biol Educ. 2003;2(3):133-6. [Abstract/Link to Full Text]

Novak JD
The promise of new ideas and new technology for improving teaching and learning.
Cell Biol Educ. 2003;2(2):122-32.
There have been enormous advances in our understanding of human learning in the past three decades. There have also been important advances in our understanding of the nature of knowledge and new knowledge creation. These advances, when combined with the explosive development of the Internet and other technologies, permit advances in educational practices at least as important as the invention of the printing press in 1460. We have built on the cognitive learning theory of David Ausubel and various sources of new ideas on epistemology. Our research program has focused on understanding meaningful learning and on developing better methods to achieve such learning and to assess progress in meaningful learning. The concept map tool developed in our program has proved to be highly effective both in promoting meaningful learning and in assessing learning outcomes. Concept mapping strategies are also proving powerful for eliciting, capturing, and archiving knowledge of experts and organizations. New technology for creating concept maps developed at the University of West Florida permits easier and better concept map construction, thus facilitating learning, knowledge capture, and local or distance creation and sharing of structured knowledge, especially when utilized with the Internet. A huge gap exists between what we now know to improve learning and use of knowledge and the practices currently in place in most schools and corporations. There are promising projects in progress that may help to achieve accelerated advances. These include projects in schools at all educational levels, including projects in Colombia, Costa Rica, Italy, Spain, and the United States, and collaborative projects with corporate organizations and distance learning projects. Results to date have been encouraging and suggest that we may be moving from the lag phase of educational innovation to a phase of exponential growth. [Abstract/Link to Full Text]

Matsui J, Liu R, Kane CM
Evaluating a science diversity program at UC Berkeley: more questions than answers.
Cell Biol Educ. 2003;2(2):117-21.
For the past three decades, much attention has been focused on developing diversity programs designed to improve the academic success of underrepresented minorities, primarily in mathematics, science, and engineering. However, ethnic minorities remain underrepresented in science majors and careers. Over the last 10 years, the Biology Scholars Program (BSP), a diversity program at the University of California (UC), Berkeley, has worked to increase the participation and success of students majoring in the biological sciences. A quantitative comparison of students in and out of the program indicates that students in BSP graduate with a degree in biology at significantly higher rates than students not in BSP regardless of race/ethnicity. Furthermore, students who are in BSP have statistically lower high school grade point averages (GPAs) and Scholastic Achievement Test (SAT) scores than students not in BSP. African-American and Hispanic students who join BSP graduate with significantly higher UC Berkeley biology GPAs than non-BSP African-American and Hispanic students, respectively. Majority (Asian and White) students in BSP graduate with statistically similar UC GPAs despite having lower SAT scores than non-BSP majority students. Although BSP students are more successful in completing a biology degree than non-program members, the results raise a series of questions about why the program works and for whom. [Abstract/Link to Full Text]

Wood WB
Inquiry-based undergraduate teaching in the life sciences at large research universities: a perspective on the Boyer Commission Report.
Cell Biol Educ. 2003;2(2):112-6.
The 1998 Boyer Commission Report advocated improvement of undergraduate education at large research universities through large-scale participation of undergraduates in the universities' research mission. At a recent conference sponsored by the Reinvention Center, which is dedicated to furthering the goals of the Boyer Commission, participants discussed progress toward these goals and recommendations for future action. A breakout group representing the life sciences concluded that independent research experience for every undergraduate may not be feasible or desirable but that transformation of lecture courses to more inquiry-based and interactive formats can effectively further the Commission's goals. [Abstract/Link to Full Text]

Campbell AM
Public access for teaching genomics, proteomics, and bioinformatics.
Cell Biol Educ. 2003;2(2):98-111.
When the human genome project was conceived, its leaders wanted all researchers to have equal access to the data and associated research tools. Their vision of equal access provides an unprecedented teaching opportunity. Teachers and students have free access to the same databases that researchers are using. Furthermore, the recent movement to deliver scientific publications freely has presented a second source of current information for teaching. I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals. These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics. In this essay, I outline how these fields are especially well suited for inclusion in the undergraduate curriculum. Assessment data indicate that my students were able to utilize online information to achieve the educational goals of the course and that the experience positively influenced their perceptions of how they might contribute to biology. [Abstract/Link to Full Text]

Rose M
The awesome power of genetics education.
Cell Biol Educ. 2003;2(2):96-7. [Abstract/Link to Full Text]

Goodenough U
Experiencing cellularity.
Cell Biol Educ. 2003;2(2):94-5. [Abstract/Link to Full Text]

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Recent Articles in BMC Medical Informatics and Decision Making

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Sutton DR, Taylor P, Earle K
Evaluation of PROforma as a language for implementing medical guidelines in a practical context.
BMC Med Inform Decis Mak. 2006;620.
BACKGROUND: PROforma is one of several languages that allow clinical guidelines to be expressed in a computer-interpretable manner. How these languages should be compared, and what requirements they should meet, are questions that are being actively addressed by a community of interested researchers. METHODS: We have developed a system to allow hypertensive patients to be monitored and assessed without visiting their GPs (except in the most urgent cases). Blood pressure measurements are performed at the patients' pharmacies and a web-based system, created using PROforma, makes recommendations for continued monitoring, and/or changes in medication. The recommendations and measurements are transmitted electronically to a practitioner with authority to issue and change prescriptions. We evaluated the use of PROforma during the knowledge acquisition, analysis, design and implementation of this system. The analysis focuses on the logical adequacy, heuristic power, notational convenience, and explanation support provided by the PROforma language. RESULTS: PROforma proved adequate as a language for the implementation of the clinical reasoning required by this project. However a lack of notational convenience led us to use UML activity diagrams, rather than PROforma process descriptions, to create the models that were used during the knowledge acquisition and analysis phases of the project. These UML diagrams were translated into PROforma during the implementation of the project. CONCLUSION: The experience accumulated during this study highlighted the importance of structure preserving design, that is to say that the models used in the design and implementation of a knowledge-based system should be structurally similar to those created during knowledge acquisition and analysis. Ideally the same language should be used for all of these models. This means that great importance has to be attached to the notational convenience of these languages, by which we mean the ease with which they can be read, written, and understood by human beings. The importance of notational convenience arises from the fact that a language used during knowledge acquisition and analysis must be intelligible to the potential users of a system, and to the domain experts who provide the knowledge that will be used in its construction. [Abstract/Link to Full Text]

Cuticchia AJ, Cooley PC, Hall RD, Qin Y
NIDDK data repository: a central collection of clinical trial data.
BMC Med Inform Decis Mak. 2006;619.
BACKGROUND: The National Institute of Diabetes and Digestive and Kidney Diseases have established central repositories for the collection of DNA, biological samples, and clinical data to be catalogued at a single site. Here we present an overview of the site which stores the clinical data and links to biospecimens. DESCRIPTION: The NIDDK Data repository is a web-enabled resource cataloguing clinical trial data and supporting information from NIDDK supported studies. The Data Repository allows for the co-location of multiple electronic datasets that were created as part of clinical investigations. The Data Repository does not serve the role of a Data Coordinating Center, but rather as a warehouse for the clinical findings once the trials have been completed. Because both biological and genetic samples are collected from many of the studies, a data management system for the cataloguing and retrieval of samples was developed. CONCLUSION: The Data Repository provides a unique resource for researchers in the clinical areas supported by NIDDK. In addition to providing a warehouse of data, Data Repository staff work with the users to educate them on the datasets as well as assist them in the acquisition of multiple data sets for cross-study analysis. Unlike the majority of biological databases, the Data Repository acts both as a catalogue for data, biosamples, and genetic materials and as a central processing point for the requests for all biospecimens. Due to regulations on the use of clinical data, the ultimate release of that data is governed under NIDDK data release policies. The Data Repository serves as the conduit for such requests. [Abstract/Link to Full Text]

Florentinus SR, Souverein PC, Griens FA, Groenewegen PP, Leufkens HG, Heerdink ER
Linking community pharmacy dispensing data to prescribing data of general practitioners.
BMC Med Inform Decis Mak. 2006;618.
BACKGROUND: Databases are frequently used for pharmacoepidemiological research. However, most of these databases consist either of prescribing, dispensing or administrative data and therefore lack insight in the interaction between the several health professionals around the patient. METHODS: To determine the success rate of linking records from the dispensing database of the Foundation for Pharmaceutical Statistics to the prescribing database of the second Dutch national survey of general practice, conducted by NIVEL (Netherlands Institute for Health Services Research), a deterministic record linkage approach was used with patient and prescription characteristics as matching variables between the two databases. RESULTS: The catchment area included 123 community pharmacies, 90 GP practices and approximately 170,000 unique patients. Overall 110,102 (64.8%) unique patients were linked using the matching variables patient's gender, year of birth, the 4-digit part of the postal code, date of dispensing/prescribing and ATC-code. The final database contains of the 110,102 both prescribing data from 83 GP practices and dispensing data of 112 community pharmacies. CONCLUSION: This study shows that linkage of dispensing to prescribing data is feasible with a combination of patient characteristics, such as gender, year of birth and postal code, and prescription characteristics like prescription date and ATC-code. We obtained a linkage proportion of 64.8% resulting in complete prescribing and dispensing history of 110,102 patients. This offers an opportunity to gain insight in the mechanisms and factors influencing drug utilisation in general practice. [Abstract/Link to Full Text]

Lagoe RJ, Westert GP
Community wide electronic distribution of summary health care utilization data.
BMC Med Inform Decis Mak. 2006;617.
BACKGROUND: In recent years, the use of digital technology has supported widespread sharing of electronic health care data. Although this approach holds considerable promise, it promises to be a complicated and expensive undertaking. This study described the development and implementation of a community wide system for electronic sharing of summary health care utilization data. METHODS: The development of the community wide data system focused on the following objectives: ongoing monitoring of the health care system, evaluation of community wide individual provider initiatives, identification and development of new initiatives. The system focused on the sharing of data related to hospital acute care, emergency medical services, long term care, and mental health. It was based on the daily distribution of reports among all health care providers related to these services. RESULTS: The development of the summary reports concerning health care utilization produced a system wide view of health care in Syracuse, New York on a daily basis. It was not possible to isolate the results of these reports because of the impact of specific projects and other factors. At the same time, the reports were associated with reduction of hospital inpatient stays, improvement of access to hospital emergency departments, reductions in stays for patients discharged to nursing homes, and increased access of mental health patients to hospital inpatient units. CONCLUSION: The implementation of the system demonstrated that summary electronic utilization data could provide daily information that would support the improvement of health care outcomes and efficiency. This approach could be implemented in a simple, direct manner with minimal expenses. [Abstract/Link to Full Text]

Schwartz A, Millam G
A web-based library consult service for evidence-based medicine: Technical development.
BMC Med Inform Decis Mak. 2006;616.
BACKGROUND: Incorporating evidence based medicine (EBM) into clinical practice requires clinicians to learn to efficiently gain access to clinical evidence and effectively appraise its validity. Even using current electronic systems, selecting literature-based data to solve a single patient-related problem can require more time than practicing physicians or residents can spare. Clinical librarians, as informationists, are uniquely suited to assist physicians in this endeavor. RESULTS: To improve support for evidence-based practice, we have developed a web-based EBM library consult service application (LCS). Librarians use the LCS system to provide full text evidence-based literature with critical appraisal in response to a clinical question asked by a remote physician. LCS uses an entirely Free/Open Source Software platform and will be released under a Free Software license. In the first year of the LCS project, the software was successfully developed and a reference implementation put into active use. Two years of evaluation of the clinical, educational, and attitudinal impact on physician-users and librarian staff are underway, and expected to lead to refinement and wide dissemination of the system. CONCLUSION: A web-based EBM library consult model may provide a useful way for informationists to assist clinicians, and is feasible to implement. [Abstract/Link to Full Text]

Macario A, Chow JL, Dexter F
A Markov computer simulation model of the economics of neuromuscular blockade in patients with acute respiratory distress syndrome.
BMC Med Inform Decis Mak. 2006;615.
BACKGROUND: Management of acute respiratory distress syndrome (ARDS) in the intensive care unit (ICU) is clinically challenging and costly. Neuromuscular blocking agents may facilitate mechanical ventilation and improve oxygenation, but may result in prolonged recovery of neuromuscular function and acute quadriplegic myopathy syndrome (AQMS). The goal of this study was to address a hypothetical question via computer modeling: Would a reduction in intubation time of 6 hours and/or a reduction in the incidence of AQMS from 25% to 21%, provide enough benefit to justify a drug with an additional expenditure of $267 (the difference in acquisition cost between a generic and brand name neuromuscular blocker)? METHODS: The base case was a 55 year-old man in the ICU with ARDS who receives neuromuscular blockade for 3.5 days. A Markov model was designed with hypothetical patients in 1 of 6 mutually exclusive health states: ICU-intubated, ICU-extubated, hospital ward, long-term care, home, or death, over a period of 6 months. The net monetary benefit was computed. RESULTS: Our computer simulation modeling predicted the mean cost for ARDS patients receiving standard care for 6 months to be $62,238 (5%-95% percentiles $42,259-$83,766), with an overall 6-month mortality of 39%. Assuming a ceiling ratio of $35,000, even if a drug (that cost $267 more) hypothetically reduced AQMS from 25% to 21% and decreased intubation time by 6 hours, the net monetary benefit would only equal $137. CONCLUSION: ARDS patients receiving a neuromuscular blocker have a high mortality, and unpredictable outcome, which results in large variability in costs per case. If a patient dies, there is no benefit to any drug that reduces ventilation time or AQMS incidence. A prospective, randomized pharmacoeconomic study of neuromuscular blockers in the ICU to asses AQMS or intubation times is impractical because of the highly variable clinical course of patients with ARDS. [Abstract/Link to Full Text]

Singh S, Dolan JG, Centor RM
Optimal management of adults with pharyngitis--a multi-criteria decision analysis.
BMC Med Inform Decis Mak. 2006;614.
BACKGROUND: Current practice guidelines offer different management recommendations for adults presenting with a sore throat. The key issue is the extent to which the clinical likelihood of a Group A streptococcal infection should affect patient management decisions. To help resolve this issue, we conducted a multi-criteria decision analysis using the Analytic Hierarchy Process. METHODS: We defined optimal patient management using four criteria: 1) reduce symptom duration; 2) prevent infectious complications, local and systemic; 3) minimize antibiotic side effects, minor and anaphylaxis; and 4) achieve prudent use of antibiotics, avoiding both over-use and under-use. In our baseline analysis we assumed that all criteria and sub-criteria were equally important except minimizing anaphylactic side effects, which was judged very strongly more important than minimizing minor side effects. Management strategies included: a) No test, No treatment; b) Perform a rapid strep test and treat if positive; c) Perform a throat culture and treat if positive; d) Perform a rapid strep test and treat if positive; if negative obtain a throat culture and treat if positive; and e) treat without further tests. We defined four scenarios based on the likelihood of group A streptococcal infection using the Centor score, a well-validated clinical index. Published data were used to estimate the likelihoods of clinical outcomes and the test operating characteristics of the rapid strep test and throat culture for identifying group A streptococcal infections. RESULTS: Using the baseline assumptions, no testing and no treatment is preferred for patients with Centor scores of 1; two strategies--culture and treat if positive and rapid strep with culture of negative results--are equally preferable for patients with Centor scores of 2; and rapid strep with culture of negative results is the best management strategy for patients with Centor scores 3 or 4. These results are sensitive to the priorities assigned to the decision criteria, especially avoiding over-use versus under-use of antibiotics, and the population prevalence of Group A streptococcal pharyngitis. CONCLUSION: The optimal clinical management of adults with sore throat depends on both the clinical probability of a group A streptococcal infection and clinical judgments that incorporate individual patient and practice circumstances. [Abstract/Link to Full Text]

Siadaty MS, Knaus WA
Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method.
BMC Med Inform Decis Mak. 2006;613.
BACKGROUND: Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness), hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones. METHODS: The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance. RESULTS: We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores. CONCLUSION: The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand. The method automates the acquisition of knowledge, thus reducing dependence on the knowledge elicited from human expert, which is usually a rate-limiting step. [Abstract/Link to Full Text]

Beckwith BA, Mahaadevan R, Balis UJ, Kuo F
Development and evaluation of an open source software tool for deidentification of pathology reports.
BMC Med Inform Decis Mak. 2006;612.
BACKGROUND: Electronic medical records, including pathology reports, are often used for research purposes. Currently, there are few programs freely available to remove identifiers while leaving the remainder of the pathology report text intact. Our goal was to produce an open source, Health Insurance Portability and Accountability Act (HIPAA) compliant, deidentification tool tailored for pathology reports. We designed a three-step process for removing potential identifiers. The first step is to look for identifiers known to be associated with the patient, such as name, medical record number, pathology accession number, etc. Next, a series of pattern matches look for predictable patterns likely to represent identifying data; such as dates, accession numbers and addresses as well as patient, institution and physician names. Finally, individual words are compared with a database of proper names and geographic locations. Pathology reports from three institutions were used to design and test the algorithms. The software was improved iteratively on training sets until it exhibited good performance. 1800 new pathology reports were then processed. Each report was reviewed manually before and after deidentification to catalog all identifiers and note those that were not removed. RESULTS: 1254 (69.7 %) of 1800 pathology reports contained identifiers in the body of the report. 3439 (98.3%) of 3499 unique identifiers in the test set were removed. Only 19 HIPAA-specified identifiers (mainly consult accession numbers and misspelled names) were missed. Of 41 non-HIPAA identifiers missed, the majority were partial institutional addresses and ages. Outside consultation case reports typically contain numerous identifiers and were the most challenging to deidentify comprehensively. There was variation in performance among reports from the three institutions, highlighting the need for site-specific customization, which is easily accomplished with our tool. CONCLUSION: We have demonstrated that it is possible to create an open-source deidentification program which performs well on free-text pathology reports. [Abstract/Link to Full Text]

Mueller M, Wagner CL, Annibale DJ, Knapp RG, Hulsey TC, Almeida JS
Parameter selection for and implementation of a web-based decision-support tool to predict extubation outcome in premature infants.
BMC Med Inform Decis Mak. 2006;611.
BACKGROUND: Approximately 30% of intubated preterm infants with respiratory distress syndrome (RDS) will fail attempted extubation, requiring reintubation and mechanical ventilation. Although ventilator technology and monitoring of premature infants have improved over time, optimal extubation remains challenging. Furthermore, extubation decisions for premature infants require complex informational processing, techniques implicitly learned through clinical practice. Computer-aided decision-support tools would benefit inexperienced clinicians, especially during peak neonatal intensive care unit (NICU) census. METHODS: A five-step procedure was developed to identify predictive variables. Clinical expert (CE) thought processes comprised one model. Variables from that model were used to develop two mathematical models for the decision-support tool: an artificial neural network (ANN) and a multivariate logistic regression model (MLR). The ranking of the variables in the three models was compared using the Wilcoxon Signed Rank Test. The best performing model was used in a web-based decision-support tool with a user interface implemented in Hypertext Markup Language (HTML) and the mathematical model employing the ANN. RESULTS: CEs identified 51 potentially predictive variables for extubation decisions for an infant on mechanical ventilation. Comparisons of the three models showed a significant difference between the ANN and the CE (p = 0.0006). Of the original 51 potentially predictive variables, the 13 most predictive variables were used to develop an ANN as a web-based decision-tool. The ANN processes user-provided data and returns the prediction 0-1 score and a novelty index. The user then selects the most appropriate threshold for categorizing the prediction as a success or failure. Furthermore, the novelty index, indicating the similarity of the test case to the training case, allows the user to assess the confidence level of the prediction with regard to how much the new data differ from the data originally used for the development of the prediction tool. CONCLUSION: State-of-the-art, machine-learning methods can be employed for the development of sophisticated tools to aid clinicians' decisions. We identified numerous variables considered relevant for extubation decisions for mechanically ventilated premature infants with RDS. We then developed a web-based decision-support tool for clinicians which can be made widely available and potentially improve patient care world wide. [Abstract/Link to Full Text]

O'Grady LA
Consumer e-health education in HIV/AIDS: a pilot study of a web-based video workshop.
BMC Med Inform Decis Mak. 2006;610.
BACKGROUND: Members of the HIV/AIDS community are known to use web-based tools to support learning about treatment issues. Initial research indicated components such as message forums or web-based documentation were effectively used by persons with HIV/AIDS. Video has also shown promise as a technology to aid consumer health education. However, no research has been published thus far investigating the impact of web-based environments combining these components in an educational workshop format. METHODS: In this qualitative study HIV/AIDS community members provided feedback on an integrated web-based consumer health education environment. Participants were recruited through organizations that serve the HIV/AIDS community located in Toronto, Canada. Demographics, data on Internet use, including messages exchanged in the study environment were collected. A group interview provided feedback on usability of the study environment, preferences for information formats, use of the message forum, and other sources for learning about treatment information. RESULTS: In this pilot study analysis of the posted messages did not demonstrate use for learning of the workshop content. Participants did not generally find the environment of value for learning about treatment information. However, participants did share how they were meeting these needs. It was indicated that a combination of resources are being used to find and discuss treatment information, including in-person sources. CONCLUSION: More research on the ways in which treatment information needs are being met by HIV/AIDS community members and how technology fits in this process is necessary before investing large amounts of money into web-based interventions. Although this study had a limited number of participants, the findings were unexpected and, therefore, of interest to those who intend to implement online consumer health education initiatives or interventions. [Abstract/Link to Full Text]

Finlay DD, Nugent CD, Donnelly MP, Lux RL, McCullagh PJ, Black ND
Selection of optimal recording sites for limited lead body surface potential mapping: a sequential selection based approach.
BMC Med Inform Decis Mak. 2006;69.
BACKGROUND: In this study we propose the development of a new algorithm for selecting optimal recording sites for limited lead body surface potential mapping. The proposed algorithm differs from previously reported methods in that it is based upon a simple and intuitive data driven technique that does not make any presumptions about deterministic characteristics of the data. It uses a forward selection based search technique to find the best combination of electrocardiographic leads. METHODS: The study was conducted using a dataset consisting of body surface potential maps (BSPM) recorded from 116 subjects which included 59 normals and 57 subjects exhibiting evidence of old Myocardial Infarction (MI). The performance of the algorithm was evaluated using spatial RMS voltage error and correlation coefficient to compare original and reconstructed map frames. RESULTS: In all, three configurations of the algorithm were evaluated and it was concluded that there was little difference in the performance of the various configurations. In addition to observing the performance of the selection algorithm, several lead subsets of 32 electrodes as chosen by the various configurations of the algorithm were evaluated. The rationale for choosing this number of recording sites was to allow comparison with a previous study that used a different algorithm, where 32 leads were deemed to provide an acceptable level of reconstruction performance. CONCLUSION: It was observed that although the lead configurations suggested in this study were not identical to that suggested in the previous work, the systems did bear similar characteristics in that recording sites were chosen with greatest density in the precordial region. [Abstract/Link to Full Text]

Rashiq S, Edlund D, Dick BD
Utilities of the post-anesthesia state derived by the standard gamble method in surgical patients.
BMC Med Inform Decis Mak. 2006;68.
BACKGROUND: There are no published utilities for the post-anesthesia state obtained by the standard gamble method (SG). METHODS: We obtained utilities for postoperative pain, nausea, vomiting, urinary retention and myalgia from 100 adults prior to elective surgery using SG. RESULTS: 20% of volunteer participants could not demonstrate a satisfactory understanding of the SG process. Median utilities for each adverse effect were all very close to 1.0, and no statistically significant differences were found between them. CONCLUSION: Our results suggest that the avoidance of anesthesia related side effects and pain is not viewed by patients prior to surgery as being worthy of the taking of even a miniscule risk of death. This may affect the decision to utilize anesthesia techniques that trade a lower incidence of common side effects for a very low but finite risk of a catastrophic complication. [Abstract/Link to Full Text]

Darmoni SJ, Névéol A, Renard JM, Gehanno JF, Soualmia LF, Dahamna B, Thirion B
A MEDLINE categorization algorithm.
BMC Med Inform Decis Mak. 2006;67.
BACKGROUND: Categorization is designed to enhance resource description by organizing content description so as to enable the reader to grasp quickly and easily what are the main topics discussed in it. The objective of this work is to propose a categorization algorithm to classify a set of scientific articles indexed with the MeSH thesaurus, and in particular those of the MEDLINE bibliographic database. In a large bibliographic database such as MEDLINE, finding materials of particular interest to a specialty group, or relevant to a particular audience, can be difficult. The categorization refines the retrieval of indexed material. In the CISMeF terminology, metaterms can be considered as super-concepts. They were primarily conceived to improve recall in the CISMeF quality-controlled health gateway. METHODS: The MEDLINE categorization algorithm (MCA) is based on semantic links existing between MeSH terms and metaterms on the one hand and between MeSH subheadings and metaterms on the other hand. These links are used to automatically infer a list of metaterms from any MeSH term/subheading indexing. Medical librarians manually select the semantic links. RESULTS: The MEDLINE categorization algorithm lists the medical specialties relevant to a MEDLINE file by decreasing order of their importance. The MEDLINE categorization algorithm is available on a Web site. It can run on any MEDLINE file in a batch mode. As an example, the top 3 medical specialties for the set of 60 articles published in BioMed Central Medical Informatics & Decision Making, which are currently indexed in MEDLINE are: information science, organization and administration and medical informatics. CONCLUSION: We have presented a MEDLINE categorization algorithm in order to classify the medical specialties addressed in any MEDLINE file in the form of a ranked list of relevant specialties. The categorization method introduced in this paper is based on the manual indexing of resources with MeSH (terms/subheadings) pairs by NLM indexers. This algorithm may be used as a new bibliometric tool. [Abstract/Link to Full Text]

Sittig DF, Krall MA, Dykstra RH, Russell A, Chin HL
A survey of factors affecting clinician acceptance of clinical decision support.
BMC Med Inform Decis Mak. 2006;66.
BACKGROUND: Real-time clinical decision support (CDS) integrated into clinicians' workflow has the potential to profoundly affect the cost, quality, and safety of health care delivery. Recent reports have identified a surprisingly low acceptance rate for different types of CDS. We hypothesized that factors affecting CDS system acceptance could be categorized as relating to differences in patients, physicians, CDS-type, or environmental characteristics. METHODS: We conducted a survey of all adult primary care physicians (PCPs, n = 225) within our group model Health Maintenance Organization (HMO) to identify factors that affect their acceptance of CDS. We defined clinical decision support broadly as "clinical information" that is either provided to you or accessible by you, from the clinical workstation (e.g., enhanced flow sheet displays, health maintenance reminders, alternative medication suggestions, order sets, alerts, and access to any internet-based information resources). RESULTS: 110 surveys were returned (49%). There were no differences in the age, gender, or years of service between those who returned the survey and the entire adult PCP population. Overall, clinicians stated that the CDS provided "helps them take better care of their patients" (3.6 on scale of 1:Never-5:Always), "is worth the time it takes" (3.5), and "reminds them of something they've forgotten" (3.2). There was no difference in the perceived acceptance rate of alerts based on their type (i.e., cost, safety, health maintenance). When asked about specific patient characteristics that would make the clinicians "more", "equally" or "less" likely to accept alerts: 41% stated that they were more (8% stated "less") likely to accept alerts on elderly patients (> 65 yrs); 38% were more (14% stated less) likely to accept alerts on patients with more than 5 current medications; and 38% were more (20% stated less) likely to accept alerts on patients with more than 5 chronic clinical conditions. Interestingly, 80% said they were less likely to accept alerts when they were behind schedule and 84% of clinicians admitted to being at least 20 minutes behind schedule "some", "most", or "all of the time". CONCLUSION: Even though a majority of our clinical decision support suggestions are not explicitly followed, clinicians feel they are of benefit and would be even more beneficial if they had more time available to address them. [Abstract/Link to Full Text]

Bird SB, Lane DR
House officer procedure documentation using a Personal Digital Assistant: a longitudinal study.
BMC Med Inform Decis Mak. 2006;65.
BACKGROUND: Personal Digital Assistants (PDAs) have been integrated into daily practice for many emergency physicians and house officers. Few objective data exist that quantify the effect of PDAs on documentation. The objective of this study was to determine whether use of a PDA would improve emergency medicine house officer documentation of procedures and patient resuscitations. METHODS: Twelve first-year Emergency Medicine (EM) residents were provided a Palm V (Palm, Inc., Santa Clara, California, USA) PDA. A customizable patient procedure and encounter program was constructed and loaded into each PDA. Residents were instructed to enter information on patients who had any of 20 procedures performed, were deemed clinically unstable, or on whom follow-up was obtained. These data were downloaded to the residency coordinator's desktop computer on a weekly basis for 36 months. The mean number of procedures and encounters performed per resident over a three year period were then compared with those of 12 historical controls from a previous residency class that had recorded the same information using a handwritten card system for 36 months. Means of both groups were compared a two-tailed Student's t test with a Bonferroni correction for multiple comparisons. One hundred randomly selected entries from both the PDA and handwritten groups were reviewed for completeness. Another group of 11 residents who had used both handwritten and PDA procedure logs for one year each were asked to complete a questionnaire regarding their satisfaction with the PDA system. RESULTS: Mean documentation of three procedures significantly increased in the PDA vs handwritten groups: conscious sedation 24.0 vs 0.03 (p = 0.001); thoracentesis 3.0 vs 0.0 (p = 0.001); and ED ultrasound 24.5 vs. 0.0 (p = 0.001). In the handwritten cohort, only the number of cardioversions/defibrillations (26.5 vs 11.5) was statistically increased (p = 0.001). Of the PDA entries, 100% were entered completely, compared to only 91% of the handwritten group, including 4% that were illegible. 10 of 11 questioned residents preferred the PDA procedure log to a handwritten log (mean +/- SD Likert-scale score of 1.6 +/- 0.9). CONCLUSION: Overall use of a PDA did not significantly change EM resident procedure or patient resuscitation documentation when used over a three-year period. Statistically significant differences between the handwritten and PDA groups likely represent alterations in the standard of ED care over time. Residents overwhelmingly preferred the PDA procedure log to a handwritten log and more entries are complete using the PDA. These favorable comparisons and the numerous other uses of PDAs may make them an attractive alternative for resident documentation. [Abstract/Link to Full Text]

Liu J, Wyatt JC, Altman DG
Decision tools in health care: focus on the problem, not the solution.
BMC Med Inform Decis Mak. 2006;64.
BACKGROUND: Systematic reviews or randomised-controlled trials usually help to establish the effectiveness of drugs and other health technologies, but are rarely sufficient by themselves to ensure actual clinical use of the technology. The process from innovation to routine clinical use is complex. Numerous computerised decision support systems (DSS) have been developed, but many fail to be taken up into actual use. Some developers construct technologically advanced systems with little relevance to the real world. Others did not determine whether a clinical need exists. With NHS investing 5 billion pounds sterling in computer systems, also occurring in other countries, there is an urgent need to shift from a technology-driven approach to one that identifies and employs the most cost-effective method to manage knowledge, regardless of the technology. The generic term, 'decision tool' (DT), is therefore suggested to demonstrate that these aids, which seem different technically, are conceptually the same from a clinical viewpoint. DISCUSSION: Many computerised DSSs failed for various reasons, for example, they were not based on best available knowledge; there was insufficient emphasis on their need for high quality clinical data; their development was technology-led; or evaluation methods were misapplied. We argue that DSSs and other computer-based, paper-based and even mechanical decision aids are members of a wider family of decision tools. A DT is an active knowledge resource that uses patient data to generate case specific advice, which supports decision making about individual patients by health professionals, the patients themselves or others concerned about them. The identification of DTs as a consistent and important category of health technology should encourage the sharing of lessons between DT developers and users and reduce the frequency of decision tool projects focusing only on technology. The focus of evaluation should become more clinical, with the impact of computer-based DTs being evaluated against other computer, paper- or mechanical tools, to identify the most cost effective tool for each clinical problem. SUMMARY: We suggested the generic term 'decision tool' to demonstrate that decision-making aids, such as computerised DSSs, paper algorithms, and reminders are conceptually the same, so the methods to evaluate them should be the same. [Abstract/Link to Full Text]

Ammenwerth E, Iller C, Mahler C
IT-adoption and the interaction of task, technology and individuals: a fit framework and a case study.
BMC Med Inform Decis Mak. 2006;63.
BACKGROUND: Factors of IT adoption have largely been discussed in the literature. However, existing frameworks (such as TAM or TTF) are failing to include one important aspect, the interaction between user and task. METHOD: Based on a literature study and a case study, we developed the FITT framework to help analyse the socio-organisational-technical factors that influence IT adoption in a health care setting. RESULTS: Our FITT framework ("Fit between Individuals, Task and Technology") is based on the idea that IT adoption in a clinical environment depends on the fit between the attributes of the individual users (e.g. computer anxiety, motivation), attributes of the technology (e.g. usability, functionality, performance), and attributes of the clinical tasks and processes (e.g. organisation, task complexity). We used this framework in the retrospective analysis of a three-year case study, describing the adoption of a nursing documentation system in various departments in a German University Hospital. We will show how the FITT framework helped analyzing the process of IT adoption during an IT implementation: we were able to describe every found IT adoption problem with regard to the three fit dimensions, and any intervention on the fit can be described with regard to the three objects of the FITT framework (individual, task, technology). We also derive facilitators and barriers to IT adoption of clinical information systems. CONCLUSION: This work should support a better understanding of the reasons for IT adoption failures and therefore enable better prepared and more successful IT introduction projects. We will discuss, however, that from a more epistemological point of view, it may be difficult or even impossible to analyse the complex and interacting factors that predict success or failure of IT projects in a socio-technical environment. [Abstract/Link to Full Text]

Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz PA
The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.
BMC Med Inform Decis Mak. 2006;62.
BACKGROUND: Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. RESULTS: The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. CONCLUSION: The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development. [Abstract/Link to Full Text]

Poon EG, Jha AK, Christino M, Honour MM, Fernandopulle R, Middleton B, Newhouse J, Leape L, Bates DW, Blumenthal D, Kaushal R
Assessing the level of healthcare information technology adoption in the United States: a snapshot.
BMC Med Inform Decis Mak. 2006;61.
BACKGROUND: Comprehensive knowledge about the level of healthcare information technology (HIT) adoption in the United States remains limited. We therefore performed a baseline assessment to address this knowledge gap. METHODS: We segmented HIT into eight major stakeholder groups and identified major functionalities that should ideally exist for each, focusing on applications most likely to improve patient safety, quality of care and organizational efficiency. We then conducted a multi-site qualitative study in Boston and Denver by interviewing key informants from each stakeholder group. Interview transcripts were analyzed to assess the level of adoption and to document the major barriers to further adoption. Findings for Boston and Denver were then presented to an expert panel, which was then asked to estimate the national level of adoption using the modified Delphi approach. We measured adoption level in Boston and Denver was graded on Rogers' technology adoption curve by co-investigators. National estimates from our expert panel were expressed as percentages. RESULTS: Adoption of functionalities with financial benefits far exceeds adoption of those with safety and quality benefits. Despite growing interest to adopt HIT to improve safety and quality, adoption remains limited, especially in the area of ambulatory electronic health records and physician-patient communication. Organizations, particularly physicians' practices, face enormous financial challenges in adopting HIT, and concerns remain about its impact on productivity. CONCLUSION: Adoption of HIT is limited and will likely remain slow unless significant financial resources are made available. Policy changes, such as financial incentivesto clinicians to use HIT or pay-for-performance reimbursement, may help health care providers defray upfront investment costs and initial productivity loss. [Abstract/Link to Full Text]

Vogelzang M, Zijlstra F, Nijsten MW
Design and implementation of GRIP: a computerized glucose control system at a surgical intensive care unit.
BMC Med Inform Decis Mak. 2005;538.
BACKGROUND: Tight glucose control by intensive insulin therapy has become a key part of critical care and is an important field of study in acute coronary care. A balance has to be found between frequency of measurements and the risk of hypoglycemia. Current nurse-driven protocols are paper-based and, therefore, rely on simple rules. For safety and efficiency a computer decision support system that employs complex logic may be superior to paper protocols. METHODS: We designed and implemented GRIP, a stand-alone Java computer program. Our implementation of GRIP will be released as free software. Blood glucose values measured by a point-of-care analyzer were automatically retrieved from the central laboratory database. Additional clinical information was asked from the nurse and the program subsequently advised a new insulin pump rate and glucose sampling interval. RESULTS: Implementation of the computer program was uneventful and successful. GRIP treated 179 patients for a total of 957 patient-days. Severe hypoglycemia (< 2.2 mmol/L) only occurred once due to human error. With a median (IQR) of 4.9 (4.2-6.2) glucose measurements per day the median percentage of time in which glucose fell in the target range was 78%. Nurses rated the program as easy to work with and as an improvement over the preceding paper protocol. They reported no increase in time spent on glucose control. CONCLUSION: A computer driven protocol is a safe and effective means of glucose control at a surgical ICU. Future improvements in the recommendation algorithm may further improve safety and efficiency. [Abstract/Link to Full Text]

Muin M, Fontelo P, Liu F, Ackerman M
SLIM: an alternative Web interface for MEDLINE/PubMed searches - a preliminary study.
BMC Med Inform Decis Mak. 2005;537.
BACKGROUND: With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. RESULTS: Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. CONCLUSION: SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine. [Abstract/Link to Full Text]

Kim J, Whitney A, Hayter S, Lewis C, Campbell M, Sutherland L, Fowler B, Googe S, McCoy R, Pignone M
Development and initial testing of a computer-based patient decision aid to promote colorectal cancer screening for primary care practice.
BMC Med Inform Decis Mak. 2005;536.
BACKGROUND: Although colorectal cancer screening is recommended by major policy-making organizations, rates of screening remain low. Our aim was to develop a patient-directed, computer-based decision aid about colorectal cancer screening and investigate whether it could increase patient interest in screening. METHODS: We used content from evidence-based literature reviews and our previous decision aid research to develop a prototype. We performed two rounds of usability testing with representative patients to revise the content and format. The final decision aid consisted of an introductory segment, four test-specific segments, and information to allow comparison of the tests across several key parameters. We then conducted a before-after uncontrolled trial of 80 patients 50-75 years old recruited from an academic internal medicine practice. RESULTS: Mean viewing time was 19 minutes. The decision aid improved patients' intent to ask providers for screening from a mean score of 2.8 (1 = not at all likely to ask, 4 = very likely to ask) before viewing the decision aid to 3.2 afterwards (difference, 0.4; p < 0.0001, paired t-test). Most found the aid useful and reported that it improved their knowledge about screening. Sixty percent said they were ready to be tested, 18% needed more information, and 22% were not ready to be screened. Within 6 months of viewing, 43% of patients had completed screening tests. CONCLUSION: We conclude that a computer-based decision aid can increase patient intent to be screened and increase interest in screening. Practice Implications: This decision aid can be viewed by patients prior to provider appointments to increase motivation to be screened and to help them decide about which modality to use for screening. Further work is required to integrate the decision aid with other practice change strategies to raise screening rates to target levels. [Abstract/Link to Full Text]

Berman JJ
Automatic extraction of candidate nomenclature terms using the doublet method.
BMC Med Inform Decis Mak. 2005;535.
BACKGROUND: New terminology continuously enters the biomedical literature. How can curators identify new terms that can be added to existing nomenclatures? The most direct method, and one that has served well, involves reading the current literature. The scholarly curator adds new terms as they are encountered. Present-day scholars are severely challenged by the enormous volume of biomedical literature. Curators of medical nomenclatures need computational assistance if they hope to keep their terminologies current. The purpose of this paper is to describe a method of rapidly extracting new, candidate terms from huge volumes of biomedical text. The resulting lists of terms can be quickly reviewed by curators and added to nomenclatures, if appropriate. The candidate term extractor uses a variation of the previously described doublet coding method. The algorithm, which operates on virtually any nomenclature, derives from the observation that most terms within a knowledge domain are composed entirely of word combinations found in other terms from the same knowledge domain. Terms can be expressed as sequences of overlapping word doublets that have more specific meaning than the individual words that compose the term. The algorithm parses through text, finding contiguous sequences of word doublets that are known to occur somewhere in the reference nomenclature. When a sequence of matching word doublets is encountered, it is compared with whole terms already included in the nomenclature. If the doublet sequence is not already in the nomenclature, it is extracted as a candidate new term. Candidate new terms can be reviewed by a curator to determine if they should be added to the nomenclature. An implementation of the algorithm is demonstrated, using a corpus of published abstracts obtained through the National Library of Medicine's PubMed query service and using "The developmental lineage classification and taxonomy of neoplasms" as a reference nomenclature. RESULTS: A 31+ Megabyte corpus of pathology journal abstracts was parsed using the doublet extraction method. This corpus consisted of 4,289 records, each containing an abstract title. The total number of words included in the abstract titles was 50,547. New candidate terms for the nomenclature were automatically extracted from the titles of abstracts in the corpus. Total execution time on a desktop computer with CPU speed of 2.79 GHz was 2 seconds. The resulting output consisted of 313 new candidate terms, each consisting of concatenated doublets found in the reference nomenclature. Human review of the 313 candidate terms yielded a list of 285 terms approved by a curator. A final automatic extraction of duplicate terms yielded a final list of 222 new terms (71% of the original 313 extracted candidate terms) that could be added to the reference nomenclature. CONCLUSION: The doublet method for automatically extracting candidate nomenclature terms can be used to quickly find new terms from vast amounts of text. The method can be immediately adapted for virtually any text and any nomenclature. An implementation of the algorithm, in the Perl programming language, is provided with this article. [Abstract/Link to Full Text]

Kim GR, Bartlett EL, Lehmann HP
Information resource preferences by general pediatricians in office settings: a qualitative study.
BMC Med Inform Decis Mak. 2005;534.
BACKGROUND: Information needs and resource preferences of office-based general pediatricians have not been well characterized. METHODS: Data collected from a sample of twenty office-based urban/suburban general pediatricians consisted of: (a) a demographic survey about participants' practice and computer use, (b) semi-structured interviews on their use of different types of information resources and (c) semi-structured interviews on perceptions of information needs and resource preferences in response to clinical vignettes representing cases in Genetics and Infectious Diseases. Content analysis of interviews provided participants' perceived use of resources and their perceived questions and preferred resources in response to vignettes. RESULTS: Participants' average time in practice was 15.4 years (2-28 years). All had in-office online access.Participants identified specialist/generalist colleagues, general/specialty pediatric texts, drug formularies, federal government/professional organization Websites and medical portals (when available) as preferred information sources. They did not identify decision-making texts, evidence-based reviews, journal abstracts, medical librarians or consumer health information for routine office use.In response to clinical vignettes in Genetics and Infectious Diseases, participants identified Question Types about patient-specific (diagnosis, history and findings) and general medical (diagnostic, therapeutic and referral guidelines) information. They identified specialists and specialty textbooks, history and physical examination, colleagues and general pediatric textbooks, and federal and professional organizational Websites as information sources. Participants with access to portals identified them as information resources in lieu of texts.For Genetics vignettes, participants identified questions about prenatal history, disease etiology and treatment guidelines. For Genetics vignettes, they identified patient history, specialists, general pediatric texts, Web search engines and colleagues as information sources. For Infectious Diseases (ID) vignettes, participants identified questions about patients' clinical status at presentation and questions about disease classification, diagnosis/therapy/referral guidelines and sources of patient education. For ID vignettes, they identified history, laboratory results, colleagues, specialists and personal experience as information sources. CONCLUSION: Content analysis of office-based general pediatricians' responses to clinical vignettes provided a qualitative description of their perceptions of information needs and preferences for information resource for cases in Genetics and Infectious Diseases. This approach may provide complementary information for discovering practitioner's information needs and resource preferences in different contexts. [Abstract/Link to Full Text]

Najmi AH, Magruder SF
An adaptive prediction and detection algorithm for multistream syndromic surveillance.
BMC Med Inform Decis Mak. 2005;533.
BACKGROUND: Surveillance of Over-the-Counter pharmaceutical (OTC) sales as a potential early indicator of developing public health conditions, in particular in cases of interest to biosurvellance, has been suggested in the literature. This paper is a continuation of a previous study in which we formulated the problem of estimating clinical data from OTC sales in terms of optimal LMS linear and Finite Impulse Response (FIR) filters. In this paper we extend our results to predict clinical data multiple steps ahead using OTC sales as well as the clinical data itself. METHODS: The OTC data are grouped into a few categories and we predict the clinical data using a multichannel filter that encompasses all the past OTC categories as well as the past clinical data itself. The prediction is performed using FIR (Finite Impulse Response) filters and the recursive least squares method in order to adapt rapidly to nonstationary behaviour. In addition, we inject simulated events in both clinical and OTC data streams to evaluate the predictions by computing the Receiver Operating Characteristic curves of a threshold detector based on predicted outputs. RESULTS: We present all prediction results showing the effectiveness of the combined filtering operation. In addition, we compute and present the performance of a detector using the prediction output. CONCLUSION: Multichannel adaptive FIR least squares filtering provides a viable method of predicting public health conditions, as represented by clinical data, from OTC sales, and/or the clinical data. The potential value to a biosurveillance system cannot, however, be determined without studying this approach in the presence of transient events (nonstationary events of relatively short duration and fast rise times). Our simulated events superimposed on actual OTC and clinical data allow us to provide an upper bound on that potential value under some restricted conditions. Based on our ROC curves we argue that a biosurveillance system can provide early warning of an impending clinical event using ancillary data streams (such as OTC) with established correlations with the clinical data, and a prediction method that can react to nonstationary events sufficiently fast. Whether OTC (or other data streams yet to be identified) provide the best source of predicting clinical data is still an open question. We present a framework and an example to show how to measure the effectiveness of predictions, and compute an upper bound on this performance for the Recursive Least Squares method when the following two conditions are met: (1) an event of sufficient strength exists in both data streams, without distortion, and (2) it occurs in the OTC (or other ancillary streams) earlier than in the clinical data. [Abstract/Link to Full Text]

Sauleau EA, Paumier JP, Buemi A
Medical record linkage in health information systems by approximate string matching and clustering.
BMC Med Inform Decis Mak. 2005;532.
BACKGROUND: Multiplication of data sources within heterogeneous healthcare information systems always results in redundant information, split among multiple databases. Our objective is to detect exact and approximate duplicates within identity records, in order to attain a better quality of information and to permit cross-linkage among stand-alone and clustered databases. Furthermore, we need to assist human decision making, by computing a value reflecting identity proximity. METHODS: The proposed method is in three steps. The first step is to standardise and to index elementary identity fields, using blocking variables, in order to speed up information analysis. The second is to match similar pair records, relying on a global similarity value taken from the Porter-Jaro-Winkler algorithm. And the third is to create clusters of coherent related records, using graph drawing, agglomerative clustering methods and partitioning methods. RESULTS: The batch analysis of 300,000 "supposedly" distinct identities isolates 240,000 true unique records, 24,000 duplicates (clusters composed of 2 records) and 3,000 clusters whose size is greater than or equal to 3 records. CONCLUSION: Duplicate-free databases, used in conjunction with relevant indexes and similarity values, allow immediate (i.e. real-time) proximity detection when inserting a new identity. [Abstract/Link to Full Text]

Legare F, Godin G, Ringa V, Dodin S, Turcot L, Norton J
Variation in the psychosocial determinants of the intention to prescribe hormone therapy prior to the release of the Women's Health Initiative trial: a survey of general practitioners and gynaecologists in France and Quebec.
BMC Med Inform Decis Mak. 2005;531.
BACKGROUND: Theory-based approaches are advocated to improve our understanding of prescription behaviour. This study is an application of the theory of planned behaviour (TPB) with additional variables. It was designed to assess which variables were associated with the intention to prescribe hormone therapy (HT). In addition, variations in the measures across medical specialities (GPs and gynaecologists) and across countries (France and Quebec) were investigated. METHODS: A survey among 2,000 doctors from France and 1,044 doctors from Quebec was conducted. Data were collected by means of a self-administered questionnaire. A clinical vignette was used to elicit doctors' opinions. The following TPB variables were assessed: attitude, subjective norm, perceived behavioural control, attitudinal beliefs, normative beliefs and power of control beliefs. Additional variables (role belief, moral norm and practice pattern-related factors) were also assessed. A stepwise logistic regression was used to assess which variables were associated with the intention to prescribe HT. GPs and gynaecologists were compared to each other within countries and the two countries were compared within the specialties. RESULTS: Overall, 1,085 doctors from France returned their questionnaire and 516 doctors from Quebec (response rate = 54% and 49%, respectively). In the overall regression model, power of control beliefs, moral norm and role belief were significantly associated with intention (all at p < 0.0001). The models by specialty and country were: for GPs in Quebec, power of control beliefs (p < 0.0001), moral norm (p < 0.01) and cytology and hormonal dosage (both at p < 0.05); for GPs in France, power of control beliefs and role belief (both at p < 0.0001) and perception of behavioural control (p < 0.05) and cessation of menses (p < 0.01); for gynaecologists in Quebec, moral norm and power of control beliefs (both at p = 0.01); and for gynaecologists in France, power of control beliefs (p < 0.0001), and moral norm, role belief and lipid profile (all at p < 0.05). CONCLUSION: In both countries, compared with GPs, intention to prescribe HT was higher for gynaecologists. Psychosocial determinants of doctors' intention to prescribe HT varied according to the specialty and the country thus, suggesting an influence of contextual factors on these determinants. [Abstract/Link to Full Text]

Meystre S, Haug PJ
Automation of a problem list using natural language processing.
BMC Med Inform Decis Mak. 2005;530.
BACKGROUND: The medical problem list is an important part of the electronic medical record in development in our institution. To serve the functions it is designed for, the problem list has to be as accurate and timely as possible. However, the current problem list is usually incomplete and inaccurate, and is often totally unused. To alleviate this issue, we are building an environment where the problem list can be easily and effectively maintained. METHODS: For this project, 80 medical problems were selected for their frequency of use in our future clinical field of evaluation (cardiovascular). We have developed an Automated Problem List system composed of two main components: a background and a foreground application. The background application uses Natural Language Processing (NLP) to harvest potential problem list entries from the list of 80 targeted problems detected in the multiple free-text electronic documents available in our electronic medical record. These proposed medical problems drive the foreground application designed for management of the problem list. Within this application, the extracted problems are proposed to the physicians for addition to the official problem list. RESULTS: The set of 80 targeted medical problems selected for this project covered about 5% of all possible diagnoses coded in ICD-9-CM in our study population (cardiovascular adult inpatients), but about 64% of all instances of these coded diagnoses. The system contains algorithms to detect first document sections, then sentences within these sections, and finally potential problems within the sentences. The initial evaluation of the section and sentence detection algorithms demonstrated a sensitivity and positive predictive value of 100% when detecting sections, and a sensitivity of 89% and a positive predictive value of 94% when detecting sentences. CONCLUSION: The global aim of our project is to automate the process of creating and maintaining a problem list for hospitalized patients and thereby help to guarantee the timeliness, accuracy and completeness of this information. [Abstract/Link to Full Text]

Razavi AR, Gill H, Stål O, Sundquist M, Thorstenson S, Ahlfeldt H, Shahsavar N
Exploring cancer register data to find risk factors for recurrence of breast cancer--application of Canonical Correlation Analysis.
BMC Med Inform Decis Mak. 2005;529.
BACKGROUND: A common approach in exploring register data is to find relationships between outcomes and predictors by using multiple regression analysis (MRA). If there is more than one outcome variable, the analysis must then be repeated, and the results combined in some arbitrary fashion. In contrast, Canonical Correlation Analysis (CCA) has the ability to analyze multiple outcomes at the same time. One essential outcome after breast cancer treatment is recurrence of the disease. It is important to understand the relationship between different predictors and recurrence, including the time interval until recurrence. This study describes the application of CCA to find important predictors for two different outcomes for breast cancer patients, loco-regional recurrence and occurrence of distant metastasis and to decrease the number of variables in the sets of predictors and outcomes without decreasing the predictive strength of the model. METHODS: Data for 637 malignant breast cancer patients admitted in the south-east region of Sweden were analyzed. By using CCA and looking at the structure coefficients (loadings), relationships between tumor specifications and the two outcomes during different time intervals were analyzed and a correlation model was built. RESULTS: The analysis successfully detected known predictors for breast cancer recurrence during the first two years and distant metastasis 2-4 years after diagnosis. Nottingham Histologic Grading (NHG) was the most important predictor, while age of the patient at the time of diagnosis was not an important predictor. CONCLUSION: In cancer registers with high dimensionality, CCA can be used for identifying the importance of risk factors for breast cancer recurrence. This technique can result in a model ready for further processing by data mining methods through reducing the number of variables to important ones. [Abstract/Link to Full Text]

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Recent Articles in Bulletin of the Medical Library Association

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Slotnick HB, Harris TR, Antonenko DR
Changes in learning-resource use across physicians' learning episodes.
Bull Med Libr Assoc. 2001 Apr;89(2):194-203.
INTRODUCTION: This study explores the numbers of learning resources physicians use at each stage in self-directed learning episodes addressing general problems. MATERIALS AND METHODS: A survey of a statewide random sample of doctors estimated the number of resources used at each stage in solving various general problems. RESULTS: The 50% response rate for faculty allowed generalization of findings to the population of these physicians; the rate for nonfaculty physicians was too low to allow generalization. Faculty findings showed (1) broader resource use in learning about diseases than diagnosis or therapeutics (2) comparable numbers of resources used in deciding whether to take on the learning problem and learning the required skills and knowledge, (3) greater numbers of resources selected to evaluate the problem and to learn the required skills and knowledge than to gain experience with the newly learned skills and knowledge, and (4) support for assertions that doctors value learning resources that are accessible, applicable, familiar, and time effective. DISCUSSION: The findings were interpreted in light of theory describing physicians' self-directed learning episodes, and implications are presented for physicians-in-training, physicians, and medical librarians. [Abstract/Link to Full Text]

Williams MD, Gish KW, Giuse NB, Sathe NA, Carrell DL
The Patient Informatics Consult Service (PICS): an approach for a patient-centered service.
Bull Med Libr Assoc. 2001 Apr;89(2):185-93.
The Patient Informatics Consult Service (PICS) at the Eskind Biomedical Library at Vanderbilt University Medical Center (VUMC) provides patients with consumer-friendly information by using an information prescription mechanism. Clinicians refer patients to the PICS by completing the prescription and noting the patient's condition and any relevant factors. In response, PICS librarians critically appraise and summarize consumer-friendly materials into a targeted information report. Copies of the report are given to both patient and clinician, thus facilitating doctor-patient communication and closing the clinician-librarian feedback loop. Moreover, the prescription form also circumvents many of the usual barriers for patients in locating information, namely, patients' unfamiliarity with medical terminology and lack of knowledge of authoritative sources. PICS librarians capture the time and expertise put into these reports by creating Web-based pathfinders on prescription topics. Pathfinders contain librarian-created disease overviews and links to authoritative resources and seek to minimize the consumer's exposure to unreliable information. Pathfinders also adhere to strict guidelines that act as a model for locating, appraising, and summarizing information for consumers. These mechanisms--the information prescription, research reports, and pathfinders--serve as steps toward the long-term goal of full integration of consumer health information into patient care at VUMC. [Abstract/Link to Full Text]

Jerome RN, Giuse NB, Gish KW, Sathe NA, Dietrich MS
Information needs of clinical teams: analysis of questions received by the Clinical Informatics Consult Service.
Bull Med Libr Assoc. 2001 Apr;89(2):177-84.
OBJECTIVES: To examine the types of questions received by Clinical Informatics Consult Service (CICS) librarians from clinicians on rounds and to analyze the number of clearly differentiated viewpoints provided in response. DESIGN: Questions were retrieved from an internal database, the CICS Knowledge Base, and analyzed for redundancy by subject analysis. The unique questions were classified into ten categories by subject. Treatment-related questions were analyzed for the number of viewpoints represented in the librarian's response. RESULTS: The CICS Knowledge Base contained 476 unique questions and 71 redundant questions. Among the unique queries, the top two categories accounted for 67%: treatment (36%) and disease description (31%). Within the treatment-related subset, 138 questions (59%) required representation of more than one viewpoint in the librarian's response. DISCUSSION: Questions generated by clinicians frequently require comprehensive, critical appraisal of the medical literature, a need that can be filled by librarians trained in such techniques. This study demonstrates that many questions require representation of more than one viewpoint to answer completely. Moreover, the redundancy rate underscores the need for resources like the CICS Knowledge Base. By critically analyzing the medical literature, CICS librarians are providing a time-saving and valuable service for clinicians and charting new territory for librarians. [Abstract/Link to Full Text]

Crossno JE, Berkins B, Gotcher N, Hill JL, McConoughey M, Walters M
Assessment of Customer Service in Academic Health Care Libraries (ACSAHL): an instrument for measuring customer service.
Bull Med Libr Assoc. 2001 Apr;89(2):170-6.
OBJECTIVES: In a pilot study, the library had good results using SERVQUAL, a respected and often-used instrument for measuring customer satisfaction. The SERVQUAL instrument itself, however, received some serious and well-founded criticism from the respondents to our survey. The purpose of this study was to test the comparability of the results of SERVQUAL with a revised and shortened instrument modeled on SERVQUAL. The revised instrument, the Assessment of Customer Service in Academic Health Care Libraries (ACSAHL), was designed to better assess customer service in academic health care libraries. METHODS: Surveys were sent to clients who had used the document delivery services at three academic medical libraries in Texas over the previous twelve to eighteen months. ACSAHL surveys were sent exclusively to clients at University of Texas (UT) Southwestern, while the client pools at the two other institutions were randomly divided and provided either SERVQUAL or ACSAHL surveys. RESULTS: Results indicated that more respondents preferred the shorter ACSAHL instrument to the longer and more complex SERVQUAL instrument. Also, comparing the scores from both surveys indicated that ACSAHL elicited comparable results. CONCLUSIONS: ACSAHL appears to measure the same type of data in similar settings, but additional testing is recommended both to confirm the survey's results through data replication and to investigate whether the instrument applies to different service areas. [Abstract/Link to Full Text]

Schmidt CM, Eckerman NL
Circulation of core collection monographs in an academic medical library.
Bull Med Libr Assoc. 2001 Apr;89(2):165-9.
Academic medical librarians responsible for monograph acquisition face a challenging task. From the plethora of medical monographs published each year, academic medical librarians must select those most useful to their patrons. Unfortunately, none of the selection tools available to medical librarians are specifically intended to assist academic librarians with medical monograph selection. The few short core collection lists that are available are intended for use in the small hospital or internal medicine department library. As these are the only selection tools available, however, many academic medical librarians spend considerable time reviewing these collection lists and place heavy emphasis on the acquisition of listed books. The study reported here was initiated to determine whether the circulation of listed books in an academic library justified the emphasis placed on the acquisition of these books. Circulation statistics for "listed" and "nonlisted" books in the hematology (WH) section of Indiana University School of Medicine's Ruth Lilly Medical Library were studied. The average circulation figures for listed books were nearly two times as high as the corresponding figures for the WH books in general. These data support the policies of those academic medical libraries that place a high priority on collection of listed books. [Abstract/Link to Full Text]

Burrows SC, Moore KM, Lemkau HL
Creating a Web-accessible, point-of-care, team-based information system (PointTIS): the librarian as publisher.
Bull Med Libr Assoc. 2001 Apr;89(2):154-64.
The Internet has created new opportunities for librarians to develop information systems that are readily accessible at the point of care. This paper describes the multiyear process used to justify, fund, design, develop, promote, and evaluate a rehabilitation prototype of a point-of-care, team-based information system (PoinTIS) and train health care providers to use this prototype for their spinal cord injury and traumatic brain injury patient care and education activities. PoinTIS is a successful model for librarians in the twenty-first century to serve as publishers of information created or used by their parent organizations and to respond to the opportunities for information dissemination provided by recent technological advances. [Abstract/Link to Full Text]

Hill DR, Stickell HN
Brandon/Hill selected list of print books and journals for the small medical library.
Bull Med Libr Assoc. 2001 Apr;89(2):131-53.
After thirty-six years of biennial updates, the authors take great pride in being able to publish the nineteenth version (2001) of the "Brandon/Hill Selected List of Print Books and Journals for the Small Medical Library." This list of 630 books and 143 journals is intended as a selection guide for health sciences libraries or similar facilities. It can also function as a core collection for a library consortium. Books and journals are categorized by subject; the book list is followed by an author/editor index, and the subject list of journals, by an alphabetical title listing. Due to continuing requests from librarians, a "minimal core list" consisting of 81 titles has been pulled out from the 217 asterisked (*) initial-purchase books and marked with daggers (dagger *) before the asterisks. To purchase the entire collection of 630 books and to pay for 143 2001 journal subscriptions would require $124,000. The cost of only the asterisked items, books and journals, totals $55,000. The "minimal core list" book collection costs approximately $14,300. [Abstract/Link to Full Text]

Ebell M
The Brandon/Hill list.
J Med Libr Assoc. 2002 Jan;90(1):111. [Abstract/Link to Full Text]

Walter PL
A small window on Janet Doe's life.
Bull Med Libr Assoc. 2001 Jan;89(1):83. [Abstract/Link to Full Text]

Fuller SS
Enabling, empowering, inspiring: research and mentorship through the years.
Bull Med Libr Assoc. 2000 Jan;88(1):1-10.
The interrelationship between research and mentorship in an association such as the Medical Library Association (MLA) is revealed through the contributions of individuals and significant association activities in support of research. Research is vital to the well-being and ultimate survival of health sciences librarianship and is not an ivory tower academic activity. Mentorship plays a critical role in setting a standard and model for those individuals who want to be involved in research and, ultimately, for the preparation of the next generation of health sciences librarians. Research and mentorship are discussed in the context of personal experiences, scholarship, and problem solving in a practice environment. Through research and mentorship, we are enabled to enhance our services and programs, empowered to look beyond our own operations for information puzzles to be solved, and inspired to serve society by improving health. [Abstract/Link to Full Text]

McClure LW
A tribute to knowledge.
Bull Med Libr Assoc. 2001 Jan;89(1):81-2. [Abstract/Link to Full Text]

Tennant MR, Butson LC, Rezeau ME, Tucker PJ, Boyle ME, Clayton G
Customizing for clients: developing a library liaison program from need to plan.
Bull Med Libr Assoc. 2001 Jan;89(1):8-20.
Building on the experiences of librarian representatives to curriculum committees in the colleges of dentistry, medicine, and nursing, the Health Science Center Libraries (HSCL) Strategic Plan recommended the formation of a Library Liaison Work Group to create a formal Library Liaison Program to serve the six Health Science Center (HSC) colleges and several affiliated centers and institutes. The work group's charge was to define the purpose and scope of the program, identify models of best practice, and recommend activities for liaisons. The work group gathered background information, performed an environmental scan, and developed a philosophy statement, a program of liaison activities focusing on seven primary areas, and a forum for liaison communication. Hallmarks of the plan included intensive subject specialization (beyond collection development), extensive communication with users, and personal information services. Specialization was expected to promote competence, communication, confidence, comfort, and customization. Development of the program required close coordination with other strategic plan implementation teams, including teams for collection development, education, and marketing. This paper discusses the HSCL's planning process and the resulting Library Liaison Program. Although focusing on an academic health center, the planning process and liaison model may be applied to any library serving diverse, subject-specific user populations. [Abstract/Link to Full Text]

Lipscomb CE
The library as laboratory.
Bull Med Libr Assoc. 2001 Jan;89(1):79-80. [Abstract/Link to Full Text]

Flannery MA
The laboratory as library metaphor and some reflections on professional practice.
Bull Med Libr Assoc. 2001 Jul;89(3):309-10. [Abstract/Link to Full Text]

Plutchak TS
What we don't know.
Bull Med Libr Assoc. 2001 Jan;89(1):77-8. [Abstract/Link to Full Text]

Eldredge JD, Guenther H
Historically significant journal articles: their identification in older bound journal volumes designated for weeding and the creation of new access to these articles.
Bull Med Libr Assoc. 2001 Jan;89(1):71-5. [Abstract/Link to Full Text]

Sievert ME, Patrick TB, Reid JC
Need a bloody nose be a nosebleed? or, lexical variants cause surprising results.
Bull Med Libr Assoc. 2001 Jan;89(1):68-71. [Abstract/Link to Full Text]

Fikar CR, Corral OL
Non-librarian health professionals becoming librarians and information specialists: results of an Internet survey.
Bull Med Libr Assoc. 2001 Jan;89(1):59-67.
OBJECTIVES: To obtain basic information about non-librarian health professionals who become librarians and information specialists. METHODS: The survey was a Web-based questionnaire. A non-random sample of persons was obtained by posting messages to several large Internet electronic discussion groups. Individuals who met the selection criteria and were willing to participate filled out a Web-based form designed using common gateway interface (CGI) programming. RESULTS: 118 forms were analyzed. Three subgroups of participants were identified and statistical comparisons among these groups were carried out for many of the quantitative questions. Information concerning reasons they left their original field; factors influencing their choice of the field of library and information science; reactions of family, friends, and colleagues; and interactions with patrons and other information about this group was obtained and summarized. A health sciences background was seen as helpful in the new career as information specialist. Most people were happy with their new profession despite negative reactions from colleagues, relatives, and, occasionally, patrons. Feelings of regret and abandonment of their patients were noted by some. Many persons did not know that peers had made similar career changes. CONCLUSIONS: A health sciences background imparts an expertise in both the vocabulary and subject matter of medicine that non-biomedical individuals would not ordinarily have. Although becoming a librarian may be perceived as a very positive career change for an individual, societal opinion and pressure can make such a career change difficult. Nevertheless, participants in this survey demonstrate a high level of satisfaction with their new careers and are quite happy with their work. [Abstract/Link to Full Text]

Atlas MC
Ethics and access to teaching materials in the medical library: the case of the Pernkopf atlas.
Bull Med Libr Assoc. 2001 Jan;89(1):51-8.
Conflicts can occur between the principle of freedom of information treasured by librarians and ethical standards of scientific research involving the propriety of using data derived from immoral or dishonorable experimentation. A prime example of this conflict was brought to the attention of the medical and library communities in 1995 when articles claiming that the subjects of the illustrations in the classic anatomy atlas, Eduard Pernkopf's Topographische Anatomie des Menschen, were victims of the Nazi holocaust. While few have disputed the accuracy, artistic, or educational value of the Pernkopf atlas, some have argued that the use of such subjects violates standards of medical ethics involving inhuman and degrading treatment of subjects or disrespect of a human corpse. Efforts were made to remove the book from medical libraries. In this article, the history of the Pernkopf atlas and the controversy surrounding it are reviewed. The results of a survey of academic medical libraries concerning their treatment of the Pernkopf atlas are reported, and the ethical implications of these issues as they affect the responsibilities of librarians is discussed. [Abstract/Link to Full Text]

Hover LM
Note to "Ethics and Access to Teaching Material in the Medical Library: The Case of the Pernkopf Atlas".
Bull Med Libr Assoc. 2001 Jul;89(3):309. [Abstract/Link to Full Text]

Braude RM, Shirinyan A, Zargaryan T
Republican Scientific-Medical Library, The Republic of Armenia: progress and programs.
Bull Med Libr Assoc. 2001 Jan;89(1):45-50.
In 1990, the Republican Scientific-Medical Library (RSML) of the Ministry of Health of Armenia in collaboration with the Fund for Armenian Relief created a vision of a national library network supported by information technology. This vision incorporated four goals: (1) to develop a national resource collection of biomedical literature accessible to all health professionals, (2) to develop a national network for access to bibliographic information, (3) to develop a systematic mechanism for sharing resources, and (4) to develop a national network of health sciences libraries. During the last decade, the RSML has achieved significant progress toward all four goals and has realized its vision of becoming a fully functional national library. The RSML now provides access to the literature of the health sciences including access to the Armenian medical literature, provides education and training to health professionals and health sciences librarians, and manages a national network of libraries of the major health care institutions in Armenia. The RSML is now able to provide rapid access to the biomedical literature and train health professionals and health sciences librarians in Armenia in information system use. This paper describes the evolution of the RSML and how it was accomplished. [Abstract/Link to Full Text]

Richwine MP, McGowan JJ
A rural virtual health sciences library project: research findings with implications for next generation library services.
Bull Med Libr Assoc. 2001 Jan;89(1):37-44.
PURPOSE: The Shared Hospital Electronic Library of Southern Indiana (SHELSI) research project was designed to determine whether access to a virtual health sciences library and training in its use would support medical decision making in rural southern Indiana and achieve the same level of impact seen by targeted information services provided by health sciences librarians in urban hospitals. METHODS: Based on the results of a needs assessment, a virtual medical library was created; various levels of training were provided. Virtual library users were asked to complete a Likert-type survey, which included questions on intent of use and impact of use. At the conclusion of the project period, structured interviews were conducted. RESULTS: Impact of the virtual health sciences library showed a strong correlation with the impact of information provided by health sciences librarians. Both interventions resulted in avoidance of adverse health events. Data collected from the structured interviews confirmed the perceived value of the virtual library. CONCLUSION: While librarians continue to hold a strong position in supporting information access for health care providers, their roles in the information age must begin to move away from providing information toward selecting and organizing knowledge resources and instruction in their use. [Abstract/Link to Full Text]

Morris RC
Online tables of contents for books: effect on usage.
Bull Med Libr Assoc. 2001 Jan;89(1):29-36.
OBJECTIVES: To explore whether the presence of online tables of contents (TOC) in an online catalog affects circulation (checkouts and inhouse usage). Two major questions were posed: (1) did the presence of online tables of contents for books increase use, and, (2) if it did, what factors might cause the increase? METHOD: A randomized and stratified design was used in tracking usage of 3,957 book titles that were previously divided into two groups: one with TOC and one without TOC. Stratification was done for year of imprint, location, subject, previous use, circulating or non-circulating status, and presence of TOC. The use was tracked by the online catalog statistics in the InnoPac online catalog for fourteen months. RESULTS: The study found that tables of contents do increase usage. It also showed a correlation in the size of the effect based on the currency of the titles. In general, even after adjusting for all of the variables (publication date, location, circulation status, subject, and previous use), the odds of a title being used increased by 45% if the titles had online tables of contents, a statistically significant impact at the 0.05 level. CONCLUSIONS: This case-control study presents new information about the impact on circulation and inhouse use when tables of contents for books are added to the online catalog record. The study helps to establish the positive role of tables of contents in online catalogs. The research establishes TOC as a major parameter that can be successfully studied using quantitative methods. The study also provides information professionals with some guidance on when enhancement of TOC is likely to be most effective in increasing the use of existing collections. [Abstract/Link to Full Text]

Shaw-Kokot J, de la Varre C
Using a journal availability study to improve access.
Bull Med Libr Assoc. 2001 Jan;89(1):21-8.
PURPOSE: Identify journal collection access and use factors. SETTING AND SUBJECTS: University of North Carolina at Chapel Hill's Health Sciences Library patrons. METHODOLOGY: Survey forms and user interactions were monitored once a week for twelve weeks during the fall 1997 semester. The project was based on a 1989 New Mexico State University study and used Kantor's Branching Analysis to measure responses. RESULT: 80% of reported sought journal articles were found successfully. Along with journal usage data, the library obtained demographic and behavioral information. DISCUSSION AND CONCLUSIONS: Journals are the library's most used resource and, even as more electronic journals are offered, print journals continue to make up the majority of the collection. Several factors highlighted the need to study journal availability. User groups indicated that finding journals was problematic, and internal statistics showed people requesting interlibrary loans for owned items. The study looked at success rates, time, and ease of finding journals. A variety of reasons contributed to not finding journals. While overall user reports indicated relatively high success rate and satisfaction, there were problems to be addressed. As the library proceeds in redesigning both the physical space and electronic presence, the collected data have provided valuable direction. [Abstract/Link to Full Text]

Messerle J
The road not taken.
Bull Med Libr Assoc. 2001 Jan;89(1):1-7.
The annual Janet Doe Lecture was established in 1966 to honor Janet Doe, emerita librarian of the New York Academy of Medicine. The lecture focuses on either the history or philosophy of health sciences librarianship. This lecture addresses three fundamental values of the field, highlighting basic beliefs of the profession that are at risk: privacy, intellectual property rights, and access to quality information. It calls upon readers to make the everyday choices required to keep the value system of health sciences librarianship in place. Robert Frost's poignant poem "The Road Not Taken" provides the metaphor for examining choices in an information economy. [Abstract/Link to Full Text]

Lipscomb CE
Clinical librarianship.
Bull Med Libr Assoc. 2000 Oct;88(4):393-5. [Abstract/Link to Full Text]

Plutchak TS
Informationists and librarians.
Bull Med Libr Assoc. 2000 Oct;88(4):391-2. [Abstract/Link to Full Text]

Giuse NB
Advancing the practice of clinical medical librarianship.
Bull Med Libr Assoc. 1997 Oct;85(4):437-8. [Abstract/Link to Full Text]

Giuse NB, Kafantaris SR, Miller MD, Wilder KS, Martin SL, Sathe NA, Campbell JD
Clinical medical librarianship: the Vanderbilt experience.
Bull Med Libr Assoc. 1998 Jul;86(3):412-6. [Abstract/Link to Full Text]

Spatz MA
Providing consumer health information in the rural setting: Planetree Health Resource Center's approach.
Bull Med Libr Assoc. 2000 Oct;88(4):382-8.
Both lifestyle and geography make the delivery of consumer health information in the rural setting unique. The Planetree Health Resource Center in The Dalles, Oregon, has served the public in a rural setting for the past eight years. It is a community-based consumer health library, affiliated with a small rural hospital, Mid-Columbia Medical Center. One task of providing consumer health information in rural environments is to be in relationship with individuals in the community. Integration into community life is very important for credibility and sustainability. The resource center takes a proactive approach and employs several different outreach efforts to deepen its relationship with community members. It also works hard to foster partnerships for improved health information delivery with other community organizations, including area schools. This paper describes Planetree Health Resource Center's approach to rural outreach. [Abstract/Link to Full Text]

Guard R, Fredericka TM, Kroll S, Marine S, Roddy C, Steiner T, Wentz S
Health care, information needs, and outreach: reaching Ohio's rural citizens.
Bull Med Libr Assoc. 2000 Oct;88(4):374-81.
As a rural state, Ohio has a vital interest in addressing rural health and information needs. NetWellness is a Web-based consumer health information service that focuses on the needs of the residents of Ohio. Health sciences faculty from the state's three Carnegie Research I universities--University of Cincinnati, Case Western Reserve University, and The Ohio State University--create and evaluate content and provide Ask an Expert service to all visitors. Through partnerships at the state and local levels, involving public, private, commercial, and noncommercial organizations, NetWellness has grown from a regional demonstration project in 1995 to a key statewide service. Collaboration with public libraries, complemented by alliances with kindergarten through twelfth grade agencies, makes NetWellness Ohio's essential health information resource. [Abstract/Link to Full Text]

McCloskey KM
Library outreach: addressing Utah's "Digital Divide".
Bull Med Libr Assoc. 2000 Oct;88(4):367-73.
A "Digital Divide" in information and technological literacy exists in Utah between small hospitals and clinics in rural areas and the larger health care institutions in the major urban area of the state. The goals of the outreach program of the Spencer S. Eccles Health Sciences Library at the University of Utah address solutions to this disparity in partnership with the National Network of Libraries of Medicine-- Midcontinental Region, the Utah Department of Health, and the Utah Area Health Education Centers. In a circuit-rider approach, an outreach librarian offers classes and demonstrations throughout the state that teach information-access skills to health professionals. Provision of traditional library services to unaffiliated health professionals is integrated into the library's daily workload as a component of the outreach program. The paper describes the history, methodology, administration, funding, impact, and results of the program. [Abstract/Link to Full Text]

McDuffee DC
AHEC library services: from circuit rider to virtual librarian. Area Health Education Centers.
Bull Med Libr Assoc. 2000 Oct;88(4):362-6.
The North Carolina Area Health Education Centers Library and Information Services (NC AHEC LIS) Network provides library outreach services to rural health care providers in all nine AHEC regions of North Carolina. Over the last twenty-five years, the AHEC and university-based librarians have collaborated to create a model program for support of community-based clinical education and information access for rural health care providers. Through several collaborative projects, they have supported Internet access for rural health clinics. The NC AHEC Digital Library--under development by NC AHEC, University of North Carolina at Chapel Hill, Duke University, East Carolina University, and Wake Forest University--will further extend access to electronic biomedical information and resources to health professionals in a statewide digital library. [Abstract/Link to Full Text]

McGowan JJ
Health information outreach: the land-grant mission.
Bull Med Libr Assoc. 2000 Oct;88(4):355-61.
Service to the state is one of the core principles of the land-grant mission. This concept of service is also fundamental to a significant number of outreach activities in academic health sciences libraries, particularly those libraries affiliated with the public land-grant universities. The Dana Medical Library at the University of Vermont has a lengthy tradition of outreach to health care providers and health care consumers of the State of Vermont. Building on the foundation of the land-grant institution-which grew out of federal legislation introduced in the mid nineteenth century by Justin Morrill, Vermont's congressional representative--the Dana Medical Library has based its outreach activities on its dedication of service to the state in the promotion of healthy citizens through information dissemination in support of health care delivery. Reengineering library services designed to meet the specific information needs of its diverse clientele, partnering with disparate health care organizations, and relying on fees for service to expand its outreach activities, the Dana Medical Library has redefined the concept of health information outreach for the new millennium. [Abstract/Link to Full Text]

Dorsch JL
Information needs of rural health professionals: a review of the literature.
Bull Med Libr Assoc. 2000 Oct;88(4):346-54.
This review analyzes the existing research on the information needs of rural health professionals and relates it to the broader information-needs literature to establish whether the information needs of rural health professionals differ from those of other health professionals. The analysis of these studies indicates that rural health practitioners appear to have the same basic needs for patient-care information as their urban counterparts, and that both groups rely on colleagues and personal libraries as their main sources of information. Rural practitioners, however, tend to make less use of journals and online databases and ask fewer clinical questions; a difference that correlates with geographic and demographic factors. Rural practitioners experience pronounced barriers to information access including lack of time, isolation, inadequate library access, lack of equipment, lack of skills, costs, and inadequate Internet infrastructure. Outreach efforts to this group of underserved health professionals must be sustained to achieve equity in information access and to change information-seeking behaviors. [Abstract/Link to Full Text]

Pifalo V
The evolution of rural outreach from Package Library to Grateful Med: introduction to the symposium.
Bull Med Libr Assoc. 2000 Oct;88(4):339-45.
Outreach is now a prevailing activity in health sciences libraries. As an introduction to a series of papers on current library outreach to rural communities, this paper traces the evolution of such activities by proponents in health sciences libraries from 1924 to 1992. Definitions of rural and outreach are followed by a consideration of the expanding audience groups. The evolution in approaches covers the package library and enhancements in extension service, library development, circuit librarianship, and self-service arrangements made possible by such programs as the Georgia Interactive Network (GaIN) and Grateful Med. [Abstract/Link to Full Text]

Hartley J
Clarifying the abstracts of systematic literature reviews.
Bull Med Libr Assoc. 2000 Oct;88(4):332-7.
BACKGROUND: There is a small body of research on improving the clarity of abstracts in general that is relevant to improving the clarity of abstracts of systematic reviews. OBJECTIVES: To summarize this earlier research and indicate its implications for writing the abstracts of systematic reviews. METHOD: Literature review with commentary on three main features affecting the clarity of abstracts: their language, structure, and typographical presentation. CONCLUSIONS: The abstracts of systematic reviews should be easier to read than the abstracts of medical research articles, as they are targeted at a wider audience. The aims, methods, results, and conclusions of systematic reviews need to be presented in a consistent way to help search and retrieval. The typographic detailing of the abstracts (type-sizes, spacing, and weights) should be planned to help, rather than confuse, the reader. [Abstract/Link to Full Text]

Hersh WR, Crabtree MK, Hickam DH, Sacherek L, Rose L, Friedman CP
Factors associated with successful answering of clinical questions using an information retrieval system.
Bull Med Libr Assoc. 2000 Oct;88(4):323-31.
OBJECTIVES: Despite the growing use of online databases by clinicians, there has been very little research documenting how effectively they are used. This study assessed the ability of medical and nurse-practitioner students to answer clinical questions using an information retrieval system. It also attempted to identify the demographic, experience, cognitive, personality, search mechanics, and user-satisfaction factors associated with successful use of a retrieval system. METHODS: Twenty-nine students completed questionnaires of clinical and computer experience as well as tests of cognitive abilities and personality type. They were then administered three clinical questions to answer in a medical library setting using the MEDLINE database and electronic and print full-text resources. RESULTS: Medical students were able to answer more questions correctly than nurse-practitioner students before and after searching, but both had comparable improvements in the number of correct questions before and after searching. Successful ability to answer questions was also associated with having experience in literature searching and higher standardized test-score percentiles. CONCLUSIONS: Medical and nurse-practitioner students obtained comparable benefits in the ability to answer clinical questions from use of the information retrieval system. Future research must examine strategies that improve successful search and retrieval of clinical questions posed by clinicians in practice. [Abstract/Link to Full Text]

Wood FB, Lyon B, Schell MB, Kitendaugh P, Cid VH, Siegel ER
Public library consumer health information pilot project: results of a National Library of Medicine evaluation.
Bull Med Libr Assoc. 2000 Oct;88(4):314-22.
In October 1998, the National Library of Medicine (NLM) launched a pilot project to learn about the role of public libraries in providing health information to the public and to generate information that would assist NLM and the National Network of Libraries of Medicine (NN/LM) in learning how best to work with public libraries in the future. Three regional medical libraries (RMLs), eight resource libraries, and forty-one public libraries or library systems from nine states and the District of Columbia were selected for participation. The pilot project included an evaluation component that was carried out in parallel with project implementation. The evaluation ran through September 1999. The results of the evaluation indicated that participating public librarians were enthusiastic about the training and information materials provided as part of the project and that many public libraries used the materials and conducted their own outreach to local communities and groups. Most libraries applied the modest funds to purchase additional Internet-accessible computers and/or upgrade their health-reference materials. However, few of the participating public libraries had health information centers (although health information was perceived as a top-ten or top-five topic of interest to patrons). Also, the project generated only minimal usage of NLM's consumer health database, known as MEDLINEplus, from the premises of the monitored libraries (patron usage from home or office locations was not tracked). The evaluation results suggested a balanced follow-up by NLM and the NN/LM, with a few carefully selected national activities, complemented by a package of targeted activities that, as of January 2000, are being planned, developed, or implemented. The results also highlighted the importance of building an evaluation component into projects like this one from the outset, to assure that objectives were met and that evaluative information was available on a timely basis, as was the case here. [Abstract/Link to Full Text]

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Recent Articles in Journal of the American Medical Informatics Association

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Ford EW, Menachemi N, Phillips MT
Predicting the adoption of electronic health records by physicians: when will health care be paperless?
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):106-12.
OBJECTIVES: The purpose of this study was threefold. First, we gathered and synthesized the historic literature regarding electronic health record (EHR) adoption rates among physicians in small practices (ten or fewer members). Next, we constructed models to project estimated future EHR adoption trends and timelines. We then determined the likelihood of achieving universal EHR adoption in the near future and articulate how barriers can be overcome in the small and solo practice medical environment. DESIGN: This study used EHR adoption data from six previous surveys of small practices to estimate historic market penetration rates. Applying technology diffusion theory, three future adoption scenarios, optimistic, best estimate, and conservative, are empirically derived. MEASUREMENT: EHR adoption parameters, external and internal coefficients of influence, are estimated using Bass diffusion models. RESULTS: All three EHR scenarios display the characteristic diffusion S curve that is indicative that the technology is likely to achieve significant market penetration, given enough time. Under current conditions, EHR adoption will reach its maximum market share in 2024 in the small practice setting. CONCLUSION: The promise of improved care quality and cost control has prompted a call for universal EHR adoption by 2014. The EHR products now available are unlikely to achieve full diffusion in a critical market segment within the time frame being targeted by policy makers. [Abstract/Link to Full Text]

Shea S, Weinstock RS, Starren J, Teresi J, Palmas W, Field L, Morin P, Goland R, Izquierdo RE, Wolff LT, Ashraf M, Hilliman C, Silver S, Meyer S, Holmes D, Petkova E, Capps L, Lantigua RA
A randomized trial comparing telemedicine case management with usual care in older, ethnically diverse, medically underserved patients with diabetes mellitus.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):40-51.
BACKGROUND: Telemedicine is a promising but largely unproven technology for providing case management services to patients with chronic conditions who experience barriers to access to care or a high burden of illness. METHODS: The authors conducted a randomized, controlled trial comparing telemedicine case management to usual care, with blinding of those obtaining outcome data, in 1,665 Medicare recipients with diabetes, aged 55 years or greater, and living in federally designated medically underserved areas of New York State. The primary endpoints were HgbA1c, blood pressure, and low-density lipoprotein (LDL) cholesterol levels. RESULTS: In the intervention group (n = 844), mean HgbA1c improved over one year from 7.35% to 6.97% and from 8.35% to 7.42% in the subgroup with baseline HgbA1c > or =7% (n = 353). In the usual care group (n = 821) mean HgbA1c improved over one year from 7.42% to 7.17%. Adjusted net reductions (one-year minus baseline mean values in each group, compared between groups) favoring the intervention were as follows: HgbA1c, 0.18% (p = 0.006), systolic and diastolic blood pressure, 3.4 (p = 0.001) and 1.9 mm Hg (p < 0.001), and LDL cholesterol, 9.5 mg/dL (p < 0.001). In the subgroup with baseline HgbA1c > or =7%, net adjusted reduction in HgbA1c favoring the intervention group was 0.32% (p = 0.002). Mean LDL cholesterol level in the intervention group at one year was 95.7 mg/dL. The intervention effects were similar in magnitude in the subgroups living in New York City and upstate New York. CONCLUSION: Telemedicine case management improved glycemic control, blood pressure levels, and total and LDL cholesterol levels at one year of follow-up. [Abstract/Link to Full Text]

Miller RA, Groth T, Hasman A, Haux R, McCray AT, Safran C, Shortliffe EH
On Exemplary Scientific Conduct Regarding Submission of Manuscripts to Biomedical Informatics Journals.
J Am Med Inform Assoc. 2005 Oct 12;
As the Editors of leading international biomedical informatics journals, the authors report on a recent pattern of improper manuscript submissions to journals in our field. As a guide for future authors, we describe ethical and pragmatic issues related to submitting work for peer-reviewed journal publication. We propose a coordinated approach to the problem that our respective journals will follow. This Editorial is being jointly published in the following journals represented by the authors: Computer METHODS and Programs in Biomedicine, International Journal of Medical Informatics, Journal of Biomedical Informatics, Journal of the American Medical Informatics Association, and Methods of Information in Medicine. [Abstract/Link to Full Text]

Harris AD, McGregor JC, Perencevich EN, Furuno JP, Zhu J, Peterson DE, Finkelstein J
The use and interpretation of quasi-experimental studies in medical informatics.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):16-23.
Quasi-experimental study designs, often described as nonrandomized, pre-post intervention studies, are common in the medical informatics literature. Yet little has been written about the benefits and limitations of the quasi-experimental approach as applied to informatics studies. This paper outlines a relative hierarchy and nomenclature of quasi-experimental study designs that is applicable to medical informatics intervention studies. In addition, the authors performed a systematic review of two medical informatics journals, the Journal of the American Medical Informatics Association (JAMIA) and the International Journal of Medical Informatics (IJMI), to determine the number of quasi-experimental studies published and how the studies are classified on the above-mentioned relative hierarchy. They hope that future medical informatics studies will implement higher level quasi-experimental study designs that yield more convincing evidence for causal links between medical informatics interventions and outcomes. [Abstract/Link to Full Text]

Zhang L, Halper M, Perl Y, Geller J, Cimino JJ
Relationship structures and semantic type assignments of the UMLS Enriched Semantic Network.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):657-66.
OBJECTIVE: The Enriched Semantic Network (ESN) was introduced as an extension of the Unified Medical Language System (UMLS) Semantic Network (SN). Its multiple subsumption configuration and concomitant multiple inheritance make the ESN's relationship structures and semantic type assignments different from those of the SN. A technique for deriving the relationship structures of the ESN's semantic types and an automated technique for deriving the ESN's semantic type assignments from those of the SN are presented. DESIGN: The technique to derive the ESN's relationship structures finds all newly inherited relationships in the ESN. All such relationships are audited for semantic validity, and the blocking mechanism is used to block invalid relationships. The mapping technique to derive the ESN's semantic type assignments uses current SN semantic type assignments and preserves nonredundant categorizations, while preventing new redundant categorizations. RESULTS: Among the 426 newly inherited relationships, 326 are deemed valid. Seven blockings are applied to avoid inheritance of the 100 invalid relationships. Sixteen semantic types have different relationship structures in the ESN as compared to those in the SN. The mapping of semantic type assignments from the SN to the ESN avoids the generation of 26,950 redundant categorizations. The resulting ESN contains 138 semantic types, 149 IS-A links, 7,303 relationships, and 1,013,876 semantic type assignments. CONCLUSION: The ESN's multiple inheritance provides more complete relationship structures than in the SN. The ESN's semantic type assignments avoid the existing redundant categorizations appearing in the SN and prevent new ones that might arise due to multiple parents. Compared to the SN, the ESN provides a more accurate unifying semantic abstraction of the UMLS Metathesaurus. [Abstract/Link to Full Text]

Bath PA, Craigs C, Maheswaran R, Raymond J, Willett P
Use of graph theory to identify patterns of deprivation and high morbidity and mortality in public health data sets.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):630-41.
OBJECTIVE: An important part of public health is identifying patterns of poor health and deprivation. Specific patterns of poor health may be associated with features of the geographic environment where contamination or pollution may be occurring. For example, there may be clusters of poor health surrounding nuclear power stations, whereas major roads or rivers may be associated with areas of poor health alongside the feature in chains. Current methods are limited in their capacity to search for complex patterns in geographic data sets. The objective of this study was to determine whether graph theory could be used to identify patterns of geographic areas that have high levels of deprivation, morbidity, and mortality in a public health database. The geographic areas used in the study were enumeration districts (EDs), which are the lowest level of census geography in England and Wales, representing on average 200 households in the 1991 census. More specifically, the study aimed to identify chains of EDs with high deprivation, morbidity, and mortality that might be adjacent to specific types of geographic features, i.e., rivers or major roads. DESIGN: The maximum common subgraph (MCS) algorithm was used to search for seven query patterns of deprivation and poor health within the Trent region. Query pattern 1 represented a linear chain of five EDs and query patterns 2 to 7 represented the possible clusters of the five EDs. To identify chains of EDs with high deprivation, morbidity, and mortality, the results from the query patterns 2 to 7 were used to remove patterns (option 1) and EDs (option 2) from the results of query pattern 1. MEASUREMENTS: Data on the Townsend Material Deprivation Index, standardized long-term limiting illness and standardized all-cause mortality rates were used for the 10,665 EDs within the Trent region. RESULTS: The MCS algorithm retrieved a range of patterns and EDs from the database for the queries. Query pattern 1 identified 3,838 patterns containing a total of 195 EDs. When the patterns retrieved using query patterns 2 to 7 were removed from the 3,838 patterns using option 1, 1,704 patterns remained containing 161 EDs. When the EDs retrieved using query patterns 2 to 7 were removed from the 195 EDs identified by query pattern 1 using option 2, 12 EDs remained. The MCS algorithm was therefore able to reduce the numbers of patterns and EDs to allow manual examination for chains of EDs and for that which might be associated with them. CONCLUSION: The study demonstrates the potential of the MCS algorithm for searching for specific patterns of need. This method has potential for identifying such patterns in relation to local geographic features for public health. [Abstract/Link to Full Text]

Harris PA, Lane L, Biaggioni I
Clinical research subject recruitment: the Volunteer for Vanderbilt Research Program www.volunteer.mc.vanderbilt.edu.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):608-13.
This article provides information concerning a novel research subject recruitment registry developed at Vanderbilt University. Project goals were (1) to provide a mechanism for lay individuals to self-enter information conveying interest in volunteering for clinical research and (2) provide tools for researchers to select and contact potential volunteers based on study-specific inclusion criteria. The registry was built and offered as an institutional resource to all university scientists conducting institutional review board-approved research. The authors present (1) a model for redesigning workflow associated with subject registration, volunteer retrieval, and subject contact; (2) details of a Web-based software application used as a focal point in designing workflow for our system; (3) descriptive statistics for volunteer and researcher use of the system during the first 32 months of operation; (4) cost estimates for the project; and (5) a set of recommendations for other medical centers wishing to adopt similar methodology. [Abstract/Link to Full Text]

Moen A, Brennan PF
Health@Home: the work of health information management in the household (HIMH): implications for consumer health informatics (CHI) innovations.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):648-56.
OBJECTIVE: Contemporary health care places enormous health information management demands on laypeople. Insights into their skills and habits complements current developments in consumer health innovations, including personal health records. Using a five-element human factors model of work, health information management in the household (HIMH) is characterized by the tasks completed by individuals within household organizations, using certain tools and technologies in a given physical environment. DESIGN: We conducted a descriptive-exploratory study of the work of HIMH, involving 49 community-dwelling volunteers from a rural Midwestern community. MEASUREMENTS: During in-person interviews, we collected data using semistructured questionnaires and photographs of artifacts used for HIMH. RESULTS: The work of HIMH is largely the responsibility of a single individual, primarily engaged in the tasks of acquiring, managing, and organizing a diverse set of health information. Paper-based tools are most common, and residents develop strategies for storing information in the household environment aligned with anticipated use. Affiliative relationships, e.g., parent-child or spousal, within the household serve as the organization that gives rise to health information management practices. Synthesis of these findings led to identification of several storage strategies employed in HIMH. These strategies are labeled "just-in-time," "just-because," "just-in-case," and "just-at-hand," reflecting location of the artifacts of health information and anticipated urgency in the need to retrieve it. CONCLUSION: Laypeople develop and employ robust, complex strategies for managing health information in the home. Capitalizing on these strategies will complement and extend current consumer health innovations to provide functional support to people who face increasing demands to manage personal health information. [Abstract/Link to Full Text]

Park RW, Shin SS, Choi YI, Ahn JO, Hwang SC
Computerized physician order entry and electronic medical record systems in Korean teaching and general hospitals: results of a 2004 survey.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):642-7.
OBJECTIVE: To determine the availability of computerized physician order entry (CPOE) and electronic medical record (EMR) systems in teaching and general hospitals in the Republic of Korea. DESIGN: A combined mail and telephone survey of 283 hospitals. MEASUREMENTS: The surveys assessed the availability of CPOE and EMRs in the hospitals, as well as inducement, participation, and saturation regarding CPOE use by physicians. RESULTS: A total of 122 (43.1%) hospitals responded to the survey. The complete form of CPOE was available in 98 (80.3%) hospitals. The use of CPOE was mandatory in 92 (86.0%) of the 107 hospitals that responded to the questions regarding the requirement of CPOE use. In 85 (79.4%) of the hospitals in which CPOE was in use, more than 90% of physicians used the system. In addition, physicians entered more than 90% of their total orders through CPOE in 87 (81.3%) hospitals. In contrast, a complete EMR system was available in only 11 (9.0%) of the hospitals. CONCLUSION: Of the teaching and general hospitals in the Republic of Korea that responded to the survey, the majority (80.3%) have CPOE systems, and a complete EMR system is available in only 9%. [Abstract/Link to Full Text]

Mosis G, Vlug AE, Mosseveld M, Dieleman JP, Stricker BC, van der Lei J, Sturkenboom MC
A technical infrastructure to conduct randomized database studies facilitated by a general practice research database.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):602-7.
General practice research databases are increasingly used to study intended and unintended effects of treatments. However, confounding by indication remains a major problem. The randomized database study methodology has been proposed as a method to combine the strengths of observational database (generalizability) and the strength of the randomized clinical trial (RCT) design (randomization). We developed an infrastructure that enables the execution of randomized database studies with treatment randomization facilitated by a general practice research database. The requirements posed by the methodology of randomized database studies were facilitated by software components. Our assessment showed that it is technically possible to conduct randomized trials in general practice according to the randomized database design. The infrastructure facilitated the conduct of randomized database studies in general practice but some practical difficulties and methodological issues remain. The technical infrastructure seems to be both promising and potentially feasible to facilitate future randomized database studies, although the methodology needs to be evaluated in more detail. [Abstract/Link to Full Text]

Chapman WW, Dowling JN, Wagner MM
Generating a reliable reference standard set for syndromic case classification.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):618-29.
OBJECTIVE: To generate and measure the reliability for a reference standard set with representative cases from seven broad syndromic case definitions and several narrower syndromic definitions used for biosurveillance. DESIGN: From 527,228 eligible patients between 1990 and 2003, we generated a set of patients potentially positive for seven syndromes by classifying all eligible patients according to their ICD-9 primary discharge diagnoses. We selected a representative subset of the cases for chart review by physicians, who read emergency department reports and assigned values to 14 variables related to the seven syndromes. MEASUREMENTS: (1) Positive predictive value of the ICD-9 diagnoses; (2) prevalence of the syndromic definitions and related variables; (3) agreement between physician raters demonstrated by kappa, kappa corrected for bias and prevalence, and Finn's r; and (4) reliability of the reference standard classifications demonstrated by generalizability coefficients. RESULTS: Positive predictive value for ICD-9 classification ranged from 0.33 for botulinic to 0.86 for gastrointestinal. We generated between 80 and 566 positive cases for six of the seven syndromic definitions. Rash syndrome exhibited low prevalence (34 cases). Agreement between physician raters was high, with kappa > 0.70 for most variables. Ratings showed no bias. Finn's r was >0.70 for all variables. Generalizability coefficients were >0.70 for all variables but three. CONCLUSION: Of the 27 syndromes generated by the 14 variables, 21 showed high enough prevalence, agreement, and reliability to be used as reference standard definitions against which an automated syndromic classifier could be compared. Syndromic definitions that showed poor agreement or low prevalence include febrile botulinic syndrome, febrile and nonfebrile rash syndrome, respiratory syndrome explained by a nonrespiratory or noninfectious diagnosis, and febrile and nonfebrile gastrointestinal syndrome explained by a nongastrointestinal or noninfectious diagnosis. [Abstract/Link to Full Text]

Evans RS, Johnson KV, Flint VB, Kinder T, Lyon CR, Hawley WL, Vawdrey DK, Thomsen GE
Enhanced notification of critical ventilator events.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):589-95.
Mechanical ventilators are designed to generate alarms when patients become disconnected or experience other critical ventilator events. However, these alarms can blend in with other accustomed sounds of the intensive care unit. Ventilator alarms that go unnoticed for extended periods of time often result in permanent patient harm or death. We developed a system to monitor critical ventilator events through our existing hospital network. Whenever an event is identified, the new system takes control of every computer in the patient's intensive care unit and generates an enhanced audio and visual alert indicating that there is a critical ventilator event and identifies the room number. Once the alert is acknowledged or the event is corrected, all the computers are restored back to the pre-alert status and/or application. This paper describes the development and implementation of this system and reports the initial results, user acceptance, and the increase in valuable information and patient safety. [Abstract/Link to Full Text]

Halamka J, Aranow M, Ascenzo C, Bates D, Debor G, Glaser J, Goroll A, Stowe J, Tripathi M, Vineyard G
Health care IT collaboration in Massachusetts: the experience of creating regional connectivity.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):596-601.
The state of Massachusetts has significant early experience in planning for and implementing interoperability networks for exchange of clinical and financial data. Members of our evolving data-sharing organizations gained valuable experience that is of potential benefit to others regarding the governance, policies, and technologies underpinning regional health information organizations. We describe the history, roles, and evolution of organizations and their plans for and success with pilot projects. [Abstract/Link to Full Text]

Berner ES, Moss J
Informatics challenges for the impending patient information explosion.
J Am Med Inform Assoc. 2005 Nov-Dec;12(6):614-7.
As we move toward an era when health information is more readily accessible and transferable, there are several issues that will arise. This article addresses the challenges of information filtering, context-sensitive decision support, legal and ethical guidelines regarding obligations to obtain and use the information, aligning patient and health professionals' expectations in regard to the use and usefulness of the information, and enhancing data reliability. The authors discuss the issues and offer suggestions for addressing them. [Abstract/Link to Full Text]

Ketchell DS, St Anna L, Kauff D, Gaster B, Timberlake D
PrimeAnswers: A practical interface for answering primary care questions.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):537-45.
This paper describes an institutional approach taken to build a primary care reference portal. The objective for the site is to make access to and use of clinical reference faster and easier and to facilitate the use of evidence-based answers in daily practice. Reference objects were selected and metadata applied to a core set of sources. Metadata were used to search, sort, and filter results and to define deep-linked queries and structure the interface. User feedback resulted in an expansion in the scope of reference objects to meet the broad spectrum of information needs, including patient handouts and interactive risk management tools. RESULTS of a user satisfaction survey suggest that a simple interface to customized content makes it faster and easier for primary care clinicians to find information during the clinic day and to improve care to their patients. The PrimeAnswers portal is a first step in creating a fast search of a customized set of reference objects to match a clinician's patient care questions in the clinic. The next step is developing methods to solve the problem of matching a clinician's question to a specific answer through precise retrieval from reference sources; however, lack of internal structure and Web service standards in most clinical reference sources is an unresolved problem. [Abstract/Link to Full Text]

Poissant L, Pereira J, Tamblyn R, Kawasumi Y
The impact of electronic health records on time efficiency of physicians and nurses: a systematic review.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):505-16.
A systematic review of the literature was performed to examine the impact of electronic health records (EHRs) on documentation time of physicians and nurses and to identify factors that may explain efficiency differences across studies. In total, 23 papers met our inclusion criteria; five were randomized controlled trials, six were posttest control studies, and 12 were one-group pretest-posttest designs. Most studies (58%) collected data using a time and motion methodology in comparison to work sampling (33%) and self-report/survey methods (8%). A weighted average approach was used to combine results from the studies. The use of bedside terminals and central station desktops saved nurses, respectively, 24.5% and 23.5% of their overall time spent documenting during a shift. Using bedside or point-of-care systems increased documentation time of physicians by 17.5%. In comparison, the use of central station desktops for computerized provider order entry (CPOE) was found to be inefficient, increasing the work time from 98.1% to 328.6% of physician's time per working shift (weighted average of CPOE-oriented studies, 238.4%). Studies that conducted their evaluation process relatively soon after implementation of the EHR tended to demonstrate a reduction in documentation time in comparison to the increases observed with those that had a longer time period between implementation and the evaluation process. This review highlighted that a goal of decreased documentation time in an EHR project is not likely to be realized. It also identified how the selection of bedside or central station desktop EHRs may influence documentation time for the two main user groups, physicians and nurses. [Abstract/Link to Full Text]

Ao H, Takagi T
ALICE: an algorithm to extract abbreviations from MEDLINE.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):576-86.
OBJECTIVE: To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly. METHODS: ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules. RESULTS: It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database. CONCLUSION: ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc.jp/ALICE/ALICE_index.html. [Abstract/Link to Full Text]

Hazlehurst B, Frost HR, Sittig DF, Stevens VJ
MediClass: A system for detecting and classifying encounter-based clinical events in any electronic medical record.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):517-29.
MediClass is a knowledge-based system that processes both free-text and coded data to automatically detect clinical events in electronic medical records (EMRs). This technology aims to optimize both clinical practice and process control by automatically coding EMR contents regardless of data input method (e.g., dictation, structured templates, typed narrative). We report on the design goals, implemented functionality, generalizability, and current status of the system. MediClass could aid both clinical operations and health services research through enhancing care quality assessment, disease surveillance, and adverse event detection. [Abstract/Link to Full Text]

Baker L, Rideout J, Gertler P, Raube K
Effect of an Internet-based system for doctor-patient communication on health care spending.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):530-6.
We studied the effect of a structured electronic communication service on health care spending, comparing doctor office and laboratory spending for a group of patients before and after the service became available to them relative to changes in a control group. In the treatment group, doctor office spending and laboratory spending fell in the period after the service became available, relative to the control group (p < 0.05). A rough estimate is that average doctor office spending per treatment group member per month fell $1.71 after availability of the service, and laboratory spending fell roughly $0.12. Spending associated with use of the electronic service was $0.29 per member per month. We conclude that use of structured electronic visits can reduce health care spending. [Abstract/Link to Full Text]

Rosenbloom ST, Chiu KW, Byrne DW, Talbert DA, Neilson EG, Miller RA
Interventions to regulate ordering of serum magnesium levels: report of an unintended consequence of decision support.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):546-53.
BACKGROUND: Unintended consequences of computerized patient care system interventions may increase resource use, foster clinical errors, and reduce users' confidence. OBJECTIVE: To evaluate three successive interventions designed to reduce serum magnesium test ordering through a care provider order entry system (CPOE). The second, modeled after a previously successful intervention, caused paradoxical increases in magnesium test ordering rates. DESIGN: A time-series analysis modeled weekly rates of magnesium test ordering, underlying trends, the impact of the three successive interventions, and the impact of potential covariates. The first intervention exhorted users to discontinue unnecessary tests recurring more than 72 hours into the future. The second displayed recent magnesium, calcium, and phosphorus test results, limited testing to one test instance per order, and provided education regarding appropriate indications for testing. The third targeted only magnesium ordering, displayed recent results, limited testing to one instance per order, summarized indications for testing, and required users to select an indication. PARTICIPANTS: Clinicians at Vanderbilt University Hospital, a 609-bed academic inpatient tertiary care facility, from 1998 through 2003. MEASUREMENTS: Weekly rates of new serum magnesium test orders, instances, and results. RESULTS: At baseline, there were 539 magnesium tests ordered per week. This decreased to 380 (p = 0.001) per week after the first intervention, increased to 491 per week (p < 0.001) after the second, and decreased to 276 per week (p < 0.001) after the third. CONCLUSION: A clinical decision support intervention intended to regulate testing increased test order rates as an unintended result of decision support. CPOE implementers must carefully design resource-related interventions and monitor their impact over time. [Abstract/Link to Full Text]

McAlearney AS, Schweikhart SB, Medow MA
Organizational and physician perspectives about facilitating handheld computer use in clinical practice: results of a cross-site qualitative study.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):568-75.
OBJECTIVE: To describe strategies that organizations select to support physicians' use of handheld computers (HHCs) in clinical practice and to explore issues about facilitating HHC use. DESIGN: A multidisciplinary team used focus groups and interviews with clinical, administrative, and information technology (IT) staff to gather data from 161 informants at seven sites. Transcripts were coded using a combination of deductive and inductive approaches to both answer research questions and identify patterns and themes that emerged in the data. MEASUREMENTS: Answers to questions about strategies for HHC support and themes about (1) how to facilitate physician adoption and use and (2) organizational concerns. RESULTS: Three main organizational strategies for HHC support were characterized among sites: (1) active support for broad-based use, (2) active support for niche use, and (3) basic support for individual physician users. Three high-level themes emerged around how to best facilitate physician adoption and use of HHCs: (1) improving usability and usefulness, (2) promoting HHCs and device use, and (3) providing training and support. However, four major themes also emerged related to organizations' concerns about HHC use: (1) security-related concerns, (2) economic concerns, (3) technical concerns, and (4) strategic concerns. CONCLUSION: An organizational approach to HHC support that involves individualized attention to existing and potential physician users rather than one-size-fits-all, organization-wide implementation efforts was an important facilitator promoting physician use of HHCs. Health care organizations interested in supporting HHC use must consider issues related to security, economics, and IT strategy that may not be prominent concerns for physician users. [Abstract/Link to Full Text]

Miller RA, Gardner RM, Johnson KB, Hripcsak G
Clinical decision support and electronic prescribing systems: a time for responsible thought and action.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):403-9. [Abstract/Link to Full Text]

Teich JM, Osheroff JA, Pifer EA, Sittig DF, Jenders RA
Clinical decision support in electronic prescribing: recommendations and an action plan: report of the joint clinical decision support workgroup.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):365-76.
Clinical decision support (CDS) in electronic prescribing (eRx) systems can improve the safety, quality, efficiency, and cost-effectiveness of care. However, at present, these potential benefits have not been fully realized. In this consensus white paper, we set forth recommendations and action plans in three critical domains: (1) advances in system capabilities, including basic and advanced sets of CDS interventions and knowledge, supporting database elements, operational features to improve usability and measure performance, and management and governance structures; (2) uniform standards, vocabularies, and centralized knowledge structures and services that could reduce rework by vendors and care providers, improve dissemination of well-constructed CDS interventions, promote generally applicable research in CDS methods, and accelerate the movement of new medical knowledge from research to practice; and (3) appropriate financial and legal incentives to promote adoption. [Abstract/Link to Full Text]

Detmer DE, Safran C
AMIA's White Paper Policy Series on Timely Issues in Informatics.
J Am Med Inform Assoc. 2005 May 19; [Abstract/Link to Full Text]

Knight AM, Kravet SJ, Harper GM, Leff B
The effect of computerized provider order entry on medical student clerkship experiences.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):554-60.
OBJECTIVE: To describe medical students' attitudes toward placing orders during training, and the effect of computerized provider order entry (CPOE) on their learning experiences. DESIGN: Prospective, controlled study of all 143 Johns Hopkins University School of Medicine students who began the Basic Medicine clerkship between March 2003 and April 2004 at one of three teaching hospitals: one using CPOE, one paper orders, and one that began using CPOE midway through this study. MEASUREMENTS: Survey of students at the start and after the first month of the clerkship. RESULTS: Ninety-six percent of students responded. Students expressed a desire to place 100% of orders for their patients. Ninety-five percent of students believed that placing orders helps students learn what tests and treatments patients need. Eighty-four percent reported that being unavailable due to conferences and teaching sessions was a significant barrier to participating in the ordering process. Students at hospitals using CPOE reported placing significantly fewer of their patients' follow-up orders compared to students at hospitals using paper orders (25% vs. 50%, p < 0.01) and were more likely to report that their resident or intern did not want them to enter orders (40% vs. 16%, p < 0.01). Comparisons of students at hospitals using CPOE to each other showed that these differences were attributable to one of the hospitals. Thirty-two percent of students at both hospitals using CPOE reported that the extra length of time required for housestaff to review their orders in the computer was a significant barrier. CONCLUSION: Hospitals need to ensure that the educational potential of medical students' clinical experiences is maximized when implementing CPOE. [Abstract/Link to Full Text]

Sittig DF, Krall M, Kaalaas-Sittig J, Ash JS
Emotional aspects of computer-based provider order entry: a qualitative study.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):561-7.
OBJECTIVES: Computer-based provider order entry (CPOE) systems are implemented to increase both efficiency and accuracy in health care, but these systems often cause a myriad of emotions to arise. This qualitative research investigates the emotions surrounding CPOE implementation and use. METHODS: We performed a secondary analysis of several previously collected qualitative data sets from interviews and observations of over 50 individuals. Three researchers worked in parallel to identify themes that expressed emotional responses to CPOE. We then reviewed and classified these quotes using a validated hierarchical taxonomy of semantically homogeneous terms associated with specific emotions. RESULTS: The implementation and use of CPOE systems provoked examples of positive, negative, and neutral emotions. Negative emotional responses were the most prevalent, by far, in all the observations. CONCLUSION: Designing and implementing CPOE systems is difficult. These systems and the implementation process itself often inspire intense emotions. If designers and implementers fail to recognize that various CPOE features and implementation strategies can increase clinicians' negative emotions, then the systems may fail to become a routine part of the clinical care delivery process. We might alleviate some of these problems by designing positive feedback mechanisms for both the systems and the organizations. [Abstract/Link to Full Text]

Lehmann TM, Bredno J
Strategies to configure image analysis algorithms for clinical usage.
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):497-504.
Medical imaging informatics must exceed the mere development of algorithms. The discipline is also responsible for the establishment of methods in clinical practice to assist physicians and improve health care. From our point of view, it is commonly accepted that model-based analysis of medical images is superior to other concepts, but only a few applications are found in daily clinical use. The gap between development of model-based image analysis and its routine application can be addressed by identifying four necessary transfer steps: formulation, parameterization, instantiation, and validation. Usually, computer scientists formulate the model and define its parameterization, i.e., configure a model to handle a selected subset of clinical data. During instantiation, the algorithm adapts the model to the actual data, which is validated by physicians. Since medical a priori knowledge and particular knowledge on technical details are required for parameterization and validation, these steps are considered to be bottlenecks. In this paper, we propose general schemes that allow an application- or image-specific parameterization to be performed by medical users. Combining noncontextual and contextual approaches, we also suggest a reliable scheme that allows application-specific validation, even if a gold standard is unavailable. To emphasize our point of view, we provide examples based on unsupervised segmentation in medical imagery, which is one of the most difficult tasks. Following the proposed schemes, an exact delineation of cells in micrographs is parameterized, validated, and successfully established in daily clinical use, while automatic determination of body regions in radiographs cannot be configured to support reliable and robust clinical use. The results stress that parameterization and validation must be based on clinical data that show all potential variations and artifact sources. [Abstract/Link to Full Text]

Rosenbloom ST, Geissbuhler AJ, Dupont WD, Giuse DA, Talbert DA, Tierney WM, Plummer WD, Stead WW, Miller RA
Effect of CPOE user interface design on user-initiated access to educational and patient information during clinical care.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):458-73.
OBJECTIVE: Authors evaluated whether displaying context sensitive links to infrequently accessed educational materials and patient information via the user interface of an inpatient computerized care provider order entry (CPOE) system would affect access rates to the materials. DESIGN: The CPOE of Vanderbilt University Hospital (VUH) included "baseline" clinical decision support advice for safety and quality. Authors augmented this with seven new primarily educational decision support features. A prospective, randomized, controlled trial compared clinicians' utilization rates for the new materials via two interfaces. Control subjects could access study-related decision support from a menu in the standard CPOE interface. Intervention subjects received active notification when study-related decision support was available through context sensitive, visibly highlighted, selectable hyperlinks. MEASUREMENTS: Rates of opportunities to access and utilization of study-related decision support materials from April 1999 through March 2000 on seven VUH Internal Medicine wards. RESULTS: During 4,466 intervention subject-days, there were 240,504 (53.9/subject-day) opportunities for study-related decision support, while during 3,397 control subject-days, there were 178,235 (52.5/subject-day) opportunities for such decision support, respectively (p = 0.11). Individual intervention subjects accessed the decision support features at least once on 3.8% of subject-days logged on (278 responses); controls accessed it at least once on 0.6% of subject-days (18 responses), with a response rate ratio adjusted for decision support frequency of 9.17 (95% confidence interval 4.6-18, p < 0.0005). On average, intervention subjects accessed study-related decision support materials once every 16 days individually and once every 1.26 days in aggregate. CONCLUSION: Highlighting availability of context-sensitive educational materials and patient information through visible hyperlinks significantly increased utilization rates for study-related decision support when compared to "standard" VUH CPOE methods, although absolute response rates were low. [Abstract/Link to Full Text]

Nelson NC, Evans RS, Samore MH, Gardner RM
Detection and prevention of medication errors using real-time bedside nurse charting.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):390-7.
OBJECTIVE: Charting systems with decision support have been developed to assist with medication charting, but many of the features of these programs are not properly used in their clinical application. An analysis of medication error reports at LDS Hospital revealed the occurrence of errors that should have been detected and prevented by decision support features if real-time entry at the bedside had taken place. The aim of this study was to increase the real-time bedside charting behavior of nurses. DESIGN: A quasiexperimental before and after design was used. The study took place in two 40-bed surgical units, one of which served as the study unit, the other as control unit. The study unit received educational intervention about error avoidance through real-time bedside charting, and 12 weeks of monitoring and performance feedback. The real-time and bedside charting rates for the study and control units were measured before and after the intervention. RESULTS: Before the intervention on the study unit, the real-time charting rate was 59% and the bedside rate was 40%. At the conclusion of a 12-week intervention period, the real-time rate increased to 73% and the bedside rate increased to 63%. Postintervention real-time rates were 75% after eight weeks and remained at 75% after one year. Equivalent control unit real-time rates varied from 53% to 57%, and bedside rates varied from 34% to 44% during the same intervals. CONCLUSION: Targeted educational intervention and monitored feedback yielded measurable improvements in the effective use of the computerized medication charting system and must be an ongoing process. [Abstract/Link to Full Text]

Horsky J, Kuperman GJ, Patel VL
Comprehensive analysis of a medication dosing error related to CPOE.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):377-82.
This case study of a serious medication error demonstrates the necessity of a comprehensive methodology for the analysis of failures in interaction between humans and information systems. The authors used a novel approach to analyze a dosing error related to computer-based ordering of potassium chloride (KCl). The method included a chronological reconstruction of events and their interdependencies from provider order entry usage logs, semistructured interviews with involved clinicians, and interface usability inspection of the ordering system. Information collected from all sources was compared and evaluated to understand how the error evolved and propagated through the system. In this case, the error was the product of faults in interaction among human and system agents that methods limited in scope to their distinct analytical domains would not identify. The authors characterized errors in several converging aspects of the drug ordering process: confusing on-screen laboratory results review, system usability difficulties, user training problems, and suboptimal clinical system safeguards that all contributed to a serious dosing error. The results of the authors' analysis were used to formulate specific recommendations for interface layout and functionality modifications, suggest new user alerts, propose changes to user training, and address error-prone steps of the KCl ordering process to reduce the risk of future medication dosing errors. [Abstract/Link to Full Text]

Hsu J, Huang J, Fung V, Robertson N, Jimison H, Frankel R
Health information technology and physician-patient interactions: impact of computers on communication during outpatient primary care visits.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):474-80.
OBJECTIVE: The aim of this study was to evaluate the impact of introducing health information technology (HIT) on physician-patient interactions during outpatient visits. DESIGN: This was a longitudinal pre-post study: two months before and one and seven months after introduction of examination room computers. Patient questionnaires (n = 313) after primary care visits with physicians (n = 8) within an integrated delivery system. There were three patient satisfaction domains: (1) satisfaction with visit components, (2) comprehension of the visit, and (3) perceptions of the physician's use of the computer. RESULTS: Patients reported that physicians used computers in 82.3% of visits. Compared with baseline, overall patient satisfaction with visits increased seven months after the introduction of computers (odds ratio [OR] = 1.50; 95% confidence interval [CI]: 1.01-2.22), as did satisfaction with physicians' familiarity with patients (OR = 1.60, 95% CI: 1.01-2.52), communication about medical issues (OR = 1.61; 95% CI: 1.05-2.47), and comprehension of decisions made during the visit (OR = 1.63; 95% CI: 1.06-2.50). In contrast, there were no significant changes in patient satisfaction with comprehension of self-care responsibilities, communication about psychosocial issues, or available visit time. Seven months post-introduction, patients were more likely to report that the computer helped the visit run in a more timely manner (OR = 1.76; 95% CI: 1.28-2.42) compared with the first month after introduction. There were no other significant changes in patient perceptions of the computer use over time. CONCLUSION: The examination room computers appeared to have positive effects on physician-patient interactions related to medical communication without significant negative effects on other areas such as time available for patient concerns. Further study is needed to better understand HIT use during outpatient visits. [Abstract/Link to Full Text]

Heidt EL
Health information technology and physician-patient interactions: impact of computers on communication during outpatient primary care visits.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):236; author reply 237. [Abstract/Link to Full Text]

Fung KW, Hole WT, Nelson SJ, Srinivasan S, Powell T, Roth L
Integrating SNOMED CT into the UMLS: an exploration of different views of synonymy and quality of editing.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):486-94.
OBJECTIVE: The integration of SNOMED CT into the Unified Medical Language System (UMLS) involved the alignment of two views of synonymy that were different because the two vocabulary systems have different intended purposes and editing principles. The UMLS is organized according to one view of synonymy, but its structure also represents all the individual views of synonymy present in its source vocabularies. Despite progress in knowledge-based automation of development and maintenance of vocabularies, manual curation is still the main method of determining synonymy. The aim of this study was to investigate the quality of human judgment of synonymy. DESIGN: Sixty pairs of potentially controversial SNOMED CT synonyms were reviewed by 11 domain vocabulary experts (six UMLS editors and five noneditors), and scores were assigned according to the degree of synonymy. MEASUREMENTS: The synonymy scores of each subject were compared to the gold standard (the overall mean synonymy score of all subjects) to assess accuracy. Agreement between UMLS editors and noneditors was measured by comparing the mean synonymy scores of editors to noneditors. RESULTS: Average accuracy was 71% for UMLS editors and 75% for noneditors (difference not statistically significant). Mean scores of editors and noneditors showed significant positive correlation (Spearman's rank correlation coefficient 0.654, two-tailed p < 0.01) with a concurrence rate of 75% and an interrater agreement kappa of 0.43. CONCLUSION: The accuracy in the judgment of synonymy was comparable for UMLS editors and nonediting domain experts. There was reasonable agreement between the two groups. [Abstract/Link to Full Text]

Saleem JJ, Patterson ES, Militello L, Render ML, Orshansky G, Asch SM
Exploring barriers and facilitators to the use of computerized clinical reminders.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):438-47.
OBJECTIVE: Evidence-based practices in preventive care and chronic disease management are inconsistently implemented. Computerized clinical reminders (CRs) can improve compliance with these practices in outpatient settings. However, since clinician adherence to CR recommendations is quite variable and declines over time, we conducted observations to determine barriers and facilitators to the effective use of CRs. DESIGN: We conducted an observational study of nurses and providers interacting with CRs in outpatient primary care clinics for two days in each of four geographically distributed Veterans Administration (VA) medical centers. MEASUREMENTS: Three observers recorded interactions of 35 nurses and 55 physicians and mid-level practitioners with the CRs, which function as part of an electronic medical record. Field notes were typed, coded in a spreadsheet, and then sorted into logical categories. We then integrated findings across observations into meaningful patterns and abstracted the data into themes, such as recurrent strategies. Several of these themes translated directly to barriers and facilitators to effective CR use. RESULTS: Optimally using the CR system for its intended purpose was impeded by (1) lack of coordination between nurses and providers; (2) using the reminders while not with the patient, impairing data acquisition and/or implementation of recommended actions; (3) workload; (4) lack of CR flexibility; and (5) poor interface usability. Facilitators included (1) limiting the number of reminders at a site; (2) strategic location of the computer workstations; (3) integration of reminders into workflow; and (4) the ability to document system problems and receive prompt administrator feedback. CONCLUSION: We identified barriers that might explain some of the variability in the use of CRs. Although these barriers may be difficult to overcome, some strategies may increase user acceptance and therefore the effectiveness of the CRs. These include explicitly assigning responsibility for each CR to nurses or providers, improving visibility of positive results from CRs in the electronic medical record, creating a feedback mechanism about CR use, and limiting the overall number of CRs. [Abstract/Link to Full Text]

Reichley RM, Seaton TL, Resetar E, Micek ST, Scott KL, Fraser VJ, Dunagan WC, Bailey TC
Implementing a commercial rule base as a medication order safety net.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):383-9.
A commercial rule base (Cerner Multum) was used to identify medication orders exceeding recommended dosage limits at five hospitals within BJC HealthCare, an integrated health care system. During initial testing, clinical pharmacists determined that there was an excessive number of nuisance and clinically insignificant alerts, with an overall alert rate of 9.2%. A method for customizing the commercial rule base was implemented to increase rule specificity for problematic rules. The system was subsequently deployed at two facilities and achieved alert rates of less than 1%. Pharmacists screened these alerts and contacted ordering physicians in 21% of cases. Physicians made therapeutic changes in response to 38% of alerts presented to them. By applying simple techniques to customize rules, commercial rule bases can be used to rapidly deploy a safety net to screen drug orders for excessive dosages, while preserving the rule architecture for later implementations of more finely tuned clinical decision support. [Abstract/Link to Full Text]

Choi J, Jenkins ML, Cimino JJ, White TM, Bakken S
Toward semantic interoperability in home health care: formally representing OASIS items for integration into a concept-oriented terminology.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):410-7.
OBJECTIVE: The authors aimed to (1) formally represent OASIS-B1 concepts using the Logical Observation Identifiers, Names, and Codes (LOINC) semantic structure; (2) demonstrate integration of OASIS-B1 concepts into a concept-oriented terminology, the Medical Entities Dictionary (MED); (3) examine potential hierarchical structures within LOINC among OASIS-B1 and other nursing terms; and (4) illustrate a Web-based implementation for OASIS-B1 data entry using Dialogix, a software tool with a set of functions that supports complex data entry. DESIGN AND MEASUREMENTS: Two hundred nine OASIS-B1 items were dissected into the six elements of the LOINC semantic structure and then integrated into the MED hierarchy. Each OASIS-B1 term was matched to LOINC-coded nursing terms, Home Health Care Classification, the Omaha System, and the Sign and Symptom Check-List for Persons with HIV, and the extent of the match was judged based on a scale of 0 (no match) to 4 (exact match). OASIS-B1 terms were implemented as a Web-based survey using Dialogix. RESULTS: Of 209 terms, 204 were successfully dissected into the elements of the LOINC semantics structure and integrated into the MED with minor revisions of MED semantics. One hundred fifty-one OASIS-B1 terms were mapped to one or more of the LOINC-coded nursing terms. CONCLUSION: The LOINC semantic structure offers a standard way to add home health care data to a comprehensive patient record to facilitate data sharing for monitoring outcomes across sites and to further terminology management, decision support, and accurate information retrieval for evidence-based practice. The cross-mapping results support the possibility of a hierarchical structure of the OASIS-B1 concepts within nursing terminologies in the LOINC database. [Abstract/Link to Full Text]

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Recent Articles in Journal of the Medical Library Association

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Giuse NB
The next challenge: where do we go from here?
J Med Libr Assoc. 2007 Jan;95(1):1-2. [Abstract/Link to Full Text]

Taylor MK, Gebremichael MD, Wagner CE
Mapping the literature of health care management.
J Med Libr Assoc. 2007 Apr;95(2):e58-65.
OBJECTIVES: The research provides an overview of the health care management literature and the indexing coverage of core journal literature. METHOD: Citations from five source journals for the years 2002 through 2004 were studied using the protocols of the Mapping the Literature of Allied Health Project and Mapping the Literature of Nursing Project. The productivity of cited journals was analyzed by applying Bradford's Law of Scattering. RESULTS: Journals were the most frequently cited format, followed by books. Only 3.2% of the cited journal titles from all 5 source journals generated two-thirds of the cited titles. When only the health care management practitioner-oriented source journals were considered, two-thirds of the output of cited journal titles came from 10.8% of the titles. Science Citation Index and PubMed provided the best overall coverage of the titles cited by all 5 source journals, while the cited titles from the 2 practitioner-oriented journals were covered most completely by Social Sciences Citation Index and Business Source Complete. CONCLUSIONS: Health care management is a multidisciplinary field. Librarians must consider the needs of their users and assist them by providing the necessary materials and combination of indexes to access this field adequately. [Abstract/Link to Full Text]

McGowan JJ
Swimming with the sharks: perspectives on professional risk taking.
J Med Libr Assoc. 2007 Jan;95(1):104-13. [Abstract/Link to Full Text]

Li G
The median age technique for assessing currency of consumer health information monographic collections in public libraries.
J Med Libr Assoc. 2007 Jan;95(1):89-90. [Abstract/Link to Full Text]

Knowlton SA
Continuing use of print-only information by researchers.
J Med Libr Assoc. 2007 Jan;95(1):83-8. [Abstract/Link to Full Text]

Miller N
Analysis of user messages to MedlinePlus.gov.
J Med Libr Assoc. 2007 Jan;95(1):81-3. [Abstract/Link to Full Text]

Koonce TY, Giuse DA, Beauregard JM, Giuse NB
Toward a more informed patient: bridging health care information through an interactive communication portal.
J Med Libr Assoc. 2007 Jan;95(1):77-81. [Abstract/Link to Full Text]

Yue W, Wilson CS, Boller F
Peer assessment of journal quality in clinical neurology.
J Med Libr Assoc. 2007 Jan;95(1):70-6.
OBJECTIVE: To explore journal quality as perceived by clinicians and researchers in clinical neurology. METHODS: A survey was conducted from August 2003 to January 2004. Ratings for 41 selected clinical neurology journals were obtained from 254 members of the World Federation of Neurology (1,500 solicited; response rate 17%). Participants provided demographic information and rated each journal on a 5-point Likert scale. Average ratings for all journals were compared with the ISI's journal impact factors. Ratings for each journal were also compared across geographic regions and respondent publication productivity. RESULTS: The top 5 journals were rated much more highly than the others, with mean ratings greater than 4. Mean journal ratings were highly correlated with journal impact factors (r = 0.67). Most of the top 10 journal ratings were consistent across the subgroups of geographic regions and journal paper productivity. However, significant differences among the different geographical regions and respondent productivity groups were also found for a few journals. CONCLUSIONS: The results provide valuable insight on how neurological experts perceive journals in clinical neurology. These results will likely aid researchers and clinicians in identifying potentially desirable research outlets and indicate journal status for editors. Likewise, biomedical librarians may use these results for serials collection development. [Abstract/Link to Full Text]

Brown SR, Roush JR, Lamkin AR, Perrakis R, Kronenfeld MR
Evaluating the professional libraries of practicing physical therapists.
J Med Libr Assoc. 2007 Jan;95(1):64-9.
BACKGROUND AND PURPOSE: The primary objective of this study was to explore the use of information resources by a sample of physical therapists. METHODS: A qualitatively designed study using structured individual interviews, examination of professional libraries, and identification of information resources was initiated in three sites (Southern California, Arizona, and Georgia). Participants included forty physical therapists with between five and twenty years of experience. RESULTS: The Internet and continuing education activities appeared to be the primary information sources for the physical therapists surveyed. The personal professional libraries of participants were limited in scope and contained titles copyrighted more than ten years ago. Access to peer-reviewed journals in the sample was limited primarily to those received as a benefit of professional association membership. DISCUSSION AND CONCLUSIONS: Participants did not maintain current print professional information resources. The majority of books in the personal and workplace professional libraries held copyrights dating from the time of the participants' enrollment in an entry-level physical therapy program. Medical librarians may play an important role in shifting physical therapy towards evidence-based practice by collaborating in professional development for this group. Physical therapy educators and professional leaders should support current public collections of physical therapy-related information resources to encourage the movement towards an evidence-based practice model in physical therapy. [Abstract/Link to Full Text]

Tenopir C, King DW, Clarke MT, Na K, Zhou X
Journal reading patterns and preferences of pediatricians.
J Med Libr Assoc. 2007 Jan;95(1):56-63.
PURPOSE: To describe the journal reading patterns of pediatrician members of the American Academy of Pediatrics (AAP) and compare results to similar surveys of medical faculty and physicians. The research also explored factors that might influence changes in reading patterns in the future, such as adoption of PDA technology. METHODOLOGY: A random sample of 2,000 AAP members was drawn from the AAP membership list, with paper surveys distributed in mid-2004. SETTINGS/SUBJECTS: Six hundred sixty-six pediatrician AAP members participated in a survey of reading behavior, with a total of 1,351 members answering some questions about technology use. RESULTS: The hypotheses that pediatricians read many journal articles each month, read each article on average quite quickly, read heavily from personal subscriptions, read from both print and electronic journals, and read for many purposes were all supported. Pediatricians read journal articles primarily for current awareness and most often rely on quick reading from print journals for current awareness. Reading for research, writing, and presentations are more likely from library-provided electronic journals. DISCUSSION/CONCLUSION: Convenience and purpose of reading are key factors that explain reading patterns of pediatricians. Print personal subscriptions are convenient for current awareness reading, while electronic journals systems are convenient for reading for research because they provide access to a broader range of journals. Publishers and librarians must understand the purposes and patterns of reading to design appropriate journals and services. Pediatricians read many current articles very quickly and from many different locations. Pediatricians under the age of thirty-five are more likely to use PDAs, suggesting that articles delivered to a handheld device might be accepted as convenient in the future. [Abstract/Link to Full Text]

Joubert DJ, Lee TP
Empowering your institution through assessment.
J Med Libr Assoc. 2007 Jan;95(1):46-53.
OBJECTIVES: The objectives of this study are to describe the process of linking Association of Academic Health Sciences Libraries (AAHSL) data with 2002 LibQUAL+ data and to address four analytical questions created by the AAHSL Task Force on Quality Assessment that relate both to user satisfaction and to services provided by AAHSL libraries. METHODS: For the thirty-five AAHSL libraries that participated in the 2002 LibQUAL+ survey, nested-effect of variance was analyzed using a linear mixed model. Using the Pearson correlation coefficient, this study explored four questions about the effect of user demographics on perceived levels of satisfaction with library services. RESULTS: The supposition that library user satisfaction may differ according to library institutional reporting structure was unsupported. Regarding effect on mean overall satisfaction, size of library staff is not significant (P = 0.860), number of constituents is slightly significant (P = 0.027), and ratio of staff to constituents has a moderate and significant effect (P = 0.004). CONCLUSIONS: From a demographic perspective, the 2002 LibQUAL+ survey represents the largest cross section of AAHSL libraries. Increased understanding of how qualitative assessment can supplement quantitative data supports evidence-based decision-making and practice. It also could promote changes in data collection and usage. [Abstract/Link to Full Text]

Foust JE, Bergen P, Maxeiner GL, Pawlowski PN
Improving e-book access via a library-developed full-text search tool.
J Med Libr Assoc. 2007 Jan;95(1):40-5.
PURPOSE: This paper reports on the development of a tool for searching the contents of licensed full-text electronic book (e-book) collections. SETTING: The Health Sciences Library System (HSLS) provides services to the University of Pittsburgh's medical programs and large academic health system. BRIEF DESCRIPTION: The HSLS has developed an innovative tool for federated searching of its e-book collections. Built using the XML-based Vivísimo development environment, the tool enables a user to perform a full-text search of over 2,500 titles from the library's seven most highly used e-book collections. From a single "Google-style" query, results are returned as an integrated set of links pointing directly to relevant sections of the full text. Results are also grouped into categories that enable more precise retrieval without reformulation of the search. RESULTS/EVALUATION: A heuristic evaluation demonstrated the usability of the tool and a web server log analysis indicated an acceptable level of usage. Based on its success, there are plans to increase the number of online book collections searched. CONCLUSION: This library's first foray into federated searching has produced an effective tool for searching across large collections of full-text e-books and has provided a good foundation for the development of other library-based federated searching products. [Abstract/Link to Full Text]

Olney CA, Warner DG, Reyna G, Wood FB, Siegel ER
MedlinePlus and the challenge of low health literacy: findings from the Colonias project.
J Med Libr Assoc. 2007 Jan;95(1):31-9.
OBJECTIVE: To explore the potential of a community-based health information outreach project to overcome problems associated with health literacy in low-income Hispanic communities along the Texas-Mexico border. METHODS: Using a train-the-trainer approach, community outreach workers known as promotoras were trained by a health information outreach team to search English and Spanish versions of MedlinePlus. These 15 promotoras submitted written examples on a weekly basis of the topics they helped residents explore on MedlinePlus and the ways in which the residents used the information. These weekly reports, along with verbal interviews with promotoras and others in the communities, allowed development of a database of 161 incidents ("stories") demonstrating how community residents used MedlinePlus. These stories were thematically analyzed to explore how the program benefited participants. RESULTS: The database of stories included examples of community residents becoming better informed about their illnesses, resolving to visit doctors, making decisions about recommended treatments, reducing their anxiety about health conditions, committing to healthy or preventive behavior, and assisting family members. CONCLUSION: With the help of paraprofessionals like promotoras, community-based health information outreach projects may improve the ability of community residents to understand their health conditions and to participate actively in their health care. [Abstract/Link to Full Text]

De Groote SL, Hitchcock K, McGowan R
Trends in reference usage statistics in an academic health sciences library.
J Med Libr Assoc. 2007 Jan;95(1):23-30.
PURPOSE: To examine reference questions asked through traditional means at an academic health sciences library and place this data within the context of larger trends in reference services. METHODOLOGY: Detailed data on the types of reference questions asked were collected during two one-month periods in 2003 and 2004. General statistics documenting broad categories of questions were compiled over a fifteen-year period. RESULTS: Administrative data show a steady increase in questions from 1990 to 1997/98 (23,848 to 48,037, followed by a decline through 2004/05 to 10,031. The distribution of reference questions asked over the years has changed-including a reduction in mediated searches 2,157 in 1990/91 to 18 in 2004/05, an increase in instruction 1,284 in 1993/94 to 1,897 in 2004/05 and an increase in digital reference interactions 0 in 1999/2000 to 581 in 2004/05. The most commonly asked questions at the current reference desk are about journal holdings 19%, book holdings 12%, and directional issues 12%. CONCLUSIONS: This study provides a unique snapshot of reference services in the contemporary library, where both online and offline services are commonplace. Changes in questions have impacted the way the library provides services, but traditional reference remains the core of information services in this health sciences library. [Abstract/Link to Full Text]

Urquhart C, Turner J, Durbin J, Ryan J
Changes in information behavior in clinical teams after introduction of a clinical librarian service.
J Med Libr Assoc. 2007 Jan;95(1):14-22.
OBJECTIVES: The eighteen-month evaluation of a clinical librarian project (October 2003-March 2005) conducted in North Wales, United Kingdom (UK) assessed the benefits of clinical librarian support to clinical teams, the impact of mediated searching services, and the effectiveness of information skills training, including journal club support. METHODS: The evaluation assessed changes in teams' information-seeking behavior and their willingness to delegate searching to a clinical librarian. Baseline (n = 69 responses, 73% response rate) and final questionnaire (n = 57, 77% response rate) surveys were complemented by telephone and face-to-face interviews (n = 33) among 3 sites served. Those attending information skills training sessions (n = 130) completed evaluations at the session and were surveyed 1 month after training (n = 24 questionnaire responses, n = 12 interviews). RESULTS: Health professionals in clinical teams reported that they were more willing to undertake their own searching, but also more willing to delegate some literature searching, than at the start of the project. The extent of change depended on the team and the type of information required. Information skills training was particularly effective when organized around journal clubs. CONCLUSIONS: Collaboration with a clinical librarian increased clinician willingness to seek information. Clinical librarian services should leverage structured training opportunities such as journal clubs. [Abstract/Link to Full Text]

Murphy SA
The effects of portfolio purchasing on a specialized subject collection.
J Med Libr Assoc. 2007 Jan;95(1):9-13.
OBJECTIVE: To examine the impact of portfolio purchasing on a small, highly specialized medical collection at The Ohio State University. METHODOLOGY: In this citation analysis, cited references for articles published by faculty in the College of Veterinary Medicine between 2000 and 2004 were collected and analyzed to determine whether The Ohio State University Libraries provided print or electronic access to the publications cited or the publishers of the cited journals, and whether the university purchased a subscription to each journal or received the subscription through a consortium-sponsored portfolio purchasing agreement. RESULTS: Of the 419 journals veterinary faculty cited more than 10 times, only 13 (3.1%) were in Zone 1, and 63 (15.0%) were in Zone 2 of the Bradford distribution, a citation analysis model which demonstrates that a small number of journals account for the bulk of literature utilized in any established field. Of these, only 23 (5.5%) were procured through an OhioLINK or other consortium portfolio purchasing agreement. DISCUSSION/CONCLUSION: The costs of acquiring a publisher's portfolio, even through a consortium, should be balanced with the costs of purchasing content required to provide a balanced collection for all user populations. [Abstract/Link to Full Text]

Walden RR, Jerome RN, Miller RS
Utilizing case reports to build awareness of rare complications in critical care.
J Med Libr Assoc. 2007 Jan;95(1):3-8. [Abstract/Link to Full Text]

Detlefsen EG
The pipeline problem: where do we go from here?
J Med Libr Assoc. 2007 Apr;95(2):115-6. [Abstract/Link to Full Text]

Alpi KM, Adams MG
Mapping the literature of public health and community nursing.
J Med Libr Assoc. 2007 Jan;95(1):e6-9.
OBJECTIVES: The purpose of this study was to identify the journals most cited in public health and community nursing and to determine which databases provide the most thorough indexing access to these journals. This study is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the nursing literature. METHODS: Two source journals of public health nursing, Public Health Nursing and Journal of Community Health Nursing, were subjected to citation analysis based on Bradford's Law of Scattering. RESULTS: A group of 18 titles comprised 34% (1,387) of the 4,100 citations, another third were dispersed among 104 journal titles, with the remaining third scattered across 703 journal titles. The core 18 journals included both of the source journals, 3 major public health journals, and several general medical and nursing journals. CONCLUSIONS: PubMed provided the best overall indexing coverage for the journals, followed by Social Science Citation Index and CINAHL. In terms of source journal coverage, several databases provided complete coverage for the journal Public Health Nursing, while only EMBASE provided complete coverage for the Journal of Community Health Nursing. [Abstract/Link to Full Text]

Lynch FH, Rieke JL
Proceedings of the 106th annual meeting of the Medical Library Association.
J Med Libr Assoc. 2007 Jan;95(1):e10-47. [Abstract/Link to Full Text]

Shams ML, Dixon LS
Mapping selected general literature of international nursing.
J Med Libr Assoc. 2007 Jan;95(1):e1-5.
OBJECTIVES: This study, part of a wider project to map the literature of nursing, identifies core journals cited in non-US nursing journals and determines the extent of their coverage by indexing services. METHODS: Four general English-language journals were analyzed for format types and publication dates. Core titles were identified and nine bibliographic databases were scanned for indexing coverage. RESULTS: Findings show that 57.5% (13,391/23,271) of the cited references from the 4 core journals were to journal articles, 27.8% (6,471/23,271) to books, 9.5% (2,208/23,271) to government documents, 4.9% (1,131/23,271) to miscellaneous sources, and less than 1% (70/23,271) to Internet resources. Eleven journals produced one-third of the citations; the next third included 146 journals, followed by a dispersion of 1,622 titles. PubMed received the best database coverage scores, followed by CINAHL and Science Citation Index. None of the databases provided complete coverage of all 11 core titles. CONCLUSION: The four source journals contain a diverse group of cited references. The currency of citations to government documents makes these journals a good source for regulatory and legislative awareness. Nurses consult nursing and biomedical journals and must search both nursing and biomedical databases to cover the literature. [Abstract/Link to Full Text]

Fulda PO, Satterthwaite RK
Proceedings, 104th Annual Meeting Medical Library Association, Inc., Washington, DC, May 21-26, 2004.
J Med Libr Assoc. 2005 Jan;93(1):143-88. [Abstract/Link to Full Text]

Locatis C, Gaines C, Liu WL, Gill M, Carney J, Foster J, McCall V, Woods M
A blended training approach using videoconferencing for distance education.
J Med Libr Assoc. 2006 Oct;94(4):464-8. [Abstract/Link to Full Text]

Sampson M, McGowan J, Cogo E, Horsley T
Managing database overlap in systematic reviews using Batch Citation Matcher: case studies using Scopus.
J Med Libr Assoc. 2006 Oct;94(4):461-3, e219. [Abstract/Link to Full Text]

McCabe JA
An assignment for building an awareness of the intersection of health literacy and cultural competence skills.
J Med Libr Assoc. 2006 Oct;94(4):458-61. [Abstract/Link to Full Text]

Hersey DP
Reviving the corporate medical library: using technology to become a cost center.
J Med Libr Assoc. 2006 Oct;94(4):456-8. [Abstract/Link to Full Text]

Wong SS, Wilczynski NL, Haynes RB
Comparison of top-performing search strategies for detecting clinically sound treatment studies and systematic reviews in MEDLINE and EMBASE.
J Med Libr Assoc. 2006 Oct;94(4):451-5. [Abstract/Link to Full Text]

Hernández-Borges AA, Cabrera-Rodríguez R, Montesdeoca-Melián A, Martínez-Pineda B, Torres-Alvarez de Arcaya ML, Jiménez-Sosa A
Awareness and attitude of Spanish medical authors to open access publishing and the "author pays" model.
J Med Libr Assoc. 2006 Oct;94(4):449-51, e218. [Abstract/Link to Full Text]

Cataldo TT, Tennant MR, Sherwill-Navarro P, Jesano R
Subject specialization in a liaison librarian program.
J Med Libr Assoc. 2006 Oct;94(4):446-8. [Abstract/Link to Full Text]

Dvorkin L, Whelan JS, Timarac S
Harvesting the best: evidence-based analysis of herbal handbooks for clinicians.
J Med Libr Assoc. 2006 Oct;94(4):442, e208-13. [Abstract/Link to Full Text]

Wallis LC
Information-seeking behavior of faculty in one school of public health.
J Med Libr Assoc. 2006 Oct;94(4):442-6, e214-7. [Abstract/Link to Full Text]

Campbell R, Ash J
An evaluation of five bedside information products using a user-centered, task-oriented approach.
J Med Libr Assoc. 2006 Oct;94(4):435-41, e206-7.
PURPOSE: The paper compares several bedside information tools using user-centered, task-oriented measures to assist those making or supporting purchasing decisions. METHODS: Eighteen potential users were asked to attempt to answer clinical questions using five commercial products (ACP's PIER, DISEASEDEX, FIRSTConsult, InfoRetriever, and UpToDate). Users evaluated each tool for ease-of-use and user satisfaction. The average number of questions answered and user satisfaction were measured for each product. RESULTS: Results show no significant differences in user perceptions of content quality. However, user interaction measures (such as screen layout) show a significant preference for the UpToDate product. In addition, users found answers to significantly more questions using UpToDate. CONCLUSION: When evaluating electronic products designed for use at the point of care, the user interaction aspects of a product become as important as more traditional content-based measures of quality. Actual or potential users of such products are appropriately equipped to identify which products rate the highest on these measures. [Abstract/Link to Full Text]

Crawley-Low J
Bibliometric analysis of the American Journal of Veterinary Research to produce a list of core veterinary medicine journals.
J Med Libr Assoc. 2006 Oct;94(4):430-4.
OBJECTIVE: Bibliometric techniques were used to analyze the citation patterns of researchers publishing in the American Journal of Veterinary Research (AJVR). METHODS: The more than 25,000 bibliographic references appearing in the AJVR from 2001 to 2003 were examined for material type, date of publication, and frequency of journals cited. Journal titles were ranked in decreasing order of productivity to create a core list of journals most frequently used by veterinary medical researchers. RESULTS: The majority of items cited were journals (88.8%), followed by books (9.8%) and gray literature (2.1%). Current sources of information were favored; 65% of the journals and 77% of the books were published in 1990 or later. Dividing the cited articles into 3 even zones revealed that 24 journals produced 7,361 cited articles in the first zone. One hundred thirty-nine journals were responsible for 7,414 cited articles in zone 2, and 1,409 journals produced 7,422 cited articles in zone 3. CONCLUSIONS: A core collection of veterinary medicine journals would include 49 veterinary medicine journals from zones 1 and 2. Libraries supporting a veterinary curriculum or veterinary research should also include veterinary medical journals from Zone 3, as well as provide access to journals in non-veterinary subjects such as biochemistry, virology, orthopedics, and surgery and a selection of general science and medical journals. [Abstract/Link to Full Text]

Booth A
"Brimful of STARLITE": toward standards for reporting literature searches.
J Med Libr Assoc. 2006 Oct;94(4):421-9, e205.
CONTEXT: Systematic reviews of qualitative research studies extend understanding of health care beyond effectiveness to acceptability and user views. OBJECTIVE: The paper surveys reports of qualitative systematic reviews and, by characterizing techniques used to identify articles for inclusion, proposes standards for reporting of literature searches. DATA SOURCES AND STUDY SELECTION: A search of MEDLINE was performed for qualitative systematic reviews published from 1988 to December 2004, supported by searches of CINAHL, Web of Knowledge (including the Science and Social Sciences Citation Index), and the Cochrane Methodology Register, and Internet searches using the Copernic Agent Professional meta-search agent. Studies were included if they used techniques of qualitative synthesis in reviewing research studies in health care. Narrative reviews were excluded. DATA EXTRACTION: Authors, year of publication, sampling strategy, databases, keywords, and other approaches used were extracted. DATA SYNTHESIS: Sixty-four studies were identified, and forty-three met inclusion criteria for this review. A summary of searching methods was produced and used to construct the STARLITE mnemonic (sampling strategy, type of study, approaches, range of years, limits, inclusion and exclusions, terms used, electronic sources). CONCLUSIONS: Considerable variation exists in search methods for qualitative systematic reviews. While diversity in methods is appropriate during the development of review methodology, major concerns remain about the absence of an accepted standard and the consequent poor quality of reporting. [Abstract/Link to Full Text]

Sandelowski M
In response to "Brimful of STARLITE".
J Med Libr Assoc. 2007 Jul;95(3):233; author reply 233. [Abstract/Link to Full Text]

Hofman K, Ryce A, Prudhomme W, Kotzin S
Reporting of non-communicable disease research in low- and middle-income countries: a pilot bibliometric analysis.
J Med Libr Assoc. 2006 Oct;94(4):415-20.
OBJECTIVE: The paper identifies the relative amount of research devoted to non-communicable disease in low- and middle-income countries (LMICs). DESIGN: A bibliometric analysis of a subset of journals published in LMICs was performed. MEASUREMENTS: Seventy-six peer-reviewed journals focused on general medicine or public health published in 46 LMICs and indexed from 1998 to 2003 in MEDLINE. A total of 24 journals were selected, 4 journals from each of 6 LMIC regions. Searches were refined using 18 non-communicable disease topics with 7,012 articles identified for analysis. RESULTS: More than 40% of articles in LMIC regions focused on non-communicable disease research. The percentage was highest in Eastern Europe/Central Asia (47%) and lowest in Latin America (36%). The percentage of articles published in Sub-Saharan Africa (38%) did not differ significantly from that of Latin America or South Asia. Cardiovascular disease and cancer led the list of the top ten most-indexed published topics by region. CONCLUSIONS: Even in regions rampant with infectious diseases, some capability exists to conduct research on non-communicable diseases. Greater attention should be paid to the conduct and support of such research in LMICs, which will benefit these countries and may yield clues to lower-cost solutions to the burden of these diseases worldwide. [Abstract/Link to Full Text]